diff --git a/404.html b/404.html new file mode 100644 index 00000000000..9b2734d2f9e --- /dev/null +++ b/404.html @@ -0,0 +1,78 @@ + + + + + +Page not found — TraitMech + + + + +
+
+ TraitMech + +
+
+
+ +
+

TraitMech › Page not found

+

Page not found

+

Nothing is published at this address. It may be mistyped, or the page may + have moved: a trait page is addressed by its category and record file name, so a record + that changes category gets a new address.

+
+ + + +
+ + + + \ No newline at end of file diff --git a/app/discussions/index.html b/app/discussions/index.html index c2f61c123cb..097800331ae 100644 --- a/app/discussions/index.html +++ b/app/discussions/index.html @@ -181,5 +181,8 @@

Knowledge gaps & discussions

} catch (error) { loadError(); } })(); + + + diff --git a/app/discussions/style.css b/app/discussions/style.css index d729b10300b..18aef2caea8 100644 --- a/app/discussions/style.css +++ b/app/discussions/style.css @@ -15,3 +15,5 @@ .badge { background:var(--badge); color:var(--badge-fg); } .badge.gap { background:var(--gap); color:var(--gap-fg); } a:focus-visible, button:focus-visible, input:focus-visible { outline-color:var(--accent); } +.shell-footer { max-width:1200px; margin:1.5rem auto 2rem; padding:1rem 1.25rem; + border-top:1px solid var(--line); color:var(--muted); font-size:.85rem; } diff --git a/pages/assets/style.css b/pages/assets/style.css index 41b18f7f31b..97b82107110 100644 --- a/pages/assets/style.css +++ b/pages/assets/style.css @@ -361,7 +361,8 @@ table.trait-list tr:hover { background: var(--accent-soft); } .protein-example-table-wrap, .detail-table-scroll { max-width: 100%; overflow-x: auto; overflow-wrap: normal; } .protein-example-table-wrap:focus-visible, -.detail-table-scroll:focus-visible { outline: 3px solid var(--accent); outline-offset: 2px; } +.detail-table-scroll:focus-visible, +.data-table-scroll:focus-visible { outline: 3px solid var(--accent); outline-offset: 2px; } .protein-example-table { border-collapse: collapse; font-size: 0.8rem; @@ -610,6 +611,11 @@ label.facet-opt .cnt { padding: 1rem; margin: 0; } +/* Stacked above the content on a narrow screen, a sticky sidebar stayed pinned + over the catalogue table or map plot it filters while the reader scrolled. */ +@media (max-width: 860px) { + .facet-sidebar { position: static; max-height: none; } +} .facet-sidebar h2, .facet-sidebar h3 { font-size: 0.78rem; text-transform: uppercase; @@ -685,3 +691,35 @@ label.facet-opt .cnt { /* Category names and provenance remain readable on narrow screens. */ h1 { overflow-wrap: anywhere; } .pathograph-status { padding: .75rem; color: var(--muted); } + +/* Generated schema reference (pages/schema.html). Built from existing tokens so + both themes are inherited; the slot tables keep their columns and scroll + inside their own region on a narrow screen. */ +.schema-contents, .schema-class, .schema-enum { margin: 1rem 0; overflow-wrap: anywhere; } +.schema-class h3, .schema-enum h3 { margin: 0 0 0.4rem; } +.schema-table { min-width: 720px; } +.schema-table td:last-child { min-width: 20rem; } +.schema-table caption { text-align: left; padding: 0 0 0.4rem; } +/* Slot names are case-sensitive identifiers: undo the uppercase column-header + treatment table.trait-list gives every th. */ +.schema-table th[scope="row"] { font-weight: 400; white-space: nowrap; text-transform: none; + letter-spacing: normal; background: none; color: var(--fg); font-size: inherit; } +.schema-table th[scope="row"], .schema-table td { vertical-align: top; } +.schema-values dt { margin-top: 0.5rem; } +.schema-values dd { margin-left: 1rem; color: var(--muted); } + +/* Skip link: the first tab stop on every page, shown only while focused. */ +.skip-link { position: absolute; left: 1rem; top: -4rem; z-index: 2100; padding: 0.5rem 0.75rem; + background: var(--card-bg); color: var(--accent); border: 2px solid var(--accent); border-radius: 4px; } +.skip-link:focus { top: 0.5rem; } +main:focus { outline: none; } + +/* Curation status explained beside the status on record pages. */ +.status-meaning { margin-top: 0.35rem; } +.status-meaning summary { cursor: pointer; color: var(--accent); font-size: 0.85rem; } +.status-meaning p { margin: 0.35rem 0 0; } + +/* Not-found page (404.html at the publishing root). */ +.not-found-search { margin: 1.25rem 0; flex-wrap: wrap; } +.not-found-search label { flex-basis: 100%; font-weight: 600; } +.not-found-links { line-height: 1.9; } diff --git a/pages/browse.html b/pages/browse.html index 2c95c10f94a..4eddb2cd41e 100644 --- a/pages/browse.html +++ b/pages/browse.html @@ -7,6 +7,7 @@ +
TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
-
+

TraitMech › Record browser

@@ -2452,12 +2453,14 @@

QUANTITATIVE_PROPERTY

kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
- Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
+ Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
Corpus as of 2026-10-25 21:40 UTC diff --git a/pages/category/ecology.html b/pages/category/ecology.html index b4576c69812..aad88826dfa 100644 --- a/pages/category/ecology.html +++ b/pages/category/ecology.html @@ -7,6 +7,7 @@ +
TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
-
+

TraitMech › Ecology

@@ -173,12 +174,14 @@

Filter records

kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
-
- Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
+ Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
Corpus as of 2026-10-25 21:40 UTC diff --git a/pages/category/environment.html b/pages/category/environment.html index 2eb1ea08aaf..24c12619507 100644 --- a/pages/category/environment.html +++ b/pages/category/environment.html @@ -7,6 +7,7 @@ +
TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
-
+

TraitMech › Environment

@@ -337,12 +338,14 @@

Filter records

kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
-
- Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
+ Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
Corpus as of 2026-10-25 21:40 UTC diff --git a/pages/category/genomics.html b/pages/category/genomics.html index 348c413d5c0..a334f3117a3 100644 --- a/pages/category/genomics.html +++ b/pages/category/genomics.html @@ -7,6 +7,7 @@ +
TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
-
+

TraitMech › Genomics

@@ -867,12 +868,14 @@

Filter records

kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
-
- Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
+ Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
Corpus as of 2026-10-25 21:40 UTC diff --git a/pages/category/metabolism.html b/pages/category/metabolism.html index d24d20d85bd..419d94fbf36 100644 --- a/pages/category/metabolism.html +++ b/pages/category/metabolism.html @@ -7,6 +7,7 @@ +
TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
-
+

TraitMech › Metabolism

@@ -457,12 +458,14 @@

Filter records

kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
-
- Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
+ Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
Corpus as of 2026-10-25 21:40 UTC diff --git a/pages/category/morphology.html b/pages/category/morphology.html index 6ec84ff03ae..1a5c349e8f1 100644 --- a/pages/category/morphology.html +++ b/pages/category/morphology.html @@ -7,6 +7,7 @@ +
TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
-
+

TraitMech › Morphology

@@ -351,12 +352,14 @@

Filter records

kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
-
- Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
+ Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
Corpus as of 2026-10-25 21:40 UTC diff --git a/pages/category/observation.html b/pages/category/observation.html index 8bb4a3762fb..fbbb1a0e91a 100644 --- a/pages/category/observation.html +++ b/pages/category/observation.html @@ -7,6 +7,7 @@ +
TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
-
+

TraitMech › Observation

@@ -133,12 +134,14 @@

Filter records

kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
-
- Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
+ Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
Corpus as of 2026-10-25 21:40 UTC diff --git a/pages/category/other.html b/pages/category/other.html index 6e7699b09f8..ebb4f02dba3 100644 --- a/pages/category/other.html +++ b/pages/category/other.html @@ -7,6 +7,7 @@ +
TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
-
+

TraitMech › Other

@@ -157,12 +158,14 @@

Filter records

kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
-
- Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
+ Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
Corpus as of 2026-10-25 21:40 UTC diff --git a/pages/category/physiology.html b/pages/category/physiology.html index 18939d1095e..9227c023de1 100644 --- a/pages/category/physiology.html +++ b/pages/category/physiology.html @@ -7,6 +7,7 @@ +
TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
-
+

TraitMech › Physiology

@@ -503,12 +504,14 @@

Filter records

kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
-
- Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
+ Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
Corpus as of 2026-10-25 21:40 UTC diff --git a/pages/category/quantitative_property.html b/pages/category/quantitative_property.html index cfae06be5a9..4fa15136163 100644 --- a/pages/category/quantitative_property.html +++ b/pages/category/quantitative_property.html @@ -7,6 +7,7 @@ +
TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
-
+

TraitMech › Quantitative Property

@@ -107,12 +108,14 @@

Filter records

kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
-
- Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
+ Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
Corpus as of 2026-10-25 21:40 UTC diff --git a/pages/category/upper.html b/pages/category/upper.html index be634623b2c..6cff949ba55 100644 --- a/pages/category/upper.html +++ b/pages/category/upper.html @@ -7,6 +7,7 @@ +
TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
-
+

TraitMech › Upper

@@ -109,12 +110,14 @@

Filter records

kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
-
- Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
+ Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
Corpus as of 2026-10-25 21:40 UTC diff --git a/pages/graph.html b/pages/graph.html index c064bc1cfe0..745c2be0a26 100644 --- a/pages/graph.html +++ b/pages/graph.html @@ -7,6 +7,7 @@ +
TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
-
+

TraitMech › Graph layout

@@ -54,7 +55,7 @@

Trait graph layout (sfdp)

View data as table
-
+
@@ -286,12 +287,14 @@

Trait graph layout (sfdp)

kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
- Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
+ Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
Corpus as of 2026-10-25 21:40 UTC diff --git a/pages/index.html b/pages/index.html index 72de900eee4..ea0edc3db9f 100644 --- a/pages/index.html +++ b/pages/index.html @@ -50,6 +50,18 @@ .btn{display:inline-block;background:var(--accent);color:#fff;padding:.5em 1.15em; border-radius:999px;font-size:.9rem;font-weight:600} .btn:hover{filter:brightness(.93);text-decoration:none} + .skip-link{position:absolute;left:1rem;top:-4rem;z-index:2100;padding:.5rem .75rem; + background:var(--card);color:var(--accent);border:2px solid var(--accent);border-radius:6px} + .skip-link:focus{top:.5rem} + main:focus{outline:none} + .notice{margin-top:28px;background:var(--card);border:1px solid var(--line);border-radius:16px;padding:22px 28px} + .notice h2{margin:0 0 .4em;font-size:1.15rem} + .notice p{margin:.4em 0;color:var(--muted);font-size:.95rem} + .notice dl{margin:.6em 0 0;display:grid;grid-template-columns:max-content 1fr;gap:.45em 1em} + .notice dt{font-weight:600} + .notice dt span{display:block;font-weight:400;color:var(--muted);font-size:.85rem} + .notice dd{margin:0;color:var(--muted);font-size:.95rem;overflow-wrap:anywhere} + @media (max-width:560px){.notice dl{grid-template-columns:1fr}.notice dd{margin-bottom:.4em}} footer{border-top:1px solid var(--line);background:rgba(255,255,255,.45); padding:30px 24px;text-align:center;font-size:.9rem;color:var(--muted)} footer .fam{margin:.2em 0} @@ -113,6 +125,7 @@ +

TraitMech

@@ -136,7 +149,7 @@

TraitMech

100.0%embedded
-
+
🔎
@@ -152,23 +165,47 @@

Embedding browser

💻
-
View on GitHub →Download traits.json →LinkML schema →
+
View on GitHub →Download traits.json →Schema reference →

Data, Schema & GitHub

-

Source code, bulk corpus JSON export, LinkML schema, and the curation workflow.

+

Source code, bulk corpus JSON export, LinkML schema documentation generated from the schema, and the curation workflow.

+ +
+

Curation status

+

Records carry one of these statuses. Each definition is quoted from the + schema; a record page explains its own + status beside it and lists every recorded curation event with its curator.

+
+ +
SEEDED 38 records
+
Imported verbatim from metpo.owl; not yet curator-reviewed.
+ +
PROPOSED 615 records
+
Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.
+ +
REVIEWED 427 records
+
Curator has signed off on label / definition / parents.
+ +
DEPRECATED 50 records
+
Superseded by another TraitRecord.
+ +
+
+
LabelCURIECategoryLayout xLayout y
@@ -85,7 +86,9 @@

Full-corpus text embedding map (BGE-large + PaCMAP)

const margin = { top: 20, right: 20, bottom: 30, left: 30 }; const svg = d3.select("#umap-plot").append("svg") - .attr("width", W).attr("height", H); + .attr("width", W).attr("height", H) + .attr("viewBox", "0 0 " + W + " " + H) + .style("width", "100%").style("height", "auto"); const g = svg.append("g") .attr("transform", `translate(${margin.left},${margin.top})`); @@ -264,12 +267,14 @@

Full-corpus text embedding map (BGE-large + PaCMAP)

kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
- Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
+ Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
Corpus as of 2026-10-25 21:40 UTC diff --git a/pages/schema.html b/pages/schema.html new file mode 100644 index 00000000000..2b75aef90e6 --- /dev/null +++ b/pages/schema.html @@ -0,0 +1,1715 @@ + + + + + +LinkML schema — TraitMech + + + + +
+
+ TraitMech + +
+
+
+ +
+

TraitMech › Schema

+

TraitMech - Microbial Trait Schema

+

LinkML schema for modeling microbial ecophysiological traits and phenotypes. +Each TraitRecord is a single trait (e.g. "pH optimum", "flagellar arrangement", +"growth temperature minimum") with provenance back to its METPO class and +optional cross-references to PATO / GO / NCIT / ENVO / CHEBI. + +Records are seeded from METPO (https://w3id.org/metpo) and curated incrementally, +mirroring the dismech / CultureMech / MIM workflow: one YAML per trait, optional +evidence-bearing audit trail, validation via `just validate-all`. +

+

Generated by just gen-pages from the LinkML schema + src/traitmech/schema/mech_shared.yaml, src/traitmech/schema/traitmech.yaml. + Slots are listed as LinkML resolves them for each class, with imports and slot usage applied. + Descriptions are shown as written in the schema, without links: the identifiers in them are often format examples. + Schema licence: BSD-3-Clause.

+
+ + + +
+

Classes (15)

+ +
+

TraitRecord

+

A single microbial trait (phenotype, capability, or quality) with provenance back to its METPO source class. One YAML per record.

+ + +
+
LabelCURIECategoryTerm kindPaCMAP xPaCMAP y
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TraitRecord slots (24)
SlotRangeCardinalityDescription
identifier (identifier)stringRequiredStable CURIE for this trait. Seeded records use the METPO CURIE directly (e.g. METPO:1000331). Curator-minted records may use the `traitmech:` prefix.
Pattern ^[A-Za-z][A-Za-z0-9._-]*:[A-Za-z0-9._-]+$
labelstringRequiredHuman-readable trait label (rdfs:label of the source class).
definitionstringOptionalTextual definition. For seeded records this is the IAO:0000115 annotation from METPO; curator can extend.
definition_sourcestringOptionalIAO:0000119 — citation for the definition (e.g. PMID:12345678, DOI:10.1234/abc, or "TODO:add_citation" when missing upstream).
synonymsTraitSynonymOptional, multivaluedAlternate labels (oboInOwl:hasExactSynonym, hasNarrowSynonym, hasBroadSynonym, hasRelatedSynonym).
parent_traitsstringOptional, multivaluedrdfs:subClassOf parents — CURIEs of broader METPO/upper-ontology classes. Multivalued because METPO uses multi-parent classification.
Pattern ^[A-Za-z][A-Za-z0-9._-]*:[A-Za-z0-9._-]+$
xrefsstringOptional, multivaluedoboInOwl:hasDbXref — equivalents in other ontologies (PATO, GO, NCIT, ENVO, CHEBI, UO, RO, MICRO, OBI). Use only for *true* equivalences; record broader/narrower relations as `parent_traits:` or notes instead.
Pattern ^[A-Za-z][A-Za-z0-9._-]*:[A-Za-z0-9._-]+$
canonical_examplesCanonicalExampleOptional, multivaluedCanonical exemplar organisms for this trait — the textbook / reference taxa a curator would point to as "this trait, archetypally". Each example carries an NCBITaxon CURIE, the organism name, an optional role note, and an optional citation. Distinct from the causal graphs (which model *how* the trait works, taxon-agnostically): these answer *who* canonically exhibits it. Curation-sourced — there is no trait→taxon edge table upstream — so each example should be backed by a reference where practical.
replacesstringOptional, multivalueddcterms:replaces — CURIEs of records that this trait supersedes. Used to track genuine record lineage, such as a curator splitting one trait into two or replacing a renumbered upstream class. It is not used to precompose a relation and its object: substrate use remains an organism-level METPO predicate composed with a CHEBI class at the assertion site. The replaced record remains resolvable with mapping_status: DEPRECATED; this field carries the structured forward link from the new record to the old. The reverse direction (deprecated → replacement) is the OBO/IAO `IAO:0100001` (term replaced by); we use dcterms:replaces because the field lives on the *new* record and points to the *old*.
Pattern ^[A-Za-z][A-Za-z0-9._-]*:[A-Za-z0-9._-]+$
trait_categoryTraitCategoryEnumOptionalCoarse-grained bucket for filesystem organisation and reporting. Inferred from the METPO upper-class lineage when seeding; curator can override.
term_kindTermKindEnumOptionalWhether this entry is an OWL Class (most METPO traits) or a DatatypeProperty / ObjectProperty (the value-bearing companions like METPO:has_pH_optimum).
domainstringOptionalFor DatatypeProperty / ObjectProperty entries — the typed subject (typically biolink:OrganismTaxon).
range_stringOptionalFor DatatypeProperty / ObjectProperty entries — the value range (e.g. xsd:decimal, xsd:string, or a TraitRecord identifier).
priorityPriorityEnumOptionalRelative editorial priority (CRITICAL/HIGH/MEDIUM/LOW) for the curation backlog — surfaced from METPO's internal proposals.
subsetstringOptionaloboInOwl:inSubset tag (e.g. metpo_proposal_2026_04).
observation_countintegerOptionalNumber of underlying source observations (from METPO's proposal TSVs); useful for ranking high-yield curation targets.
created_bystringOptionalIAO:0000117 — original term author from METPO.
contributorsstringOptional, multivaluedAdditional curators who have edited this record locally.
evidenceEvidenceItemOptional, multivaluedOptional citation list — populated when a curator backs the trait with literature support beyond METPO's own provenance. Intentionally *not* `required: true` (compare CausalEdge.evidence): a TraitRecord inherits provenance from the underlying METPO term, so requiring trait-level citations would force every SEEDED row to carry duplicate boilerplate. Causal claims are different — they are curator-asserted and must carry their own support.
mapping_statusMappingStatusEnumOptionalLifecycle flag. SEEDED rows came directly from metpo.owl; REVIEWED rows have curator sign-off; DEPRECATED rows are retained for traceability but flagged as superseded.
curation_historyCurationEventOptional, multivaluedAppend-only audit trail.
causal_graphsCausalGraphOptional, multivaluedOptional causal mechanism graphs for this trait. Nodes represent traits, pathways, environmental or experimental factors, genes/proteins, chemicals, cellular locations, molecular functions, and biological processes. Edges must carry evidence.
discussionsDiscussionOptional, multivaluedOpen questions, knowledge gaps, controversies, and curation todos attached to this trait (shared Discussion supertype; anchor `attaches_to` into e.g. `causal_graphs#<edge>`).
datasetsDatasetOptional, multivaluedPublic datasets (omics/sequence/phenotype) relevant to this trait.
+
+ + + +
+

TraitSynonym

+

A synonym entry with its scope.

+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
TraitSynonym slots (3)
SlotRangeCardinalityDescription
synonym_textstringRequired
synonym_typeSynonymTypeEnumOptional
sourcestringOptionalWhere the synonym came from (e.g. "metpo.owl", "PMID:...").
+
+ +
+ +
+

EvidenceItem

+

A literature or database citation supporting a TraitRecord.

+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
EvidenceItem slots (3)
SlotRangeCardinalityDescription
referencestringRequiredPMID:..., DOI:..., or an opaque URL.
snippetstringOptionalVerbatim quote from the source supporting the trait claim.
notesstringOptional
+
+ +
+ +
+

CanonicalExample

+

A canonical exemplar organism for a trait — a reference taxon that archetypally exhibits the trait. Curation-sourced; back with a citation where practical (compare EvidenceItem).

+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
CanonicalExample slots (4)
SlotRangeCardinalityDescription
taxon_idstringRequiredNCBITaxon CURIE for the exemplar organism (e.g. NCBITaxon:1423).
Pattern ^NCBITaxon:[0-9]+$
taxon_labelstringRequiredScientific name of the exemplar organism (e.g. Bacillus subtilis).
notestringOptionalWhy this organism is canonical for the trait (e.g. "model rod-shaped Gram-positive", "type strain for acidophily studies").
referencestringOptionalIAO:0000119-style citation supporting the exemplar claim (PMID:..., DOI:..., or an opaque URL). Optional but recommended.
+
+ +
+ +
+

CausalGraph

+

A directed causal mechanism graph associated with a trait.

+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
CausalGraph slots (7)
SlotRangeCardinalityDescription
graph_id (identifier)stringRequiredStable local graph identifier within the TraitRecord.
titlestringOptionalHuman-readable graph title.
descriptionstringOptionalShort scope note for the graph.
scope_statusCausalGraphScopeEnumOptionalCurator disposition for whether this graph represents a biological mechanism. NONMECHANISTIC is reserved for an explicitly reviewed measurement, classification, or upper-ontology context and must be explained in scope_notes. Omission is treated as REVIEW_NEEDED and is a blocking coverage-audit gap; the slot remains schema-optional only for protected legacy records.
scope_notesstringOptionalEvidence-based rationale for the graph scope disposition.
nodesCausalNodeRequired, multivaluedNodes participating in the causal graph.
edgesCausalEdgeRequired, multivaluedEvidence-backed directed causal or mechanistic edges.
+
+ +
+ +
+

CausalNode

+

A node in a trait causal graph. GENE_OR_PROTEIN is a legacy enum label; within TraitMech it is restricted to proteins and protein complexes. Genes, operons, and gene clusters are metadata, not primary graph nodes.

+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
CausalNode slots (12)
SlotRangeCardinalityDescription
node_id (identifier)stringRequiredStable local node identifier used by graph edges.
labelstringRequiredHuman-readable node label.
node_typeCausalNodeTypeEnumRequiredBroad semantic category used for rendering and curation.
groundingstringOptionalPreferred ontology or database CURIE for the node when available. A taxon-agnostic gene/protein node should use a semantic family, function, or complex CURIE such as GO, InterPro, NCBIfam, or ComplexPortal. UniProtKB accessions are organism-specific instances and belong in protein_examples, not here.
Pattern ^[A-Za-z][A-Za-z0-9._-]*:[A-Za-z0-9._-]+$
grounding_statusProteinGroundingStatusEnumOptionalExplicit review disposition for a GENE_OR_PROTEIN node that has no exact semantic grounding. REVIEWED_LABEL_ONLY requires a reason in grounding_notes. Grounded nodes do not need this field.
grounding_notesstringOptionalCurator rationale for retaining a GENE_OR_PROTEIN node label without an exact semantic grounding.
xrefsstringOptional, multivaluedAdditional ontology/database CURIEs for this node.
Pattern ^[A-Za-z][A-Za-z0-9._-]*:[A-Za-z0-9._-]+$
descriptionstringOptionalOptional node-specific scope note.
gene_symbolsstringOptional, multivaluedGene symbols encoding this protein or the explicit components of this protein complex. Gene symbols are metadata and do not denote primary causal nodes.
operonstringOptionalOperon or gene-cluster name encoding this protein or protein-complex module. Operons are metadata and do not denote primary causal nodes.
protein_examplesProteinExampleOptional, multivaluedOrganism-specific UniProt protein instances illustrating this taxon-agnostic GENE_OR_PROTEIN node. Each example names the source taxon in which its mechanistic role was established and carries mechanistic evidence. That source need not be a canonical example of the trait; the UniProt record verifies identity and taxonomy but does not by itself prove the causal role.
+
+ +
+ + + +
+

ProteinExample

+

A source-backed UniProt protein example paired with the organism in which its mechanistic role was established. Reviewed Swiss-Prot entries are preferred. One component accession must not be presented as an entire multisubunit complex.

+ + +
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ProteinExample slots (12)
SlotRangeCardinalityDescription
uniprot_idstringRequiredCurrent UniProtKB primary accession.
Pattern ^UniProtKB:(?:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2})$
protein_labelstringRequiredCurrent UniProt protein name or concise source-backed name.
gene_symbolstringOptionalGene symbol used by UniProt or the mechanistic source.
taxon_idstringRequiredUniProt organism taxon for this protein instance. This source taxon need not also be a canonical example of the owning trait.
Pattern ^NCBITaxon:[0-9]+$
taxon_labelstringRequiredScientific name corresponding to taxon_id.
entry_statusUniProtEntryStatusEnumRequiredUniProtKB reviewed or unreviewed entry status.
proteome_idstringOptionalUniProt proteome accession. Required by policy when an unreviewed reference-proteome entry is used as the only available exact example.
Pattern ^UP[0-9]{9}$
retrieved_ondateRequiredDate on which the UniProt metadata was verified.
entry_versionintegerOptionalUniProt entry version at retrieval time.
sequence_versionintegerOptionalUniProt sequence version at retrieval time.
rolestringRequiredSource-backed role in this mechanism, including an explicit component role when the causal node denotes a multisubunit complex.
evidenceEvidenceItemRequired, multivaluedPrimary-source evidence for this protein's mechanistic role in this taxon. Every item must include reference, snippet, and notes.
+
+ +
+ +
+

CausalEdge

+

An evidence-backed directed relationship in a trait causal graph.

+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
CausalEdge slots (6)
SlotRangeCardinalityDescription
subjectstringRequiredLocal node_id of the upstream/source node.
predicatestringRequiredHuman-readable predicate label or relation CURIE.
predicate_idstringOptionalOptional ontology CURIE grounding the predicate.
Pattern ^[A-Za-z][A-Za-z0-9._-]*:[A-Za-z0-9._-]+$
objectstringRequiredLocal node_id of the downstream/target node.
descriptionstringOptionalShort explanation of the causal claim.
evidenceEvidenceItemRequired, multivaluedEdge-level literature, database, or curated source support. `required: true` (in contrast to TraitRecord.evidence, which is optional): every causal claim must carry at least one citation because, unlike trait classification, mechanism assertions are not backed by METPO's own provenance.
+
+ +
+ +
+

CurationEvent

+

A timestamped curator action on a TraitRecord.

+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
CurationEvent slots (5)
SlotRangeCardinalityDescription
timestampdatetimeRequired
Pattern ^20[0-9]{2}-
curatorstringOptional
actionstringOptional
changesstringOptional
llm_assistedbooleanOptional
+
+ +
+ + + +
+

SupportingReference

+

A lightweight literature/database citation supporting a Discussion or Dataset. Self-contained (so this module has no dependency on each repo's EvidenceItem); carries a verbatim `snippet` so the same anti-hallucination snippet-vs-cached-abstract check the Mechs already run can validate it.

+

Defined in the shared module src/traitmech/schema/mech_shared.yaml.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
SupportingReference slots (7)
SlotRangeCardinalityDescription
referencestringRequiredPMID:..., DOI:..., a repository accession/CURIE, or an opaque URL.
reference_titlestringOptionalTitle of the cited source (optional; populated by tooling).
supportsSupportLevelEnumOptional
evidence_sourcestringOptionalHow the snippet was obtained (e.g. abstract, full_text, figure, supplement, database). Free-form to stay self-contained.
snippetstringOptionalVerbatim quote from the source supporting the attached claim.
explanationstringOptionalWhy this source bears on the claim.
notesstringOptional
+
+ +
+ +
+

Discussion

+

A thread-like record of an open question, controversy, curation todo, emerging hypothesis, knowledge gap, or interpretation debate attached to a record or one of its sub-objects. Captures the discourse / knowledge-gap layer of curation. External thread links (GitHub issues, forum posts) are cited via the `evidence` block, not a separate slot.

+

Defined in the shared module src/traitmech/schema/mech_shared.yaml.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Discussion slots (13)
SlotRangeCardinalityDescription
discussion_idstringRequiredStable local identifier for this discussion thread.
promptstringRequiredThe open question, gap statement, or todo, in one or two sentences.
kindDiscussionKindEnumOptional
statusDiscussionStatusEnumOptional
attaches_tostringOptional, multivaluedHash-anchor pointers into the sections/nodes this discussion concerns: `<section>#<anchor>`, e.g. `causal_graphs#edge_x`, `composition#ingredient_y`, `ecological_interactions#z`, `ontology_mapping#m`. Free-form so each Mech can anchor into its own record structure.
rationalestringOptionalWhy this matters / what resolving it would change.
proposed_experimentsProposedExperimentOptional, multivaluedOptional sketches of how the gap could be resolved.
evidenceSupportingReferenceOptional, multivaluedSupporting / contextual citations.
posed_bystringOptionalCurator or agent that raised the discussion.
posed_datedateOptional
resolved_datedateOptional
resolution_notestringOptionalHow it was resolved (when status is RESOLVED).
notesstringOptional
+
+ +
+ +
+

ProposedExperiment

+

A lightweight, domain-neutral sketch of an experiment or analysis that could resolve a knowledge gap. Records the idea and how its outcome would decide the gap; intentionally simpler than a full study design.

+

Defined in the shared module src/traitmech/schema/mech_shared.yaml.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ProposedExperiment slots (10)
SlotRangeCardinalityDescription
experiment_idstringOptionalStable local id (optional; for cross-reference).
namestringOptional
descriptionstringOptional
approachstringOptionalMethod/assay in brief (e.g. "defined-coculture growth assay", "isolate WGS").
model_systemsstringOptional, multivaluedSystems to use (e.g. isolate, enrichment, defined coculture, metagenome).
perturbationsstringOptional, multivaluedInterventions applied (e.g. gene knockout, nutrient removal).
readoutsstringOptional, multivaluedWhat would be measured.
decision_criterionstringOptionalThe observation that would settle the question.
would_supportstringOptionalOutcome that would support the hypothesis/assertion.
would_refutestringOptionalOutcome that would refute it.
+
+ +
+ +
+

Dataset

+

A reference to a publicly available dataset (omics, sequence, phenotype) relevant to this record. A lightweight repository-accession reference, not a full Datasheets-for-Datasets / DCAT description.

+

Defined in the shared module src/traitmech/schema/mech_shared.yaml.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Dataset slots (15)
SlotRangeCardinalityDescription
accessionstringOptionalRepository accession or CURIE, e.g. `geo:GSE36701`, `NCBI_SRA:SRP...`. (CultureMech `dataset_id` migrates here.)
titlestringOptionalShort dataset title. (CommunityMech `name` migrates here.)
descriptionstringOptionalHuman-readable description; may add nuance beyond the title.
organismstringOptionalSource organism / community label (free text or CURIE).
dataset_typeDatasetTypeEnumOptional
repositoryDatasetRepositoryEnumOptional
sample_typesstringOptional, multivaluedSample/material types represented (free text or term labels).
sample_countintegerOptional
conditionsstringOptional, multivaluedExperimental conditions / groups represented.
platformstringOptionalSequencing/assay platform.
urluriOptionalDirect URL to the dataset landing page, if no CURIE applies.
publicationstringOptionalAssociated publication reference (e.g. PMID:...).
findingsstringOptionalBrief note on what the dataset shows relevant to this record.
evidenceSupportingReferenceOptional, multivaluedSupporting citations.
notesstringOptional
+
+ +
+ + + +
+

Enumerations (15)

+ +
+

DiscussionKindEnum

+

Kind of unresolved / in-progress item captured by a Discussion. Knowledge gaps are represented as a discussion kind so they reuse the shared pointer, evidence, and lifecycle machinery, while optional proposed experiments capture how a gap could be resolved.

+

Defined in the shared module src/traitmech/schema/mech_shared.yaml.

+
+ +
OPEN_QUESTION
+
An unresolved scientific question posed by curators or experts.
+ +
KNOWLEDGE_GAP
+
A missing causal, evidentiary, model-system, or measurement assertion whose resolution would materially improve the record.
+ +
CONTROVERSY
+
A live disagreement or competing interpretation between published positions.
+ +
CURATION_TODO
+
A curation task captured inline (e.g. "ingredient needs CHEBI refinement").
+ +
EMERGING_HYPOTHESIS
+
A recently reported hypothesis under active discussion in the community.
+ +
INTERPRETATION
+
A discussion about how to interpret existing evidence or model an edge.
+ +
HUMAN_MODEL_MISMATCH
+
A gap where evidence exists in one system but its fidelity to the target context is uncertain (e.g. an in-vitro/model result whose transfer to the in-situ or host-associated setting is unverified).
+ +
+
+ +
+

DiscussionStatusEnum

+

Lifecycle status for a Discussion.

+

Defined in the shared module src/traitmech/schema/mech_shared.yaml.

+
+ +
OPEN
+
Posed but not yet under active discussion.
+ +
UNDER_DISCUSSION
+
Actively being discussed in one or more linked venues.
+ +
RESOLVED
+
Closed with a documented resolution; kept for provenance.
+ +
ARCHIVED
+
No longer active and not resolved (deferred, stale, or superseded).
+ +
+
+ +
+

SupportLevelEnum

+

How a SupportingReference bears on the claim it is attached to (mirrors the supports semantics already used in the Mech EvidenceItem models).

+

Defined in the shared module src/traitmech/schema/mech_shared.yaml.

+
+ +
SUPPORT
+
The source supports the claim.
+ +
REFUTE
+
The source contradicts the claim.
+ +
PARTIAL
+
The source partially supports the claim or supports it with caveats.
+ +
NO_EVIDENCE
+
The source is relevant context but does not directly bear on the claim.
+ +
WRONG_STATEMENT
+
The cited statement was found to be incorrect (kept for provenance).
+ +
+
+ +
+

DatasetTypeEnum

+

Type of dataset or data resource. Canonical UNION of CultureMech's and CommunityMech's enums plus microbial additions. Migration map (old → this): CultureMech values carry over unchanged; CommunityMech GENOME→GENOMICS, METAGENOME→METAGENOMICS, METATRANSCRIPTOME→METATRANSCRIPTOMICS, METAPROTEOME→METAPROTEOMICS (AMPLICON_16S / AMPLICON_ITS / METABOLOMICS / PHENOTYPE / MULTI_OMICS / OTHER are unchanged).

+

Defined in the shared module src/traitmech/schema/mech_shared.yaml.

+
+ +
GENOMICS
+
Isolate / single-organism genome data. (CultureMech GENOMICS; CommunityMech GENOME)
+ +
METAGENOMICS
+
Shotgun metagenome sequencing. (CommunityMech METAGENOME)
+ +
AMPLICON_16S
+
16S rRNA marker-gene amplicon sequencing.
+ +
AMPLICON_ITS
+
ITS marker-gene amplicon sequencing.
+ +
AMPLICON_OTHER
+
Marker-gene amplicon sequencing other than 16S/ITS (e.g. 18S, rpoB).
+ +
TRANSCRIPTOMICS
+
Single-organism RNA sequencing / expression.
+ +
METATRANSCRIPTOMICS
+
Community-level RNA sequencing. (CommunityMech METATRANSCRIPTOME)
+ +
PROTEOMICS
+
Single-organism protein expression profiling.
+ +
METAPROTEOMICS
+
Community-level proteomics. (CommunityMech METAPROTEOME)
+ +
METABOLOMICS
+
Metabolite profiling.
+ +
FLUXOMICS
+
Metabolic flux profiling.
+ +
PHENOMICS
+
High-throughput phenotype profiling.
+ +
PHENOTYPE
+
Phenotype / trait measurement collection (e.g. growth, biochemical).
+ +
MULTI_OMICS
+
Integrated multi-omics profiling.
+ +
OTHER
+
A dataset type not covered by the above.
+ +
+
+ +
+

DatasetRepositoryEnum

+

Public repository hosting the dataset. Superset of CommunityMech's enum (all values preserved) plus common additions; CultureMech datasets have no repository field today and migrate with repository unset / OTHER.

+

Defined in the shared module src/traitmech/schema/mech_shared.yaml.

+
+ +
NCBI_SRA
+
NCBI Sequence Read Archive.
+ +
NCBI_BIOPROJECT
+
NCBI BioProject.
+ +
NCBI_GEO
+
NCBI Gene Expression Omnibus.
+ +
NCBI_ASSEMBLY
+
NCBI Assembly (genome assemblies).
+ +
ENA
+
European Nucleotide Archive.
+ +
ARRAYEXPRESS
+
EBI ArrayExpress / BioStudies.
+ +
MGNIFY
+
EBI MGnify metagenomics resource.
+ +
JGI_GOLD
+
JGI Genomes OnLine Database.
+ +
JGI_IMG
+
JGI Integrated Microbial Genomes & Microbiomes.
+ +
NMDC
+
National Microbiome Data Collaborative.
+ +
METABOLOMICS_WORKBENCH
+
NIH Metabolomics Workbench.
+ +
METABOLIGHTS
+
EBI MetaboLights metabolomics repository.
+ +
MASSIVE
+
MassIVE mass-spectrometry repository.
+ +
GNPS
+
Global Natural Products Social Molecular Networking.
+ +
PRIDE
+
EBI PRIDE proteomics repository.
+ +
DBGAP
+
NCBI database of Genotypes and Phenotypes.
+ +
GTEX
+
Genotype-Tissue Expression project.
+ +
FIGSHARE
+
Figshare general-purpose research data archive.
+ +
ZENODO
+
Zenodo general-purpose research data archive.
+ +
BIOMODELS
+
EBI BioModels repository of computational models.
+ +
KBASE
+
DOE Systems Biology Knowledgebase (KBase).
+ +
OTHER
+
A repository not covered by the above.
+ +
+
+ +
+

PathwayContextRelationEnum

+ + +
+ +
PATHWAY_CONTEXT
+
An organism-scoped pathway record provides biochemical context for this node; the basis states the shared route or component and limits of the correspondence. This is not an exact-equivalence mapping.
+ +
+
+ +
+

TraitCategoryEnum

+

Coarse-grained trait bucket — used for filesystem layout.

+ +
+ +
MORPHOLOGY
+
Cell shape, motility apparatus, Gram type, etc.
+ +
PHYSIOLOGY
+
Metabolic mode, oxygen tolerance, fermentation capability.
+ +
ENVIRONMENT
+
pH / temperature / salinity / pressure tolerances and optima.
+ +
METABOLISM
+
Substrate utilisation, electron donor/acceptor, fermentation.
+ +
GENOMICS
+
GC content, genome size, ploidy.
+ +
ECOLOGY
+
Habitat, host association, symbiosis class.
+ +
DETECTION
+
Differential / selective media growth, biochemical assays.
+ +
QUANTITATIVE_PROPERTY
+
Datatype property carrying a numeric value (e.g. has_pH_optimum).
+ +
OBSERVATION
+
Observation-class entries (METPO:1001000 subtree) — not traits per se, but data-collection units (e.g. "growth pH observation", "NaCl range observation") that link a trait to a measurement event.
+ +
UPPER
+
Upper-level classifier (e.g. "quality", "biological process").
+ +
OTHER
+
No description.
+ +
+
+ +
+

TermKindEnum

+ + +
+ +
CLASS
+
No description.
+ +
DATATYPE_PROPERTY
+
No description.
+ +
OBJECT_PROPERTY
+
No description.
+ +
ANNOTATION_PROPERTY
+
No description.
+ +
+
+ +
+

SynonymTypeEnum

+ + +
+ +
EXACT_SYNONYM
+
No description.
+ +
NARROW_SYNONYM
+
No description.
+ +
BROAD_SYNONYM
+
No description.
+ +
RELATED_SYNONYM
+
No description.
+ +
+
+ +
+

PriorityEnum

+ + +
+ +
CRITICAL
+
No description.
+ +
HIGH
+
No description.
+ +
MEDIUM
+
No description.
+ +
LOW
+
No description.
+ +
+
+ +
+

MappingStatusEnum

+ + +
+ +
SEEDED
+
Imported verbatim from metpo.owl; not yet curator-reviewed.
+ +
PROPOSED
+
Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.
+ +
REVIEWED
+
Curator has signed off on label / definition / parents.
+ +
DEPRECATED
+
Superseded by another TraitRecord.
+ +
+
+ +
+

CausalGraphScopeEnum

+

Curator disposition for a graph's mechanistic scope.

+ +
+ +
MECHANISTIC
+
The graph represents a source-backed biological mechanism.
+ +
NONMECHANISTIC
+
The record is a measurement, classification, hazard, or upper-level context for which a protein-mediated causal mechanism is inapplicable.
+ +
REVIEW_NEEDED
+
The graph still requires an explicit scope decision.
+ +
+
+ +
+

ProteinGroundingStatusEnum

+

Review disposition for a protein node without an exact CURIE.

+ +
+ +
REVIEWED_LABEL_ONLY
+
The graph evidence supports the protein label, but no exact family, function, or complex term can be asserted without overclaiming.
+ +
+
+ +
+

UniProtEntryStatusEnum

+

Curation status of a UniProtKB protein entry.

+ +
+ +
REVIEWED
+
Manually reviewed UniProtKB/Swiss-Prot entry.
+ +
UNREVIEWED
+
Automatically annotated UniProtKB/TrEMBL entry.
+ +
+
+ +
+

CausalNodeTypeEnum

+

Broad categories for nodes in trait causal graphs.

+ +
+ +
TRAIT
+
A TraitMech or METPO trait.
+ +
PATHWAY
+
A pathway or pathway-like mechanism.
+ +
ENVIRONMENTAL_FACTOR
+
An environmental exposure or condition.
+ +
EXPERIMENTAL_FACTOR
+
An assay, perturbation, or experimental condition.
+ +
GENE_OR_PROTEIN
+
Legacy enum name restricted in TraitMech to a protein, protein family, or protein complex. Genes and operons belong in node metadata.
+ +
RNA
+
A functional RNA molecule or RNA-containing causal entity.
+ +
GENETIC_ELEMENT
+
A non-protein mobile or chromosomal genetic element such as a plasmid or prophage.
+ +
CHEMICAL
+
A chemical entity.
+ +
ORGANELLE
+
A cellular organelle or microbial subcellular structure.
+ +
CELLULAR_LOCALIZATION
+
A cellular component or localization.
+ +
MOLECULAR_FUNCTION
+
A molecular activity or function.
+ +
BIOLOGICAL_PROCESS
+
A biological process.
+ +
STATE
+
A bioenergetic or molecular state of the cell (e.g. proton motive force, redox state of the quinone pool) that mediates a trait mechanism. Distinct from a process: the state is the gradient / steady-value, not its establishment.
+ +
QUALITY
+
A quality or measurable attribute of a cellular component (e.g. membrane fluidity, GC content, motility speed) — a PATO-style axis attached to a microbial entity that modulates the trait mechanism.
+ +
CAPACITY
+
A metabolic or functional capacity — an electron-donating pool, ATP charge, or other reservoir-of-X notion that is neither a single chemical species nor a process. Examples include reducing power (NADH/NADPH pool) and energy charge.
+ +
+
+ +
+ +
+ + + + \ No newline at end of file diff --git a/pages/sequence-map.html b/pages/sequence-map.html index cbd28f9696d..a73c1d99e44 100644 --- a/pages/sequence-map.html +++ b/pages/sequence-map.html @@ -7,6 +7,7 @@ +
TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
-
+

TraitMech › Protein sequence map (pLM)

@@ -53,7 +54,7 @@

Protein sequence embedding map (ESM-2 pLM + PaCMAP)

View protein embeddings as table
-
+
@@ -86,7 +87,9 @@

Protein sequence embedding map (ESM-2 pLM + PaCMAP)

const margin = { top: 24, right: 24, bottom: 32, left: 32 }; const svg = d3.select("#umap-plot").append("svg") - .attr("width", W).attr("height", H); + .attr("width", W).attr("height", H) + .attr("viewBox", "0 0 " + W + " " + H) + .style("width", "100%").style("height", "auto"); const g = svg.append("g") .attr("transform", `translate(${margin.left},${margin.top})`); @@ -243,12 +246,14 @@

Protein sequence embedding map (ESM-2 pLM + PaCMAP)

kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
- Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
+ Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
Corpus as of 2026-10-25 21:40 UTC diff --git a/pages/traits/ecology/animal_pathogen.html b/pages/traits/ecology/animal_pathogen.html index c17c0826068..f068c70e92b 100644 --- a/pages/traits/ecology/animal_pathogen.html +++ b/pages/traits/ecology/animal_pathogen.html @@ -7,6 +7,7 @@ +
TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
-
+
@@ -443,7 +444,7 @@

kg-microbe context

via direct_metpo.

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

@@ -526,7 +527,7 @@

Deep research

The trait should represent the **realized, strain-level capacity of a microorganism to establish infection in a host belonging to Metazoa**, rather than the mere presence of a virulence-associated gene. A defensible general graph should center on five recurring functions: **host attachment/colonization, acquisition of host-limited nutrients, resistance or manipulation of host defenses, host damage, and persistence/dissemination**. Individual adhesins, secretion systems, toxins, capsules, and metabolic pathways should normally be modeled as taxon- or niche-specific implementations of those functions. -A 2024 authoritative review frames bacterial host adaptation around colonization, nutrient acquisition, and immune evasion and emphasizes that host range varies from single-host restriction to infection of diverse vertebrates and invertebrates. It also notes that successful establishment requires adaptation to host-specific anatomy, physiology, immunity, and nutrient availability (published 13 July 2024; https://doi.org/10.1093/femsre/fuae019). (barber2024mechanismsofhost pages 1-2) +A 2024 authoritative review frames bacterial host adaptation around colonization, nutrient acquisition, and immune evasion and emphasizes that host range varies from single-host restriction to infection of diverse vertebrates and invertebrates. It also notes that successful establishment requires adaptation to host-specific anatomy, physiology, immunity, and nutrient availability (published 13 July 2024; https://doi.org/10.1093/femsre/fuae019). (barber2024mechanismsofhost pages 1-2) | module | recommended graph status | representative nodes | strongest evidence type | principal caveat | |---|---|---|---|---| @@ -554,7 +555,7 @@

Deep research

### Important distinctions 1. **Pathogenicity versus virulence.** Pathogenicity is the ability to cause infection/disease; virulence is its degree or severity. A low-virulence pathogen still belongs in the class. -2. **Colonizer/commensal versus pathogen.** Colonization may precede infection but is not sufficient by itself. Staphylococci illustrate this boundary: all are members of mammalian epithelial microbiota, yet only some species or lineages commonly cause disease, and colonization is a frequent source of infection (published 26 September 2023; https://doi.org/10.3390/ijms241914587). (cheung2023virulencemechanismsof pages 1-2) +2. **Colonizer/commensal versus pathogen.** Colonization may precede infection but is not sufficient by itself. Staphylococci illustrate this boundary: all are members of mammalian epithelial microbiota, yet only some species or lineages commonly cause disease, and colonization is a frequent source of infection (published 26 September 2023; https://doi.org/10.3390/ijms241914587). (cheung2023virulencemechanismsof pages 1-2) 3. **Opportunistic pathogen.** Opportunism is compatible with the trait, but host compromise, barrier disruption, device implantation, or dysbiosis should be represented as contextual enabling factors—not as microbial mechanisms. 4. **Zoonotic/vector-borne/reservoir status.** These are transmission/ecological traits. A strain can be an animal pathogen without transmission between animal species. 5. **Toxigenic but non-invasive microbes.** Intoxication from a preformed toxin does not automatically demonstrate infection; distinguish toxin producer, foodborne intoxication, and pathogen. @@ -692,7 +693,7 @@

Proposed experiments

Provenance -

Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for animal pathogen: Prokaryotes in such plastispheres are unknown to date.', whose sentence came from PMID:40891913. That sentence is about prokaryotes of marine plastispheres, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:40891913 'Prokaryotes in such plastispheres are unknown to date.'; PMID:42279816 'However, in South America, their use is still limited because of complicated regulations and inconsistent evidence requirements.'; PMID:41639266 'However, the interacting effects of climate factors and seasonal variations in nutritional components on PMCs remain poorly understood.'; PMID:42197358 'While plant growth-promoting bacteria (PGPB) are known to alleviate heavy metal toxicity, their role under MP-HM co-contamination and the differential responses of rhizosphere microbial communities remain unclear.'.

+

Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for animal pathogen: Prokaryotes in such plastispheres are unknown to date.', whose sentence came from PMID:40891913. That sentence is about prokaryotes of marine plastispheres, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:40891913 'Prokaryotes in such plastispheres are unknown to date.'; PMID:42279816 'However, in South America, their use is still limited because of complicated regulations and inconsistent evidence requirements.'; PMID:41639266 'However, the interacting effects of climate factors and seasonal variations in nutritional components on PMCs remain poorly understood.'; PMID:42197358 'While plant growth-promoting bacteria (PGPB) are known to alleviate heavy metal toxicity, their role under MP-HM co-contamination and the differential responses of rhizosphere microbial communities remain unclear.'.

@@ -818,7 +819,16 @@

Identifier

Term kind
CLASS
Status
-
REVIEWED
+
REVIEWED + + +
+ What this status means +

Curator has signed off on label / definition / parents.

+

Quoted from the schema's status definitions.

+
+ +
@@ -1182,12 +1192,14 @@

kg-microbe

kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
-
- Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
+ Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/ecology/bacterial_cannibalism.html b/pages/traits/ecology/bacterial_cannibalism.html index 8c0f279808b..e81ee20d120 100644 --- a/pages/traits/ecology/bacterial_cannibalism.html +++ b/pages/traits/ecology/bacterial_cannibalism.html @@ -7,6 +7,7 @@ +
TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
-
+
@@ -55,19 +56,19 @@

Trait evidence (3)

DOI:10.1126/science.1086462
The sporulating cells feed on the nutrients thereby released, which allows them to keep growing rather than to complete morphogenesis.
-

Gonzalez-Pastor et al. (2003), PMID:12817086, scientific abstract directly retrieved from Europe PMC. The author-posted main text at https://www.researchgate.net/publication/10699307_Cannibalism_by_Sporulating_Bacteria was also read. It reports sibling killing in the PY79 laboratory background, while the nutritional explanation is proposed from killing and sporulation phenotypes, not traced nutrient uptake. The snippet preserves the abstract's stronger wording without upgrading that inference. Actual figures and supplements were not inspected; no numerical or protein-resolved claim is imported.

+

Gonzalez-Pastor et al. (2003), PMID:12817086, scientific abstract directly retrieved from Europe PMC. The author-posted main text at https://www.researchgate.net/publication/10699307_Cannibalism_by_Sporulating_Bacteria was also read. It reports sibling killing in the PY79 laboratory background, while the nutritional explanation is proposed from killing and sporulation phenotypes, not traced nutrient uptake. The snippet preserves the abstract's stronger wording without upgrading that inference. Actual figures and supplements were not inspected; no numerical or protein-resolved claim is imported.

  • DOI:10.1111/j.1365-2958.2009.06882.x
    Cannibal cells express the skf and sdp toxin systems to lyse a fraction of their sensitive siblings.
    -

    Lopez et al. (2009), PMID:19775247, PMC2983100, scientific Summary, directly checked in NCBI BioC full text at https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_xml/PMC2983100/unicode. Results, Discussion and Experimental Procedures were read. NCIB3610 is the wild-type background; prominent hypercannibal phenotypes concern engineered derivatives. Nutrient-mediated sporulation delay remains an interpretation, not a nutrient-flux measurement. Actual figures and supplements were not inspected.

    +

    Lopez et al. (2009), PMID:19775247, PMC2983100, scientific Summary, directly checked in NCBI BioC full text at https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_xml/PMC2983100/unicode. Results, Discussion and Experimental Procedures were read. NCIB3610 is the wild-type background; prominent hypercannibal phenotypes concern engineered derivatives. Nutrient-mediated sporulation delay remains an interpretation, not a nutrient-flux measurement. Actual figures and supplements were not inspected.

  • DOI:10.1128/mbio.00525-26
    our data challenge the established role of cannibalism-dependent killing as the mechanism behind this sporulation delay.
    -

    Friebel et al. (2026), PMID:42294941, PMC13343845.1, published 2026-06-15, IMPORTANCE section, not the scientific Abstract. Directly checked against Europe PMC full-text XML and https://pmc.ncbi.nlm.nih.gov/articles/PMC13343845.1/. Results, Discussion and Methods were read; actual figures and supplements were not inspected. DK1042 is an NCIB3610-derived laboratory background. Biofilm differentiation and membrane-integrity readouts do not directly establish nutrient transfer. This is counterevidence to a universal killing-based explanation, not a new positive demonstration of the nutritional phenotype.

    +

    Friebel et al. (2026), PMID:42294941, PMC13343845.1, published 2026-06-15, IMPORTANCE section, not the scientific Abstract. Directly checked against Europe PMC full-text XML and https://pmc.ncbi.nlm.nih.gov/articles/PMC13343845.1/. Results, Discussion and Methods were read; actual figures and supplements were not inspected. DK1042 is an NCIB3610-derived laboratory background. Biofilm differentiation and membrane-integrity readouts do not directly establish nutrient transfer. This is counterevidence to a universal killing-based explanation, not a new positive demonstration of the nutritional phenotype.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 19:24 UTC diff --git a/pages/traits/ecology/bacterial_mycophagy.html b/pages/traits/ecology/bacterial_mycophagy.html index 58047db4389..b542c5e45b8 100644 --- a/pages/traits/ecology/bacterial_mycophagy.html +++ b/pages/traits/ecology/bacterial_mycophagy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1111/j.1469-8137.2007.02325.x
    phenotypic behaviours that make available nutrients from living fungi and allow the conversion of living fungal biomass into bacterial biomass.
    -

    Leveau and Preston 2008, PMID:18086226, section I, p. 860 (author PDF page 2), visually checked contiguous quotation. Definition authority, not experimental replication. Summary, section I, strategy overview and selected diagnostic passages in section III read; remaining review and referenced experiments not comprehensively assessed. Section I explicitly includes oomycetes while acknowledging they are not true fungi. Section III requires growth controls and distinguishes inferred nutrient acquisition from direct flux measurement. Author full text: https://leveau.faculty.ucdavis.edu/wp-content/uploads/sites/220/2015/05/Leveau2008.pdf. DOI AND SRC:MED metadata matched PMID, title and DOI on 2026-10-11.

    +

    Leveau and Preston 2008, PMID:18086226, section I, p. 860 (author PDF page 2), visually checked contiguous quotation. Definition authority, not experimental replication. Summary, section I, strategy overview and selected diagnostic passages in section III read; remaining review and referenced experiments not comprehensively assessed. Section I explicitly includes oomycetes while acknowledging they are not true fungi. Section III requires growth controls and distinguishes inferred nutrient acquisition from direct flux measurement. Author full text: https://leveau.faculty.ucdavis.edu/wp-content/uploads/sites/220/2015/05/Leveau2008.pdf. DOI AND SRC:MED metadata matched PMID, title and DOI on 2026-10-11.

  • DOI:10.1099/ijs.0.02920-0
    All Ter isolates proliferated in sand when hyphae of the fungi C. globosum, F. culmorum or M. hiemalis invaded.
    -

    de Boer et al. 2004, PMID:15143036, Results, p. 860 (PDF page 4), visually checked quotation. Methods tested all isolates against intact living hyphae, using plate counts at three weeks corrected for uninoculated controls. Growth is indirect nutritional evidence, not isotope-traced transfer. Heat-fixed-hypha adhesion is a separate observation. Abstract, Introduction, Methods, relevant Results and taxonomic descriptions read; pages 4/7 visually inspected; supplement unread. Author full text: https://leveau.faculty.ucdavis.edu/wp-content/uploads/sites/220/2015/05/deBoer2004.pdf. EXT_ID:15143036 AND SRC:MED matched source, ID, title and DOI on 2026-10-11.

    +

    de Boer et al. 2004, PMID:15143036, Results, p. 860 (PDF page 4), visually checked quotation. Methods tested all isolates against intact living hyphae, using plate counts at three weeks corrected for uninoculated controls. Growth is indirect nutritional evidence, not isotope-traced transfer. Heat-fixed-hypha adhesion is a separate observation. Abstract, Introduction, Methods, relevant Results and taxonomic descriptions read; pages 4/7 visually inspected; supplement unread. Author full text: https://leveau.faculty.ucdavis.edu/wp-content/uploads/sites/220/2015/05/deBoer2004.pdf. EXT_ID:15143036 AND SRC:MED matched source, ID, title and DOI on 2026-10-11.

  • DOI:10.1038/ismej.2008.97
    The growth of collimonads did not cause a significant reduction in the Absidia biomass.
    -

    Hoppener-Ogawa et al. 2009, PMID:18923455, scientific Abstract, directly matched. Abstract, Introduction, Methods, Results, Discussion, Table 1 and actual Figures 1/2 read; Figure 3 and supplement unread. Indigenous soil populations and a four-strain sand mixture grew with invading fungus; this is not individual strain proof or direct nutrient tracing. Nonsignificant biomass loss does not establish no fitness cost. Methods samples at three weeks, whereas Figure 2 caption names two and three; no time-specific quantitative claim adopted. Overlapping authors with 2004, not independent-group replication. Author full text: https://leveau.ucdavis.edu/wp-content/uploads/sites/220/2015/05/HoppenerOgawa2009.pdf. EXT_ID:18923455 AND SRC:MED matched source, ID, title and DOI on 2026-10-11.

    +

    Hoppener-Ogawa et al. 2009, PMID:18923455, scientific Abstract, directly matched. Abstract, Introduction, Methods, Results, Discussion, Table 1 and actual Figures 1/2 read; Figure 3 and supplement unread. Indigenous soil populations and a four-strain sand mixture grew with invading fungus; this is not individual strain proof or direct nutrient tracing. Nonsignificant biomass loss does not establish no fitness cost. Methods samples at three weeks, whereas Figure 2 caption names two and three; no time-specific quantitative claim adopted. Overlapping authors with 2004, not independent-group replication. Author full text: https://leveau.ucdavis.edu/wp-content/uploads/sites/220/2015/05/HoppenerOgawa2009.pdf. EXT_ID:18923455 AND SRC:MED matched source, ID, title and DOI on 2026-10-11.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1099/ijs.0.02920-0 - Qualified to natural dune-soil isolate Ter6 (type strain, NCCB 100033 = LMG 21973), not every species member. Primary Methods establish provenance and hyphal-growth testing; species description on p. 863 identifies Ter6. Provenance: https://doi.org/10.1099/ijs.0.02920-0. NCBI species ID/name and Ter6 type material independently resolved on 2026-10-11: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=158899. Do not assign all 22 Ter isolates to this species from the 2004 circumscription. + Qualified to natural dune-soil isolate Ter6 (type strain, NCCB 100033 = LMG 21973), not every species member. Primary Methods establish provenance and hyphal-growth testing; species description on p. 863 identifies Ter6. Provenance: https://doi.org/10.1099/ijs.0.02920-0. NCBI species ID/name and Ter6 type material independently resolved on 2026-10-11: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=158899. Do not assign all 22 Ter isolates to this species from the 2004 circumscription. @@ -270,7 +271,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Causal graphs and protein examples are deferred, not claimed absent. Separate fungal damage, nutrient release and bacterial assimilation; require functional evidence and taxon-paired accessions before encoding protein mechanisms. CommunityMech CommunityMech:000364 led to DOI:10.1093/ismejo/wrag201 (PMID:42523014, PMC13615538). Its Abstract, antagonistic-assay Methods and mycophagy Results/Discussion passages were read: CFU after five days with sclerotia is compared with glass beads. This is a follow-up lead, not counted evidence of active feeding rather than released-nutrient consumption. Figures and supplement remain unread; no additional canonical taxon or independent replication is inferred from the assay name.

    +

    Causal graphs and protein examples are deferred, not claimed absent. Separate fungal damage, nutrient release and bacterial assimilation; require functional evidence and taxon-paired accessions before encoding protein mechanisms. CommunityMech CommunityMech:000364 led to DOI:10.1093/ismejo/wrag201 (PMID:42523014, PMC13615538). Its Abstract, antagonistic-assay Methods and mycophagy Results/Discussion passages were read: CFU after five days with sclerotia is compared with glass beads. This is a follow-up lead, not counted evidence of active feeding rather than released-nutrient consumption. Figures and supplement remain unread; no additional canonical taxon or independent replication is inferred from the assay name.

    @@ -340,7 +341,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -369,12 +379,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-11 10:23 UTC diff --git a/pages/traits/ecology/biofilm_formation.html b/pages/traits/ecology/biofilm_formation.html index 423d7de90bb..dd180805415 100644 --- a/pages/traits/ecology/biofilm_formation.html +++ b/pages/traits/ecology/biofilm_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    GO:0042710 confers biofilm formation - traitmech:000053 + traitmech:000053 METPO:2007700

    Biofilm-formation activity realizes the biofilm-forming trait.

      @@ -364,8 +365,8 @@

      Protein and taxon examples

    ProteinUniProtGeneTaxonTraitLength (aa)PaCMAP xPaCMAP y
    - Pseudomonas aeruginosa PAO1 -
    NCBITaxon:208964 + Pseudomonas aeruginosa PAO1 +
    NCBITaxon:208964         		UNREVIEWED
    @@ -431,7 +432,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -447,7 +448,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -696,7 +697,7 @@

    Proposed experiments

    Provenance -

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for biofilm formation: How immune homeostasis is maintained in this constantly challenged environment remains however a central and largely unanswered question.', whose sentence came from PMID:42039744. That sentence is about immune homeostasis at the gut mucosa, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:42039744 'How immune homeostasis is maintained in this constantly challenged environment remains however a central and largely unanswered question.'; PMID:41245847 'We present a research agenda identifying key research gaps and organizing them into priority areas to guide future investigations in this high-risk population.'; PMID:41661098 'Finally, we identify major knowledge gaps and research priorities necessary to advance a more integrated understanding of maternal microbial influences on reproductive and neonatal health.'; PMID:42125129 "However, contradictions persist regarding pH's effect on microbial diversity, with unresolved questions about how specific environmental conditions regulate microbial taxa.".

    +

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for biofilm formation: How immune homeostasis is maintained in this constantly challenged environment remains however a central and largely unanswered question.', whose sentence came from PMID:42039744. That sentence is about immune homeostasis at the gut mucosa, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:42039744 'How immune homeostasis is maintained in this constantly challenged environment remains however a central and largely unanswered question.'; PMID:41245847 'We present a research agenda identifying key research gaps and organizing them into priority areas to guide future investigations in this high-risk population.'; PMID:41661098 'Finally, we identify major knowledge gaps and research priorities necessary to advance a more integrated understanding of maternal microbial influences on reproductive and neonatal health.'; PMID:42125129 "However, contradictions persist regarding pH's effect on microbial diversity, with unresolved questions about how specific environmental conditions regulate microbial taxa.".

    @@ -807,7 +808,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1171,12 +1181,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/ecology/biosafety_level.html b/pages/traits/ecology/biosafety_level.html index 5202b03e561..c32d9da083d 100644 --- a/pages/traits/ecology/biosafety_level.html +++ b/pages/traits/ecology/biosafety_level.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -134,11 +135,11 @@

    Edge evidence

  • biosafety level 1 - METPO:1001102 + METPO:1001102 is a biosafety level METPO:1001101 - rdfs:subClassOf + rdfs:subClassOf

    BSL-1 is a biosafety-level classification.

    • @@ -420,7 +421,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -653,7 +654,7 @@

    Proposed experiments

    Provenance -

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for biosafety level: Additionally, it identifies ongoing challenges and critical knowledge gaps for future research.', whose sentence came from PMID:41494000. That sentence is about a review's boilerplate statement that gaps exist, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:41494000 'Additionally, it identifies ongoing challenges and critical knowledge gaps for future research.'; PMID:41556562 'This review outlines the possibilities, as well as the limitations of their use in food production.'; PMID:41647993 'Given the knowledge gap on the characteristics and significance of microbiome in early-onset pancreatic ductal adenocarcinoma (eoPDAC, age 50 years).'; PMID:41683313 'Background : Untargeted microbiome modulation has achieved conflicting results in post-infectious irritable bowel syndrome (PI-IBS).'.

    +

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for biosafety level: Additionally, it identifies ongoing challenges and critical knowledge gaps for future research.', whose sentence came from PMID:41494000. That sentence is about a review's boilerplate statement that gaps exist, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:41494000 'Additionally, it identifies ongoing challenges and critical knowledge gaps for future research.'; PMID:41556562 'This review outlines the possibilities, as well as the limitations of their use in food production.'; PMID:41647993 'Given the knowledge gap on the characteristics and significance of microbiome in early-onset pancreatic ductal adenocarcinoma (eoPDAC, age 50 years).'; PMID:41683313 'Background : Untargeted microbiome modulation has achieved conflicting results in post-infectious irritable bowel syndrome (PI-IBS).'.

    @@ -716,7 +717,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; PMID:21208457). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; PMID:21208457). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -749,7 +750,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1113,12 +1123,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/ecology/biosafety_level_1.html b/pages/traits/ecology/biosafety_level_1.html index 1b838f12466..fd8fc184370 100644 --- a/pages/traits/ecology/biosafety_level_1.html +++ b/pages/traits/ecology/biosafety_level_1.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1001102 is a biosafety level - METPO:1001101 - rdfs:subClassOf + METPO:1001101 + rdfs:subClassOf

    BSL-1 is a quantitative class within the biosafety-level classification axis.

      @@ -226,7 +227,7 @@

      Edge evidence

      assigns biosafety level - METPO:1001101 + METPO:1001101

      The selection process assigns a biosafety level on the classification axis.

        @@ -305,7 +306,7 @@

        Parent traits (1)

        Synonyms (1)

          -
        • 1 RELATED_SYNONYM · metpo.owl
          • +
        • 1 RELATED_SYNONYM · metpo.owl
    @@ -321,7 +322,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -588,7 +589,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -952,12 +962,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/ecology/biosafety_level_2.html b/pages/traits/ecology/biosafety_level_2.html index f50a1d454a4..c1e184a86f9 100644 --- a/pages/traits/ecology/biosafety_level_2.html +++ b/pages/traits/ecology/biosafety_level_2.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1001103 is a biosafety level - METPO:1001101 - rdfs:subClassOf + METPO:1001101 + rdfs:subClassOf

    BSL-2 is a member of the biosafety-level classification.

      @@ -286,7 +287,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • 2 RELATED_SYNONYM · metpo.owl
        • +
      • 2 RELATED_SYNONYM · metpo.owl
    @@ -302,7 +303,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -551,7 +552,7 @@

    Proposed experiments

    Provenance -

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for biosafety level 2: Background : Untargeted microbiome modulation has achieved conflicting results in post-infectious irritable bowel syndrome (PI-IBS).', whose sentence came from PMID:41683313. That sentence is about microbiome modulation in post-infectious IBS, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:41683313 'Background : Untargeted microbiome modulation has achieved conflicting results in post-infectious irritable bowel syndrome (PI-IBS).'; PMID:41413233 'Recently, the gut microbiota (GM) has gained attention for its potential involvement in blood pressure regulation; however, polyamine metabolism involvement remains poorly understood.'; PMID:41640410 'However, their clinical translation is hampered by challenges within the harsh gastrointestinal milieu, including low viability, poor colonization, and insufficient target specificity.'; PMID:41490313 'However, how these core strains interact with each other and with other gut microbes is largely unknown.'.

    +

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for biosafety level 2: Background : Untargeted microbiome modulation has achieved conflicting results in post-infectious irritable bowel syndrome (PI-IBS).', whose sentence came from PMID:41683313. That sentence is about microbiome modulation in post-infectious IBS, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:41683313 'Background : Untargeted microbiome modulation has achieved conflicting results in post-infectious irritable bowel syndrome (PI-IBS).'; PMID:41413233 'Recently, the gut microbiota (GM) has gained attention for its potential involvement in blood pressure regulation; however, polyamine metabolism involvement remains poorly understood.'; PMID:41640410 'However, their clinical translation is hampered by challenges within the harsh gastrointestinal milieu, including low viability, poor colonization, and insufficient target specificity.'; PMID:41490313 'However, how these core strains interact with each other and with other gut microbes is largely unknown.'.

    @@ -635,7 +636,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -999,12 +1009,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/ecology/biosafety_level_3.html b/pages/traits/ecology/biosafety_level_3.html index f4ccc023138..6badfcef94e 100644 --- a/pages/traits/ecology/biosafety_level_3.html +++ b/pages/traits/ecology/biosafety_level_3.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1001104 is a biosafety level - METPO:1001101 - rdfs:subClassOf + METPO:1001101 + rdfs:subClassOf

    BSL-3 is a member of the biosafety-level classification.

      @@ -286,9 +287,9 @@

      Parent traits (1)

      Synonyms (2)

        -
      • 3 RELATED_SYNONYM · metpo.owl
        • +
      • 3 RELATED_SYNONYM · metpo.owl
        • -
      • 3** RELATED_SYNONYM · metpo.owl
        • +
      • 3** RELATED_SYNONYM · metpo.owl
    @@ -304,7 +305,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -553,7 +554,7 @@

    Proposed experiments

    Provenance -

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for biosafety level 3: Additionally, it identifies ongoing challenges and critical knowledge gaps for future research.', whose sentence came from PMID:41494000. That sentence is about a review's boilerplate statement that gaps exist, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:41494000 'Additionally, it identifies ongoing challenges and critical knowledge gaps for future research.'; PMID:40514544 'Although T cells are essential for immunity to TB, the mechanisms that provide protective immunity are poorly understood.'; PMID:41552424 'In the field of microbiological diagnosis, HTS provides a complementary or alternative approach to traditional diagnostic tests, particularly in cases with non-specific symptoms or when the etiology is unknown.'; PMID:41917383 'While its virulence genes critically regulate intracellular survival and replication, the molecular mechanisms underlying pathogenesis remain elusive.'.

    +

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for biosafety level 3: Additionally, it identifies ongoing challenges and critical knowledge gaps for future research.', whose sentence came from PMID:41494000. That sentence is about a review's boilerplate statement that gaps exist, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:41494000 'Additionally, it identifies ongoing challenges and critical knowledge gaps for future research.'; PMID:40514544 'Although T cells are essential for immunity to TB, the mechanisms that provide protective immunity are poorly understood.'; PMID:41552424 'In the field of microbiological diagnosis, HTS provides a complementary or alternative approach to traditional diagnostic tests, particularly in cases with non-specific symptoms or when the etiology is unknown.'; PMID:41917383 'While its virulence genes critically regulate intracellular survival and replication, the molecular mechanisms underlying pathogenesis remain elusive.'.

    @@ -643,7 +644,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1007,12 +1017,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/ecology/biosafety_level_4.html b/pages/traits/ecology/biosafety_level_4.html index fcb3a2985a1..a9513aa6e37 100644 --- a/pages/traits/ecology/biosafety_level_4.html +++ b/pages/traits/ecology/biosafety_level_4.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1001105 is a biosafety level - METPO:1001101 - rdfs:subClassOf + METPO:1001101 + rdfs:subClassOf

    BSL-4 is a member of the biosafety-level classification.

      @@ -323,7 +324,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • 4 RELATED_SYNONYM · metpo.owl
        • +
      • 4 RELATED_SYNONYM · metpo.owl
    @@ -339,7 +340,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -432,27 +433,27 @@

    Deep research

    ## Key Evidence-Backed Causal Edges | Subject | Predicate | Object | Source (DOI/URL) | Key snippet | Node type(s) | Curation uncertainty | |---|---|---|---|---|---|---| -| Biosafety level 4 (BSL-4) | is_defined_as | highest containment level for dangerous/life-threatening pathogens | https://doi.org/10.3390/laboratories1030013 | “BSL-4 is characterized… as the highest containment level for dangerous and life-threatening pathogens” (gao2024frombiosafetyto pages 5-6) | trait class; containment level | Low | -| Biosafety level 3 (BSL-3) | differs_from | BSL-4 by handling serious/lethal inhalation agents with less complex containment | https://doi.org/10.3390/laboratories1030013 | “BSL-3 addresses agents causing serious or lethal diseases via inhalation… while BSL-4 requires more complex self-contained facilities for maximum containment” (gao2024frombiosafetyto pages 5-6) | trait class; containment level | Low | -| Global BSL-4 governance | has_current_count | 51 operational BSL-4 laboratories globally | https://doi.org/10.3390/laboratories1030013 | “51 BSL-4 laboratories currently operational globally, with 18 additional facilities in planning or construction” (gao2024frombiosafetyto pages 10-12) | governance/statistic | Low | -| External biorisk assessment of BSL-4 laboratories | found | only 7 of 27 assessed labs met high standards | https://doi.org/10.3390/laboratories1030013 | “A 2023 King's College London report assessing 27 BSL-4 laboratories found only seven met high standards of biorisk management” (gao2024frombiosafetyto pages 10-12) | governance/statistic | Medium | -| WHO Laboratory Biosafety Guideline (2024) | supports | countries lacking biosafety frameworks and emphasizes national oversight committees | https://doi.org/10.3390/laboratories1030013 | “the 2024 WHO Laboratory Biosafety Guideline was released to support countries lacking biosafety frameworks… emphasizing national biosafety oversight committees” (gao2024frombiosafetyto pages 10-12) | governance/policy | Medium | -| Lassa virus | requires_handling_in | BSL-4 conditions | https://doi.org/10.1080/22221751.2024.2356149 | “Lassa virus (LASV), a risk-group 4 pathogen, must be handled in biosafety level-4 (BSL-4) conditions” (nunez2024treatmentofhighly pages 26-28) | agent; containment assignment | Low | -| Lassa virus research constraints | motivate_development_of | BSL-2 surrogate reverse genetics systems | https://doi.org/10.1080/22221751.2024.2356149 | “thereby limiting its research and antiviral development… the first to study the complete LASV life cycle under BSL-2 conditions” (nunez2024treatmentofhighly pages 26-28) | application/model system | Low | -| Ebola virus VP35 | inhibits | type I interferon production/induction | https://doi.org/10.1007/s40121-023-00913-y | “VP35 inhibits both the production of type I interferon (IFN)” (ndayambaje2024molecularcharacterizationof pages 4-6) | viral protein; host process | Medium | -| Ebola/filovirus VP35 | binds | dsRNA and blocks RIG-I/PACT-dependent IFN-I induction | https://doi.org/10.3390/cells13010071 | “the viral VP35 protein, which binds dsRNA… inhibit RIG-I activation, blocking IFNα/β induction” (vogel2023viraltargetingof pages 4-6) | viral protein; ligand; innate immune pathway | Low | -| Ebola virus VP24 | competes_for_binding_to | importin alpha (IMPA5/6/7) | https://doi.org/10.3390/cells13010071 | “VP24 competes for this interaction, preventing STAT1 nuclear accumulation… by competitive binding to importin-alpha (IMPA) proteins, specifically IMPA5, 6, and 7” (vogel2023viraltargetingof pages 4-6) | viral protein; host transport protein | Low | -| Ebola virus VP24 | prevents | STAT1 nuclear accumulation and ISG expression | https://doi.org/10.3390/cells13010071 | “preventing STAT1 nuclear accumulation and subsequent ISG expression” (vogel2023viraltargetingof pages 4-6) | viral protein; transcription factor; antiviral gene expression | Low | -| VP24-IMPA antagonism | is_conserved_in | Orthoebolavirus but not Marburg virus | https://doi.org/10.3390/cells13010071 | “VP24-IMPA interaction is conserved in Orthoebolavirus genus but not Marburg virus” (vogel2023viraltargetingof pages 4-6) | comparative mechanism; taxon scope | Medium | -| Ebola virus GP1 | binds_and_undergoes_conformational_change_to_enable | GP2-mediated membrane fusion | https://doi.org/10.1186/s43042-024-00600-8 | “GP1 binds to host cells and undergoes conformational change to expose GP2, enabling viral fusion with host cell membranes” (ndayambaje2024molecularcharacterizationof pages 4-6) | viral glycoprotein; entry/fusion process | Medium | -| Ebola virus shed glycoprotein (GP) | acts_as | antibody decoy/antigen sink | https://doi.org/10.1186/s43042-024-00600-8 | “The shed glycoprotein (GP) acts as an antigen sink/decoy that absorbs antibodies” (ndayambaje2024molecularcharacterizationof pages 4-6) | secreted viral protein; immune evasion | Medium | -| Ebola virus shed glycoprotein (GP) | stimulates | macrophages and dendritic cells causing cytokine production and vascular permeability | https://doi.org/10.1186/s43042-024-00600-8 | “stimulating macrophages and dendritic cells, resulting in large-scale cytokine production and heightened vascular permeability” (ndayambaje2024molecularcharacterizationof pages 4-6) | viral protein; immune cells; pathophysiology | Medium | -| Filovirus infection | causes | organ injury via inflammation and endothelial dysfunction | https://doi.org/10.1038/s41390-023-02873-y | “organ injury due to inflammation, endothelial dysfunction” (ndayambaje2024molecularcharacterizationof pages 4-6) | disease process; host pathology | High | -| LASV infection | can_use | LAMP1 for entry in a BSL-2 surrogate system | https://doi.org/10.1080/22221751.2024.2356149 | “membrane protein 1 (LAMP1), but not α-dystroglycan (α-DG)” (nunez2024treatmentofhighly pages 26-28) | viral entry; host receptor | Medium | -| Alpha-dystroglycan | is_dispensable_for | LASVmg infection in helper-cell BSL-2 system | https://doi.org/10.1080/22221751.2024.2356149 | “a previously reported cellular receptor α-dystroglycan is dispensable for LASVmg infection” (nunez2024treatmentofhighly pages 26-28) | host receptor; surrogate assay finding | High | -| Mammarenavirus NP | functions_as | interferon antagonist | https://doi.org/10.1080/17460441.2024.2340494 | “Like NP, Z is an interferon antagonist” (nunez2024treatmentofhighly pages 26-28) | viral protein; innate immune antagonism | Medium | -| Mammarenavirus Z | functions_as | interferon antagonist | https://doi.org/10.1080/17460441.2024.2340494 | “Like NP, Z is an interferon antagonist” (nunez2024treatmentofhighly pages 26-28) | viral matrix protein; innate immune antagonism | Medium | -| Mammarenavirus Z | mediates | virion budding | https://doi.org/10.1080/17460441.2024.2340494 | “Z-mediated virion budding” (nunez2024treatmentofhighly pages 26-28) | viral matrix protein; egress process | Medium | +| Biosafety level 4 (BSL-4) | is_defined_as | highest containment level for dangerous/life-threatening pathogens | https://doi.org/10.3390/laboratories1030013 | “BSL-4 is characterized… as the highest containment level for dangerous and life-threatening pathogens” (gao2024frombiosafetyto pages 5-6) | trait class; containment level | Low | +| Biosafety level 3 (BSL-3) | differs_from | BSL-4 by handling serious/lethal inhalation agents with less complex containment | https://doi.org/10.3390/laboratories1030013 | “BSL-3 addresses agents causing serious or lethal diseases via inhalation… while BSL-4 requires more complex self-contained facilities for maximum containment” (gao2024frombiosafetyto pages 5-6) | trait class; containment level | Low | +| Global BSL-4 governance | has_current_count | 51 operational BSL-4 laboratories globally | https://doi.org/10.3390/laboratories1030013 | “51 BSL-4 laboratories currently operational globally, with 18 additional facilities in planning or construction” (gao2024frombiosafetyto pages 10-12) | governance/statistic | Low | +| External biorisk assessment of BSL-4 laboratories | found | only 7 of 27 assessed labs met high standards | https://doi.org/10.3390/laboratories1030013 | “A 2023 King's College London report assessing 27 BSL-4 laboratories found only seven met high standards of biorisk management” (gao2024frombiosafetyto pages 10-12) | governance/statistic | Medium | +| WHO Laboratory Biosafety Guideline (2024) | supports | countries lacking biosafety frameworks and emphasizes national oversight committees | https://doi.org/10.3390/laboratories1030013 | “the 2024 WHO Laboratory Biosafety Guideline was released to support countries lacking biosafety frameworks… emphasizing national biosafety oversight committees” (gao2024frombiosafetyto pages 10-12) | governance/policy | Medium | +| Lassa virus | requires_handling_in | BSL-4 conditions | https://doi.org/10.1080/22221751.2024.2356149 | “Lassa virus (LASV), a risk-group 4 pathogen, must be handled in biosafety level-4 (BSL-4) conditions” (nunez2024treatmentofhighly pages 26-28) | agent; containment assignment | Low | +| Lassa virus research constraints | motivate_development_of | BSL-2 surrogate reverse genetics systems | https://doi.org/10.1080/22221751.2024.2356149 | “thereby limiting its research and antiviral development… the first to study the complete LASV life cycle under BSL-2 conditions” (nunez2024treatmentofhighly pages 26-28) | application/model system | Low | +| Ebola virus VP35 | inhibits | type I interferon production/induction | https://doi.org/10.1007/s40121-023-00913-y | “VP35 inhibits both the production of type I interferon (IFN)” (ndayambaje2024molecularcharacterizationof pages 4-6) | viral protein; host process | Medium | +| Ebola/filovirus VP35 | binds | dsRNA and blocks RIG-I/PACT-dependent IFN-I induction | https://doi.org/10.3390/cells13010071 | “the viral VP35 protein, which binds dsRNA… inhibit RIG-I activation, blocking IFNα/β induction” (vogel2023viraltargetingof pages 4-6) | viral protein; ligand; innate immune pathway | Low | +| Ebola virus VP24 | competes_for_binding_to | importin alpha (IMPA5/6/7) | https://doi.org/10.3390/cells13010071 | “VP24 competes for this interaction, preventing STAT1 nuclear accumulation… by competitive binding to importin-alpha (IMPA) proteins, specifically IMPA5, 6, and 7” (vogel2023viraltargetingof pages 4-6) | viral protein; host transport protein | Low | +| Ebola virus VP24 | prevents | STAT1 nuclear accumulation and ISG expression | https://doi.org/10.3390/cells13010071 | “preventing STAT1 nuclear accumulation and subsequent ISG expression” (vogel2023viraltargetingof pages 4-6) | viral protein; transcription factor; antiviral gene expression | Low | +| VP24-IMPA antagonism | is_conserved_in | Orthoebolavirus but not Marburg virus | https://doi.org/10.3390/cells13010071 | “VP24-IMPA interaction is conserved in Orthoebolavirus genus but not Marburg virus” (vogel2023viraltargetingof pages 4-6) | comparative mechanism; taxon scope | Medium | +| Ebola virus GP1 | binds_and_undergoes_conformational_change_to_enable | GP2-mediated membrane fusion | https://doi.org/10.1186/s43042-024-00600-8 | “GP1 binds to host cells and undergoes conformational change to expose GP2, enabling viral fusion with host cell membranes” (ndayambaje2024molecularcharacterizationof pages 4-6) | viral glycoprotein; entry/fusion process | Medium | +| Ebola virus shed glycoprotein (GP) | acts_as | antibody decoy/antigen sink | https://doi.org/10.1186/s43042-024-00600-8 | “The shed glycoprotein (GP) acts as an antigen sink/decoy that absorbs antibodies” (ndayambaje2024molecularcharacterizationof pages 4-6) | secreted viral protein; immune evasion | Medium | +| Ebola virus shed glycoprotein (GP) | stimulates | macrophages and dendritic cells causing cytokine production and vascular permeability | https://doi.org/10.1186/s43042-024-00600-8 | “stimulating macrophages and dendritic cells, resulting in large-scale cytokine production and heightened vascular permeability” (ndayambaje2024molecularcharacterizationof pages 4-6) | viral protein; immune cells; pathophysiology | Medium | +| Filovirus infection | causes | organ injury via inflammation and endothelial dysfunction | https://doi.org/10.1038/s41390-023-02873-y | “organ injury due to inflammation, endothelial dysfunction” (ndayambaje2024molecularcharacterizationof pages 4-6) | disease process; host pathology | High | +| LASV infection | can_use | LAMP1 for entry in a BSL-2 surrogate system | https://doi.org/10.1080/22221751.2024.2356149 | “membrane protein 1 (LAMP1), but not α-dystroglycan (α-DG)” (nunez2024treatmentofhighly pages 26-28) | viral entry; host receptor | Medium | +| Alpha-dystroglycan | is_dispensable_for | LASVmg infection in helper-cell BSL-2 system | https://doi.org/10.1080/22221751.2024.2356149 | “a previously reported cellular receptor α-dystroglycan is dispensable for LASVmg infection” (nunez2024treatmentofhighly pages 26-28) | host receptor; surrogate assay finding | High | +| Mammarenavirus NP | functions_as | interferon antagonist | https://doi.org/10.1080/17460441.2024.2340494 | “Like NP, Z is an interferon antagonist” (nunez2024treatmentofhighly pages 26-28) | viral protein; innate immune antagonism | Medium | +| Mammarenavirus Z | functions_as | interferon antagonist | https://doi.org/10.1080/17460441.2024.2340494 | “Like NP, Z is an interferon antagonist” (nunez2024treatmentofhighly pages 26-28) | viral matrix protein; innate immune antagonism | Medium | +| Mammarenavirus Z | mediates | virion budding | https://doi.org/10.1080/17460441.2024.2340494 | “Z-mediated virion budding” (nunez2024treatmentofhighly pages 26-28) | viral matrix protein; egress process | Medium | *Table: This table summarizes candidate evidence-backed causal graph edges relevant to the biosafety level 4 trait, combining containment definitions and representative taxon-specific mechanisms from Ebola and Lassa virus literature. It is useful for deciding which edges are appropriate for TraitMech curation and which should remain flagged as taxon-specific or uncertain.* @@ -463,19 +464,19 @@

    Deep research

    * Some model findings (e.g., alpha-dystroglycan dispensability for LASV infection in surrogate BSL-2 systems) must be considered with caution for universal applicability. ## Bibliography and URLs (DOI-first) -- Gao W et al. (2024) From Biosafety to National Security: The Evolution and Challenges of Biosafety Laboratories. Laboratories. https://doi.org/10.3390/laboratories1030013 (gao2024frombiosafetyto pages 5-6, gao2024frombiosafetyto pages 10-12) -- Nuñez IA et al. (2024) Treatment of highly virulent mammarenavirus infections—status quo and future directions. Expert Opin Drug Discov. https://doi.org/10.1080/17460441.2024.2340494 (nunez2024treatmentofhighly pages 26-28) -- Vogel OA et al. (2023) Viral targeting of importin alpha-mediated nuclear import to block innate immunity. Cells. https://doi.org/10.3390/cells13010071 (vogel2023viraltargetingof pages 4-6) -- Ndayambaje M et al. (2024) Molecular characterization of ebola virus, immune response, and therapeutic challenges: a narrative review. Egyptian Journal of Medical Human Genetics. https://doi.org/10.1186/s43042-024-00600-8 (ndayambaje2024molecularcharacterizationof pages 4-6, ndayambaje2024molecularcharacterizationof pages 14-15) +- Gao W et al. (2024) From Biosafety to National Security: The Evolution and Challenges of Biosafety Laboratories. Laboratories. https://doi.org/10.3390/laboratories1030013 (gao2024frombiosafetyto pages 5-6, gao2024frombiosafetyto pages 10-12) +- Nuñez IA et al. (2024) Treatment of highly virulent mammarenavirus infections—status quo and future directions. Expert Opin Drug Discov. https://doi.org/10.1080/17460441.2024.2340494 (nunez2024treatmentofhighly pages 26-28) +- Vogel OA et al. (2023) Viral targeting of importin alpha-mediated nuclear import to block innate immunity. Cells. https://doi.org/10.3390/cells13010071 (vogel2023viraltargetingof pages 4-6) +- Ndayambaje M et al. (2024) Molecular characterization of ebola virus, immune response, and therapeutic challenges: a narrative review. Egyptian Journal of Medical Human Genetics. https://doi.org/10.1186/s43042-024-00600-8 (ndayambaje2024molecularcharacterizationof pages 4-6, ndayambaje2024molecularcharacterizationof pages 14-15) ## Summary Significant progress has occurred from 2023–2024 in clarifying BSL-4 as a laboratory/containment trait, standardizing governance, and detailing viral-host mechanisms for classically assigned BSL-4 agents. Curation for TraitMech must distinguish between universal containment features and taxon-specific molecular mechanisms. See the embedded table for detailed evidence and curation assessment. References -1. (gao2024frombiosafetyto pages 5-6): Wanying Gao, Zongzhen Wu, Kunlan Zuo, Qiangyu Xiang, Lu Zhang, Xiaoya Chen, Feng Tan, and Huan Liu. From biosafety to national security: the evolution and challenges of biosafety laboratories. Laboratories, 1:158-173, Dec 2024. URL: https://doi.org/10.3390/laboratories1030013, doi:10.3390/laboratories1030013. This article has 11 citations. +1. (gao2024frombiosafetyto pages 5-6): Wanying Gao, Zongzhen Wu, Kunlan Zuo, Qiangyu Xiang, Lu Zhang, Xiaoya Chen, Feng Tan, and Huan Liu. From biosafety to national security: the evolution and challenges of biosafety laboratories. Laboratories, 1:158-173, Dec 2024. URL: https://doi.org/10.3390/laboratories1030013, doi:10.3390/laboratories1030013. This article has 11 citations. -2. (gao2024frombiosafetyto pages 10-12): Wanying Gao, Zongzhen Wu, Kunlan Zuo, Qiangyu Xiang, Lu Zhang, Xiaoya Chen, Feng Tan, and Huan Liu. From biosafety to national security: the evolution and challenges of biosafety laboratories. Laboratories, 1:158-173, Dec 2024. URL: https://doi.org/10.3390/laboratories1030013, doi:10.3390/laboratories1030013. This article has 11 citations. +2. (gao2024frombiosafetyto pages 10-12): Wanying Gao, Zongzhen Wu, Kunlan Zuo, Qiangyu Xiang, Lu Zhang, Xiaoya Chen, Feng Tan, and Huan Liu. From biosafety to national security: the evolution and challenges of biosafety laboratories. Laboratories, 1:158-173, Dec 2024. URL: https://doi.org/10.3390/laboratories1030013, doi:10.3390/laboratories1030013. This article has 11 citations.

    Showing the first 60 of 68 lines of findings; the linked file also carries the @@ -573,7 +574,7 @@

    Proposed experiments

    Provenance -

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for biosafety level 4: Finally, this review examines the largely unknown microbiology and infection implications of celestial body habitation with an emphasis placed on Mars.', whose sentence came from PMID:37362850. That sentence is about microbiology and infection during celestial body habitation, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:37362850 'Finally, this review examines the largely unknown microbiology and infection implications of celestial body habitation with an emphasis placed on Mars.'; PMID:41914886 'Both Old World arenaviruses LASV and LCMV exploit host tyrosine kinase signaling to establish infection, though the molecular mechanisms remain incompletely understood.'; PMID:40044492 'However, the comparatively low scientific commitment of countries that are usually among the major players in global scientific publications and the declining scientific interest in NiV research combined with the prevailing knowledge gaps in NiV infectiology in conjunction with the risk of NiV spreading to other areas is extremely threatening.'; PMID:39682751 'The COVID-19 pandemic has underscored the limitations of focusing solely on the pathogen-killing strategies of immunology and microbiology to address complex, multisystemic infectious diseases.'.

    +

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for biosafety level 4: Finally, this review examines the largely unknown microbiology and infection implications of celestial body habitation with an emphasis placed on Mars.', whose sentence came from PMID:37362850. That sentence is about microbiology and infection during celestial body habitation, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:37362850 'Finally, this review examines the largely unknown microbiology and infection implications of celestial body habitation with an emphasis placed on Mars.'; PMID:41914886 'Both Old World arenaviruses LASV and LCMV exploit host tyrosine kinase signaling to establish infection, though the molecular mechanisms remain incompletely understood.'; PMID:40044492 'However, the comparatively low scientific commitment of countries that are usually among the major players in global scientific publications and the declining scientific interest in NiV research combined with the prevailing knowledge gaps in NiV infectiology in conjunction with the risk of NiV spreading to other areas is extremely threatening.'; PMID:39682751 'The COVID-19 pandemic has underscored the limitations of focusing solely on the pathogen-killing strategies of immunology and microbiology to address complex, multisystemic infectious diseases.'.

    @@ -630,7 +631,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Zaire ebolavirus (NCBITaxon:186538; https://www.canada.ca/en/public-health/services/laboratory-biosafety-biosecurity/pathogen-safety-data-sheets-risk-assessment/ebolavirus.html). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Zaire ebolavirus (NCBITaxon:186538; https://www.canada.ca/en/public-health/services/laboratory-biosafety-biosecurity/pathogen-safety-data-sheets-risk-assessment/ebolavirus.html). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -663,7 +664,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1027,12 +1037,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/ecology/biosafety_level_5.html b/pages/traits/ecology/biosafety_level_5.html index 7e8ac584095..336820d9b2b 100644 --- a/pages/traits/ecology/biosafety_level_5.html +++ b/pages/traits/ecology/biosafety_level_5.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,8 +119,8 @@

    Edge evidence

    METPO:1001106 is a biosafety level - METPO:1001101 - rdfs:subClassOf + METPO:1001101 + rdfs:subClassOf

    BSL-5 is a proposed member of the biosafety-level classification.

      @@ -178,7 +179,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • 5 RELATED_SYNONYM · metpo.owl
        • +
      • 5 RELATED_SYNONYM · metpo.owl
    @@ -194,7 +195,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -422,7 +423,7 @@

    Recorded curation sessions

  • · codex
    • REVIEW — Repair PR 664 BSL-5 definition evidence -

      Addressed adversarial review issue #668 by restoring DOI:10.1146/annurev.micro.62.081307.162938 as the biosafety_level_5 definition source and DOI-backed top-level evidence while keeping the SAE PPL-alpha source as additional record and graph evidence; the focused replay tests verify the patched script and curated YAML stay in sync.

    +

    Addressed adversarial review issue #668 by restoring DOI:10.1146/annurev.micro.62.081307.162938 as the biosafety_level_5 definition source and DOI-backed top-level evidence while keeping the SAE PPL-alpha source as additional record and graph evidence; the focused replay tests verify the patched script and curated YAML stay in sync.

    • Read this curation session @@ -454,7 +455,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -818,12 +828,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-07 07:24 UTC diff --git a/pages/traits/ecology/collective_bacterial_predation.html b/pages/traits/ecology/collective_bacterial_predation.html index f0bf7e442e2..186c9563955 100644 --- a/pages/traits/ecology/collective_bacterial_predation.html +++ b/pages/traits/ecology/collective_bacterial_predation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1038/s41467-023-41193-x
    Myxococcus xanthus forages and moves collectively to prey and feed on other bacterial species.
    -

    Rombouts et al. 2023, PMID:37696789, PMC10495355, scientific abstract, not the separate editor summary. Identity checked with EXT_ID:37696789 AND SRC:MED plus matching title and DOI. Results on cell-state transitions, A/S motility, trail following and prey lysis, Discussion and relevant Methods were read directly. Figure 5 and Supplementary Table 1 (p. 12) were visually inspected. The table identifies DZ2 laboratory material and engineered reporters or motility mutants; the paper's wild-type designation does not establish an untouched natural isolate. The prey is E. coli MG1655 with HU-mCherry for the lysis readout. Figure 5 measures prey fluorescence loss relative to an uninvaded zone, not direct nutrient assimilation or individual fitness benefits. Motility perturbations support contributions to efficient predation in this assay, not universal group obligacy. Raw movies and source data were not independently reanalyzed. MED and Crossref exposed a preprint relationship, not a linked correction/retraction; none was identified on the retrieved publisher page. Source: https://www.nature.com/articles/s41467-023-41193-x.

    +

    Rombouts et al. 2023, PMID:37696789, PMC10495355, scientific abstract, not the separate editor summary. Identity checked with EXT_ID:37696789 AND SRC:MED plus matching title and DOI. Results on cell-state transitions, A/S motility, trail following and prey lysis, Discussion and relevant Methods were read directly. Figure 5 and Supplementary Table 1 (p. 12) were visually inspected. The table identifies DZ2 laboratory material and engineered reporters or motility mutants; the paper's wild-type designation does not establish an untouched natural isolate. The prey is E. coli MG1655 with HU-mCherry for the lysis readout. Figure 5 measures prey fluorescence loss relative to an uninvaded zone, not direct nutrient assimilation or individual fitness benefits. Motility perturbations support contributions to efficient predation in this assay, not universal group obligacy. Raw movies and source data were not independently reanalyzed. MED and Crossref exposed a preprint relationship, not a linked correction/retraction; none was identified on the retrieved publisher page. Source: https://www.nature.com/articles/s41467-023-41193-x.

  • DOI:10.1128/AEM.02286-19
    In addition to group hunting, individual M. xanthus cells are able to kill and lyse prey cells
    -

    Zhang et al. 2020, PMID:31704687, PMC6974655, scientific ABSTRACT, not the separate IMPORTANCE text. Qualified MED identity and title/DOI checked. The PMC Results and Discussion subsections on post-killing behavior and conclusions, Methods strain table and tracking analysis were also read. This is primary counterevidence to obligate group-only killing: DK1622 cells can kill E. coli individually. Prey-fragment consumption inferences do not constitute a direct assimilation assay. The delta-aglZ analysis also included individuals in groups of two or three and is not uniformly a solitary-cell dataset. This paper is boundary evidence, not independent replication of the 2023 collective-motility experiment. MED and Crossref exposed no linked correction/retraction; publisher access returned HTTP 403, leaving publisher notice status unverified. Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC6974655/.

    +

    Zhang et al. 2020, PMID:31704687, PMC6974655, scientific ABSTRACT, not the separate IMPORTANCE text. Qualified MED identity and title/DOI checked. The PMC Results and Discussion subsections on post-killing behavior and conclusions, Methods strain table and tracking analysis were also read. This is primary counterevidence to obligate group-only killing: DK1622 cells can kill E. coli individually. Prey-fragment consumption inferences do not constitute a direct assimilation assay. The delta-aglZ analysis also included individuals in groups of two or three and is not uniformly a solitary-cell dataset. This paper is boundary evidence, not independent replication of the 2023 collective-motility experiment. MED and Crossref exposed no linked correction/retraction; publisher access returned HTTP 403, leaving publisher notice status unverified. Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC6974655/.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -271,7 +272,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add collective bacterial predation with explicit cooperation limits -

      Added traitmech:000701 using Rombouts et al. 2023 DOI:10.1038/s41467-023-41193-x and Zhang et al. 2020 DOI:10.1128/AEM.02286-19. Two directly checked scientific-abstract snippets distinguish collective feeding from obligate cooperation or solitary-cell incapacity. Relevant Results and Methods, Figure 5 and the 2023 supplementary strain table were inspected; laboratory reporter evidence is not asserted a natural canonical example. Ignored/hidden worktree and complete open-PR checks support v577 block 1065400-1065499. Dry run and validated writer applied. No existing trait, including protected spore_germination, changed. Full validation and immutable adversarial review follow; no human scientific approval or upstream METPO acceptance is claimed.

    +

    Added traitmech:000701 using Rombouts et al. 2023 DOI:10.1038/s41467-023-41193-x and Zhang et al. 2020 DOI:10.1128/AEM.02286-19. Two directly checked scientific-abstract snippets distinguish collective feeding from obligate cooperation or solitary-cell incapacity. Relevant Results and Methods, Figure 5 and the 2023 supplementary strain table were inspected; laboratory reporter evidence is not asserted a natural canonical example. Ignored/hidden worktree and complete open-PR checks support v577 block 1065400-1065499. Dry run and validated writer applied. No existing trait, including protected spore_germination, changed. Full validation and immutable adversarial review follow; no human scientific approval or upstream METPO acceptance is claimed.

    • Read this curation session @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-11 17:03 UTC diff --git a/pages/traits/ecology/commensalism.html b/pages/traits/ecology/commensalism.html index b8bcb825565..2c3f57d842d 100644 --- a/pages/traits/ecology/commensalism.html +++ b/pages/traits/ecology/commensalism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    confers commensalism - traitmech:000042 + traitmech:000042 METPO:2007700

    Persistent colonization without harm or benefit to the host realizes the commensal lifestyle.

      @@ -115,7 +116,7 @@

      Edge evidence

    • commensalism - traitmech:000042 + traitmech:000042 associated with neutral host fitness effect @@ -270,7 +271,7 @@

      Edge evidence

      operationalizes commensalism - traitmech:000042 + traitmech:000042

      Benefit to the microbe with no detectable host cost operationalizes commensalism.

        @@ -330,7 +331,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -346,7 +347,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -580,7 +581,7 @@

    Proposed experiments

    Provenance -

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for commensalism: MicroRNAs (miRNAs) are small, noncoding RNAs involved in posttranscriptional gene regulation in both animal and plant. miRNAs derived from edible plants, referred to as xenomiRs, are proposed to cross-kingdom barriers and to modulate mammalian gene expression.', whose sentence came from PMID:40945860. That sentence is about plant-derived xenomiRs crossing kingdom barriers, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:40945860 'MicroRNAs (miRNAs) are small, noncoding RNAs involved in posttranscriptional gene regulation in both animal and plant. miRNAs derived from edible plants, referred to as xenomiRs, are proposed to cross-kingdom barriers and to modulate mammalian gene expression.'; PMID:40574831 'Emerging evidence suggests the gut microbiota plays a role in immune regulation, yet its impact on ITP remains unclear.'; PMID:42197356 'Examining the existing literature may identify knowledge gaps regarding precise mechanisms through which the development of GM influences the maturation of the immune system.'; PMID:41808832 'Given its promising anti-inflammatory properties, further research is warranted.'.

    +

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for commensalism: MicroRNAs (miRNAs) are small, noncoding RNAs involved in posttranscriptional gene regulation in both animal and plant. miRNAs derived from edible plants, referred to as xenomiRs, are proposed to cross-kingdom barriers and to modulate mammalian gene expression.', whose sentence came from PMID:40945860. That sentence is about plant-derived xenomiRs crossing kingdom barriers, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:40945860 'MicroRNAs (miRNAs) are small, noncoding RNAs involved in posttranscriptional gene regulation in both animal and plant. miRNAs derived from edible plants, referred to as xenomiRs, are proposed to cross-kingdom barriers and to modulate mammalian gene expression.'; PMID:40574831 'Emerging evidence suggests the gut microbiota plays a role in immune regulation, yet its impact on ITP remains unclear.'; PMID:42197356 'Examining the existing literature may identify knowledge gaps regarding precise mechanisms through which the development of GM influences the maturation of the immune system.'; PMID:41808832 'Given its promising anti-inflammatory properties, further research is warranted.'.

    @@ -670,7 +671,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1034,12 +1044,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/ecology/cytoplasmic_bacterial_predation.html b/pages/traits/ecology/cytoplasmic_bacterial_predation.html index cb9086af6a1..80dc1386a29 100644 --- a/pages/traits/ecology/cytoplasmic_bacterial_predation.html +++ b/pages/traits/ecology/cytoplasmic_bacterial_predation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1073/pnas.83.7.2138
    Daptobacter penetrates both membranes of the prey cell walls and reproduces in their degrading cytoplasm.
    -

    Guerrero et al. 1986, PMID:11542073, PMC323246, Figure 2E caption continued on p. 2141. Full five-page primary paper read from the Europe PMC PDF, including Methods, Results and Discussion, Table 2 and the note added in proof; actual Figure 2E/F micrographs and continued caption visually inspected. Enrichment-culture thin sections support prey-cytoplasmic invasion, degradation and division; these are not live-cell time courses or nutrient-tracing experiments. Figure 3 is a schematic, not additional experimental imaging. The scientific abstract was independently retrieved with EXT_ID:11542073 AND SRC:MED and title/DOI checked. MED and Crossref exposed no linked correction/retraction; publisher notice access returned HTTP 403, so that status is unverified. Source: https://europepmc.org/articles/PMC323246?pdf=render.

    +

    Guerrero et al. 1986, PMID:11542073, PMC323246, Figure 2E caption continued on p. 2141. Full five-page primary paper read from the Europe PMC PDF, including Methods, Results and Discussion, Table 2 and the note added in proof; actual Figure 2E/F micrographs and continued caption visually inspected. Enrichment-culture thin sections support prey-cytoplasmic invasion, degradation and division; these are not live-cell time courses or nutrient-tracing experiments. Figure 3 is a schematic, not additional experimental imaging. The scientific abstract was independently retrieved with EXT_ID:11542073 AND SRC:MED and title/DOI checked. MED and Crossref exposed no linked correction/retraction; publisher notice access returned HTTP 403, so that status is unverified. Source: https://europepmc.org/articles/PMC323246?pdf=render.

  • https://lpsn.dsmz.de/genus/daptobacter
    invade their host cells and replicate in the cytoplasm, consuming their prey from the inside out
    -

    LPSN genus Daptobacter, Notes, directly retrieved 2026-10-11. LPSN quotes this description from Madigan et al. 2019; that book was not independently read. Supports established terminology, not independent experimental replication of Guerrero et al. LPSN marks the genus name not validly published and preferred rather than correct. Its permanent record link is https://doi.org/10.83108/rn.684. The nomenclatural record is not evidence for a sequence-defined lineage or an NCBITaxon mapping.

    +

    LPSN genus Daptobacter, Notes, directly retrieved 2026-10-11. LPSN quotes this description from Madigan et al. 2019; that book was not independently read. Supports established terminology, not independent experimental replication of Guerrero et al. LPSN marks the genus name not validly published and preferred rather than correct. Its permanent record link is https://doi.org/10.83108/rn.684. The nomenclatural record is not evidence for a sequence-defined lineage or an NCBITaxon mapping.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -271,7 +272,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed cytoplasmic bacterial predation -

      Added traitmech:000700 at PROPOSED under predatory bacterium, with a primary Figure 2E caption snippet from DOI:10.1073/pnas.83.7.2138 (PMID:11542073; full PDF and actual microscopy read) and explicitly secondary LPSN terminology evidence at https://lpsn.dsmz.de/genus/daptobacter. No taxon ID or protein mechanism inferred; two open scope and evidence discussions retained. Main/worktree ignored-and-hidden novelty searches, full-block reservation checks, live upstream snapshots and complete open/draft PR file lists support v576 METPO:1065300-1065399. Native writer dry run and schema prevalidation were used. Existing TraitRecords are unchanged; generated products and full validation/review follow in this branch.

    +

    Added traitmech:000700 at PROPOSED under predatory bacterium, with a primary Figure 2E caption snippet from DOI:10.1073/pnas.83.7.2138 (PMID:11542073; full PDF and actual microscopy read) and explicitly secondary LPSN terminology evidence at https://lpsn.dsmz.de/genus/daptobacter. No taxon ID or protein mechanism inferred; two open scope and evidence discussions retained. Main/worktree ignored-and-hidden novelty searches, full-block reservation checks, live upstream snapshots and complete open/draft PR file lists support v576 METPO:1065300-1065399. Native writer dry run and schema prevalidation were used. Existing TraitRecords are unchanged; generated products and full validation/review follow in this branch.

    • Read this curation session @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-11 15:34 UTC diff --git a/pages/traits/ecology/endophytic.html b/pages/traits/ecology/endophytic.html index 61c70af60bb..ec7e42aa4ce 100644 --- a/pages/traits/ecology/endophytic.html +++ b/pages/traits/ecology/endophytic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    confers endophytic - traitmech:000442 + traitmech:000442 METPO:2007700

    Endophytic colonization realizes the endophytic ecological trait.

      @@ -178,9 +179,9 @@

      Parent traits (1)

      Synonyms (2)

    @@ -196,7 +197,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -324,7 +325,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -688,12 +698,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 19:39 UTC diff --git a/pages/traits/ecology/endosymbiosis.html b/pages/traits/ecology/endosymbiosis.html index c5a7ac89e1b..01a1eb1d0d3 100644 --- a/pages/traits/ecology/endosymbiosis.html +++ b/pages/traits/ecology/endosymbiosis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    confers endosymbiosis - traitmech:000045 + traitmech:000045 METPO:2007700

    Sustained residence inside host cells defines endosymbiosis.

      @@ -115,7 +116,7 @@

      Edge evidence

    • endosymbiosis - traitmech:000045 + traitmech:000045 causes reductive genome evolution METPO:1007721 @@ -273,7 +274,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • endosymbiont RELATED_SYNONYM · DOI:10.1038/nrmicro2670
        • +
      • endosymbiont RELATED_SYNONYM · DOI:10.1038/nrmicro2670
    @@ -289,7 +290,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -522,7 +523,7 @@

    Proposed experiments

    Provenance -

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for endosymbiosis: Growth anomalies (GAs) are coral diseases characterised by tumour-like skeletal lesions reported globally, yet their causes remain poorly understood.', whose sentence came from PMID:42130304. That sentence is about growth anomalies in corals, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:42130304 'Growth anomalies (GAs) are coral diseases characterised by tumour-like skeletal lesions reported globally, yet their causes remain poorly understood.'; PMID:41612704 'Disrupting this obligate symbiosis represents a promising pest control strategy, yet the molecular mechanisms maintaining host-symbiont homeostasis remain poorly understood.'; PMID:40831140 'This review explores the origin and evolution of plastids, their protein-import machinery, compartmentalization, and interactions with other cellular compartments, and highlights key unanswered questions in these areas.'; PMID:41764142 'Detritivorous E. murphyi larvae can increase soil nitrogen levels by up to five times compared with similar uncolonized substrates, although the mechanisms involved remain unknown.'.

    +

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for endosymbiosis: Growth anomalies (GAs) are coral diseases characterised by tumour-like skeletal lesions reported globally, yet their causes remain poorly understood.', whose sentence came from PMID:42130304. That sentence is about growth anomalies in corals, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:42130304 'Growth anomalies (GAs) are coral diseases characterised by tumour-like skeletal lesions reported globally, yet their causes remain poorly understood.'; PMID:41612704 'Disrupting this obligate symbiosis represents a promising pest control strategy, yet the molecular mechanisms maintaining host-symbiont homeostasis remain poorly understood.'; PMID:40831140 'This review explores the origin and evolution of plastids, their protein-import machinery, compartmentalization, and interactions with other cellular compartments, and highlights key unanswered questions in these areas.'; PMID:41764142 'Detritivorous E. murphyi larvae can increase soil nitrogen levels by up to five times compared with similar uncolonized substrates, although the mechanisms involved remain unknown.'.

    @@ -612,7 +613,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -976,12 +986,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/ecology/epibiotic_bacterial_predation.html b/pages/traits/ecology/epibiotic_bacterial_predation.html index f14542a4801..de3b909bc37 100644 --- a/pages/traits/ecology/epibiotic_bacterial_predation.html +++ b/pages/traits/ecology/epibiotic_bacterial_predation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1038/ismej.2013.164
    epibiotic, where they attach to the prey from outside.
    -

    Pasternak et al. 2014, PMID:24088628, PMC3930308, Introduction; contiguous quotation defining the external predation strategy. Abstract, Introduction, culture/prey-range/electron-microscopy Methods, growth Results, Discussion and actual Figure 1 read. JSS and Micavibrio aeruginosavorus EPB observations support external feeding; genome comparisons are not functional proof. Do not make the paper's binary-division generalization defining: the 2024 JSS time-lapse study demonstrates nonbinary division. Other figures, genomic analyses and supplements not fully assessed. Full text: https://pmc.ncbi.nlm.nih.gov/articles/PMC3930308/.

    +

    Pasternak et al. 2014, PMID:24088628, PMC3930308, Introduction; contiguous quotation defining the external predation strategy. Abstract, Introduction, culture/prey-range/electron-microscopy Methods, growth Results, Discussion and actual Figure 1 read. JSS and Micavibrio aeruginosavorus EPB observations support external feeding; genome comparisons are not functional proof. Do not make the paper's binary-division generalization defining: the 2024 JSS time-lapse study demonstrates nonbinary division. Other figures, genomic analyses and supplements not fully assessed. Full text: https://pmc.ncbi.nlm.nih.gov/articles/PMC3930308/.

  • DOI:10.1099/ijs.0.039701-0
    No periplasmic growth stage was observed and no bdelloplast was formed.
    -

    Koval et al. 2013, PMID:22368169, directly read scientific Abstract on the publisher site and source-qualified MED metadata. JSS was isolated from sewage in London, Ontario, with Caulobacter crescentus prey; attached external predation left emptied cells. This supports natural strain provenance and noninvasive feeding, not its frequency in undisturbed sewage. Full text, figures and supplement unavailable to this review; no Methods claim imported. Publisher: https://doi.org/10.1099/ijs.0.039701-0.

    +

    Koval et al. 2013, PMID:22368169, directly read scientific Abstract on the publisher site and source-qualified MED metadata. JSS was isolated from sewage in London, Ontario, with Caulobacter crescentus prey; attached external predation left emptied cells. This supports natural strain provenance and noninvasive feeding, not its frequency in undisturbed sewage. Full text, figures and supplement unavailable to this review; no Methods claim imported. Publisher: https://doi.org/10.1099/ijs.0.039701-0.

  • DOI:10.1038/s41467-024-48042-5
    Bdellovibrio exovorus is an obligate epibiotic predator that attaches on the prey cell surface, where it grows and proliferates.
    -

    Santin et al. 2024, PMID:38678033, PMC11055950, scientific Abstract; direct contiguous match. Abstract, Introduction, Results, Discussion, selected culture/killing/live-imaging/cryo-EM/statistics Methods and actual Figures 2-5 read; other Methods, actual Figures 1/6, supplements and movies not fully assessed. JSS time-lapse growth and prey-content loss support feeding, not direct molecular nutrient tracing. The 2025 correction DOI:10.1038/s41467-025-58758-7 (PMID:40234419, PMC12000597) was read: retain its qualified prey-range wording and removal of the S-layer-defense recommendation. It is not another independent experiment. Full corrected text: https://pmc.ncbi.nlm.nih.gov/articles/PMC11055950/.

    +

    Santin et al. 2024, PMID:38678033, PMC11055950, scientific Abstract; direct contiguous match. Abstract, Introduction, Results, Discussion, selected culture/killing/live-imaging/cryo-EM/statistics Methods and actual Figures 2-5 read; other Methods, actual Figures 1/6, supplements and movies not fully assessed. JSS time-lapse growth and prey-content loss support feeding, not direct molecular nutrient tracing. The 2025 correction DOI:10.1038/s41467-025-58758-7 (PMID:40234419, PMC12000597) was read: retain its qualified prey-range wording and removal of the S-layer-defense recommendation. It is not another independent experiment. Full corrected text: https://pmc.ncbi.nlm.nih.gov/articles/PMC11055950/.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1038/s41467-024-48042-5 - Qualified to JSS (ATCC BAA-2330 = DSM 25223), not every species member. Studied as Bdellovibrio exovorus on C. crescentus; the predator's natural sewage-isolate provenance and type-strain identity are stated in the primary Abstract at https://doi.org/10.1099/ijs.0.039701-0. Some 2024 prey strains carry engineered labels or deletions; this natural-provenance qualification concerns the predator. NCBI species ID/name and JSS type material independently resolved on 2026-10-11: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=453816. + Qualified to JSS (ATCC BAA-2330 = DSM 25223), not every species member. Studied as Bdellovibrio exovorus on C. crescentus; the predator's natural sewage-isolate provenance and type-strain identity are stated in the primary Abstract at https://doi.org/10.1099/ijs.0.039701-0. Some 2024 prey strains carry engineered labels or deletions; this natural-provenance qualification concerns the predator. NCBI species ID/name and JSS type material independently resolved on 2026-10-11: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=453816. @@ -302,7 +303,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed epibiotic bacterial predation -

      Added PROPOSED traitmech:000697 beneath predatory bacterium with DOI:10.1038/ismej.2013.164, DOI:10.1099/ijs.0.039701-0 and DOI:10.1038/s41467-024-48042-5; all three carry directly checked snippets. The 2025 correction DOI:10.1038/s41467-025-58758-7 is context, not independent experimental evidence. Qualified NCBITaxon:453816 example to natural JSS; retained two OPEN discussions and deferred protein mechanisms/exact mappings. Ignored-and-hidden main/worktree and pending-PR checks supported local ID and v573 block 1065000-1065099. Guarded writer dry run and 23 focused tests passed before this history was scaffolded.

    +

    Added PROPOSED traitmech:000697 beneath predatory bacterium with DOI:10.1038/ismej.2013.164, DOI:10.1099/ijs.0.039701-0 and DOI:10.1038/s41467-024-48042-5; all three carry directly checked snippets. The 2025 correction DOI:10.1038/s41467-025-58758-7 is context, not independent experimental evidence. Qualified NCBITaxon:453816 example to natural JSS; retained two OPEN discussions and deferred protein mechanisms/exact mappings. Ignored-and-hidden main/worktree and pending-PR checks supported local ID and v573 block 1065000-1065099. Guarded writer dry run and 23 focused tests passed before this history was scaffolded.

    • Read this curation session @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-11 11:45 UTC diff --git a/pages/traits/ecology/epiphytic.html b/pages/traits/ecology/epiphytic.html index 0dde2fe1f16..923b39f61e2 100644 --- a/pages/traits/ecology/epiphytic.html +++ b/pages/traits/ecology/epiphytic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    confers epiphytic - traitmech:000443 + traitmech:000443 METPO:2007700

    Epiphytic colonization realizes the plant-surface epiphytic ecological trait.

      @@ -178,9 +179,9 @@

      Parent traits (1)

      Synonyms (2)

    @@ -196,7 +197,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -324,7 +325,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -688,12 +698,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 20:21 UTC diff --git a/pages/traits/ecology/free_living.html b/pages/traits/ecology/free_living.html index 4fd24ee3ff1..d5cd07cc112 100644 --- a/pages/traits/ecology/free_living.html +++ b/pages/traits/ecology/free_living.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    confers free-living - traitmech:000048 + traitmech:000048 METPO:2007700

    Persistent occupancy of environmental habitats realizes the free-living lifestyle.

      @@ -115,7 +116,7 @@

      Edge evidence

    • free-living - traitmech:000048 + traitmech:000048 associated with biogeographic community structure @@ -137,7 +138,7 @@

      Edge evidence

      required for free-living - traitmech:000048 + traitmech:000048

      Self-sufficient metabolic pathways for carbon, nitrogen, sulfur and cofactors are required for a host-independent free-living life strategy.

        @@ -225,7 +226,7 @@

        Edge evidence

        promotes free-living - traitmech:000048 + traitmech:000048 RO:0002213

        Osmoadaptation supports persistence in unstable/saline environments characteristic of the free-living lifestyle.

          @@ -339,7 +340,7 @@

          kg-microbe context

          via parent_proxy.

            -
          • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
            • +
          • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

          512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

          @@ -583,14 +584,14 @@

          Proposed experiments

          -

          Resolution: Refuted. The record's own would_refute criterion was 'the trehalose knockout is osmotically impaired', and it is: in Bradyrhizobium diazoefficiens USDA 110 the otsCB-otsA deletion loses viability at 400 mM sorbitol, a nonionic challenge that separates osmotic pressure from ion toxicity, as well as at 27 mM NaCl, 50 mM MgCl2 and 75 mM MgSO4 (DOI:10.1128/mBio.00390-21). A cytoplasmic trehalase phenocopies the deletion and exogenous trehalose rescues the otsA deletion but not the transporter-deficient strains, so the phenotype tracks intracellular trehalose. Independently constructed mutants in the same background are inhibited on 60 mM NaCl (DOI:10.1128/AEM.02483-09). The split was therefore not real, and trehalose_biosynthesis now enables osmotic_stress_tolerance alongside ectoine and glycine betaine. Two things were deliberately NOT decided here and are tracked in issue 614: the weaker pre-existing trehalose_biosynthesis to environmental_stress_tolerance edge was retained rather than deleted, and the observation that the same AEM study found no desiccation defect for low-trehalose otsA mutants argues trehalose's role is specifically osmotic.

          +

          Resolution: Refuted. The record's own would_refute criterion was 'the trehalose knockout is osmotically impaired', and it is: in Bradyrhizobium diazoefficiens USDA 110 the otsCB-otsA deletion loses viability at 400 mM sorbitol, a nonionic challenge that separates osmotic pressure from ion toxicity, as well as at 27 mM NaCl, 50 mM MgCl2 and 75 mM MgSO4 (DOI:10.1128/mBio.00390-21). A cytoplasmic trehalase phenocopies the deletion and exogenous trehalose rescues the otsA deletion but not the transporter-deficient strains, so the phenotype tracks intracellular trehalose. Independently constructed mutants in the same background are inhibited on 60 mM NaCl (DOI:10.1128/AEM.02483-09). The split was therefore not real, and trehalose_biosynthesis now enables osmotic_stress_tolerance alongside ectoine and glycine betaine. Two things were deliberately NOT decided here and are tracked in issue 614: the weaker pre-existing trehalose_biosynthesis to environmental_stress_tolerance edge was retained rather than deleted, and the observation that the same AEM study found no desiccation defect for low-trehalose otsA mutants argues trehalose's role is specifically osmotic.

          Provenance -

          Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for free-living: Interactions between parasites and the gut microbiota play a key role in immune responses and susceptibility to zoonotic diseases; however, many aspects of how protozoan infections alter microbial diversity and how these changes influence parasite pathogenicity and host defense remain poorly understood.', whose sentence came from PMID:41989588. That sentence is about protozoan infection and gut microbial diversity, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:41989588 'Interactions between parasites and the gut microbiota play a key role in immune responses and susceptibility to zoonotic diseases; however, many aspects of how protozoan infections alter microbial diversity and how these changes influence parasite pathogenicity and host defense remain poorly understood.'; PMID:42039802 'Engineered microbial assemblies tailored to specific host plants and environmental conditions have shown potential in stabilizing crop performance during drought, salinity, and nutrient limitations.'; PMID:41943163 'OBJECTIVES: Oxo-polyethylene (oxo-PE) is marketed as a biodegradable plastic, yet its environmental degradation remains poorly understood, particularly in marine contexts.'; PMID:42125129 "However, contradictions persist regarding pH's effect on microbial diversity, with unresolved questions about how specific environmental conditions regulate microbial taxa.".

          +

          Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for free-living: Interactions between parasites and the gut microbiota play a key role in immune responses and susceptibility to zoonotic diseases; however, many aspects of how protozoan infections alter microbial diversity and how these changes influence parasite pathogenicity and host defense remain poorly understood.', whose sentence came from PMID:41989588. That sentence is about protozoan infection and gut microbial diversity, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:41989588 'Interactions between parasites and the gut microbiota play a key role in immune responses and susceptibility to zoonotic diseases; however, many aspects of how protozoan infections alter microbial diversity and how these changes influence parasite pathogenicity and host defense remain poorly understood.'; PMID:42039802 'Engineered microbial assemblies tailored to specific host plants and environmental conditions have shown potential in stabilizing crop performance during drought, salinity, and nutrient limitations.'; PMID:41943163 'OBJECTIVES: Oxo-polyethylene (oxo-PE) is marketed as a biodegradable plastic, yet its environmental degradation remains poorly understood, particularly in marine contexts.'; PMID:42125129 "However, contradictions persist regarding pH's effect on microbial diversity, with unresolved questions about how specific environmental conditions regulate microbial taxa.".

    @@ -653,7 +654,7 @@

    Curation history

  • · CONNECT_CAUSAL_GRAPH · claude -

    Added trehalose_biosynthesis -[RO:0002327 enables]-> osmotic_stress_tolerance to free_living_environmental_habitat, resolving the record's x-compatible-solute-partitioning knowledge gap (#614) against its own stated would_refute criterion. Loss-of-function, trehalase-depletion and metabolite-rescue evidence from DOI:10.1128/mBio.00390-21, replicated by independent mutants in DOI:10.1128/AEM.02483-09, show the trehalose knockout is osmotically impaired, so the trehalose/ectoine split the graph asserted is not a real distinction. This also merges the graph's stranded {trehalose_biosynthesis, environmental_stress_tolerance} component into the main one. The pre-existing edge to environmental_stress_tolerance is retained rather than deleted: its comparative-genomics evidence is weaker but removing a cited edge is a semantic decision, tracked in #614.

    +

    Added trehalose_biosynthesis -[RO:0002327 enables]-> osmotic_stress_tolerance to free_living_environmental_habitat, resolving the record's x-compatible-solute-partitioning knowledge gap (#614) against its own stated would_refute criterion. Loss-of-function, trehalase-depletion and metabolite-rescue evidence from DOI:10.1128/mBio.00390-21, replicated by independent mutants in DOI:10.1128/AEM.02483-09, show the trehalose knockout is osmotically impaired, so the trehalose/ectoine split the graph asserted is not a real distinction. This also merges the graph's stranded {trehalose_biosynthesis, environmental_stress_tolerance} component into the main one. The pre-existing edge to environmental_stress_tolerance is retained rather than deleted: its comparative-genomics evidence is weaker but removing a cited edge is a semantic decision, tracked in #614.

  • @@ -671,7 +672,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1038/nrmicro1341 (already present on sibling record soil_dwelling.yaml evidence[1]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-014 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.1038/nrmicro1341 (already present on sibling record soil_dwelling.yaml evidence[1]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-014 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -681,7 +682,7 @@

    Recorded curation sessions

  • · claude-code
    • EDIT — Connect trehalose biosynthesis to osmotic stress tolerance in free_living -

      Resolves the record's own x-compatible-solute-partitioning knowledge gap against its stated would_refute criterion. Added trehalose_biosynthesis -[RO:0002327 enables]-> osmotic_stress_tolerance to free_living_environmental_habitat with two independent experimental references and verbatim snippets: DOI:10.1128/mBio.00390-21 (Bradyrhizobium diazoefficiens USDA 110; the otsCB-otsA deletion loses viability at 400 mM sorbitol, 27 mM NaCl, 50 mM MgCl2 and 75 mM MgSO4, the nonionic sorbitol condition separating osmotic pressure from ion toxicity; a cytoplasmic trehalase phenocopies it and exogenous trehalose rescues the otsA deletion but not the transporter-deficient strains) and DOI:10.1128/AEM.02483-09 (independently constructed mutants in the same background inhibited on 60 mM NaCl). Both DOIs and both snippets were verified against the primary sources this session, not taken from the research artifact. The edit merges the graph's stranded trehalose_biosynthesis/environmental_stress_tolerance component into the main one, taking the graph from 2 wired components to 1 with no unwired nodes; that fragmentation was invisible to audit-graphs because the graph is NONMECHANISTIC, filed as issue 613. The pre-existing trehalose_biosynthesis to environmental_stress_tolerance edge was RETAINED, not deleted: its comparative-genomics evidence is weaker than what is added here and the desiccation result in AEM.02483-09 argues trehalose's role is specifically osmotic, but removing a cited edge is a semantic decision and evidence removal without provenance is the issue 520 failure mode. Written through write_validated_trait with a CONNECT_CAUSAL_GRAPH curation event. Gates: validate-strict 0 errors, audit-snippets 2592 findings all baselined with 0 new, audit-graphs 0 new, audit-derived-reports clean after just gen-pages. Also set the x-compatible-solute-partitioning discussion to RESOLVED with resolved_date 2026-08-31 and a resolution_note recording the verdict, the two references, and the two questions deliberately left open (the retained environmental_stress_tolerance edge, and the absence of a desiccation defect for low-trehalose otsA mutants). Regenerated pages/ via just gen-pages and app/discussions/data.js via just gen-discussions-data. This record is one record for one coherent change to one target, per history/README.md.

    +

    Resolves the record's own x-compatible-solute-partitioning knowledge gap against its stated would_refute criterion. Added trehalose_biosynthesis -[RO:0002327 enables]-> osmotic_stress_tolerance to free_living_environmental_habitat with two independent experimental references and verbatim snippets: DOI:10.1128/mBio.00390-21 (Bradyrhizobium diazoefficiens USDA 110; the otsCB-otsA deletion loses viability at 400 mM sorbitol, 27 mM NaCl, 50 mM MgCl2 and 75 mM MgSO4, the nonionic sorbitol condition separating osmotic pressure from ion toxicity; a cytoplasmic trehalase phenocopies it and exogenous trehalose rescues the otsA deletion but not the transporter-deficient strains) and DOI:10.1128/AEM.02483-09 (independently constructed mutants in the same background inhibited on 60 mM NaCl). Both DOIs and both snippets were verified against the primary sources this session, not taken from the research artifact. The edit merges the graph's stranded trehalose_biosynthesis/environmental_stress_tolerance component into the main one, taking the graph from 2 wired components to 1 with no unwired nodes; that fragmentation was invisible to audit-graphs because the graph is NONMECHANISTIC, filed as issue 613. The pre-existing trehalose_biosynthesis to environmental_stress_tolerance edge was RETAINED, not deleted: its comparative-genomics evidence is weaker than what is added here and the desiccation result in AEM.02483-09 argues trehalose's role is specifically osmotic, but removing a cited edge is a semantic decision and evidence removal without provenance is the issue 520 failure mode. Written through write_validated_trait with a CONNECT_CAUSAL_GRAPH curation event. Gates: validate-strict 0 errors, audit-snippets 2592 findings all baselined with 0 new, audit-graphs 0 new, audit-derived-reports clean after just gen-pages. Also set the x-compatible-solute-partitioning discussion to RESOLVED with resolved_date 2026-08-31 and a resolution_note recording the verdict, the two references, and the two questions deliberately left open (the retained environmental_stress_tolerance edge, and the absence of a desiccation defect for low-trehalose otsA mutants). Regenerated pages/ via just gen-pages and app/discussions/data.js via just gen-discussions-data. This record is one record for one coherent change to one target, per history/README.md.

    • Read this curation session @@ -713,7 +714,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1077,12 +1087,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/ecology/fungal_nematode_egg_parasitism.html b/pages/traits/ecology/fungal_nematode_egg_parasitism.html index 26901eb28a0..5333a6d875d 100644 --- a/pages/traits/ecology/fungal_nematode_egg_parasitism.html +++ b/pages/traits/ecology/fungal_nematode_egg_parasitism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.3389/fmicb.2021.617710
    The egg-pathogenic fungus Purpureocillium lilacinum parasitizes on nematode eggs
    -

    Xu et al. 2021, PMID:33897634, PMCID:PMC8058359, scientific Abstract; direct JATS match and native VERIFIED. Own JZD02 experiment, Methods and actual Figure 1 A-C support infection of Meloidogyne incognita eggs. Supplementary Table 1 defines infection by hyphal penetration through an individual egg, not mere surface contact. Its 30-hour printed mean disagrees with the replicate counts; no numerical infection rates are adopted. The 6-hour control and 42-hour infected transcriptomes differ in time and include mixed infection stages. Expression associations are not causal protein evidence.

    +

    Xu et al. 2021, PMID:33897634, PMCID:PMC8058359, scientific Abstract; direct JATS match and native VERIFIED. Own JZD02 experiment, Methods and actual Figure 1 A-C support infection of Meloidogyne incognita eggs. Supplementary Table 1 defines infection by hyphal penetration through an individual egg, not mere surface contact. Its 30-hour printed mean disagrees with the replicate counts; no numerical infection rates are adopted. The 6-hour control and 42-hour infected transcriptomes differ in time and include mixed infection stages. Expression associations are not causal protein evidence.

  • DOI:10.3389/fmicb.2016.01084
    Infected eggs by P. lilacinum 36-1.
    -

    Xie et al. 2016, PMID:27486440, PMCID:PMC4949223, Figure 5 caption, panel B; actual panels A-C and Methods/Results inspected. P. lilacinum denotes Purpureocillium lilacinum. Direct JATS match; native NOT_IN_ABSTRACT is retained. This is its own 36-1 infection experiment, not a repetition of Xu's citation. Eggs were supplied as the only nourishment for the reported 24-hour comparison, but microscopy does not quantify nutrient assimilation. RNA-seq replicates were pooled; gene homology and expression do not demonstrate a required effector.

    +

    Xie et al. 2016, PMID:27486440, PMCID:PMC4949223, Figure 5 caption, panel B; actual panels A-C and Methods/Results inspected. P. lilacinum denotes Purpureocillium lilacinum. Direct JATS match; native NOT_IN_ABSTRACT is retained. This is its own 36-1 infection experiment, not a repetition of Xu's citation. Eggs were supplied as the only nourishment for the reported 24-hour comparison, but microscopy does not quantify nutrient assimilation. RNA-seq replicates were pooled; gene homology and expression do not demonstrate a required effector.

  • DOI:10.3389/fmicb.2021.617710
    Infection defined by Purpureocillium lilacinum mycelium penetrating through the whole individual Meloidogyne incognita egg
    -

    Xu et al. 2021, Supplementary Table 1 footnote, Table_1.DOCX from the PMC8058359 Europe PMC supplementaryFiles archive. Direct DOCX text match and complete rendered page inspected; native NOT_IN_ABSTRACT is retained. This operational scoring criterion supports individual-egg penetration, not another independent experiment or a direct nutrient-flux measurement. The two Xu excerpts total 23 words. The printed 30-hour mean discrepancy remains unresolved; no infection rate is imported.

    +

    Xu et al. 2021, Supplementary Table 1 footnote, Table_1.DOCX from the PMC8058359 Europe PMC supplementaryFiles archive. Direct DOCX text match and complete rendered page inspected; native NOT_IN_ABSTRACT is retained. This operational scoring criterion supports individual-egg penetration, not another independent experiment or a direct nutrient-flux measurement. The two Xu excerpts total 23 words. The printed 30-hour mean discrepancy remains unresolved; no infection rate is imported.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -351,7 +352,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -380,12 +390,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-14 12:53 UTC diff --git a/pages/traits/ecology/fungal_nematode_endoparasitism.html b/pages/traits/ecology/fungal_nematode_endoparasitism.html index 915b501ab45..8b6cb8ca852 100644 --- a/pages/traits/ecology/fungal_nematode_endoparasitism.html +++ b/pages/traits/ecology/fungal_nematode_endoparasitism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (3)

    DOI:10.1371/journal.pgen.1006017
    Drechmeria coniospora is an obligate fungal pathogen that infects nematodes via the adhesion of specialized spores to the host cuticle.
    -

    Lebrigand et al. 2016, PMID:27153332, PMCID:PMC4859500, scientific Abstract. Direct JATS match and native VERIFIED. Author Summary and Discussion distinguish spore-initiated endoparasitism from hyphal traps and egg infection. Actual Figures 8 and 9 show recombinant fungal growth in C. elegans, not unmodified natural exemplars. S1 Text was fully read and visually checked: the laboratory line was serially passaged for about 15 years; its source isolate and ARSEF 6962 share provenance. Obligate is the authors' species description, not a universal class requirement or inability to grow on their artificial medium. Predicted genes and expression are not a universal mechanism.

    +

    Lebrigand et al. 2016, PMID:27153332, PMCID:PMC4859500, scientific Abstract. Direct JATS match and native VERIFIED. Author Summary and Discussion distinguish spore-initiated endoparasitism from hyphal traps and egg infection. Actual Figures 8 and 9 show recombinant fungal growth in C. elegans, not unmodified natural exemplars. S1 Text was fully read and visually checked: the laboratory line was serially passaged for about 15 years; its source isolate and ARSEF 6962 share provenance. Obligate is the authors' species description, not a universal class requirement or inability to grow on their artificial medium. Predicted genes and expression are not a universal mechanism.

  • DOI:10.3390/jof10010068
    Then, the fungal hyphae penetrate into the nematode body cavity and grow in the nematode body
    -

    Sun et al. 2024, PMID:38248977, PMCID:PMC10820206, Results 3.2. Direct JATS match; native NOT_IN_ABSTRACT retained. Methods 2.5 and actual Figure 2c,d concern GFP-engineered HR-eGFP1 on Bursaphelenchus xylophilus; Figure 2 distinguishes attachment, entry, internal growth and emergence. The entire two-page supplement, including S1-S3, was inspected. Methods 2.6 scores attached spores or colonization as parasitism; no rate is imported as an internal-infection rate. Main-text intestinal infection after swallowing is tentative; do not silently strengthen it using the supplement caption. No field efficacy or safety is inferred.

    +

    Sun et al. 2024, PMID:38248977, PMCID:PMC10820206, Results 3.2. Direct JATS match; native NOT_IN_ABSTRACT retained. Methods 2.5 and actual Figure 2c,d concern GFP-engineered HR-eGFP1 on Bursaphelenchus xylophilus; Figure 2 distinguishes attachment, entry, internal growth and emergence. The entire two-page supplement, including S1-S3, was inspected. Methods 2.6 scores attached spores or colonization as parasitism; no rate is imported as an internal-infection rate. Main-text intestinal infection after swallowing is tentative; do not silently strengthen it using the supplement caption. No field efficacy or safety is inferred.

  • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -339,7 +340,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -368,12 +378,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-14 15:22 UTC diff --git a/pages/traits/ecology/fungal_nematophagy.html b/pages/traits/ecology/fungal_nematophagy.html index 2487e32b634..d87fb92d84b 100644 --- a/pages/traits/ecology/fungal_nematophagy.html +++ b/pages/traits/ecology/fungal_nematophagy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -73,7 +74,7 @@

    Trait evidence (4)

    DOI:10.1371/journal.pbio.3002400
    At mid to late time points, we observed hyphal growth inside nematodes following penetration of the cuticle, corresponding to digestion.
    -

    Lin et al. 2023, PMID:37988381; Results subsection on late-time protease induction, publisher XML sec018. Native verifier: NOT_IN_ABSTRACT; exact full-text match. Actual Figure 5, Table 1 and S7 inspected. GFP-labeled reference TWF3407 is engineered, not an unmodified natural exemplar. Protease inhibition delays internal growth at 12 h without proving complete feeding loss or quantifying assimilation. Remaining figures and raw S1 spreadsheet were not fully audited.

    +

    Lin et al. 2023, PMID:37988381; Results subsection on late-time protease induction, publisher XML sec018. Native verifier: NOT_IN_ABSTRACT; exact full-text match. Actual Figure 5, Table 1 and S7 inspected. GFP-labeled reference TWF3407 is engineered, not an unmodified natural exemplar. Protease inhibition delays internal growth at 12 h without proving complete feeding loss or quantifying assimilation. Remaining figures and raw S1 spreadsheet were not fully audited.

    @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Canonical examples DOI:10.3390/f10050404 - Qualified Figure 2a example: unnamed culture isolated from grocery-store mushrooms and identified morphologically, per Methods 2.1 at https://doi.org/10.3390/f10050404. The water-agar assay used 20 mixed-age nematodes and assessed this fungus after one week. No strain deposit, molecular identification or genetic provenance is inferred. NCBI EFetch resolved the species on 2026-10-13. + Qualified Figure 2a example: unnamed culture isolated from grocery-store mushrooms and identified morphologically, per Methods 2.1 at https://doi.org/10.3390/f10050404. The water-agar assay used 20 mixed-age nematodes and assessed this fungus after one week. No strain deposit, molecular identification or genetic provenance is inferred. NCBI EFetch resolved the species on 2026-10-13. @@ -306,7 +307,7 @@

    Discussions and Knowledge Gaps (3)

    mechanism it concerns.

    -

    Marlin's Table 2 conflicts with its Introduction on two host responses; Table 3 and Results differ for P. artyukhovskii. Those disputed host ranges are not imported. den Belder's Figure 2 panel labels/caption, Table 3 direction and significance notation disagree with prose; no numerical rates are adopted. Lin's Results uses mep1 where Table 1 and Figure 5 use mcp1; no protein identity is silently reconciled. Its linked DOI:10.1371/journal.pbio.3003178 is a later Update Article, not a correction or independent laboratory replication. Capture and digestion have distinct assays; expression associations do not establish universal effectors. No causal graph, protein example or chemical mechanism is asserted. Source-status checks are bounded: MDPI's notice page returned 403, and no comprehensive notice clearance is claimed. Source hashes, inspected sections and actual native verdicts are retained in the verification sidecar.

    +

    Marlin's Table 2 conflicts with its Introduction on two host responses; Table 3 and Results differ for P. artyukhovskii. Those disputed host ranges are not imported. den Belder's Figure 2 panel labels/caption, Table 3 direction and significance notation disagree with prose; no numerical rates are adopted. Lin's Results uses mep1 where Table 1 and Figure 5 use mcp1; no protein identity is silently reconciled. Its linked DOI:10.1371/journal.pbio.3003178 is a later Update Article, not a correction or independent laboratory replication. Capture and digestion have distinct assays; expression associations do not establish universal effectors. No causal graph, protein example or chemical mechanism is asserted. Source-status checks are bounded: MDPI's notice page returned 403, and no comprehensive notice clearance is claimed. Source hashes, inspected sections and actual native verdicts are retained in the verification sidecar.

    @@ -338,7 +339,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed fungal nematophagy -

      Added traitmech:000719 as PROPOSED with four contiguous excerpts from Marlin 2019 DOI:10.3390/f10050404, den Belder and Jansen 1994 stable IRD PDF, and Lin 2023 DOI:10.1371/journal.pbio.3002400. Includes a source-qualified Pleurotus ostreatus example, conservative phenotype parent, explicit source discrepancies and no inferred causal graph. Local ID, cohort v595 and block 1067200-1067299 passed bounded ignored/hidden, retained-history and open/draft PR reservation checks; proposal and source receipts accompany the record. Writer dry-run and validated application passed; full QC and review remain pending.

    +

    Added traitmech:000719 as PROPOSED with four contiguous excerpts from Marlin 2019 DOI:10.3390/f10050404, den Belder and Jansen 1994 stable IRD PDF, and Lin 2023 DOI:10.1371/journal.pbio.3002400. Includes a source-qualified Pleurotus ostreatus example, conservative phenotype parent, explicit source discrepancies and no inferred causal graph. Local ID, cohort v595 and block 1067200-1067299 passed bounded ignored/hidden, retained-history and open/draft PR reservation checks; proposal and source receipts accompany the record. Writer dry-run and validated application passed; full QC and review remain pending.

    • Read this curation session @@ -370,7 +371,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -399,12 +409,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-13 15:36 UTC diff --git a/pages/traits/ecology/gut_associated.html b/pages/traits/ecology/gut_associated.html index dc18f8ce72f..1201f9185d6 100644 --- a/pages/traits/ecology/gut_associated.html +++ b/pages/traits/ecology/gut_associated.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    confers gut-associated - traitmech:000052 + traitmech:000052 METPO:2007700

    The intestinal environment supports persistent residency.

      @@ -115,7 +116,7 @@

      Edge evidence

    • gut-associated - traitmech:000052 + traitmech:000052 contributes to host metabolic contribution @@ -156,7 +157,7 @@

      Edge evidence

      prerequisite for gut-associated - traitmech:000052 + traitmech:000052

      Adhesion to mucus/epithelium is a prerequisite for long-term gut colonization.

        @@ -386,7 +387,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -402,7 +403,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -631,14 +632,14 @@

    Proposed experiments

    -

    Resolution: Supported, with two bounds. The would_support criterion was 'oxygen rises on depletion and falls again on re-colonisation', and both arms hold: streptomycin depletion of butyrate-producing Clostridia lowers cecal butyrate and raises epithelial oxygenation, tributyrin supplementation reverses it, and recolonisation with 17 human Clostridia isolates raises butyrate and restores colonocyte hypoxia (DOI:10.1016/j.chom.2016.03.004), replicated independently by DOI:10.1016/j.chom.2015.03.005. The pair is therefore a feedback loop, now modelled as such. Bound 1: the return arm is HOST-MEDIATED, running through butyrate and colonocyte beta-oxidation rather than direct microbial oxygen consumption (DOI:10.1126/science.aam9949), so the graph routes it through the new butyrate and colonocyte_oxidative_metabolism nodes rather than drawing a direct reverse edge. Bound 2: the community is NOT responsible for bulk centre-lumen anoxia -- direct phosphorescent-probe measurement finds germ-free and conventional mice nearly indistinguishable (DOI:10.1073/pnas.1718635115) -- so the closing edge is scoped to mucosal-to-luminal oxygen flux and carries that source as bounding evidence. Left open and tracked in issue 617: whether abiotic luminal oxygen consumption deserves its own node, and whether this component should attach to the trait node, which no current source supports.

    +

    Resolution: Supported, with two bounds. The would_support criterion was 'oxygen rises on depletion and falls again on re-colonisation', and both arms hold: streptomycin depletion of butyrate-producing Clostridia lowers cecal butyrate and raises epithelial oxygenation, tributyrin supplementation reverses it, and recolonisation with 17 human Clostridia isolates raises butyrate and restores colonocyte hypoxia (DOI:10.1016/j.chom.2016.03.004), replicated independently by DOI:10.1016/j.chom.2015.03.005. The pair is therefore a feedback loop, now modelled as such. Bound 1: the return arm is HOST-MEDIATED, running through butyrate and colonocyte beta-oxidation rather than direct microbial oxygen consumption (DOI:10.1126/science.aam9949), so the graph routes it through the new butyrate and colonocyte_oxidative_metabolism nodes rather than drawing a direct reverse edge. Bound 2: the community is NOT responsible for bulk centre-lumen anoxia -- direct phosphorescent-probe measurement finds germ-free and conventional mice nearly indistinguishable (DOI:10.1073/pnas.1718635115) -- so the closing edge is scoped to mucosal-to-luminal oxygen flux and carries that source as bounding evidence. Left open and tracked in issue 617: whether abiotic luminal oxygen consumption deserves its own node, and whether this component should attach to the trait node, which no current source supports.

    Provenance -

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for gut-associated: MicroRNAs (miRNAs) are small, noncoding RNAs involved in posttranscriptional gene regulation in both animal and plant. miRNAs derived from edible plants, referred to as xenomiRs, are proposed to cross-kingdom barriers and to modulate mammalian gene expression.', whose sentence came from PMID:40945860. That sentence is about plant-derived xenomiRs crossing kingdom barriers, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:40945860 'MicroRNAs (miRNAs) are small, noncoding RNAs involved in posttranscriptional gene regulation in both animal and plant. miRNAs derived from edible plants, referred to as xenomiRs, are proposed to cross-kingdom barriers and to modulate mammalian gene expression.'; PMID:42278360 'By integrating microbiological, immunological, and clinical perspectives, this review highlights key knowledge gaps and outlines future research directions aimed at harnessing the gut microbiome as a novel therapeutic avenue in HIV management and eradication.'; PMID:41808832 'Given its promising anti-inflammatory properties, further research is warranted.'; PMID:42197356 'Examining the existing literature may identify knowledge gaps regarding precise mechanisms through which the development of GM influences the maturation of the immune system.'.

    +

    Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for gut-associated: MicroRNAs (miRNAs) are small, noncoding RNAs involved in posttranscriptional gene regulation in both animal and plant. miRNAs derived from edible plants, referred to as xenomiRs, are proposed to cross-kingdom barriers and to modulate mammalian gene expression.', whose sentence came from PMID:40945860. That sentence is about plant-derived xenomiRs crossing kingdom barriers, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:40945860 'MicroRNAs (miRNAs) are small, noncoding RNAs involved in posttranscriptional gene regulation in both animal and plant. miRNAs derived from edible plants, referred to as xenomiRs, are proposed to cross-kingdom barriers and to modulate mammalian gene expression.'; PMID:42278360 'By integrating microbiological, immunological, and clinical perspectives, this review highlights key knowledge gaps and outlines future research directions aimed at harnessing the gut microbiome as a novel therapeutic avenue in HIV management and eradication.'; PMID:41808832 'Given its promising anti-inflammatory properties, further research is warranted.'; PMID:42197356 'Examining the existing literature may identify knowledge gaps regarding precise mechanisms through which the development of GM influences the maturation of the immune system.'.

    @@ -713,7 +714,7 @@

    Curation history

  • · CONNECT_CAUSAL_GRAPH · claude -

    Closed the oxygen/fermenter feedback loop in gut_associated_microbiota_metabolism (#617), resolving the record's x-gut-oxygen-causal-direction knowledge gap in favour of its would_support criterion. Added nodes butyrate (CHEBI:17968) and colonocyte_oxidative_metabolism, and three edges: primary_fermenter_community -[biolink:produces]-> butyrate -[RO:0002213]-> colonocyte_oxidative_metabolism -[RO:0002326]-> luminal_oxygen_limitation. The return arm is modelled as HOST-MEDIATED rather than as direct microbial oxygen consumption, because that is what the sources show. The closing edge carries DOI:10.1073/pnas.1718635115 as bounding evidence: bulk centre-lumen pO2 is near-identical in germ-free and conventional mice, so the claim is scoped to mucosal-to-luminal oxygen flux and must not drift into bulk anoxia. No connectivity-only edge was invented to attach this component to the trait node.

    +

    Closed the oxygen/fermenter feedback loop in gut_associated_microbiota_metabolism (#617), resolving the record's x-gut-oxygen-causal-direction knowledge gap in favour of its would_support criterion. Added nodes butyrate (CHEBI:17968) and colonocyte_oxidative_metabolism, and three edges: primary_fermenter_community -[biolink:produces]-> butyrate -[RO:0002213]-> colonocyte_oxidative_metabolism -[RO:0002326]-> luminal_oxygen_limitation. The return arm is modelled as HOST-MEDIATED rather than as direct microbial oxygen consumption, because that is what the sources show. The closing edge carries DOI:10.1073/pnas.1718635115 as bounding evidence: bulk centre-lumen pO2 is near-identical in germ-free and conventional mice, so the claim is scoped to mucosal-to-luminal oxygen flux and must not drift into bulk anoxia. No connectivity-only edge was invented to attach this component to the trait node.

  • @@ -725,7 +726,7 @@

    Curation history

  • · CORRECT_EVIDENCE_SNIPPETS · claude -

    Adversarial review of PR 618 before merge. Corrected two snippets and one note. Issue 619: the DOI:10.1073/pnas.1718635115 snippet was a PARAPHRASE presented as a verbatim quote and has been replaced with the source sentence retrieved from the Europe PMC REST API. Issue 620: the DOI:10.1016/j.chom.2016.03.004 snippet silently dropped '(P < 0.05)' from mid-quote and is now contiguous. Issue 621: the same evidence item's notes asserted the microbiota is not responsible for bulk anoxia, a stronger negative than the source supports; the source concludes that both microbes and oxidative chemistry regulate luminal oxygen, so the note now bounds SOLE causation rather than denying a microbial contribution. No causal claim changed.

    +

    Adversarial review of PR 618 before merge. Corrected two snippets and one note. Issue 619: the DOI:10.1073/pnas.1718635115 snippet was a PARAPHRASE presented as a verbatim quote and has been replaced with the source sentence retrieved from the Europe PMC REST API. Issue 620: the DOI:10.1016/j.chom.2016.03.004 snippet silently dropped '(P < 0.05)' from mid-quote and is now contiguous. Issue 621: the same evidence item's notes asserted the microbiota is not responsible for bulk anoxia, a stronger negative than the source supports; the source concludes that both microbes and oxidative chemistry regulate luminal oxygen, so the note now bounds SOLE causation rather than denying a microbial contribution. No causal claim changed.

    • @@ -735,13 +736,13 @@

    Recorded curation sessions

  • · claude-code
    • EDIT — Close the gut_associated oxygen loop through colonocyte metabolism -

      Resolves the record's x-gut-oxygen-causal-direction knowledge gap in favour of its would_support criterion. Added nodes butyrate (CHEBI:17968, CHEMICAL) and colonocyte_oxidative_metabolism (BIOLOGICAL_PROCESS), plus three edges closing the loop against the existing luminal_oxygen_limitation to primary_fermenter_community edge: primary_fermenter_community -[biolink:produces]-> butyrate -[RO:0002213 positively regulates]-> colonocyte_oxidative_metabolism -[RO:0002326 contributes to]-> luminal_oxygen_limitation. Six evidence items across the three edges, every snippet verbatim and verified against the primary source this session, from four studies: DOI:10.1016/j.chom.2016.03.004 (depletion, tributyrin rescue, 17-strain recolonisation), DOI:10.1126/science.aam9949 (PPAR-gamma and beta-oxidation), DOI:10.1016/j.chom.2015.03.005 (independent replication; butyrate raises epithelial oxygen consumption) and DOI:10.1073/pnas.1718635115. That last one is attached as BOUNDING evidence on the closing edge: direct phosphorescent-probe measurement shows bulk centre-lumen pO2 is near-identical in germ-free and conventional mice, so the community does not create bulk anoxia and this edge asserts only a limit on mucosal-to-luminal oxygen flux, which is how the target node is already defined. The return arm is deliberately modelled as host-mediated rather than as direct microbial oxygen consumption. Two things were deliberately NOT done: no abiotic_luminal_oxygen_consumption node was added, and no connectivity-only edge was invented to attach this component to gut_associated_trait, since no source supports one and issue 183 warns explicitly against edges added to satisfy a check. The graph therefore still has three components; that fragmentation is invisible to audit-graphs because the graph is NONMECHANISTIC, which is issue 613. Also set the discussion to RESOLVED with resolved_date 2026-08-31 and a resolution_note recording both bounds. Written through write_validated_trait with CONNECT_CAUSAL_GRAPH and RESOLVE_DISCUSSION events. Gates: validate-strict 0 errors, audit-predicate-domains 0 findings, audit-snippets 2592 all baselined with 0 new, audit-graphs 0 new.

    +

    Resolves the record's x-gut-oxygen-causal-direction knowledge gap in favour of its would_support criterion. Added nodes butyrate (CHEBI:17968, CHEMICAL) and colonocyte_oxidative_metabolism (BIOLOGICAL_PROCESS), plus three edges closing the loop against the existing luminal_oxygen_limitation to primary_fermenter_community edge: primary_fermenter_community -[biolink:produces]-> butyrate -[RO:0002213 positively regulates]-> colonocyte_oxidative_metabolism -[RO:0002326 contributes to]-> luminal_oxygen_limitation. Six evidence items across the three edges, every snippet verbatim and verified against the primary source this session, from four studies: DOI:10.1016/j.chom.2016.03.004 (depletion, tributyrin rescue, 17-strain recolonisation), DOI:10.1126/science.aam9949 (PPAR-gamma and beta-oxidation), DOI:10.1016/j.chom.2015.03.005 (independent replication; butyrate raises epithelial oxygen consumption) and DOI:10.1073/pnas.1718635115. That last one is attached as BOUNDING evidence on the closing edge: direct phosphorescent-probe measurement shows bulk centre-lumen pO2 is near-identical in germ-free and conventional mice, so the community does not create bulk anoxia and this edge asserts only a limit on mucosal-to-luminal oxygen flux, which is how the target node is already defined. The return arm is deliberately modelled as host-mediated rather than as direct microbial oxygen consumption. Two things were deliberately NOT done: no abiotic_luminal_oxygen_consumption node was added, and no connectivity-only edge was invented to attach this component to gut_associated_trait, since no source supports one and issue 183 warns explicitly against edges added to satisfy a check. The graph therefore still has three components; that fragmentation is invisible to audit-graphs because the graph is NONMECHANISTIC, which is issue 613. Also set the discussion to RESOLVED with resolved_date 2026-08-31 and a resolution_note recording both bounds. Written through write_validated_trait with CONNECT_CAUSAL_GRAPH and RESOLVE_DISCUSSION events. Gates: validate-strict 0 errors, audit-predicate-domains 0 findings, audit-snippets 2592 all baselined with 0 new, audit-graphs 0 new.

    • Read this curation session
  • · claude-code
    • REVIEW — Correct two fabricated or elided snippets and one overstated note found reviewing PR 618 -

      Adversarial review of my own PR 618 before merge, correcting three defects. Issue 619 (critical): the DOI:10.1073/pnas.1718635115 snippet was a PARAPHRASE presented as a verbatim quote; the sentence it claimed does not exist in the source. Replaced with the real abstract sentence retrieved from the Europe PMC REST API, and verified as an exact substring. Issue 620: the DOI:10.1016/j.chom.2016.03.004 snippet on the fermenter-to-butyrate edge silently dropped the statistic (P < 0.05) from mid-quote; restored to the contiguous source text and confirmed against the PMC full text. Issue 621: the notes on the Friedman evidence asserted that the microbiota is NOT responsible for bulk centre-lumen anoxia, which is a stronger negative than the source supports; the paper concludes that both the microbes and the oxidative chemical reactions regulate luminal oxygen levels and credits microbial biomass with the proximal-to-distal gradient, so the note now bounds SOLE causation rather than denying a microbial contribution. No causal claim, edge, node or predicate changed. Root cause recorded in issue 623: the snippets were obtained through a summarising fetch layer that paraphrases and silently drops markup, and audit_evidence_snippets.py checks snippet SHAPE only, so all three defects passed it cleanly. Verification now uses the Europe PMC REST API. Gates after correction: qc 0, validate-strict 0 errors, audit-snippets 2592 all baselined with 0 new.

    +

    Adversarial review of my own PR 618 before merge, correcting three defects. Issue 619 (critical): the DOI:10.1073/pnas.1718635115 snippet was a PARAPHRASE presented as a verbatim quote; the sentence it claimed does not exist in the source. Replaced with the real abstract sentence retrieved from the Europe PMC REST API, and verified as an exact substring. Issue 620: the DOI:10.1016/j.chom.2016.03.004 snippet on the fermenter-to-butyrate edge silently dropped the statistic (P < 0.05) from mid-quote; restored to the contiguous source text and confirmed against the PMC full text. Issue 621: the notes on the Friedman evidence asserted that the microbiota is NOT responsible for bulk centre-lumen anoxia, which is a stronger negative than the source supports; the paper concludes that both the microbes and the oxidative chemical reactions regulate luminal oxygen levels and credits microbial biomass with the proximal-to-distal gradient, so the note now bounds SOLE causation rather than denying a microbial contribution. No causal claim, edge, node or predicate changed. Root cause recorded in issue 623: the snippets were obtained through a summarising fetch layer that paraphrases and silently drops markup, and audit_evidence_snippets.py checks snippet SHAPE only, so all three defects passed it cleanly. Verification now uses the Europe PMC REST API. Gates after correction: qc 0, validate-strict 0 errors, audit-snippets 2592 all baselined with 0 new.

    • Read this curation session @@ -773,7 +774,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1137,12 +1147,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-02 05:09 UTC diff --git a/pages/traits/ecology/habitat_association.html b/pages/traits/ecology/habitat_association.html index f1077919a7e..3acf2d46a66 100644 --- a/pages/traits/ecology/habitat_association.html +++ b/pages/traits/ecology/habitat_association.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    ENVO:01000739 causes habitat association - traitmech:000047 + traitmech:000047 biolink:causes

    The organism's primary habitat sets its habitat-association classification.

      @@ -115,7 +116,7 @@

      Edge evidence

    • habitat association - traitmech:000047 + traitmech:000047 associated with biogeographic community structure @@ -307,7 +308,7 @@

      Children (4)

      Synonyms (1)

        -
      • niche association RELATED_SYNONYM · DOI:10.1038/nrmicro1341
        • +
      • niche association RELATED_SYNONYM · DOI:10.1038/nrmicro1341
    @@ -323,7 +324,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -542,13 +543,13 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Candidatus Pelagibacter ubique HTCC1062 (NCBITaxon:335992; PMID:16109880). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Candidatus Pelagibacter ubique HTCC1062 (NCBITaxon:335992; PMID:16109880). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1038/nrmicro1341 (already present on child records free_living.yaml evidence[0] and soil_dwelling.yaml evidence[1]) to record-level evidence[0] to match definition_source (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-001 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.1038/nrmicro1341 (already present on child records free_living.yaml evidence[0] and soil_dwelling.yaml evidence[1]) to record-level evidence[0] to match definition_source (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-001 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -581,7 +582,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -945,12 +955,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/ecology/host_associated.html b/pages/traits/ecology/host_associated.html index 5a2fa55b61f..1699d38a540 100644 --- a/pages/traits/ecology/host_associated.html +++ b/pages/traits/ecology/host_associated.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    confers host-associated - traitmech:000049 + traitmech:000049 METPO:2007700

    Persistent host colonization realizes the host-associated lifestyle.

      @@ -369,7 +370,7 @@

      kg-microbe context

      via parent_proxy.

        -
      • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
        • +
      • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

      512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

      @@ -642,7 +643,16 @@

      Identifier

      Term kind
      CLASS
      Status
      -
      REVIEWED
      +
      REVIEWED + + +
      + What this status means +

      Curator has signed off on label / definition / parents.

      +

      Quoted from the schema's status definitions.

      +
      + +
    @@ -1006,12 +1016,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/ecology/human_pathogen.html b/pages/traits/ecology/human_pathogen.html index 7d32abb5096..6f7c7374436 100644 --- a/pages/traits/ecology/human_pathogen.html +++ b/pages/traits/ecology/human_pathogen.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -368,7 +369,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • human_pathogens_all RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • human_pathogens_all RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -384,7 +385,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -711,7 +712,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1075,12 +1085,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/ecology/ixotrophy.html b/pages/traits/ecology/ixotrophy.html index 16717c1ea73..5081bcad2ce 100644 --- a/pages/traits/ecology/ixotrophy.html +++ b/pages/traits/ecology/ixotrophy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1126/science.adp0614
    Single-cell analyses with stable isotope-labeled prey revealed that prey components are taken up by the attacker.
    -

    Lien et al. 2024, PMID:39418385, scientific Abstract, not the separate article summary; directly matched source-qualified MED text. Introduction and contact/capture Results support the surface-trapping differentia. Nutrient-uptake Results, culture, killing, imaging and Raman Methods, Discussion and actual Figures 1, 5 and 6 read. Raman labeling supports uptake from killed prey; Figure 6 is a model, not independent flux data. On solid surfaces, gliding can establish contact without flagellar trapping; this record denotes a capability, not a mandatory sequence for every feeding event. Other figures, supplements and movies not fully assessed. Author-hosted published full text: https://stockerlab.ethz.ch/wp-content/uploads/2024/10/183.Lien-et-al_Science_Kang.pdf. MED linked a commentary and preprint, not a correction/retraction; publisher status page was inaccessible, so that check remains limited.

    +

    Lien et al. 2024, PMID:39418385, scientific Abstract, not the separate article summary; directly matched source-qualified MED text. Introduction and contact/capture Results support the surface-trapping differentia. Nutrient-uptake Results, culture, killing, imaging and Raman Methods, Discussion and actual Figures 1, 5 and 6 read. Raman labeling supports uptake from killed prey; Figure 6 is a model, not independent flux data. On solid surfaces, gliding can establish contact without flagellar trapping; this record denotes a capability, not a mandatory sequence for every feeding event. Other figures, supplements and movies not fully assessed. Author-hosted published full text: https://stockerlab.ethz.ch/wp-content/uploads/2024/10/183.Lien-et-al_Science_Kang.pdf. MED linked a commentary and preprint, not a correction/retraction; publisher status page was inaccessible, so that check remains limited.

  • DOI:10.1007/s002489900052
    can subsist on other microbes and can even catch motile bacteria by their flagella before killing and digesting them.
    -

    Lewin 1997, PMID:9337418, directly retrieved publisher Abstract. The subject is Saprospira grandis; supports prey capture, killing and nutrition, not universal dependence on flagellated prey. MED metadata matched title and DOI but exposed no abstract; do not report an abstract-resolver verification for this quote. Full text, figures and strain provenance were unavailable. Publisher page and qualified MED metadata showed no linked correction/retraction at access, not proof none exists. Source: https://link.springer.com/article/10.1007/s002489900052.

    +

    Lewin 1997, PMID:9337418, directly retrieved publisher Abstract. The subject is Saprospira grandis; supports prey capture, killing and nutrition, not universal dependence on flagellated prey. MED metadata matched title and DOI but exposed no abstract; do not report an abstract-resolver verification for this quote. Full text, figures and strain provenance were unavailable. Publisher page and qualified MED metadata showed no linked correction/retraction at access, not proof none exists. Source: https://link.springer.com/article/10.1007/s002489900052.

  • DOI:10.1099/mic.0.000158
    The ability of cells to aggregate or adhere is thought to be a significant initial step in ixotrophy.
    -

    Furusawa et al. 2015, PMID:26306656, scientific Abstract directly read at the publisher and matched qualified MED metadata. CCB-QB1 adhesion/capture assays support an initial interaction, not by themselves nutrient transfer. Calcium and acidic polysaccharide interpretations are model-specific, not defining requirements. Full-text delivery failed; Methods, figures and supplement remain unread. Publisher page and MED record exposed no linked correction/retraction. Authors and CCB-QB1 material overlap with 2024, so these are not independent-group replications. Source: https://doi.org/10.1099/mic.0.000158.

    +

    Furusawa et al. 2015, PMID:26306656, scientific Abstract directly read at the publisher and matched qualified MED metadata. CCB-QB1 adhesion/capture assays support an initial interaction, not by themselves nutrient transfer. Calcium and acidic polysaccharide interpretations are model-specific, not defining requirements. Full-text delivery failed; Methods, figures and supplement remain unread. Publisher page and MED record exposed no linked correction/retraction. Authors and CCB-QB1 material overlap with 2024, so these are not independent-group replications. Source: https://doi.org/10.1099/mic.0.000158.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1126/science.adp0614 - Qualified to the ixotrophy-positive WT studied with Vibrio campbellii, not all culture derivatives or the entire genus. The primary scientific Abstract at https://pubmed.ncbi.nlm.nih.gov/25468060/ (DOI:10.1016/j.margen.2014.10.006) directly identifies CCB-QB1 as an isolate from the coastal area of Penang, Malaysia; this is provenance, not another predation experiment. NCBI identifier/name independently checked on 2026-10-11: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1313421. The 2024 IS-inactivated predator derivatives are not the exemplar. + Qualified to the ixotrophy-positive WT studied with Vibrio campbellii, not all culture derivatives or the entire genus. The primary scientific Abstract at https://pubmed.ncbi.nlm.nih.gov/25468060/ (DOI:10.1016/j.margen.2014.10.006) directly identifies CCB-QB1 as an isolate from the coastal area of Penang, Malaysia; this is provenance, not another predation experiment. NCBI identifier/name independently checked on 2026-10-11: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1313421. The 2024 IS-inactivated predator derivatives are not the exemplar. @@ -240,7 +241,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Use phenotype METPO:1000059 as parent. Predatory bacterium traitmech:000054 requires bacterial prey, whereas ixotrophy literature also includes nonbacterial microbial prey. Epibiotic bacterial predation traitmech:000697 denotes attached external growth on bacterial prey and is not an exact synonym or proven broader parent. Heng et al. 2026 (DOI:10.1007/s00248-026-02864-6), publisher Abstract only, calls ixotrophy epibiotic in a broader usage; retain that attribution without equating the scopes. Gliding, aggregation, adhesive surfaces, antagonism and prey lysis alone do not establish ixotrophy. No universal prey range, obligate dependence or organism-level disjointness is asserted. No exact external xrefs or synonyms assigned pending authority and scope reconciliation.

    +

    Use phenotype METPO:1000059 as parent. Predatory bacterium traitmech:000054 requires bacterial prey, whereas ixotrophy literature also includes nonbacterial microbial prey. Epibiotic bacterial predation traitmech:000697 denotes attached external growth on bacterial prey and is not an exact synonym or proven broader parent. Heng et al. 2026 (DOI:10.1007/s00248-026-02864-6), publisher Abstract only, calls ixotrophy epibiotic in a broader usage; retain that attribution without equating the scopes. Gliding, aggregation, adhesive surfaces, antagonism and prey lysis alone do not establish ixotrophy. No universal prey range, obligate dependence or organism-level disjointness is asserted. No exact external xrefs or synonyms assigned pending authority and scope reconciliation.

    @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-11 12:58 UTC diff --git a/pages/traits/ecology/kin_discrimination.html b/pages/traits/ecology/kin_discrimination.html index 0e4deee7b2d..c7663b0b7ca 100644 --- a/pages/traits/ecology/kin_discrimination.html +++ b/pages/traits/ecology/kin_discrimination.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1371/journal.pbio.0060287
    Our findings demonstrate that D. discoideum cells co-aggregate more with genetically similar than dissimilar individuals
    -

    Ostrowski et al. 2008, PMID:19067487; scientific abstract, publisher PDF page 1, contiguous span visually checked. Mixtures with AX4-GFP and natural-isolate dye controls support partial sorting during aggregation, not complete clonal exclusion. The measured endpoint is variation in fluorescent spore proportions among fruiting bodies; genetic distance uses 12 microsatellite loci, not genome-wide identity. Main text and all four figures were inspected; Figure 1 is hypothetical. Supplementary Tables S1 and S2 were read by text extraction. Main Methods names QS45, absent from the retrieved S1 strain table; no strain alias is inferred. Kin-selected benefit is an interpretation, not a measured fitness endpoint here. Natural provenance of every laboratory derivative and a molecular recognition mechanism remain unresolved. Native abstract verifier: VERIFIED.

    +

    Ostrowski et al. 2008, PMID:19067487; scientific abstract, publisher PDF page 1, contiguous span visually checked. Mixtures with AX4-GFP and natural-isolate dye controls support partial sorting during aggregation, not complete clonal exclusion. The measured endpoint is variation in fluorescent spore proportions among fruiting bodies; genetic distance uses 12 microsatellite loci, not genome-wide identity. Main text and all four figures were inspected; Figure 1 is hypothetical. Supplementary Tables S1 and S2 were read by text extraction. Main Methods names QS45, absent from the retrieved S1 strain table; no strain alias is inferred. Kin-selected benefit is an interpretation, not a measured fitness endpoint here. Natural provenance of every laboratory derivative and a molecular recognition mechanism remain unresolved. Native abstract verifier: VERIFIED.

  • DOI:10.1073/pnas.1512671112
    Some swarms did merge, and most interestingly, this behavior was only seen in the most highly related strain pairs.
    -

    Stefanic et al. 2015, PMID:26438858, PMC4653157; directly retrieved scientific abstract from Europe PMC with the namespace-qualified query EXT_ID:26438858 AND SRC:MED. Title, PMID and DOI were checked together. The authors define a conspecific scope and report relatedness-associated swarm merging versus boundary formation among sympatric Bacillus subtilis isolates. The separately reported root-colonization outcome is not a direct killing measurement. Full text, figures and supplements were inaccessible and are not claimed as inspected; indexed search passages were not used as excerpts or quantitative evidence. Native abstract verifier: VERIFIED. Linked PMID:26512099 is commentary, not a correction or experimental replication.

    +

    Stefanic et al. 2015, PMID:26438858, PMC4653157; directly retrieved scientific abstract from Europe PMC with the namespace-qualified query EXT_ID:26438858 AND SRC:MED. Title, PMID and DOI were checked together. The authors define a conspecific scope and report relatedness-associated swarm merging versus boundary formation among sympatric Bacillus subtilis isolates. The separately reported root-colonization outcome is not a direct killing measurement. Full text, figures and supplements were inaccessible and are not claimed as inspected; indexed search passages were not used as excerpts or quantitative evidence. Native abstract verifier: VERIFIED. Linked PMID:26512099 is commentary, not a correction or experimental replication.

  • DOI:10.1128/mBio.00723-17
    The effects of kin discrimination extend to nearby species, as the other subtilis clade species were treated with the same antagonism as nonkin.
    -

    Lyons and Kolter 2017, PMID:28679746, PMC5573675; scientific abstract, NLM version 1 PDF page 1 and JATS article-meta abstract without abstract-type. This is not the separate IMPORTANCE summary. Introduction distinguishes preferential kin association from nonkin exclusion and supports the definition's two modes; the paper's own experiments support the nearby-species extension. The comparison concerns interactions with B. subtilis NCIB3610: nearby species can be antagonized, while more distant lineages show varied outcomes. This is not a universal monotonic relation between distance and antagonism. Relatedness uses type-strain 16S, not whole-genome identity of every isolate. Swarm, biofilm and halo assays differ in medium and endpoint. Figure 2A and 2C assign WNC032 to different species; Data Set S1 identifies it as B. megaterium. No silent panel correction or taxon anchor is inferred. Actual Figures 2 and 4 and selected spreadsheet rows/totals were inspected, not all figures or raw assays. Native abstract verifier: VERIFIED. Shares an investigator with 2015; not an independent-laboratory replication.

    +

    Lyons and Kolter 2017, PMID:28679746, PMC5573675; scientific abstract, NLM version 1 PDF page 1 and JATS article-meta abstract without abstract-type. This is not the separate IMPORTANCE summary. Introduction distinguishes preferential kin association from nonkin exclusion and supports the definition's two modes; the paper's own experiments support the nearby-species extension. The comparison concerns interactions with B. subtilis NCIB3610: nearby species can be antagonized, while more distant lineages show varied outcomes. This is not a universal monotonic relation between distance and antagonism. Relatedness uses type-strain 16S, not whole-genome identity of every isolate. Swarm, biofilm and halo assays differ in medium and endpoint. Figure 2A and 2C assign WNC032 to different species; Data Set S1 identifies it as B. megaterium. No silent panel correction or taxon anchor is inferred. Actual Figures 2 and 4 and selected spreadsheet rows/totals were inspected, not all figures or raw assays. Native abstract verifier: VERIFIED. Shares an investigator with 2015; not an independent-laboratory replication.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -283,13 +284,13 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed microbial kin discrimination -

      Added PROPOSED traitmech:000716 under METPO:1000059 with three DOI-backed snippets (10.1371/journal.pbio.0060287, 10.1073/pnas.1512671112, 10.1128/mBio.00723-17), two OPEN discussions and companion v592 proposal reserving 1066900-1066999. Retained relational scope, nonmonotonic and assay-dependent outcomes, 2015 abstract-only access, strain-label discrepancies and unresolved mechanisms. No canonical taxa, exact mappings or causal graph inferred. Guarded writer dry-run and apply passed; broader validation and review follow. Existing trait records remain unchanged.

    +

    Added PROPOSED traitmech:000716 under METPO:1000059 with three DOI-backed snippets (10.1371/journal.pbio.0060287, 10.1073/pnas.1512671112, 10.1128/mBio.00723-17), two OPEN discussions and companion v592 proposal reserving 1066900-1066999. Retained relational scope, nonmonotonic and assay-dependent outcomes, 2015 abstract-only access, strain-label discrepancies and unresolved mechanisms. No canonical taxa, exact mappings or causal graph inferred. Guarded writer dry-run and apply passed; broader validation and review follow. Existing trait records remain unchanged.

    • Read this curation session
  • · codex
    • EDIT — Correct kin-discrimination evidence and definition provenance -

      Addresses #1909 and #1910 from the saved initial adversarial review: replaces two insufficiently self-contained snippets with explicit merging and antagonism results, changes definition_source to DOI:10.1128/mBio.00723-17 for the nearby-species scope, preserves DOI:10.1073/pnas.1512671112 for its own excerpt, and updates the 2017 scientific-abstract locator and discussion. Preserves the original event and history/records/kin_discrimination/2026-10-13T091229Z-codex-2c345e.yaml. Does not alter the phenotype definition, identifiers, parent, PROPOSED status or source limitations. Guarded correction dry-run and apply passed; broader validation follows.

    +

    Addresses #1909 and #1910 from the saved initial adversarial review: replaces two insufficiently self-contained snippets with explicit merging and antagonism results, changes definition_source to DOI:10.1128/mBio.00723-17 for the nearby-species scope, preserves DOI:10.1073/pnas.1512671112 for its own excerpt, and updates the 2017 scientific-abstract locator and discussion. Preserves the original event and history/records/kin_discrimination/2026-10-13T091229Z-codex-2c345e.yaml. Does not alter the phenotype definition, identifiers, parent, PROPOSED status or source limitations. Guarded correction dry-run and apply passed; broader validation follows.

    • Read this curation session @@ -321,7 +322,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -350,12 +360,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-13 09:19 UTC diff --git a/pages/traits/ecology/mutualism.html b/pages/traits/ecology/mutualism.html index 17f6e7d7f12..da124fceb10 100644 --- a/pages/traits/ecology/mutualism.html +++ b/pages/traits/ecology/mutualism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    confers mutualism - traitmech:000041 + traitmech:000041 METPO:2007700

    Sustained mutual benefit realizes the mutualistic lifestyle.

      @@ -156,7 +157,7 @@

      Edge evidence

      confers mutualism - traitmech:000041 + traitmech:000041 METPO:2007700

      Selection for host-beneficial microbial traits sustains the mutualistic relationship.

        @@ -194,7 +195,7 @@

        Edge evidence

        confers mutualism - traitmech:000041 + traitmech:000041 METPO:2007700

        Exchange of N-sources, vitamins, and micronutrients supports mutualistic associations.

          @@ -282,7 +283,7 @@

          Children (1)

          Synonyms (1)

    @@ -298,7 +299,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -559,7 +560,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -923,12 +933,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/ecology/nitrogen_fixing_symbiosis.html b/pages/traits/ecology/nitrogen_fixing_symbiosis.html index 4ef801b9bf4..58760e7d5a7 100644 --- a/pages/traits/ecology/nitrogen_fixing_symbiosis.html +++ b/pages/traits/ecology/nitrogen_fixing_symbiosis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    confers nitrogen-fixing symbiosis - traitmech:000044 + traitmech:000044 METPO:2007700

    Nod-factor signalling between rhizobia and legume hosts establishes the symbiosis.

      @@ -115,7 +116,7 @@

      Edge evidence

    • nitrogen-fixing symbiosis - traitmech:000044 + traitmech:000044 enables nitrogen fixation GO:0009399 @@ -307,8 +308,8 @@

      Protein and taxon examples

    		 - Sinorhizobium meliloti 1021 -
    NCBITaxon:266834 + Sinorhizobium meliloti 1021 +
    NCBITaxon:266834         		REVIEWED
    @@ -374,9 +375,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • nitrogen-fixing symbiont RELATED_SYNONYM · DOI:10.1038/nrmicro.2017.171
      • +
    • nitrogen-fixing symbiont RELATED_SYNONYM · DOI:10.1038/nrmicro.2017.171
      • -
    • root-nodule symbiosis RELATED_SYNONYM · DOI:10.1038/nrmicro2990
      • +
    • root-nodule symbiosis RELATED_SYNONYM · DOI:10.1038/nrmicro2990
    @@ -392,7 +393,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -671,7 +672,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1035,12 +1045,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/ecology/nutritional_fungal_mycoparasitism.html b/pages/traits/ecology/nutritional_fungal_mycoparasitism.html index 5c9395ebcef..49ba0578918 100644 --- a/pages/traits/ecology/nutritional_fungal_mycoparasitism.html +++ b/pages/traits/ecology/nutritional_fungal_mycoparasitism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1139/b95-389
    The term mycoparasitism applies strictly to those relationships in which one living fungus acts as a nutrient source for another
    -

    Jeffries 1995 review; scientific abstract directly retrieved from https://kar.kent.ac.uk/19621/. This strict sense contrasts with broader fungicolous usage in the same abstract. Selected main text and actual PDF pages 1 and 3 support detrimental nutrition with either a living host or killing before use. The record restricts actor and host to fungi, excluding historically grouped oomycetes. The review supplies terminology, not an independent experiment. Not every figure or table was inspected. Native abstract verifier: UNRESOLVED; the direct institutional excerpt was separately matched, not relabeled VERIFIED.

    +

    Jeffries 1995 review; scientific abstract directly retrieved from https://kar.kent.ac.uk/19621/. This strict sense contrasts with broader fungicolous usage in the same abstract. Selected main text and actual PDF pages 1 and 3 support detrimental nutrition with either a living host or killing before use. The record restricts actor and host to fungi, excluding historically grouped oomycetes. The review supplies terminology, not an independent experiment. Not every figure or table was inspected. Native abstract verifier: UNRESOLVED; the direct institutional excerpt was separately matched, not relabeled VERIFIED.

  • DOI:10.1002/rcm.6131
    In dual-culture the mycelia of T. atroviride which remained in direct contact with labeled A. mellea showed an increased δ(13)C value
    -

    Pellegrini et al. 2012, PMID:22302490; directly retrieved scientific abstract, Results, using DOI and SRC:MED together. Title, DOI and PMID agree. After 29 days in contact, the reported carbon isotope value was 66.4 per mille versus -26.6 per mille with unlabeled host. This supports host-derived carbon assimilation, not by itself host killing, a penetration mechanism or exclusion of all alternative transfer routes. The journal full text was not retrieved; the restricted institutional deposit was not bypassed. The bacterial comparator is not an example of this fungal-actor trait. Native abstract verifier: VERIFIED.

    +

    Pellegrini et al. 2012, PMID:22302490; directly retrieved scientific abstract, Results, using DOI and SRC:MED together. Title, DOI and PMID agree. After 29 days in contact, the reported carbon isotope value was 66.4 per mille versus -26.6 per mille with unlabeled host. This supports host-derived carbon assimilation, not by itself host killing, a penetration mechanism or exclusion of all alternative transfer routes. The journal full text was not retrieved; the restricted institutional deposit was not bypassed. The bacterial comparator is not an example of this fungal-actor trait. Native abstract verifier: VERIFIED.

  • DOI:10.1016/j.apsoil.2012.12.005
    Only T. harzianum maintained mycoparasitic activity in the soil microcosm
    -

    Pellegrini et al. 2013; scientific abstract directly read at https://iris.unipv.it/handle/11571/604013?mode=complete. Native verifier: VERIFIED via AGR:IND500606635, not PubMed. The author-deposited Corneo thesis chapter identifies this DOI; its version is not presumed identical to the unread journal full text. Its experiment selects three microorganisms: the positive soil result concerns a sterile microcosm at 20 C after 29 days, followed by three-day culture-out before isotope measurement, not direct field flux or all 158 isolates. Dual-culture enrichment accompanies growth inhibition; the host viability endpoint comes from a separate broth assay. Washing and host-specific PCR address contamination without excluding every route of carbon transfer. Leakage versus direct parasitism remains partly interpretive. Shares all six authors with 2012, not independent-laboratory replication.

    +

    Pellegrini et al. 2013; scientific abstract directly read at https://iris.unipv.it/handle/11571/604013?mode=complete. Native verifier: VERIFIED via AGR:IND500606635, not PubMed. The author-deposited Corneo thesis chapter identifies this DOI; its version is not presumed identical to the unread journal full text. Its experiment selects three microorganisms: the positive soil result concerns a sterile microcosm at 20 C after 29 days, followed by three-day culture-out before isotope measurement, not direct field flux or all 158 isolates. Dual-culture enrichment accompanies growth inhibition; the host viability endpoint comes from a separate broth assay. Washing and host-specific PCR address contamination without excluding every route of carbon transfer. Leakage versus direct parasitism remains partly interpretive. Shares all six authors with 2012, not independent-laboratory replication.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-13 11:26 UTC diff --git a/pages/traits/ecology/opportunistic_pathogen.html b/pages/traits/ecology/opportunistic_pathogen.html index ec6c9df10ce..e0bbe4635d7 100644 --- a/pages/traits/ecology/opportunistic_pathogen.html +++ b/pages/traits/ecology/opportunistic_pathogen.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    confers opportunistic pathogen - traitmech:000046 + traitmech:000046 METPO:2007700

    Context-dependent infection realizes the opportunistic-pathogen lifestyle.

      @@ -311,7 +312,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • opportunistic infection RELATED_SYNONYM · DOI:10.1016/j.tim.2012.04.005
        • +
      • opportunistic infection RELATED_SYNONYM · DOI:10.1016/j.tim.2012.04.005
    @@ -327,7 +328,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -573,7 +574,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -937,12 +947,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/ecology/parasitism.html b/pages/traits/ecology/parasitism.html index 52a329ba16a..2e37482bd7d 100644 --- a/pages/traits/ecology/parasitism.html +++ b/pages/traits/ecology/parasitism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    confers parasitism - traitmech:000043 + traitmech:000043 METPO:2007700

    Chronic host fitness cost realizes the parasitic lifestyle.

      @@ -349,7 +350,7 @@

      Parent traits (1)

      Synonyms (1)

    @@ -365,7 +366,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -611,7 +612,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -975,12 +985,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/ecology/pathogenic_to_host.html b/pages/traits/ecology/pathogenic_to_host.html index bb4a4a574cb..b81c73d1a54 100644 --- a/pages/traits/ecology/pathogenic_to_host.html +++ b/pages/traits/ecology/pathogenic_to_host.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -240,7 +241,7 @@

    Edge evidence

  • DOI:10.3390/bacteria3030008 - EPS matrix protects deeper-layer cells from antimicrobials; biofilm bacteria increase resistance about 1000 fold (DOI:10.3390/ijms25052655). + EPS matrix protects deeper-layer cells from antimicrobials; biofilm bacteria increase resistance about 1000 fold (DOI:10.3390/ijms25052655).
    • @@ -383,9 +384,9 @@

    Children (4)

    Synonyms (2)

      -
    • General.keywords RELATED_SYNONYM · metpo.owl
      • +
    • General.keywords RELATED_SYNONYM · metpo.owl
      • -
    • Safety information.risk assessment RELATED_SYNONYM · metpo.owl
      • +
    • Safety information.risk assessment RELATED_SYNONYM · metpo.owl
    @@ -401,7 +402,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -686,7 +687,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1050,12 +1060,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/ecology/periplasmic_bacterial_predation.html b/pages/traits/ecology/periplasmic_bacterial_predation.html index 5719ea2c7e1..ba879ed3a57 100644 --- a/pages/traits/ecology/periplasmic_bacterial_predation.html +++ b/pages/traits/ecology/periplasmic_bacterial_predation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1038/s42003-025-09010-x
    establishes itself in the prey periplasm, feeding on the prey’s cytoplasmic contents as a main nutrient source.
    -

    Lai et al. 2025, PMID:41125861, PMC12546842, Introduction, second paragraph; the subject is B. bacteriovorus. Direct publisher HTML and Europe PMC full-text XML match. Scientific Abstract, Introduction, selected growth/exit Results and culture, sampling, time-lapse and statistics Methods, Discussion and actual Figures 1 and 4 read. Figure 1a is a lifecycle schematic, not direct imaging; Figure 4a includes WT exit measurements. Other figures and supplements not fully assessed. Publisher and MED showed no linked notice; MED linked the earlier preprint, not a correction. Published source: https://doi.org/10.1038/s42003-025-09010-x.

    +

    Lai et al. 2025, PMID:41125861, PMC12546842, Introduction, second paragraph; the subject is B. bacteriovorus. Direct publisher HTML and Europe PMC full-text XML match. Scientific Abstract, Introduction, selected growth/exit Results and culture, sampling, time-lapse and statistics Methods, Discussion and actual Figures 1 and 4 read. Figure 1a is a lifecycle schematic, not direct imaging; Figure 4a includes WT exit measurements. Other figures and supplements not fully assessed. Publisher and MED showed no linked notice; MED linked the earlier preprint, not a correction. Published source: https://doi.org/10.1038/s42003-025-09010-x.

  • DOI:10.1128/JB.00914-10
    Nutrients for the replication of Bdellovibrio bacteria come entirely from the digestion of the single invaded bacterium
    -

    Fenton et al. 2010, PMID:20935099, scientific Abstract retrieved from source-qualified MED metadata. Supports prey-derived nutrition during intrabacterial replication; do not generalize its single-prey wording to a fixed predator occupancy or universal prey dependence. Full-text delivery failed; Methods, actual figures and supplement remain unread. MED links a commentary, not a correction/retraction; publisher notice check was inaccessible. Source: https://pubmed.ncbi.nlm.nih.gov/20935099/.

    +

    Fenton et al. 2010, PMID:20935099, scientific Abstract retrieved from source-qualified MED metadata. Supports prey-derived nutrition during intrabacterial replication; do not generalize its single-prey wording to a fixed predator occupancy or universal prey dependence. Full-text delivery failed; Methods, actual figures and supplement remain unread. MED links a commentary, not a correction/retraction; publisher notice check was inaccessible. Source: https://pubmed.ncbi.nlm.nih.gov/20935099/.

  • DOI:10.1128/jb.96.4.1366-1381.1968
    Although partial disruption of the cytoplasmic membrane was always apparent, the parasite did not appear to actively penetrate through this barrier.
    -

    Burnham et al. 1968, PMID:4879563, scientific Abstract directly read at PubMed and matched source-qualified MED metadata. Electron microscopy supports entry without observed active penetration of the prey cytoplasmic membrane, not an intact membrane throughout predation or direct nutrient tracing. Full text and actual figures were unavailable; no strain-level example inferred. MED/PubMed exposed no linked notice, but publisher notice status was not verified. Source: https://pubmed.ncbi.nlm.nih.gov/4879563/.

    +

    Burnham et al. 1968, PMID:4879563, scientific Abstract directly read at PubMed and matched source-qualified MED metadata. Electron microscopy supports entry without observed active penetration of the prey cytoplasmic membrane, not an intact membrane throughout predation or direct nutrient tracing. Full text and actual figures were unavailable; no strain-level example inferred. MED/PubMed exposed no linked notice, but publisher notice status was not verified. Source: https://pubmed.ncbi.nlm.nih.gov/4879563/.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1038/s42003-025-09010-x - Qualified to wild-type HD100, not deletion, complemented or host-independent derivatives. Lai et al. used E. coli laboratory prey; this is not direct field observation. DSM 50701 is HD100 and is recorded as a soil isolate at https://webshop.dsmz.de/en/bacteria/Bdellovibrio-bacteriovorus.html; this establishes natural provenance, not another predation assay. NCBI strain identifier, scientific name and DSM 50701 synonym independently checked on 2026-10-11: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=264462. + Qualified to wild-type HD100, not deletion, complemented or host-independent derivatives. Lai et al. used E. coli laboratory prey; this is not direct field observation. DSM 50701 is HD100 and is recorded as a soil isolate at https://webshop.dsmz.de/en/bacteria/Bdellovibrio-bacteriovorus.html; this establishes natural provenance, not another predation assay. NCBI strain identifier, scientific name and DSM 50701 synonym independently checked on 2026-10-11: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=264462. @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-11 14:22 UTC diff --git a/pages/traits/ecology/plant_pathogen.html b/pages/traits/ecology/plant_pathogen.html index 6cd1d240586..69c25dbb2c9 100644 --- a/pages/traits/ecology/plant_pathogen.html +++ b/pages/traits/ecology/plant_pathogen.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -375,7 +376,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -687,7 +688,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1051,12 +1061,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/ecology/predatory_bacterium.html b/pages/traits/ecology/predatory_bacterium.html index 30224a9821c..49759f490b6 100644 --- a/pages/traits/ecology/predatory_bacterium.html +++ b/pages/traits/ecology/predatory_bacterium.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • predatory bacterium - traitmech:000054 + traitmech:000054 enables bacteriolytic killing @@ -385,7 +386,7 @@

    Children (5)

    Synonyms (1)

    • @@ -401,7 +402,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -674,7 +675,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1038,12 +1048,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-11 11:45 UTC diff --git a/pages/traits/ecology/rhizosphere_association.html b/pages/traits/ecology/rhizosphere_association.html index 842024e47c1..fda92ed0c63 100644 --- a/pages/traits/ecology/rhizosphere_association.html +++ b/pages/traits/ecology/rhizosphere_association.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    confers rhizosphere association - traitmech:000051 + traitmech:000051 METPO:2007700

    The rhizosphere habitat supports the rhizosphere-associated lifestyle.

      @@ -194,7 +195,7 @@

      Edge evidence

      positively regulates rhizosphere association - traitmech:000051 + traitmech:000051 RO:0002213

      Flagellar motility is required for efficient root colonization / rhizosphere association.

        @@ -232,7 +233,7 @@

        Edge evidence

        GO:0042710 positively regulates rhizosphere association - traitmech:000051 + traitmech:000051 RO:0002213

        Biofilms provide nutrient-rich microenvironments and protection supporting rhizosphere persistence.

          @@ -292,7 +293,7 @@

          Parent traits (1)

          Synonyms (1)

            -
          • rhizosphere-associated RELATED_SYNONYM · DOI:10.1038/nrmicro3109
            • +
          • rhizosphere-associated RELATED_SYNONYM · DOI:10.1038/nrmicro3109
    @@ -308,7 +309,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -566,7 +567,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -930,12 +940,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/ecology/saprotrophy.html b/pages/traits/ecology/saprotrophy.html index c09c6306a08..51e2bcb78bc 100644 --- a/pages/traits/ecology/saprotrophy.html +++ b/pages/traits/ecology/saprotrophy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • saprotrophy - traitmech:000055 + traitmech:000055 enables organic matter decomposition @@ -311,9 +312,9 @@

    Parent traits (1)

    Synonyms (2)

    • @@ -329,7 +330,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -632,7 +633,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -996,12 +1006,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-07 20:05 UTC diff --git a/pages/traits/ecology/soil_dwelling.html b/pages/traits/ecology/soil_dwelling.html index e28db3f93b9..6c68ca53a66 100644 --- a/pages/traits/ecology/soil_dwelling.html +++ b/pages/traits/ecology/soil_dwelling.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • soil-dwelling - traitmech:000050 + traitmech:000050 contributes to biogeochemical cycling @@ -346,7 +347,7 @@

    Edge evidence

    associated with soil-dwelling - traitmech:000050 + traitmech:000050 biolink:associated_with

    Soil habitat is associated with soil-resident microbes.

      @@ -406,7 +407,7 @@

      Parent traits (1)

      Synonyms (1)

    • @@ -422,7 +423,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -717,7 +718,7 @@

    Recorded curation sessions

  • · claude-code
    • REVIEW — Reviewed soil-dwelling causal evidence for issue #183 -

      Reviewed data/traits/ecology/soil_dwelling.yaml after the issue #183 priority pass. Added source-verified verbatim snippets to the two record-level evidence items and all eight causal-edge evidence items in soil_dwelling_biogeochemistry; regrounded the five broad observational ecology edges to biolink:associated_with; and narrowed the climate-extreme edge to the heat treatment supported by DOI:10.1038/s41586-024-08185-3. The transform is dry-run by default, uses write_validated_trait for LinkML validation before writes, and has focused regression tests for idempotence, source drift, migrated drift, and partial replay.

    +

    Reviewed data/traits/ecology/soil_dwelling.yaml after the issue #183 priority pass. Added source-verified verbatim snippets to the two record-level evidence items and all eight causal-edge evidence items in soil_dwelling_biogeochemistry; regrounded the five broad observational ecology edges to biolink:associated_with; and narrowed the climate-extreme edge to the heat treatment supported by DOI:10.1038/s41586-024-08185-3. The transform is dry-run by default, uses write_validated_trait for LinkML validation before writes, and has focused regression tests for idempotence, source drift, migrated drift, and partial replay.

    • Read this curation session
  • @@ -761,7 +762,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -1125,12 +1135,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-07 20:05 UTC diff --git a/pages/traits/ecology/symbiosis.html b/pages/traits/ecology/symbiosis.html index 07c9ee40bfe..356c1412e1c 100644 --- a/pages/traits/ecology/symbiosis.html +++ b/pages/traits/ecology/symbiosis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    GO:0044403 confers symbiosis - traitmech:000040 + traitmech:000040 METPO:2007700

    Sustained symbiotic interaction realizes the symbiotic lifestyle.

      @@ -364,7 +365,7 @@

      Children (4)

      Synonyms (1)

    @@ -380,7 +381,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -467,12 +468,12 @@

    Deep research

    | Proposed mechanism / edge module | Strongest model system | Evidence design | Confidence / curation recommendation | Key quantitative result | DOI | |---|---|---|---|---|---| -| SRRP adhesins + aSec secretion system -> stable host-specific foregut colonization | *Lactiplantibacillus plantarum* in *Drosophila melanogaster* gut | Live imaging of single cells, experimental evolution, colonization-island loss mutant, CRISPRi of adhesins | **High; curate as taxon-specific direct edge** | Stable wild-type colonization of ~20,000-50,000 CFU per gut; high-affinity binding diffusion coefficient 0.001 µm2/s versus 0.10 µm2/s for transient binders; colonization-island loss increased diffusion to 0.122 µm2/s; CRISPRi colonization defect ****P<0.0001 (gutierrezgarcia2024aconservedbacterial pages 6-7, gutierrezgarcia2024aconservedbacterial pages 3-4, gutierrezgarcia2024aconservedbacterial pages 9-13) | 10.1126/science.adp7748 | -| *mglB* allele / type IV pili-dependent motility -> increased colonization in non-native host | *Snodgrassella* from *Bombus terrestris* serially passaged in *Apis mellifera* | ARTP mutagenesis, in vivo serial passage, gnotobiotic bees, competition assays | **High; curate as taxon-specific direct edge** | Mutant alleles in the mutual gliding locus out-competed the ancestral strain in the non-native honeybee gut but not in the native host; effect interpreted as altered type IV pili-dependent motility (meng2024identificationofthe pages 1-2) | 10.1186/s40168-024-01813-0 | -| Rhizobial Nod factors -> NFR1/NFR5 signaling -> altered root exudate composition -> altered microbiota assembly | *Lotus japonicus* with rhizobial symbionts | Host mutant comparison (*nfr5*, *nfr1/nfre*, *chit5*), metabolomics, microbiome profiling across nitrogen states | **High for plant-side causal chain; curate as taxon-specific direct edge** | Distinct “starved, symbiotic, or inorganic” nitrogen states produced different root/rhizosphere microbiomes; Nod-factor-signaling mutants had altered community assembly and exudate profiles (tao2024nitrogenandnod pages 9-11, tao2024nitrogenandnod pages 1-2) | 10.1038/s41467-024-47752-0 | -| Rhizobial nitrogenase: N2 -> NH4+ and plant photosynthate/carbon exchange supports persistent symbiosis | Legume-rhizobium root nodules | Integrative physiological/genetic review drawing on split-root, metabolomic, transcriptomic, and mutant literature | **Moderate-High; curate only at generic process level unless adding species-specific supporting primary data** | No single effect size extracted here, but source states bacteria reduce N2 to NH4+ and plant supplies photosynthates/dicarboxylates; nitrogen demand and sugar allocation tune nodule function and senescence (lepetit2023controlofthe pages 1-2) | 10.3389/fpls.2023.1114840 | -| Host ApGLNT1 glutamine transporter + arginine feedback -> metabolic integration with *Buchnera* amino-acid biosynthesis | *Acyrthosiphon pisum*–*Buchnera aphidicola* | Functional transporter characterization, modeling, comparative phylogeny, metabolite concentration comparison | **High; curate as taxon-specific direct edge** | Arginine IC50 values for GLNT1 orthologs are within/near phloem sap arginine range of 4.4-15.2 mM; aphid hemolymph arginine was insufficient to inhibit ApGLNT1, whereas hemolymph glutamine approached saturating levels (duncan2023cooptionofa pages 7-8) | 10.1073/pnas.2308448120 | -| Conserved host-association module: chemotaxis/host sensing + TCS + biofilm + secretion systems + immune evasion -> persistent host association across symbiosis continuum | Cross-system review emphasizing *Pseudomonas*, *Sinorhizobium*, *Brucella*, *Agrobacterium* and other plant/animal associates | Comparative review of shared mechanisms; includes mutant examples for TCS/biofilm systems but mostly umbrella synthesis | **Moderate; curate as umbrella background only, not as a single universal edge** | Review identifies five shared features across pathogenic, commensal, and mutualistic bacteria; no unified cross-taxon effect size, though individual TCS mutants show impaired symbiosis/virulence in cited systems (wiesmann2023originsofsymbiosis pages 6-8, wiesmann2023originsofsymbiosis pages 1-2) | 10.1093/femsre/fuac048 | +| SRRP adhesins + aSec secretion system -> stable host-specific foregut colonization | *Lactiplantibacillus plantarum* in *Drosophila melanogaster* gut | Live imaging of single cells, experimental evolution, colonization-island loss mutant, CRISPRi of adhesins | **High; curate as taxon-specific direct edge** | Stable wild-type colonization of ~20,000-50,000 CFU per gut; high-affinity binding diffusion coefficient 0.001 µm2/s versus 0.10 µm2/s for transient binders; colonization-island loss increased diffusion to 0.122 µm2/s; CRISPRi colonization defect ****P<0.0001 (gutierrezgarcia2024aconservedbacterial pages 6-7, gutierrezgarcia2024aconservedbacterial pages 3-4, gutierrezgarcia2024aconservedbacterial pages 9-13) | 10.1126/science.adp7748 | +| *mglB* allele / type IV pili-dependent motility -> increased colonization in non-native host | *Snodgrassella* from *Bombus terrestris* serially passaged in *Apis mellifera* | ARTP mutagenesis, in vivo serial passage, gnotobiotic bees, competition assays | **High; curate as taxon-specific direct edge** | Mutant alleles in the mutual gliding locus out-competed the ancestral strain in the non-native honeybee gut but not in the native host; effect interpreted as altered type IV pili-dependent motility (meng2024identificationofthe pages 1-2) | 10.1186/s40168-024-01813-0 | +| Rhizobial Nod factors -> NFR1/NFR5 signaling -> altered root exudate composition -> altered microbiota assembly | *Lotus japonicus* with rhizobial symbionts | Host mutant comparison (*nfr5*, *nfr1/nfre*, *chit5*), metabolomics, microbiome profiling across nitrogen states | **High for plant-side causal chain; curate as taxon-specific direct edge** | Distinct “starved, symbiotic, or inorganic” nitrogen states produced different root/rhizosphere microbiomes; Nod-factor-signaling mutants had altered community assembly and exudate profiles (tao2024nitrogenandnod pages 9-11, tao2024nitrogenandnod pages 1-2) | 10.1038/s41467-024-47752-0 | +| Rhizobial nitrogenase: N2 -> NH4+ and plant photosynthate/carbon exchange supports persistent symbiosis | Legume-rhizobium root nodules | Integrative physiological/genetic review drawing on split-root, metabolomic, transcriptomic, and mutant literature | **Moderate-High; curate only at generic process level unless adding species-specific supporting primary data** | No single effect size extracted here, but source states bacteria reduce N2 to NH4+ and plant supplies photosynthates/dicarboxylates; nitrogen demand and sugar allocation tune nodule function and senescence (lepetit2023controlofthe pages 1-2) | 10.3389/fpls.2023.1114840 | +| Host ApGLNT1 glutamine transporter + arginine feedback -> metabolic integration with *Buchnera* amino-acid biosynthesis | *Acyrthosiphon pisum*–*Buchnera aphidicola* | Functional transporter characterization, modeling, comparative phylogeny, metabolite concentration comparison | **High; curate as taxon-specific direct edge** | Arginine IC50 values for GLNT1 orthologs are within/near phloem sap arginine range of 4.4-15.2 mM; aphid hemolymph arginine was insufficient to inhibit ApGLNT1, whereas hemolymph glutamine approached saturating levels (duncan2023cooptionofa pages 7-8) | 10.1073/pnas.2308448120 | +| Conserved host-association module: chemotaxis/host sensing + TCS + biofilm + secretion systems + immune evasion -> persistent host association across symbiosis continuum | Cross-system review emphasizing *Pseudomonas*, *Sinorhizobium*, *Brucella*, *Agrobacterium* and other plant/animal associates | Comparative review of shared mechanisms; includes mutant examples for TCS/biofilm systems but mostly umbrella synthesis | **Moderate; curate as umbrella background only, not as a single universal edge** | Review identifies five shared features across pathogenic, commensal, and mutualistic bacteria; no unified cross-taxon effect size, though individual TCS mutants show impaired symbiosis/virulence in cited systems (wiesmann2023originsofsymbiosis pages 6-8, wiesmann2023originsofsymbiosis pages 1-2) | 10.1093/femsre/fuac048 | *Table: This table ranks the strongest candidate mechanism modules for curating microbial symbiosis (traitmech:000040), separating direct taxon-specific causal edges from broader cross-system umbrella claims. It is useful for deciding which nodes and edges are ready for TraitMech curation versus which should remain as background or warning-level context.* @@ -653,7 +654,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1017,12 +1027,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/acidophilic.html b/pages/traits/environment/acidophilic.html index 138b180e5a7..4a32325345d 100644 --- a/pages/traits/environment/acidophilic.html +++ b/pages/traits/environment/acidophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -343,9 +344,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • acidophil EXACT_SYNONYM · metpo.owl
      • +
    • acidophil EXACT_SYNONYM · metpo.owl
      • -
    • acidophile EXACT_SYNONYM · metpo.owl
      • +
    • acidophile EXACT_SYNONYM · metpo.owl
    @@ -361,7 +362,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -655,7 +656,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1019,12 +1029,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/acidotolerant.html b/pages/traits/environment/acidotolerant.html index 345aef46841..1d9fa4d5eef 100644 --- a/pages/traits/environment/acidotolerant.html +++ b/pages/traits/environment/acidotolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -305,7 +306,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • aciduric EXACT_SYNONYM · metpo.owl
      • +
    • aciduric EXACT_SYNONYM · metpo.owl
    @@ -321,7 +322,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -624,7 +625,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -988,12 +998,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/aerobic.html b/pages/traits/environment/aerobic.html index 1c5f6b67057..20e18f44374 100644 --- a/pages/traits/environment/aerobic.html +++ b/pages/traits/environment/aerobic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -358,9 +359,9 @@

    Children (1)

    Synonyms (2)

      -
    • Ox_aerobic RELATED_SYNONYM · metpo.owl
      • +
    • Ox_aerobic RELATED_SYNONYM · metpo.owl
      • -
    • aerobe RELATED_SYNONYM · metpo.owl
      • +
    • aerobe RELATED_SYNONYM · metpo.owl
    @@ -383,7 +384,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000602 [-37.032, +29.784, -5.356, +74.090, …]
      • +
    • aerobic METPO:1000602 [-37.032, +29.784, -5.356, +74.090, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -716,7 +717,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1080,12 +1090,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 06:15 UTC diff --git a/pages/traits/environment/aerotolerant.html b/pages/traits/environment/aerotolerant.html index e750b7dfbf8..aa17090d2a5 100644 --- a/pages/traits/environment/aerotolerant.html +++ b/pages/traits/environment/aerotolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -308,7 +309,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -641,7 +642,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1005,12 +1015,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/alkalotolerant.html b/pages/traits/environment/alkalotolerant.html index d3640508783..00f8d4fd507 100644 --- a/pages/traits/environment/alkalotolerant.html +++ b/pages/traits/environment/alkalotolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -324,7 +325,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • alkalitolerant EXACT_SYNONYM · metpo.owl
      • +
    • alkalitolerant EXACT_SYNONYM · metpo.owl
    @@ -340,7 +341,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -643,7 +644,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1007,12 +1017,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/alkaphilic.html b/pages/traits/environment/alkaphilic.html index 07c931d26ce..c3eb01bc063 100644 --- a/pages/traits/environment/alkaphilic.html +++ b/pages/traits/environment/alkaphilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -333,11 +334,11 @@

    Children (1)

    Synonyms (3)

      -
    • alkaliphile EXACT_SYNONYM · metpo.owl
      • +
    • alkaliphile EXACT_SYNONYM · metpo.owl
      • -
    • alkalophile EXACT_SYNONYM · metpo.owl
      • +
    • alkalophile EXACT_SYNONYM · metpo.owl
      • -
    • alkalophilic EXACT_SYNONYM · metpo.owl
      • +
    • alkalophilic EXACT_SYNONYM · metpo.owl
    @@ -353,7 +354,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -680,7 +681,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1044,12 +1054,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 07:35 UTC diff --git a/pages/traits/environment/anaerobic.html b/pages/traits/environment/anaerobic.html index ae9e1166a15..80ca75e3a54 100644 --- a/pages/traits/environment/anaerobic.html +++ b/pages/traits/environment/anaerobic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -330,9 +331,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • Ox_anaerobic RELATED_SYNONYM · metpo.owl
      • +
    • Ox_anaerobic RELATED_SYNONYM · metpo.owl
      • -
    • anaerobe RELATED_SYNONYM · metpo.owl
      • +
    • anaerobe RELATED_SYNONYM · metpo.owl
    @@ -355,7 +356,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000603 [+295.383, -195.343, -25.409, +1.165, …]
      • +
    • anaerobic METPO:1000603 [+295.383, -195.343, -25.409, +1.165, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -658,7 +659,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1022,12 +1032,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 06:15 UTC diff --git a/pages/traits/environment/arsenic_tolerant.html b/pages/traits/environment/arsenic_tolerant.html index b755d847159..e228dd526a0 100644 --- a/pages/traits/environment/arsenic_tolerant.html +++ b/pages/traits/environment/arsenic_tolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    CHEBI:29242 challenges arsenic tolerant - traitmech:000017 + traitmech:000017 METPO:2007406

    Cytoplasmic arsenite is the toxic challenge the trait counters.

      @@ -345,8 +346,8 @@

      Protein and taxon examples

    		 - Cupriavidus metallidurans CH34 -
    NCBITaxon:266264 + Cupriavidus metallidurans CH34 +
    NCBITaxon:266264         		UNREVIEWED
    @@ -412,7 +413,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -428,7 +429,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -728,7 +729,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1092,12 +1102,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/environment/cadmium_tolerant.html b/pages/traits/environment/cadmium_tolerant.html index debf53e1300..5ebf597f056 100644 --- a/pages/traits/environment/cadmium_tolerant.html +++ b/pages/traits/environment/cadmium_tolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -105,7 +106,7 @@

    Edge evidence

    CHEBI:48775 challenges cadmium tolerant - traitmech:000013 + traitmech:000013 METPO:2007406

    Cytoplasmic cadmium is the toxic challenge the trait counters.

      @@ -256,8 +257,8 @@

      Protein and taxon examples

    		 - Cupriavidus metallidurans CH34 -
    NCBITaxon:266264 + Cupriavidus metallidurans CH34 +
    NCBITaxon:266264         		REVIEWED
    @@ -330,7 +331,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -582,7 +583,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added PMID:12829273 (Nies 2003) with verified verbatim snippet to record-level evidence to match definition_source (Stage 5 remediation of F-DEF-SRC-CADMIUM-002 in group G-STAGE4-RECORD-LEVEL-DEFINITION-SOURCE, issue #1981).

    +

    Added PMID:12829273 (Nies 2003) with verified verbatim snippet to record-level evidence to match definition_source (Stage 5 remediation of F-DEF-SRC-CADMIUM-002 in group G-STAGE4-RECORD-LEVEL-DEFINITION-SOURCE, issue #1981).

    • @@ -615,7 +616,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -979,12 +989,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 05:20 UTC diff --git a/pages/traits/environment/capnophilic.html b/pages/traits/environment/capnophilic.html index 79842c87078..3bc058fefba 100644 --- a/pages/traits/environment/capnophilic.html +++ b/pages/traits/environment/capnophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -155,8 +156,8 @@

    Protein and taxon examples

    		 - Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) -
    NCBITaxon:192222 + Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) +
    NCBITaxon:192222         		UNREVIEWED
    @@ -229,7 +230,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -388,7 +389,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -752,12 +762,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 21:12 UTC diff --git a/pages/traits/environment/cobalt_tolerant.html b/pages/traits/environment/cobalt_tolerant.html index dea542957ca..9760b66c156 100644 --- a/pages/traits/environment/cobalt_tolerant.html +++ b/pages/traits/environment/cobalt_tolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -105,7 +106,7 @@

    Edge evidence

    CHEBI:48828 challenges cobalt tolerant - traitmech:000015 + traitmech:000015 METPO:2007406

    Cytoplasmic cobalt is the toxic challenge the trait counters.

      @@ -219,7 +220,7 @@

      Edge evidence

      confers resistance to cobalt tolerant - traitmech:000015 + traitmech:000015

      The cnrCBAYXHT operon confers cobalt (and nickel) resistance.

        @@ -313,8 +314,8 @@

        Protein and taxon examples

    		 - Cupriavidus metallidurans CH34 -
    NCBITaxon:266264 + Cupriavidus metallidurans CH34 +
    NCBITaxon:266264         		REVIEWED
    @@ -387,7 +388,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -627,7 +628,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added PMID:12829273 (Nies 2003) with verified verbatim snippet to record-level evidence to match definition_source (Stage 5 remediation of F-DEF-SRC-COBALT-003 in group G-STAGE4-RECORD-LEVEL-DEFINITION-SOURCE, issue #1981).

    +

    Added PMID:12829273 (Nies 2003) with verified verbatim snippet to record-level evidence to match definition_source (Stage 5 remediation of F-DEF-SRC-COBALT-003 in group G-STAGE4-RECORD-LEVEL-DEFINITION-SOURCE, issue #1981).

    • @@ -660,7 +661,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1024,12 +1034,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 05:20 UTC diff --git a/pages/traits/environment/copper_tolerant.html b/pages/traits/environment/copper_tolerant.html index c0f1a1a41bf..9c2fad8a5bb 100644 --- a/pages/traits/environment/copper_tolerant.html +++ b/pages/traits/environment/copper_tolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    CHEBI:29036 challenges copper tolerant - traitmech:000018 + traitmech:000018 METPO:2007406

    Elevated cytoplasmic copper is the toxic challenge the trait counters.

      @@ -250,8 +251,8 @@

      Protein and taxon examples

    		 - Cupriavidus metallidurans CH34 -
    NCBITaxon:266264 + Cupriavidus metallidurans CH34 +
    NCBITaxon:266264         		UNREVIEWED
    @@ -317,7 +318,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -333,7 +334,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -454,18 +455,18 @@

    Deep research

    | subject | predicate | object | taxon/condition | confidence | DOI | |---|---|---|---|---|---| -| Cu(I)-bound CueR | activates transcription of | copA | *Escherichia coli*; cytoplasmic copper stress; Cue regulon (hyre2021copperhomeostaticmechanisms pages 2-4, bittner2017thecopperefflux pages 1-2, gautam2023linkingcopperassociatedsignal pages 3-5) | high | 10.1128/ecosalplus.esp-0014-2020 | -| Cu(I)-bound CueR | activates transcription of | cueO | *Escherichia coli*; cytoplasmic copper stress; Cue regulon (hyre2021copperhomeostaticmechanisms pages 2-4, bittner2017thecopperefflux pages 1-2, gautam2023linkingcopperassociatedsignal pages 3-5) | high | 10.1128/ecosalplus.esp-0014-2020 | -| CopZ copper chaperone | delivers cytoplasmic Cu(I) to | CopA Cu(+)-ATPase | *Pseudomonas aeruginosa*; cytoplasmic copper trafficking (virieuxpetit2022fromcoppertolerance pages 5-7, andrei2020cuhomeostasisin pages 10-12, giachino2020coppertolerancein pages 3-5) | medium | 10.3390/genes13020301 | -| CopA/CupA P1B-type ATPase | exports | cytoplasmic Cu(I) to the periplasm | Gram-negative bacteria; strongest primary evidence in *Cupriavidus metallidurans* and reviewed broadly (hirth2023fullcopperresistance pages 16-18, andrei2020cuhomeostasisin pages 16-19, hyre2021copperhomeostaticmechanisms pages 2-4) | high | 10.1128/aem.00567-23 | -| CueO/PcoA/CopA multicopper oxidase | oxidizes | periplasmic Cu(I) to Cu(II) | Enterobacteria and *C. metallidurans*; oxygen-dependent periplasmic detoxification (hirth2023fullcopperresistance pages 16-18, chaturvedi2014pathogenicadaptationsto pages 6-7, giachino2020coppertolerancein pages 3-5, andrei2020cuhomeostasisin pages 21-23) | high | 10.1128/aem.00567-23 | -| CusS/CusR two-component system | activates transcription of | cusCFBA | *Escherichia coli*; periplasmic copper sensing, strongest under anaerobic conditions (rismondo2023thesensoryhistidine pages 8-10, rismondo2023thesensoryhistidine pages 2-5) | high | 10.1128/spectrum.00291-23 | -| CusCFBA/CusCBA efflux complex | exports | periplasmic Cu(I) to the extracellular space | *E. coli* and *C. metallidurans*; especially important when oxygen is limiting (rismondo2023thesensoryhistidine pages 1-2, andrei2020cuhomeostasisin pages 19-21, hirth2023fullcopperresistance pages 16-18) | high | 10.1128/spectrum.00291-23 | -| Glutathione (via GshA) | cooperates with | Cop/Cus/Cup copper-defense systems | *C. metallidurans*; deletion analysis showed GSH amplifies resistance but is insufficient alone (hirth2023fullcopperresistance pages 1-3, hirth2023fullcopperresistance pages 7-9, hirth2023fullcopperresistance pages 11-12) | high | 10.1128/aem.00567-23 | -| Extracellular polymeric substances (EPS) | sequester/adsorb | copper | Deep-sea vent isolates; Cu induced EPS and adsorption of ~40–50 mg·g−1 Cu (yu2024isolationofhighly pages 4-6, yu2024isolationofhighly pages 1-2, yu2024isolationofhighly pages 2-3) | medium | 10.3389/fmicb.2024.1390451 | -| CopA/CupA-mediated copper export | decreases | intracellular copper accumulation | *Haemophilus influenzae* and *C. metallidurans*; ΔcopZA accumulated 97% more Cu, Cup reduced accumulation at high Cu (hirth2023fullcopperresistance pages 16-18, hirth2023fullcopperresistance pages 11-12, wong2023coppereffluxsystem pages 10-12) | high | 10.1128/iai.00091-23 | -| Reduced intracellular/periplasmic copper burden | enables | growth/survival at elevated copper | Broad bacterial trait; strongest mutant IC50/survival evidence in *C. metallidurans* and hospital-adapted *P. aeruginosa* (hirth2023fullcopperresistance pages 16-18, hirth2023fullcopperresistance pages 4-6, virieuxpetit2022fromcoppertolerance pages 8-9) | high | 10.1128/aem.00567-23 | -| copZA copper efflux locus | promotes | lung infection fitness under host copper stress | Nontypeable *Haemophilus influenzae*; copA mutant ~4-fold and copZA mutant ~20-fold underrepresented in murine lung infection (wong2023coppereffluxsystem pages 10-12) | high | 10.1128/iai.00091-23 | +| Cu(I)-bound CueR | activates transcription of | copA | *Escherichia coli*; cytoplasmic copper stress; Cue regulon (hyre2021copperhomeostaticmechanisms pages 2-4, bittner2017thecopperefflux pages 1-2, gautam2023linkingcopperassociatedsignal pages 3-5) | high | 10.1128/ecosalplus.esp-0014-2020 | +| Cu(I)-bound CueR | activates transcription of | cueO | *Escherichia coli*; cytoplasmic copper stress; Cue regulon (hyre2021copperhomeostaticmechanisms pages 2-4, bittner2017thecopperefflux pages 1-2, gautam2023linkingcopperassociatedsignal pages 3-5) | high | 10.1128/ecosalplus.esp-0014-2020 | +| CopZ copper chaperone | delivers cytoplasmic Cu(I) to | CopA Cu(+)-ATPase | *Pseudomonas aeruginosa*; cytoplasmic copper trafficking (virieuxpetit2022fromcoppertolerance pages 5-7, andrei2020cuhomeostasisin pages 10-12, giachino2020coppertolerancein pages 3-5) | medium | 10.3390/genes13020301 | +| CopA/CupA P1B-type ATPase | exports | cytoplasmic Cu(I) to the periplasm | Gram-negative bacteria; strongest primary evidence in *Cupriavidus metallidurans* and reviewed broadly (hirth2023fullcopperresistance pages 16-18, andrei2020cuhomeostasisin pages 16-19, hyre2021copperhomeostaticmechanisms pages 2-4) | high | 10.1128/aem.00567-23 | +| CueO/PcoA/CopA multicopper oxidase | oxidizes | periplasmic Cu(I) to Cu(II) | Enterobacteria and *C. metallidurans*; oxygen-dependent periplasmic detoxification (hirth2023fullcopperresistance pages 16-18, chaturvedi2014pathogenicadaptationsto pages 6-7, giachino2020coppertolerancein pages 3-5, andrei2020cuhomeostasisin pages 21-23) | high | 10.1128/aem.00567-23 | +| CusS/CusR two-component system | activates transcription of | cusCFBA | *Escherichia coli*; periplasmic copper sensing, strongest under anaerobic conditions (rismondo2023thesensoryhistidine pages 8-10, rismondo2023thesensoryhistidine pages 2-5) | high | 10.1128/spectrum.00291-23 | +| CusCFBA/CusCBA efflux complex | exports | periplasmic Cu(I) to the extracellular space | *E. coli* and *C. metallidurans*; especially important when oxygen is limiting (rismondo2023thesensoryhistidine pages 1-2, andrei2020cuhomeostasisin pages 19-21, hirth2023fullcopperresistance pages 16-18) | high | 10.1128/spectrum.00291-23 | +| Glutathione (via GshA) | cooperates with | Cop/Cus/Cup copper-defense systems | *C. metallidurans*; deletion analysis showed GSH amplifies resistance but is insufficient alone (hirth2023fullcopperresistance pages 1-3, hirth2023fullcopperresistance pages 7-9, hirth2023fullcopperresistance pages 11-12) | high | 10.1128/aem.00567-23 | +| Extracellular polymeric substances (EPS) | sequester/adsorb | copper | Deep-sea vent isolates; Cu induced EPS and adsorption of ~40–50 mg·g−1 Cu (yu2024isolationofhighly pages 4-6, yu2024isolationofhighly pages 1-2, yu2024isolationofhighly pages 2-3) | medium | 10.3389/fmicb.2024.1390451 | +| CopA/CupA-mediated copper export | decreases | intracellular copper accumulation | *Haemophilus influenzae* and *C. metallidurans*; ΔcopZA accumulated 97% more Cu, Cup reduced accumulation at high Cu (hirth2023fullcopperresistance pages 16-18, hirth2023fullcopperresistance pages 11-12, wong2023coppereffluxsystem pages 10-12) | high | 10.1128/iai.00091-23 | +| Reduced intracellular/periplasmic copper burden | enables | growth/survival at elevated copper | Broad bacterial trait; strongest mutant IC50/survival evidence in *C. metallidurans* and hospital-adapted *P. aeruginosa* (hirth2023fullcopperresistance pages 16-18, hirth2023fullcopperresistance pages 4-6, virieuxpetit2022fromcoppertolerance pages 8-9) | high | 10.1128/aem.00567-23 | +| copZA copper efflux locus | promotes | lung infection fitness under host copper stress | Nontypeable *Haemophilus influenzae*; copA mutant ~4-fold and copZA mutant ~20-fold underrepresented in murine lung infection (wong2023coppereffluxsystem pages 10-12) | high | 10.1128/iai.00091-23 | *Table: This table lists the strongest candidate causal triples for TraitMech curation of microbial copper tolerance, prioritizing experimentally supported sensing, efflux, oxidation, sequestration, and fitness relationships. It is useful as a compact starting set for graph curation while preserving evidence strength and assay context.* @@ -594,7 +595,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -958,12 +968,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/environment/delta_phenotype_with_numerical_limits.html b/pages/traits/environment/delta_phenotype_with_numerical_limits.html index 68a199bc5b2..e2a4fd994d1 100644 --- a/pages/traits/environment/delta_phenotype_with_numerical_limits.html +++ b/pages/traits/environment/delta_phenotype_with_numerical_limits.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,11 +116,11 @@

    Edge evidence

  • NaCl delta - METPO:1000335 + METPO:1000335 is a delta phenotype with numerical limits METPO:1000534 - rdfs:subClassOf + rdfs:subClassOf

    NaCl delta is an axis-specific delta phenotype.

      @@ -134,11 +135,11 @@

      Edge evidence

    • pH delta - METPO:1000232 + METPO:1000232 is a delta phenotype with numerical limits METPO:1000534 - rdfs:subClassOf + rdfs:subClassOf

      pH delta is an axis-specific delta phenotype.

        @@ -153,11 +154,11 @@

        Edge evidence

      • temperature delta - METPO:1000303 + METPO:1000303 is a delta phenotype with numerical limits METPO:1000534 - rdfs:subClassOf + rdfs:subClassOf

        Temperature delta is an axis-specific delta phenotype.

          @@ -251,7 +252,7 @@

          Edge evidence

          maintained across temperature delta - METPO:1000303 + METPO:1000303

          Regulatory-metabolic cross talk buffers core central metabolism across a wide temperature range, supporting a broad temperature delta.

            @@ -331,7 +332,7 @@

            kg-microbe context

            via direct_metpo.

            512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

            @@ -562,7 +563,7 @@

            Curation history

          • · ADD_CANONICAL_EXAMPLES · codex -

            Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Psychrobacter arcticus (NCBITaxon:334543; DOI:10.1128/JB.01377-08). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

            +

            Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Psychrobacter arcticus (NCBITaxon:334543; DOI:10.1128/JB.01377-08). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

          • @@ -610,7 +611,16 @@

            Identifier

            Term kind
            CLASS
            Status
            -
            REVIEWED
            +
            REVIEWED + + +
            + What this status means +

            Curator has signed off on label / definition / parents.

            +

            Quoted from the schema's status definitions.

            +
            + +
    • @@ -974,12 +984,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 07:07 UTC diff --git a/pages/traits/environment/desiccation_tolerant.html b/pages/traits/environment/desiccation_tolerant.html index c0da8160554..03f2470f65b 100644 --- a/pages/traits/environment/desiccation_tolerant.html +++ b/pages/traits/environment/desiccation_tolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    confers desiccation tolerant - traitmech:000010 + traitmech:000010 METPO:2007700

    Reversible anhydrobiosis is the basis of desiccation survival.

      @@ -137,7 +138,7 @@

      Edge evidence

      GO:0006302 confers desiccation tolerant - traitmech:000010 + traitmech:000010 METPO:2007700

      Efficient DNA double-strand-break repair restores integrity on rehydration.

        @@ -330,7 +331,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -346,7 +347,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -610,7 +611,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -974,12 +984,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/euryhaline.html b/pages/traits/environment/euryhaline.html index cf71a625339..2204d98a7f0 100644 --- a/pages/traits/environment/euryhaline.html +++ b/pages/traits/environment/euryhaline.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -413,7 +414,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000627 [-3.209, -1.862, -0.407, -3.229, …]
      • +
    • euryhaline METPO:1000627 [-3.209, -1.862, -0.407, -3.229, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -758,7 +759,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1122,12 +1132,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/extreme_hyperthermophilic.html b/pages/traits/environment/extreme_hyperthermophilic.html index 32277d13dd7..26f581aa067 100644 --- a/pages/traits/environment/extreme_hyperthermophilic.html +++ b/pages/traits/environment/extreme_hyperthermophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -311,9 +312,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • extreme hyperthermophile RELATED_SYNONYM · metpo.owl
      • +
    • extreme hyperthermophile RELATED_SYNONYM · metpo.owl
      • -
    • extremely hyperthermophilic RELATED_SYNONYM · metpo.owl
      • +
    • extremely hyperthermophilic RELATED_SYNONYM · metpo.owl
    @@ -329,7 +330,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -647,7 +648,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1011,12 +1021,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/extremely_halophilic.html b/pages/traits/environment/extremely_halophilic.html index d904b3285a6..91f5c0cfc99 100644 --- a/pages/traits/environment/extremely_halophilic.html +++ b/pages/traits/environment/extremely_halophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -343,7 +344,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • extreme-halophilic RELATED_SYNONYM · metpo.owl
      • +
    • extreme-halophilic RELATED_SYNONYM · metpo.owl
    @@ -359,7 +360,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -653,7 +654,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1017,12 +1027,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/facultative_oxygen_preference.html b/pages/traits/environment/facultative_oxygen_preference.html index 3bcecd5e7ae..0807973d3e9 100644 --- a/pages/traits/environment/facultative_oxygen_preference.html +++ b/pages/traits/environment/facultative_oxygen_preference.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -292,7 +293,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Ox_facultative_aerobe_anaerobe RELATED_SYNONYM · metpo.owl
      • +
    • Ox_facultative_aerobe_anaerobe RELATED_SYNONYM · metpo.owl
    @@ -308,7 +309,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -587,7 +588,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -951,12 +961,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/facultative_psychrophilic.html b/pages/traits/environment/facultative_psychrophilic.html index 523c442e91a..15d06729e67 100644 --- a/pages/traits/environment/facultative_psychrophilic.html +++ b/pages/traits/environment/facultative_psychrophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -343,7 +344,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • facultative psychrophile RELATED_SYNONYM · metpo.owl
      • +
    • facultative psychrophile RELATED_SYNONYM · metpo.owl
    @@ -359,7 +360,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -683,7 +684,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1047,12 +1057,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/facultatively_acidophilic.html b/pages/traits/environment/facultatively_acidophilic.html index dce12999224..6c994e5aadb 100644 --- a/pages/traits/environment/facultatively_acidophilic.html +++ b/pages/traits/environment/facultatively_acidophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -400,7 +401,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • facultative acidophile EXACT_SYNONYM · metpo.owl
      • +
    • facultative acidophile EXACT_SYNONYM · metpo.owl
    @@ -416,7 +417,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -707,7 +708,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Paludibaculum fermentans (NCBITaxon:1473598; DOI:10.1099/ijs.0.066175-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Paludibaculum fermentans (NCBITaxon:1473598; DOI:10.1099/ijs.0.066175-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -740,7 +741,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1104,12 +1114,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/facultatively_aerobic.html b/pages/traits/environment/facultatively_aerobic.html index bcf3f326536..2d0a9169416 100644 --- a/pages/traits/environment/facultatively_aerobic.html +++ b/pages/traits/environment/facultatively_aerobic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -330,9 +331,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • facultative RELATED_SYNONYM · metpo.owl
      • +
    • facultative RELATED_SYNONYM · metpo.owl
      • -
    • facultative aerobe RELATED_SYNONYM · metpo.owl
      • +
    • facultative aerobe RELATED_SYNONYM · metpo.owl
    @@ -348,7 +349,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -624,7 +625,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -988,12 +998,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 10:54 UTC diff --git a/pages/traits/environment/facultatively_alkaphilic.html b/pages/traits/environment/facultatively_alkaphilic.html index 27f717eae96..5aaf24707a8 100644 --- a/pages/traits/environment/facultatively_alkaphilic.html +++ b/pages/traits/environment/facultatively_alkaphilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -324,9 +325,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • facultative alkaliphile EXACT_SYNONYM · metpo.owl
      • +
    • facultative alkaliphile EXACT_SYNONYM · metpo.owl
      • -
    • facultative alkaphilic EXACT_SYNONYM · metpo.owl
      • +
    • facultative alkaphilic EXACT_SYNONYM · metpo.owl
    @@ -342,7 +343,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -666,7 +667,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1030,12 +1040,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 07:35 UTC diff --git a/pages/traits/environment/facultatively_anaerobic.html b/pages/traits/environment/facultatively_anaerobic.html index 4c97c92df6b..84400fc70a1 100644 --- a/pages/traits/environment/facultatively_anaerobic.html +++ b/pages/traits/environment/facultatively_anaerobic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -292,9 +293,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • facultative RELATED_SYNONYM · metpo.owl
      • +
    • facultative RELATED_SYNONYM · metpo.owl
      • -
    • facultative anaerobe RELATED_SYNONYM · metpo.owl
      • +
    • facultative anaerobe RELATED_SYNONYM · metpo.owl
    @@ -310,7 +311,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -577,7 +578,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -941,12 +951,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/growth_range_phenotype_with_numerical_limits.html b/pages/traits/environment/growth_range_phenotype_with_numerical_limits.html index b70e46d7805..96b09a22c0e 100644 --- a/pages/traits/environment/growth_range_phenotype_with_numerical_limits.html +++ b/pages/traits/environment/growth_range_phenotype_with_numerical_limits.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,11 +116,11 @@

    Edge evidence

  • NaCl range - METPO:1000334 + METPO:1000334 is a growth range phenotype with numerical limits METPO:1000535 - rdfs:subClassOf + rdfs:subClassOf

    NaCl range is an axis-specific growth-range phenotype.

      @@ -134,11 +135,11 @@

      Edge evidence

    • pH range - METPO:1000332 + METPO:1000332 is a growth range phenotype with numerical limits METPO:1000535 - rdfs:subClassOf + rdfs:subClassOf

      pH range is an axis-specific growth-range phenotype.

        @@ -153,11 +154,11 @@

        Edge evidence

      • temperature range - METPO:1000306 + METPO:1000306 is a growth range phenotype with numerical limits METPO:1000535 - rdfs:subClassOf + rdfs:subClassOf

        Temperature range is an axis-specific growth-range phenotype.

          @@ -172,7 +173,7 @@

          Edge evidence

        • pH range - METPO:1000332 + METPO:1000332 requires maintenance of near-neutral cytoplasmic pH @@ -213,7 +214,7 @@

          Edge evidence

          contributes to pH range - METPO:1000332 + METPO:1000332 RO:0002326

          Antiporter-driven cytoplasmic acidification supports growth at the alkaline end of the pH range.

            @@ -308,7 +309,7 @@

            Edge evidence

            contributes to NaCl range - METPO:1000334 + METPO:1000334 RO:0002326

            Compatible-solute accumulation counteracts hyperosmotic stress, supporting growth across the NaCl salinity range.

              @@ -388,7 +389,7 @@

              kg-microbe context

              via direct_metpo.

              512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

              @@ -625,7 +626,7 @@

              Curation history

            • · ADD_CANONICAL_EXAMPLES · codex -

              Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Natranaerobius thermophilus (NCBITaxon:375929; DOI:10.1128/aem.00145-24). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

              +

              Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Natranaerobius thermophilus (NCBITaxon:375929; DOI:10.1128/aem.00145-24). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

              • @@ -658,7 +659,16 @@

              Identifier

              Term kind
              CLASS
              Status
              -
              REVIEWED
              +
              REVIEWED + + +
              + What this status means +

              Curator has signed off on label / definition / parents.

              +

              Quoted from the schema's status definitions.

              +
              + +
    • @@ -1022,12 +1032,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/haloalkaliphilic.html b/pages/traits/environment/haloalkaliphilic.html index 0c635ba9148..aefee6dd988 100644 --- a/pages/traits/environment/haloalkaliphilic.html +++ b/pages/traits/environment/haloalkaliphilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -369,7 +370,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -684,7 +685,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1048,12 +1058,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/halophilic.html b/pages/traits/environment/halophilic.html index 74d041ff0be..25adb626db2 100644 --- a/pages/traits/environment/halophilic.html +++ b/pages/traits/environment/halophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -303,7 +304,7 @@

    Edge evidence

    is a compatible solutes CHEBI:25728 - rdfs:subClassOf + rdfs:subClassOf

    Ectoine is a major organic compatible solute used in osmoadaptation.

      @@ -369,7 +370,7 @@

      kg-microbe context

      via direct_metpo.

        -
      • METPO:1000620 [-1.039, -0.924, -1.635, -0.067, …]
        • +
      • halophilic METPO:1000620 [-1.039, -0.924, -1.635, -0.067, …]

      512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

      @@ -467,7 +468,7 @@

      Deep research

      * **Haloalkaliphilic, halothermophilic, or chaotolerant:** compound traits requiring separate evidence for pH, temperature, or chaotropic-ion dependence. For example, *Natranaerobius thermophilus* grows optimally at 3.3–3.9 M Na⁺, pH 9.5, and 53°C; its salt phenotype should be represented separately from alkaliphily and thermophily. (xing2024thepolyextremophilenatranaerobius pages 1-2) * **Habitat occurrence:** recovery from a saltern, salt mine, saline lake, or brine is supporting ecological context, not sufficient evidence of physiological salt requirement. -The supplied *Salinicoccus albus* example is valid organism-level evidence, but the DOI-first reference is **10.1099/ijs.0.003251-0** (published April 2009; PMID:19329623). Its species description should support an organism-to-trait association, not a universal mechanism. +The supplied *Salinicoccus albus* example is valid organism-level evidence, but the DOI-first reference is **10.1099/ijs.0.003251-0** (published April 2009; PMID:19329623). Its species description should support an organism-to-trait association, not a universal mechanism. ## 2. Mechanistic model and current understanding @@ -708,7 +709,16 @@

      Identifier

      Term kind
      CLASS
      Status
      -
      REVIEWED
      +
      REVIEWED + + +
      + What this status means +

      Curator has signed off on label / definition / parents.

      +

      Quoted from the schema's status definitions.

      +
      + +
    @@ -1072,12 +1082,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/halophily_preference.html b/pages/traits/environment/halophily_preference.html index 2445fbf4cdb..ee40c04a0f9 100644 --- a/pages/traits/environment/halophily_preference.html +++ b/pages/traits/environment/halophily_preference.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -406,9 +407,9 @@

    Children (9)

    Synonyms (2)

      -
    • Physiology and metabolism.halophily.halophily level RELATED_SYNONYM · metpo.owl
      • +
    • Physiology and metabolism.halophily.halophily level RELATED_SYNONYM · metpo.owl
      • -
    • range_salinity RELATED_SYNONYM · metpo.owl
      • +
    • range_salinity RELATED_SYNONYM · metpo.owl
    @@ -424,7 +425,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -736,13 +737,13 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 2 direct source-backed canonical example(s): Halomonas elongata (NCBITaxon:2746; PMID:20849449), Escherichia coli (NCBITaxon:562; PMC8415458). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 2 direct source-backed canonical example(s): Halomonas elongata (NCBITaxon:2746; PMID:20849449), Escherichia coli (NCBITaxon:562; PMC8415458). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • · REPAIR_CANONICAL_CITATION_SCOPE_1626 · codex -

    Resolved issue 1626 by normalizing PMC8415458 to its verified DOI 10.3389/fmicb.2021.705326 (PMID:34484145), preserving the same paper. Qualified the non-halophilic comparator to BW25113 in LB at 37 C and the reported 24-h viable-count comparison across 0%, 1%, 3.5% and 5% NaCl supplementation. Retained NCBITaxon:562 and its independently checked NCBI label. The broad-class role, Halomonas example, definition, hierarchy and graph are unchanged; no species-wide salt requirement or sodium-free growth is asserted.

    +

    Resolved issue 1626 by normalizing PMC8415458 to its verified DOI 10.3389/fmicb.2021.705326 (PMID:34484145), preserving the same paper. Qualified the non-halophilic comparator to BW25113 in LB at 37 C and the reported 24-h viable-count comparison across 0%, 1%, 3.5% and 5% NaCl supplementation. Retained NCBITaxon:562 and its independently checked NCBI label. The broad-class role, Halomonas example, definition, hierarchy and graph are unchanged; no species-wide salt requirement or sodium-free growth is asserted.

  • @@ -758,13 +759,13 @@

    Recorded curation sessions

  • · codex
    • EDIT — Normalize and scope the non-halophilic branch comparator citation -

      Resolved legacy reference PMC8415458 to DOI:10.3389/fmicb.2021.705326, the same Li et al. 2021 paper independently identified as PMID:34484145. Qualified the existing E. coli comparator to wild-type BW25113 in LB at 37 C and the reported 24-h viable-count comparison across 0%, 1%, 3.5% and 5% NaCl supplementation. Retained the broad-class comparator role and NCBITaxon:562 with its live NCBI label; no sodium-free or species-wide requirement is asserted. Preserved the Halomonas example, all top-level evidence, definition, hierarchy, graph, mapping status and old history. Guarded prevalidation and 91 focused tests passed; full downstream checks and independent review remain required.

    +

    Resolved legacy reference PMC8415458 to DOI:10.3389/fmicb.2021.705326, the same Li et al. 2021 paper independently identified as PMID:34484145. Qualified the existing E. coli comparator to wild-type BW25113 in LB at 37 C and the reported 24-h viable-count comparison across 0%, 1%, 3.5% and 5% NaCl supplementation. Retained the broad-class comparator role and NCBITaxon:562 with its live NCBI label; no sodium-free or species-wide requirement is asserted. Preserved the Halomonas example, all top-level evidence, definition, hierarchy, graph, mapping status and old history. Guarded prevalidation and 91 focused tests passed; full downstream checks and independent review remain required.

    • Read this curation session
  • · codex
    • EDIT — Keep the parent comparator at branch scope without duplicating the child measurement -

      Addressed optional independent PR 1628 review feedback. Retained verified DOI:10.3389/fmicb.2021.705326 and BW25113 in LB as the non-halophilic branch comparator contrasting with Halomonas, but removed the repeated 24-hour numerical comparison. The exact snippet and measured comparison remain on non_halophilic. No sodium-free or species-wide claim is introduced. Appended a second event; preserved original repository/per-record history, Halomonas row, evidence, identity, definition, hierarchy and graph. Exact reviewed-successor guards remain; comparing arbitrary live examples would weaken drift detection. All 102 focused repair/rendering tests passed; generated products and full checks must be rerun before independent re-review.

    +

    Addressed optional independent PR 1628 review feedback. Retained verified DOI:10.3389/fmicb.2021.705326 and BW25113 in LB as the non-halophilic branch comparator contrasting with Halomonas, but removed the repeated 24-hour numerical comparison. The exact snippet and measured comparison remain on non_halophilic. No sodium-free or species-wide claim is introduced. Appended a second event; preserved original repository/per-record history, Halomonas row, evidence, identity, definition, hierarchy and graph. Exact reviewed-successor guards remain; comparing arbitrary live examples would weaken drift detection. All 102 focused repair/rendering tests passed; generated products and full checks must be rerun before independent re-review.

    • Read this curation session @@ -796,7 +797,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1160,12 +1170,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 17:32 UTC diff --git a/pages/traits/environment/halotolerant.html b/pages/traits/environment/halotolerant.html index f12c9a5fe36..200dd4d1069 100644 --- a/pages/traits/environment/halotolerant.html +++ b/pages/traits/environment/halotolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -375,7 +376,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -699,7 +700,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1063,12 +1073,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/hyperthermophilic.html b/pages/traits/environment/hyperthermophilic.html index 834bcd83813..9c239044a91 100644 --- a/pages/traits/environment/hyperthermophilic.html +++ b/pages/traits/environment/hyperthermophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -349,7 +350,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • extreme thermophilic RELATED_SYNONYM · metpo.owl
      • +
    • extreme thermophilic RELATED_SYNONYM · metpo.owl
    @@ -365,7 +366,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -464,11 +465,11 @@

    Deep research

    ## 2. Recent developments, 2023–2024 -The strongest recent primary evidence is Grünberger et al.’s integrated RNA-sequencing/proteomics study of *Pyrococcus furiosus*. Heat shock caused rapid, extensive transcriptome reprogramming controlled in substantial part by the transcriptional regulator Phr. Heat-signature RNAs rapidly returned toward baseline during recovery, whereas corresponding proteins remained elevated, demonstrating that transcript abundance alone incompletely represents the sustained response. Heat shock also increased energy-production and transcription-related proteins while reducing CRISPR–Cas expression, the latter being interpreted cautiously as possible resource reallocation. The study’s relative quantification and discrete sampling cannot establish new protein synthesis for every target or resolve cell-to-cell heterogeneity. Published December 2023; DOI URL: https://doi.org/10.1128/mbio.02174-23. (grunberger2023uncoveringthetemporal pages 1-2, grunberger2023uncoveringthetemporal pages 23-24) +The strongest recent primary evidence is Grünberger et al.’s integrated RNA-sequencing/proteomics study of *Pyrococcus furiosus*. Heat shock caused rapid, extensive transcriptome reprogramming controlled in substantial part by the transcriptional regulator Phr. Heat-signature RNAs rapidly returned toward baseline during recovery, whereas corresponding proteins remained elevated, demonstrating that transcript abundance alone incompletely represents the sustained response. Heat shock also increased energy-production and transcription-related proteins while reducing CRISPR–Cas expression, the latter being interpreted cautiously as possible resource reallocation. The study’s relative quantification and discrete sampling cannot establish new protein synthesis for every target or resolve cell-to-cell heterogeneity. Published December 2023; DOI URL: https://doi.org/10.1128/mbio.02174-23. (grunberger2023uncoveringthetemporal pages 1-2, grunberger2023uncoveringthetemporal pages 23-24) -A 2024 biochemical study of Sulfolobales group-II chaperonins found that HSPα and HSPβ are induced by thermal shock and form ATP/Mg²⁺-dependent 18-subunit complexes that shelter client proteins in an internal folding chamber. Circular dichroism and fluorescence measurements showed broad thermal structural resilience at neutral pH, but compromised integrity at pH 2 and tertiary-structure changes around pH 4. This is important negative evidence: proteins selected in hot, acidic habitats need not themselves be maximally acid-stable because Sulfolobales maintain an intracellular pH near 6.5. Published November 2024; DOI URL: https://doi.org/10.3390/microorganisms12112348. (furr2024structuralstabilitycomparisons pages 1-2) +A 2024 biochemical study of Sulfolobales group-II chaperonins found that HSPα and HSPβ are induced by thermal shock and form ATP/Mg²⁺-dependent 18-subunit complexes that shelter client proteins in an internal folding chamber. Circular dichroism and fluorescence measurements showed broad thermal structural resilience at neutral pH, but compromised integrity at pH 2 and tertiary-structure changes around pH 4. This is important negative evidence: proteins selected in hot, acidic habitats need not themselves be maximally acid-stable because Sulfolobales maintain an intracellular pH near 6.5. Published November 2024; DOI URL: https://doi.org/10.3390/microorganisms12112348. (furr2024structuralstabilitycomparisons pages 1-2) -A 2024 synthesis of thermophile genome organization identifies reverse gyrase, archaeal histones, Alba/Cren7/Sul7 proteins, SMC-family complexes, and polyamines as major candidate genome-maintenance modules. It emphasizes, however, that thermophile lineages use different architectural systems and that a causal relationship between higher-order chromosome organization and thermophily remains incompletely tested. Published June 2024; DOI URL: https://doi.org/10.1264/jsme2.me23087. (takemata2024howdothermophiles pages 4-5) +A 2024 synthesis of thermophile genome organization identifies reverse gyrase, archaeal histones, Alba/Cren7/Sul7 proteins, SMC-family complexes, and polyamines as major candidate genome-maintenance modules. It emphasizes, however, that thermophile lineages use different architectural systems and that a causal relationship between higher-order chromosome organization and thermophily remains incompletely tested. Published June 2024; DOI URL: https://doi.org/10.1264/jsme2.me23087. (takemata2024howdothermophiles pages 4-5) | module | strongest candidate edge | evidence class | curation status | |---|---|---|---| @@ -689,7 +690,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1053,12 +1063,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/ionizing_radiation_tolerant.html b/pages/traits/environment/ionizing_radiation_tolerant.html index e8693c2498c..41ef209b624 100644 --- a/pages/traits/environment/ionizing_radiation_tolerant.html +++ b/pages/traits/environment/ionizing_radiation_tolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    challenges ionizing radiation tolerant - traitmech:000008 + traitmech:000008 METPO:2007406

    Gamma exposure is the environmental challenge the trait counters.

      @@ -118,7 +119,7 @@

      Edge evidence

      GO:0006302 confers ionizing radiation tolerant - traitmech:000008 + traitmech:000008 METPO:2007700

      Efficient DSB repair restores chromosomal integrity after ionizing-radiation damage.

        @@ -137,7 +138,7 @@

        Edge evidence

        confers ionizing radiation tolerant - traitmech:000008 + traitmech:000008 METPO:2007700

        Mn-antioxidant proteome protection preserves repair capacity under irradiation.

          @@ -194,7 +195,7 @@

          Edge evidence

          positively correlates with ionizing radiation tolerant - traitmech:000008 + traitmech:000008

          A high intracellular Mn/Fe ratio correlates with antioxidant proteome protection and survival of ionizing radiation.

            @@ -273,7 +274,7 @@

            Parent traits (1)

            Synonyms (1)

              -
            • gamma radiation resistant NARROW_SYNONYM · DOI:10.3390/genes14091803
              • +
            • gamma radiation resistant NARROW_SYNONYM · DOI:10.3390/genes14091803
    @@ -289,7 +290,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -535,7 +536,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -899,12 +909,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/mercury_tolerant.html b/pages/traits/environment/mercury_tolerant.html index 3092f52807f..8902e35ece8 100644 --- a/pages/traits/environment/mercury_tolerant.html +++ b/pages/traits/environment/mercury_tolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    CHEBI:25195 challenges mercury tolerant - traitmech:000016 + traitmech:000016 METPO:2007406

    Reactive Hg(II) is the toxic challenge the trait counters.

      @@ -269,8 +270,8 @@

      Protein and taxon examples

    		 - Cupriavidus metallidurans CH34 -
    NCBITaxon:266264 + Cupriavidus metallidurans CH34 +
    NCBITaxon:266264         		UNREVIEWED
    @@ -336,7 +337,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -352,7 +353,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -634,7 +635,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -998,12 +1008,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/mesophilic.html b/pages/traits/environment/mesophilic.html index de2a7dcd349..da673a6c040 100644 --- a/pages/traits/environment/mesophilic.html +++ b/pages/traits/environment/mesophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -413,7 +414,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000615 [+102.284, -178.453, -111.655, -113.199, …]
      • +
    • mesophilic METPO:1000615 [+102.284, -178.453, -111.655, -113.199, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -732,7 +733,7 @@

    Recorded curation sessions

  • · codex
    • REVIEW — Repair PR 664 mesophilic snippets -

      Addressed adversarial review issue #665 by replacing two sigma-32 snippets in the mesophilic graph with exact RpoH wording from DOI:10.1128/jb.183.18.5302-5310.2001; the focused replay tests verify the patched script and curated YAML stay in sync.

    +

    Addressed adversarial review issue #665 by replacing two sigma-32 snippets in the mesophilic graph with exact RpoH wording from DOI:10.1128/jb.183.18.5302-5310.2001; the focused replay tests verify the patched script and curated YAML stay in sync.

    • Read this curation session @@ -764,7 +765,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1128,12 +1138,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-06 17:10 UTC diff --git a/pages/traits/environment/metal_tolerant.html b/pages/traits/environment/metal_tolerant.html index a0aaaed7189..14c115c8225 100644 --- a/pages/traits/environment/metal_tolerant.html +++ b/pages/traits/environment/metal_tolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    challenges metal tolerant - traitmech:000012 + traitmech:000012 METPO:2007406

    Elevated heavy-metal concentrations are the environmental challenge the trait counters.

      @@ -137,7 +138,7 @@

      Edge evidence

      GO:0030001 confers metal tolerant - traitmech:000012 + traitmech:000012 METPO:2007700

      Cytoplasmic detoxification by export realizes the metal-tolerant phenotype.

        @@ -213,8 +214,8 @@

        Edge evidence

        is a metal tolerant - traitmech:000012 - rdfs:subClassOf + traitmech:000012 + rdfs:subClassOf

        Arsenic (metalloid) tolerance is a component of the broad metal-tolerant phenotype.

          @@ -232,7 +233,7 @@

          Edge evidence

          mediates metal tolerant - traitmech:000012 + traitmech:000012

          P-type ATPase, CDF, and RND efflux transporters mediate heavy-metal resistance in most bacteria.

            @@ -311,9 +312,9 @@

            Children (6)

            Synonyms (2)

              -
            • metallophilic RELATED_SYNONYM · DOI:10.3389/fmicb.2020.00047
              • +
            • metallophilic RELATED_SYNONYM · DOI:10.3389/fmicb.2020.00047
              • -
            • heavy metal resistant RELATED_SYNONYM · PMID:12829273
              • +
            • heavy metal resistant RELATED_SYNONYM · PMID:12829273
    @@ -329,7 +330,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -593,7 +594,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -957,12 +967,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/microaerophilic.html b/pages/traits/environment/microaerophilic.html index 255b4915ab2..3aab1f25f85 100644 --- a/pages/traits/environment/microaerophilic.html +++ b/pages/traits/environment/microaerophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -330,9 +331,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • Ox_microerophile RELATED_SYNONYM · metpo.owl
      • +
    • Ox_microerophile RELATED_SYNONYM · metpo.owl
      • -
    • microaerophile RELATED_SYNONYM · metpo.owl
      • +
    • microaerophile RELATED_SYNONYM · metpo.owl
    @@ -348,7 +349,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -660,7 +661,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1024,12 +1034,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/microaerotolerant.html b/pages/traits/environment/microaerotolerant.html index b0adb1381fc..64ee6dfca96 100644 --- a/pages/traits/environment/microaerotolerant.html +++ b/pages/traits/environment/microaerotolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -356,7 +357,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -656,7 +657,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1020,12 +1030,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 10:54 UTC diff --git a/pages/traits/environment/moderately_halophilic.html b/pages/traits/environment/moderately_halophilic.html index e45722412ce..eb1c1042217 100644 --- a/pages/traits/environment/moderately_halophilic.html +++ b/pages/traits/environment/moderately_halophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -343,7 +344,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • moderate-halophilic RELATED_SYNONYM · metpo.owl
      • +
    • moderate-halophilic RELATED_SYNONYM · metpo.owl
    @@ -359,7 +360,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -653,7 +654,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1017,12 +1027,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/nacl_delta.html b/pages/traits/environment/nacl_delta.html index 015bb059873..cd3057af953 100644 --- a/pages/traits/environment/nacl_delta.html +++ b/pages/traits/environment/nacl_delta.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -335,7 +336,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000335 [-3.596, -2.760, -3.043, +0.053, …]
      • +
    • NaCl delta METPO:1000335 [-3.596, -2.760, -3.043, +0.053, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -584,7 +585,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Lederbergia graminis (NCBITaxon:735518; DOI:10.1099/ijs.0.023820-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Lederbergia graminis (NCBITaxon:735518; DOI:10.1099/ijs.0.023820-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -632,7 +633,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -996,12 +1006,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-04 07:20 UTC diff --git a/pages/traits/environment/nacl_delta_high.html b/pages/traits/environment/nacl_delta_high.html index 9db0920e768..4de42b092ce 100644 --- a/pages/traits/environment/nacl_delta_high.html +++ b/pages/traits/environment/nacl_delta_high.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,8 +119,8 @@

    Edge evidence

    METPO:1000482 is a NaCl delta - METPO:1000335 - rdfs:subClassOf + METPO:1000335 + rdfs:subClassOf

    NaCl delta high is a quantitative bin of the NaCl-delta phenotype.

      @@ -387,7 +388,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • Nad_>8 RELATED_SYNONYM · metpo.owl
        • +
      • Nad_>8 RELATED_SYNONYM · metpo.owl
    @@ -403,7 +404,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -691,7 +692,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1055,12 +1065,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 10:44 UTC diff --git a/pages/traits/environment/nacl_delta_low.html b/pages/traits/environment/nacl_delta_low.html index afdc14d62a8..619d30cc55e 100644 --- a/pages/traits/environment/nacl_delta_low.html +++ b/pages/traits/environment/nacl_delta_low.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000479 is a NaCl delta - METPO:1000335 - rdfs:subClassOf + METPO:1000335 + rdfs:subClassOf

    NaCl delta low is a quantitative bin of the NaCl-delta phenotype.

      @@ -131,7 +132,7 @@

      Edge evidence

      supports NaCl delta - METPO:1000335 + METPO:1000335

      Ectoine biosynthesis capacity broadens NaCl tolerance; its loss narrows the growth range.

        @@ -169,7 +170,7 @@

        Edge evidence

        supports NaCl delta - METPO:1000335 + METPO:1000335

        TrkH K+ uptake supports intracellular K+ homeostasis enabling salt tolerance; its absence may contribute to narrow breadth.

          @@ -188,7 +189,7 @@

          Edge evidence

          supports NaCl delta - METPO:1000335 + METPO:1000335

          NhaC Na+/H+ antiporters support ion homeostasis under salt stress; a candidate breadth-expanding mechanism whose absence may contribute to NaCl delta low.

            @@ -207,7 +208,7 @@

            Edge evidence

            supports NaCl delta - METPO:1000335 + METPO:1000335

            Increased intracellular proline as a compatible solute supports growth at higher NaCl, broadening tolerance.

              @@ -267,7 +268,7 @@

              Parent traits (1)

              Synonyms (1)

                -
              • Nad_<=1 RELATED_SYNONYM · metpo.owl
                • +
              • Nad_<=1 RELATED_SYNONYM · metpo.owl
    @@ -283,7 +284,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -520,7 +521,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -553,7 +554,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -917,12 +927,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/nacl_delta_mid1.html b/pages/traits/environment/nacl_delta_mid1.html index 0c6ebf24557..8b8dd4e386f 100644 --- a/pages/traits/environment/nacl_delta_mid1.html +++ b/pages/traits/environment/nacl_delta_mid1.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000480 is a NaCl delta - METPO:1000335 - rdfs:subClassOf + METPO:1000335 + rdfs:subClassOf

    NaCl delta mid1 is a quantitative bin of the NaCl-delta phenotype.

      @@ -324,7 +325,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • Nad_1_3 RELATED_SYNONYM · metpo.owl
        • +
      • Nad_1_3 RELATED_SYNONYM · metpo.owl
    @@ -340,7 +341,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -577,7 +578,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Aureivirga marina (NCBITaxon:1182451; DOI:10.1099/ijs.0.043257-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Aureivirga marina (NCBITaxon:1182451; DOI:10.1099/ijs.0.043257-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -610,7 +611,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -974,12 +984,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/nacl_delta_mid2.html b/pages/traits/environment/nacl_delta_mid2.html index 2fd0157d0d1..35bd7eebba6 100644 --- a/pages/traits/environment/nacl_delta_mid2.html +++ b/pages/traits/environment/nacl_delta_mid2.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000481 is a NaCl delta - METPO:1000335 - rdfs:subClassOf + METPO:1000335 + rdfs:subClassOf

    NaCl delta mid2 is a quantitative bin of the NaCl-delta phenotype.

      @@ -286,7 +287,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • Nad_3_8 RELATED_SYNONYM · metpo.owl
        • +
      • Nad_3_8 RELATED_SYNONYM · metpo.owl
    @@ -302,7 +303,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -533,7 +534,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Peribacillus endoradicis (NCBITaxon:718002; DOI:10.1099/ijs.0.028936-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Peribacillus endoradicis (NCBITaxon:718002; DOI:10.1099/ijs.0.028936-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -581,7 +582,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -945,12 +955,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-04 07:40 UTC diff --git a/pages/traits/environment/nacl_optimum.html b/pages/traits/environment/nacl_optimum.html index 08dabc79def..00f3ac6d39f 100644 --- a/pages/traits/environment/nacl_optimum.html +++ b/pages/traits/environment/nacl_optimum.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -449,7 +450,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -734,13 +735,13 @@

    Curation history

  • · MOVE_CANONICAL_EXAMPLE_TO_SPECIFIC_BIN · codex -

    Moved Wallemia ichthyophaga (NCBITaxon:245174; DOI:10.1128/aem.02702-13) off the NaCl-optimum parent under the #478 most-specific-placement policy. Its measured 15-20% (w/v) optimum belongs wholly in METPO:1000468; the same claim is not duplicated on parent and bin.

    +

    Moved Wallemia ichthyophaga (NCBITaxon:245174; DOI:10.1128/aem.02702-13) off the NaCl-optimum parent under the #478 most-specific-placement policy. Its measured 15-20% (w/v) optimum belongs wholly in METPO:1000468; the same claim is not duplicated on parent and bin.

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Paraliobacillus ryukyuensis (NCBITaxon:200904; DOI:10.2323/jgam.48.269). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Paraliobacillus ryukyuensis (NCBITaxon:200904; DOI:10.2323/jgam.48.269). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -806,7 +807,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -1170,12 +1180,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-06 17:10 UTC diff --git a/pages/traits/environment/nacl_optimum_high.html b/pages/traits/environment/nacl_optimum_high.html index 938f128c035..a80389569d4 100644 --- a/pages/traits/environment/nacl_optimum_high.html +++ b/pages/traits/environment/nacl_optimum_high.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -137,8 +138,8 @@

    Edge evidence

    METPO:1000468 is a NaCl optimum - METPO:1000333 - rdfs:subClassOf + METPO:1000333 + rdfs:subClassOf

    NaCl optimum high is a quantitative bin of the NaCl-optimum phenotype.

      @@ -311,9 +312,9 @@

      Parent traits (1)

      Synonyms (2)

        -
      • Extreme halophile EXACT_SYNONYM · metpo.owl
        • +
      • Extreme halophile EXACT_SYNONYM · metpo.owl
        • -
      • NaO_>8 RELATED_SYNONYM · metpo.owl
        • +
      • NaO_>8 RELATED_SYNONYM · metpo.owl
    @@ -329,7 +330,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -584,7 +585,7 @@

    Curation history

  • · MOVE_CANONICAL_EXAMPLE_TO_SPECIFIC_BIN · codex -

    Added Wallemia ichthyophaga (NCBITaxon:245174; DOI:10.1128/aem.02702-13) from the NaCl-optimum parent under the #478 most-specific-placement policy. Its complete measured optimum interval, 15-20% (w/v), is above this bin's >8% (w/v) threshold.

    +

    Added Wallemia ichthyophaga (NCBITaxon:245174; DOI:10.1128/aem.02702-13) from the NaCl-optimum parent under the #478 most-specific-placement policy. Its complete measured optimum interval, 15-20% (w/v), is above this bin's >8% (w/v) threshold.

    • @@ -617,7 +618,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -981,12 +991,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-30 20:02 UTC diff --git a/pages/traits/environment/nacl_optimum_low.html b/pages/traits/environment/nacl_optimum_low.html index 053ee8c9784..2a85ad48569 100644 --- a/pages/traits/environment/nacl_optimum_low.html +++ b/pages/traits/environment/nacl_optimum_low.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000465 is a NaCl optimum - METPO:1000333 - rdfs:subClassOf + METPO:1000333 + rdfs:subClassOf

    NaCl optimum low is a quantitative bin of the NaCl-optimum phenotype.

      @@ -170,7 +171,7 @@

      Edge evidence

      is a non-halophilic optimum NaCl (<0.2 M / ~1% w/v) - rdfs:subClassOf + rdfs:subClassOf

      Halotolerant organisms are non-halophiles (low-NaCl optimum) able to grow at high salt.

        @@ -305,11 +306,11 @@

        Parent traits (1)

        Synonyms (3)

          -
        • Halotolerant EXACT_SYNONYM · metpo.owl
          • +
        • Halotolerant EXACT_SYNONYM · metpo.owl
          • -
        • Non-halophile EXACT_SYNONYM · metpo.owl
          • +
        • Non-halophile EXACT_SYNONYM · metpo.owl
          • -
        • NaO_<=1 RELATED_SYNONYM · metpo.owl
          • +
        • NaO_<=1 RELATED_SYNONYM · metpo.owl
    @@ -325,7 +326,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -562,7 +563,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -595,7 +596,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -959,12 +969,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/nacl_optimum_mid1.html b/pages/traits/environment/nacl_optimum_mid1.html index 0a8c081d5de..8656be016e0 100644 --- a/pages/traits/environment/nacl_optimum_mid1.html +++ b/pages/traits/environment/nacl_optimum_mid1.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000466 is a NaCl optimum - METPO:1000333 - rdfs:subClassOf + METPO:1000333 + rdfs:subClassOf

    NaCl optimum mid1 is a quantitative bin of the NaCl-optimum phenotype.

      @@ -286,11 +287,11 @@

      Parent traits (1)

      Synonyms (3)

        -
      • Halotolerant EXACT_SYNONYM · metpo.owl
        • +
      • Halotolerant EXACT_SYNONYM · metpo.owl
        • -
      • Slight halophile EXACT_SYNONYM · metpo.owl
        • +
      • Slight halophile EXACT_SYNONYM · metpo.owl
        • -
      • NaO_1_to_3 RELATED_SYNONYM · metpo.owl
        • +
      • NaO_1_to_3 RELATED_SYNONYM · metpo.owl
    @@ -306,7 +307,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -543,7 +544,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Flavicella sediminum (NCBITaxon:2585141; DOI:10.1099/ijsem.0.003839). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Flavicella sediminum (NCBITaxon:2585141; DOI:10.1099/ijsem.0.003839). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -576,7 +577,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -940,12 +950,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/nacl_optimum_mid2.html b/pages/traits/environment/nacl_optimum_mid2.html index 6f7c1e0cfc9..046319d4090 100644 --- a/pages/traits/environment/nacl_optimum_mid2.html +++ b/pages/traits/environment/nacl_optimum_mid2.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000467 is a NaCl optimum - METPO:1000333 - rdfs:subClassOf + METPO:1000333 + rdfs:subClassOf

    NaCl optimum mid2 is a quantitative bin of the NaCl-optimum phenotype.

      @@ -208,7 +209,7 @@

      Edge evidence

      is a compatible-solute strategy - rdfs:subClassOf + rdfs:subClassOf

      Pronounced organic-osmolyte accumulation is an instance of the compatible-solute osmoadaptation strategy.

        @@ -324,11 +325,11 @@

        Parent traits (1)

        Synonyms (3)

          -
        • Halotolerant EXACT_SYNONYM · metpo.owl
          • +
        • Halotolerant EXACT_SYNONYM · metpo.owl
          • -
        • Moderate halophile EXACT_SYNONYM · metpo.owl
          • +
        • Moderate halophile EXACT_SYNONYM · metpo.owl
          • -
        • NaO_3_to_8 RELATED_SYNONYM · metpo.owl
          • +
        • NaO_3_to_8 RELATED_SYNONYM · metpo.owl
    @@ -344,7 +345,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -587,7 +588,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Lederbergia graminis (NCBITaxon:735518; DOI:10.1099/ijs.0.023820-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Lederbergia graminis (NCBITaxon:735518; DOI:10.1099/ijs.0.023820-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -620,7 +621,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -984,12 +994,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/nacl_range.html b/pages/traits/environment/nacl_range.html index c8d6a824f9e..1d79c079637 100644 --- a/pages/traits/environment/nacl_range.html +++ b/pages/traits/environment/nacl_range.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -335,7 +336,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000334 [-2.929, -1.954, -2.325, +0.965, …]
      • +
    • NaCl range METPO:1000334 [-2.929, -1.954, -2.325, +0.965, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -590,7 +591,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Kushneria aurantia (NCBITaxon:504092; DOI:10.1099/ijs.0.001461-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Kushneria aurantia (NCBITaxon:504092; DOI:10.1099/ijs.0.001461-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -623,7 +624,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -987,12 +997,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/nacl_range_high.html b/pages/traits/environment/nacl_range_high.html index 72e691dce0c..b978ad4bfed 100644 --- a/pages/traits/environment/nacl_range_high.html +++ b/pages/traits/environment/nacl_range_high.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,8 +119,8 @@

    Edge evidence

    METPO:1000472 is a NaCl range - METPO:1000334 - rdfs:subClassOf + METPO:1000334 + rdfs:subClassOf

    NaCl range high is a quantitative bin of the NaCl-range phenotype.

      @@ -273,9 +274,9 @@

      Parent traits (1)

      Synonyms (2)

        -
      • Extreme halophile EXACT_SYNONYM · metpo.owl
        • +
      • Extreme halophile EXACT_SYNONYM · metpo.owl
        • -
      • NaR_>8 RELATED_SYNONYM · metpo.owl
        • +
      • NaR_>8 RELATED_SYNONYM · metpo.owl
    @@ -291,7 +292,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -516,7 +517,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Amycolatopsis flava (NCBITaxon:486505; DOI:10.1007/s10482-015-0542-z). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Amycolatopsis flava (NCBITaxon:486505; DOI:10.1007/s10482-015-0542-z). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -549,7 +550,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -913,12 +923,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/nacl_range_low.html b/pages/traits/environment/nacl_range_low.html index 039262eef05..f5778c30fec 100644 --- a/pages/traits/environment/nacl_range_low.html +++ b/pages/traits/environment/nacl_range_low.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000469 is a NaCl range - METPO:1000334 - rdfs:subClassOf + METPO:1000334 + rdfs:subClassOf

    NaCl range low is a quantitative bin of the NaCl-range phenotype.

      @@ -267,11 +268,11 @@

      Parent traits (1)

      Synonyms (3)

        -
      • Halotolerant EXACT_SYNONYM · metpo.owl
        • +
      • Halotolerant EXACT_SYNONYM · metpo.owl
        • -
      • Non-halophile EXACT_SYNONYM · metpo.owl
        • +
      • Non-halophile EXACT_SYNONYM · metpo.owl
        • -
      • NaR_<=1 RELATED_SYNONYM · metpo.owl
        • +
      • NaR_<=1 RELATED_SYNONYM · metpo.owl
    @@ -287,7 +288,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -518,7 +519,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -572,7 +573,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -936,12 +946,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-06 17:10 UTC diff --git a/pages/traits/environment/nacl_range_mid1.html b/pages/traits/environment/nacl_range_mid1.html index dcd039fed98..5cced5e6b72 100644 --- a/pages/traits/environment/nacl_range_mid1.html +++ b/pages/traits/environment/nacl_range_mid1.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000470 is a NaCl range - METPO:1000334 - rdfs:subClassOf + METPO:1000334 + rdfs:subClassOf

    NaCl range mid1 is a quantitative bin of the NaCl-range phenotype.

      @@ -267,11 +268,11 @@

      Parent traits (1)

      Synonyms (3)

        -
      • Halotolerant EXACT_SYNONYM · metpo.owl
        • +
      • Halotolerant EXACT_SYNONYM · metpo.owl
        • -
      • Slight halophile EXACT_SYNONYM · metpo.owl
        • +
      • Slight halophile EXACT_SYNONYM · metpo.owl
        • -
      • NaR_1_to_3 RELATED_SYNONYM · metpo.owl
        • +
      • NaR_1_to_3 RELATED_SYNONYM · metpo.owl
    @@ -287,7 +288,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -512,7 +513,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Spongorhabdus nitratireducens (NCBITaxon:2995321; DOI:10.1099/ijsem.0.007037). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Spongorhabdus nitratireducens (NCBITaxon:2995321; DOI:10.1099/ijsem.0.007037). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -545,7 +546,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -909,12 +919,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/nacl_range_mid2.html b/pages/traits/environment/nacl_range_mid2.html index 741111ffa14..831f8953fdf 100644 --- a/pages/traits/environment/nacl_range_mid2.html +++ b/pages/traits/environment/nacl_range_mid2.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000471 is a NaCl range - METPO:1000334 - rdfs:subClassOf + METPO:1000334 + rdfs:subClassOf

    NaCl range mid2 is a quantitative bin of the NaCl-range phenotype.

      @@ -305,11 +306,11 @@

      Parent traits (1)

      Synonyms (3)

        -
      • Halotolerant EXACT_SYNONYM · metpo.owl
        • +
      • Halotolerant EXACT_SYNONYM · metpo.owl
        • -
      • Moderate halophile EXACT_SYNONYM · metpo.owl
        • +
      • Moderate halophile EXACT_SYNONYM · metpo.owl
        • -
      • NaR_3_to_8 RELATED_SYNONYM · metpo.owl
        • +
      • NaR_3_to_8 RELATED_SYNONYM · metpo.owl
    @@ -325,7 +326,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -556,7 +557,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Aureivirga marina (NCBITaxon:1182451; DOI:10.1099/ijs.0.043257-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Aureivirga marina (NCBITaxon:1182451; DOI:10.1099/ijs.0.043257-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -589,7 +590,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -953,12 +963,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/neutrophilic.html b/pages/traits/environment/neutrophilic.html index ceb5a895e53..43582fa91de 100644 --- a/pages/traits/environment/neutrophilic.html +++ b/pages/traits/environment/neutrophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -305,11 +306,11 @@

    Parent traits (1)

    Synonyms (3)

      -
    • neutralophile EXACT_SYNONYM · metpo.owl
      • +
    • neutralophile EXACT_SYNONYM · metpo.owl
      • -
    • neutralophilic EXACT_SYNONYM · metpo.owl
      • +
    • neutralophilic EXACT_SYNONYM · metpo.owl
      • -
    • neutrophile EXACT_SYNONYM · metpo.owl
      • +
    • neutrophile EXACT_SYNONYM · metpo.owl
    @@ -325,7 +326,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -637,7 +638,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Replaced elliptical record-level evidence[0].snippet on DOI:10.1038/nrmicro2549 with contiguous verbatim snippet already present on causal_graphs[0].edges[0].evidence[0] (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-002 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Replaced elliptical record-level evidence[0].snippet on DOI:10.1038/nrmicro2549 with contiguous verbatim snippet already present on causal_graphs[0].edges[0].evidence[0] (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-002 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -670,7 +671,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1034,12 +1044,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/environment/non_halophilic.html b/pages/traits/environment/non_halophilic.html index 3ae56953e5d..2024e02b2cc 100644 --- a/pages/traits/environment/non_halophilic.html +++ b/pages/traits/environment/non_halophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -67,7 +68,7 @@

    Trait evidence (3)

    DOI:10.3389/fmicb.2021.705326
    the number of viable cells in LB broth supplemented with 0% NaCl at 24 h is significantly higher than other tested groups
    -

    Li et al. 2021, Results, Bacterial Growth, Figure 2B: wild-type E. coli BW25113 was compared in LB broth supplemented with 0%, 1%, 3.5% and 5% NaCl at 37 C. This is a strain- and medium-qualified low-salt growth observation, not sodium-free growth, a complete salinity optimum curve or a universal species-wide requirement. PMCID:PMC8415458 and PMID:34484145 identify this same paper.

    +

    Li et al. 2021, Results, Bacterial Growth, Figure 2B: wild-type E. coli BW25113 was compared in LB broth supplemented with 0%, 1%, 3.5% and 5% NaCl at 37 C. This is a strain- and medium-qualified low-salt growth observation, not sodium-free growth, a complete salinity optimum curve or a universal species-wide requirement. PMCID:PMC8415458 and PMID:34484145 identify this same paper.

    @@ -336,7 +337,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • non-halophilic RELATED_SYNONYM · metpo.owl
      • +
    • non-halophilic RELATED_SYNONYM · metpo.owl
    @@ -352,7 +353,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -628,7 +629,7 @@

    Curation history

  • · REPAIR_CANONICAL_CITATION_SCOPE_1626 · codex -

    Resolved issue 1626 by normalizing PMC8415458 to its verified DOI 10.3389/fmicb.2021.705326 (PMID:34484145), without replacing the paper. Qualified the E. coli example to wild-type BW25113 growth in LB supplemented with 0% NaCl at 37 C and the 24-h comparison with 1%, 3.5% and 5% NaCl. Added an exact Results snippet and interpretation; no sodium-free or universal species-wide requirement is inferred. Retained NCBITaxon:562 and its independently checked NCBI label. Definition, hierarchy, graph and other example unchanged.

    +

    Resolved issue 1626 by normalizing PMC8415458 to its verified DOI 10.3389/fmicb.2021.705326 (PMID:34484145), without replacing the paper. Qualified the E. coli example to wild-type BW25113 growth in LB supplemented with 0% NaCl at 37 C and the 24-h comparison with 1%, 3.5% and 5% NaCl. Added an exact Results snippet and interpretation; no sodium-free or universal species-wide requirement is inferred. Retained NCBITaxon:562 and its independently checked NCBI label. Definition, hierarchy, graph and other example unchanged.

    • @@ -638,7 +639,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Resolve the E. coli citation and qualify its low-salt growth example -

      Normalized PMC8415458 to DOI:10.3389/fmicb.2021.705326 (PMID:34484145), with authoritative metadata confirming the same Li et al. 2021 paper. Direct full-text XML Results and Methods support wild-type BW25113 growth in LB at 37 C and higher viable counts at 24 h with 0% NaCl supplementation than the 1%, 3.5% and 5% groups. Added the exact Results span and qualified the example note: no sodium-free growth, complete optimum curve, or universal species-wide requirement is inferred. Retained NCBITaxon:562 and its live NCBI label. Definition, hierarchy, graph, Bacillus example and prior history are preserved. Guarded all-target prevalidation and 91 focused tests passed; full downstream checks and independent review remain required.

    +

    Normalized PMC8415458 to DOI:10.3389/fmicb.2021.705326 (PMID:34484145), with authoritative metadata confirming the same Li et al. 2021 paper. Direct full-text XML Results and Methods support wild-type BW25113 growth in LB at 37 C and higher viable counts at 24 h with 0% NaCl supplementation than the 1%, 3.5% and 5% groups. Added the exact Results span and qualified the example note: no sodium-free growth, complete optimum curve, or universal species-wide requirement is inferred. Retained NCBITaxon:562 and its live NCBI label. Definition, hierarchy, graph, Bacillus example and prior history are preserved. Guarded all-target prevalidation and 91 focused tests passed; full downstream checks and independent review remain required.

    • Read this curation session @@ -670,7 +671,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1034,12 +1044,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 17:10 UTC diff --git a/pages/traits/environment/obligately_acidophilic.html b/pages/traits/environment/obligately_acidophilic.html index f3407956930..c6be7ae515c 100644 --- a/pages/traits/environment/obligately_acidophilic.html +++ b/pages/traits/environment/obligately_acidophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -381,7 +382,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • obligate acidophile EXACT_SYNONYM · metpo.owl
      • +
    • obligate acidophile EXACT_SYNONYM · metpo.owl
    @@ -397,7 +398,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -718,7 +719,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1082,12 +1092,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/obligately_aerobic.html b/pages/traits/environment/obligately_aerobic.html index 7a1a1656bdb..3266c77e260 100644 --- a/pages/traits/environment/obligately_aerobic.html +++ b/pages/traits/environment/obligately_aerobic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -330,9 +331,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • obligate aerobe RELATED_SYNONYM · metpo.owl
      • +
    • obligate aerobe RELATED_SYNONYM · metpo.owl
      • -
    • obligate aerobic RELATED_SYNONYM · metpo.owl
      • +
    • obligate aerobic RELATED_SYNONYM · metpo.owl
    @@ -348,7 +349,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -672,7 +673,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1036,12 +1046,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/obligately_alkaphilic.html b/pages/traits/environment/obligately_alkaphilic.html index a21f6299d8b..3d427f5be1e 100644 --- a/pages/traits/environment/obligately_alkaphilic.html +++ b/pages/traits/environment/obligately_alkaphilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -381,9 +382,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • obligate alkaliphile EXACT_SYNONYM · metpo.owl
      • +
    • obligate alkaliphile EXACT_SYNONYM · metpo.owl
      • -
    • obligate alkaphilic EXACT_SYNONYM · metpo.owl
      • +
    • obligate alkaphilic EXACT_SYNONYM · metpo.owl
    @@ -399,7 +400,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -723,7 +724,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1087,12 +1097,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 07:35 UTC diff --git a/pages/traits/environment/obligately_anaerobic.html b/pages/traits/environment/obligately_anaerobic.html index c24191bf96b..fdbf5940f63 100644 --- a/pages/traits/environment/obligately_anaerobic.html +++ b/pages/traits/environment/obligately_anaerobic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -377,9 +378,9 @@

    Children (1)

    Synonyms (2)

      -
    • obligate anaerobe RELATED_SYNONYM · metpo.owl
      • +
    • obligate anaerobe RELATED_SYNONYM · metpo.owl
      • -
    • obligate anaerobic RELATED_SYNONYM · metpo.owl
      • +
    • obligate anaerobic RELATED_SYNONYM · metpo.owl
    @@ -395,7 +396,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -665,7 +666,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1029,12 +1039,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/obligately_piezophilic.html b/pages/traits/environment/obligately_piezophilic.html index 2ae55ecd57c..7733e54d3c0 100644 --- a/pages/traits/environment/obligately_piezophilic.html +++ b/pages/traits/environment/obligately_piezophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    causes obligately piezophilic - traitmech:000002 + traitmech:000002 biolink:causes

    HHP adaptation that no longer functions at 0.1 MPa makes high pressure obligatory for growth.

      @@ -118,7 +119,7 @@

      Edge evidence

      confers obligately piezophilic - traitmech:000002 + traitmech:000002 METPO:2007700

      Cellular machinery requiring HHP for function realizes the obligate-piezophile phenotype.

        @@ -137,7 +138,7 @@

        Edge evidence

        manifests as obligately piezophilic - traitmech:000002 + traitmech:000002 METPO:2007400

        Inability to grow at 0.1 MPa is the diagnostic pressure-growth failure state represented by obligate piezophily.

          @@ -254,7 +255,7 @@

          Parent traits (1)

          Synonyms (1)

            -
          • obligate piezophile EXACT_SYNONYM · DOI:10.1038/srep27289
            • +
          • obligate piezophile EXACT_SYNONYM · DOI:10.1038/srep27289
    @@ -270,7 +271,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -543,7 +544,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -907,12 +917,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-07 02:20 UTC diff --git a/pages/traits/environment/optimum_phenotype_with_numerical_limits.html b/pages/traits/environment/optimum_phenotype_with_numerical_limits.html index 5ec0216b956..9716ee32c57 100644 --- a/pages/traits/environment/optimum_phenotype_with_numerical_limits.html +++ b/pages/traits/environment/optimum_phenotype_with_numerical_limits.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,11 +116,11 @@

    Edge evidence

  • NaCl optimum - METPO:1000333 + METPO:1000333 is a optimum phenotype with numerical limits METPO:1000536 - rdfs:subClassOf + rdfs:subClassOf

    NaCl optimum is an axis-specific optimum phenotype.

      @@ -134,11 +135,11 @@

      Edge evidence

    • pH optimum - METPO:1000331 + METPO:1000331 is a optimum phenotype with numerical limits METPO:1000536 - rdfs:subClassOf + rdfs:subClassOf

      pH optimum is an axis-specific optimum phenotype.

        @@ -153,11 +154,11 @@

        Edge evidence

      • temperature optimum - METPO:1000304 + METPO:1000304 is a optimum phenotype with numerical limits METPO:1000536 - rdfs:subClassOf + rdfs:subClassOf

        Temperature optimum is an axis-specific optimum phenotype.

          @@ -350,7 +351,7 @@

          kg-microbe context

          via direct_metpo.

          512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

          @@ -593,7 +594,7 @@

          Curation history

        • · ADD_CANONICAL_EXAMPLES · codex -

          Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

          +

          Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

          • @@ -626,7 +627,16 @@

          Identifier

          Term kind
          CLASS
          Status
          -
          REVIEWED
          +
          REVIEWED + + +
          + What this status means +

          Curator has signed off on label / definition / parents.

          +

          Quoted from the schema's status definitions.

          +
          + +
    • @@ -990,12 +1000,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/oxygen_preference.html b/pages/traits/environment/oxygen_preference.html index a8fc13c5c99..233815b2068 100644 --- a/pages/traits/environment/oxygen_preference.html +++ b/pages/traits/environment/oxygen_preference.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,11 +116,11 @@

    Edge evidence

  • aerobic - METPO:1000602 + METPO:1000602 is a oxygen preference METPO:1000601 - rdfs:subClassOf + rdfs:subClassOf

    Aerobic is a child oxygen-preference phenotype.

      @@ -134,11 +135,11 @@

      Edge evidence

    • anaerobic - METPO:1000603 + METPO:1000603 is a oxygen preference METPO:1000601 - rdfs:subClassOf + rdfs:subClassOf

      Anaerobic is a child oxygen-preference phenotype.

        @@ -153,11 +154,11 @@

        Edge evidence

      • microaerophilic - METPO:1000604 + METPO:1000604 is a oxygen preference METPO:1000601 - rdfs:subClassOf + rdfs:subClassOf

        Microaerophilic is a child oxygen-preference phenotype.

          @@ -172,11 +173,11 @@

          Edge evidence

        • facultative oxygen preference - METPO:1000612 + METPO:1000612 is a oxygen preference METPO:1000601 - rdfs:subClassOf + rdfs:subClassOf

          Facultative oxygen preference is a child oxygen-preference phenotype.

            @@ -194,7 +195,7 @@

            Edge evidence

            confers aerobic - METPO:1000602 + METPO:1000602 METPO:2007700

            Obligate aerobic growth depends on molecular oxygen as terminal electron acceptor.

              @@ -378,9 +379,9 @@

              Children (11)

              Synonyms (2)

                -
              • Physiology and metabolism.oxygen tolerance.oxygen tolerance RELATED_SYNONYM · metpo.owl
                • +
              • Physiology and metabolism.oxygen tolerance.oxygen tolerance RELATED_SYNONYM · metpo.owl
                • -
              • metabolism RELATED_SYNONYM · metpo.owl
                • +
              • metabolism RELATED_SYNONYM · metpo.owl
    • @@ -396,7 +397,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -681,7 +682,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; DOI:10.1111/1751-7915.70051). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; DOI:10.1111/1751-7915.70051). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -714,7 +715,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1078,12 +1088,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/ph_delta.html b/pages/traits/environment/ph_delta.html index 49c47a99b2f..dc7d451591b 100644 --- a/pages/traits/environment/ph_delta.html +++ b/pages/traits/environment/ph_delta.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -339,7 +340,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000232 [-1.997, -1.168, -3.290, +0.199, …]
      • +
    • pH delta METPO:1000232 [-1.997, -1.168, -3.290, +0.199, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -452,14 +453,14 @@

    Deep research

    | subject | predicate | object | evidence class/taxon | DOI | |---|---|---|---|---| -| low external pH | increases | inward proton stress / proton influx pressure | review synthesis; neutralophilic bacteria broadly (krulwich2011molecularaspectsof pages 1-3, krulwich2011molecularaspectsof pages 5-6) | 10.1038/nrmicro2549 | -| glutamate decarboxylase GadB | consumes | cytoplasmic protons during glutamate decarboxylation | review-backed mechanism; *Escherichia coli* and other bacteria (krulwich2011molecularaspectsof pages 5-6, krulwich2011molecularaspectsof pages 15-17) | 10.1038/nrmicro2549 | -| urease + UreI | enables | periplasmic buffering via NH3/CO2 production and transport | direct physiological/regulatory evidence; *Helicobacter pylori* (krulwich2011molecularaspectsof pages 11-12, krulwich2011molecularaspectsof pages 27-28) | 10.1038/nrmicro2549 | -| membrane / envelope adaptations | reduces | proton leakage across the cell boundary | review synthesis; acid-stressed bacteria and extremophiles (krulwich2011molecularaspectsof pages 5-6) | 10.1038/nrmicro2549 | -| high external pH | induces | cation/proton antiporters (Na+/H+, K+/H+) | review synthesis; alkaliphile/alkali-stressed bacteria (krulwich2011molecularaspectsof pages 5-6) | 10.1038/nrmicro2549 | -| Mrp Na+/H+ antiporter | supports | proton uptake and high-pH growth | direct genetic/physiological evidence summarized in review; alkaliphilic *Bacillus* spp. including *B. pseudofirmus* OF4 (krulwich2011molecularaspectsof pages 12-14, krulwich2011molecularaspectsof pages 20-22, krulwich2011molecularaspectsof pages 22-23) | 10.1038/nrmicro2549 | -| F1Fo ATP synthase | contributes to | pH homeostasis | review synthesis with organism-specific evidence; acidophiles, alkaliphiles, and neutralophiles (krulwich2011molecularaspectsof pages 12-14, krulwich2011molecularaspectsof pages 5-6, krulwich2011molecularaspectsof pages 11-12) | 10.1038/nrmicro2549 | -| broad external pH growth range (pH delta) | inferred to reflect | pH-homeostasis flexibility | inferred terminal trait link; cross-taxon interpretation from pH-homeostasis review and comparative physiology (krulwich2011molecularaspectsof pages 1-3, maksimova2024metabolicandmorphological pages 1-2) | 10.1038/nrmicro2549; 10.1155/2024/3087296 | +| low external pH | increases | inward proton stress / proton influx pressure | review synthesis; neutralophilic bacteria broadly (krulwich2011molecularaspectsof pages 1-3, krulwich2011molecularaspectsof pages 5-6) | 10.1038/nrmicro2549 | +| glutamate decarboxylase GadB | consumes | cytoplasmic protons during glutamate decarboxylation | review-backed mechanism; *Escherichia coli* and other bacteria (krulwich2011molecularaspectsof pages 5-6, krulwich2011molecularaspectsof pages 15-17) | 10.1038/nrmicro2549 | +| urease + UreI | enables | periplasmic buffering via NH3/CO2 production and transport | direct physiological/regulatory evidence; *Helicobacter pylori* (krulwich2011molecularaspectsof pages 11-12, krulwich2011molecularaspectsof pages 27-28) | 10.1038/nrmicro2549 | +| membrane / envelope adaptations | reduces | proton leakage across the cell boundary | review synthesis; acid-stressed bacteria and extremophiles (krulwich2011molecularaspectsof pages 5-6) | 10.1038/nrmicro2549 | +| high external pH | induces | cation/proton antiporters (Na+/H+, K+/H+) | review synthesis; alkaliphile/alkali-stressed bacteria (krulwich2011molecularaspectsof pages 5-6) | 10.1038/nrmicro2549 | +| Mrp Na+/H+ antiporter | supports | proton uptake and high-pH growth | direct genetic/physiological evidence summarized in review; alkaliphilic *Bacillus* spp. including *B. pseudofirmus* OF4 (krulwich2011molecularaspectsof pages 12-14, krulwich2011molecularaspectsof pages 20-22, krulwich2011molecularaspectsof pages 22-23) | 10.1038/nrmicro2549 | +| F1Fo ATP synthase | contributes to | pH homeostasis | review synthesis with organism-specific evidence; acidophiles, alkaliphiles, and neutralophiles (krulwich2011molecularaspectsof pages 12-14, krulwich2011molecularaspectsof pages 5-6, krulwich2011molecularaspectsof pages 11-12) | 10.1038/nrmicro2549 | +| broad external pH growth range (pH delta) | inferred to reflect | pH-homeostasis flexibility | inferred terminal trait link; cross-taxon interpretation from pH-homeostasis review and comparative physiology (krulwich2011molecularaspectsof pages 1-3, maksimova2024metabolicandmorphological pages 1-2) | 10.1038/nrmicro2549; 10.1155/2024/3087296 | *Table: This table summarizes the strongest conservative candidate causal edges for curating microbial pH delta, emphasizing well-supported acid and alkaline homeostasis mechanisms and marking the terminal pH-delta interpretation as inferred.* @@ -594,7 +595,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -627,7 +628,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -991,12 +1001,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/ph_delta_high.html b/pages/traits/environment/ph_delta_high.html index 7b6ad651a88..1445e3c555d 100644 --- a/pages/traits/environment/ph_delta_high.html +++ b/pages/traits/environment/ph_delta_high.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,8 +119,8 @@

    Edge evidence

    METPO:1000478 is a pH delta - METPO:1000232 - rdfs:subClassOf + METPO:1000232 + rdfs:subClassOf

    pH delta high is a quantitative bin of the pH-delta phenotype.

      @@ -232,7 +233,7 @@

      Edge evidence

      confers growth across external pH 5.5-9.0 - METPO:1000332 + METPO:1000332 METPO:2007700

      Neutralophiles maintain narrow internal pH while growing over a broad external range.

        @@ -330,7 +331,7 @@

        Parent traits (1)

        Synonyms (1)

          -
        • pHd_5_9 RELATED_SYNONYM · metpo.owl
          • +
        • pHd_5_9 RELATED_SYNONYM · metpo.owl
    @@ -346,7 +347,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -607,7 +608,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Amycolatopsis flava (NCBITaxon:486505; DOI:10.1007/s10482-015-0542-z). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Amycolatopsis flava (NCBITaxon:486505; DOI:10.1007/s10482-015-0542-z). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -640,7 +641,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1004,12 +1014,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/ph_delta_low.html b/pages/traits/environment/ph_delta_low.html index 6944f04ff5f..525c6180b5a 100644 --- a/pages/traits/environment/ph_delta_low.html +++ b/pages/traits/environment/ph_delta_low.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000474 is a pH delta - METPO:1000232 - rdfs:subClassOf + METPO:1000232 + rdfs:subClassOf

    pH delta low is a quantitative bin of the pH-delta phenotype.

      @@ -267,7 +268,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • pHd_1_2 RELATED_SYNONYM · metpo.owl
        • +
      • pHd_1_2 RELATED_SYNONYM · metpo.owl
    @@ -283,7 +284,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -520,7 +521,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Paracoccus mangrovi (NCBITaxon:1715645; DOI:10.1099/ijsem.0.001993). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Paracoccus mangrovi (NCBITaxon:1715645; DOI:10.1099/ijsem.0.001993). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -553,7 +554,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -917,12 +927,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/ph_delta_mid1.html b/pages/traits/environment/ph_delta_mid1.html index ad70cd666ab..9eda4c80c63 100644 --- a/pages/traits/environment/ph_delta_mid1.html +++ b/pages/traits/environment/ph_delta_mid1.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000475 is a pH delta - METPO:1000232 - rdfs:subClassOf + METPO:1000232 + rdfs:subClassOf

    pH delta mid1 is a quantitative bin of the pH-delta phenotype.

      @@ -305,7 +306,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • pHd_2_3 RELATED_SYNONYM · metpo.owl
        • +
      • pHd_2_3 RELATED_SYNONYM · metpo.owl
    @@ -321,7 +322,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -576,7 +577,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Lederbergia graminis (NCBITaxon:735518; DOI:10.1099/ijs.0.023820-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Lederbergia graminis (NCBITaxon:735518; DOI:10.1099/ijs.0.023820-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -609,7 +610,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -973,12 +983,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/ph_delta_mid2.html b/pages/traits/environment/ph_delta_mid2.html index dd0b4dd96f9..4b4e80f39a7 100644 --- a/pages/traits/environment/ph_delta_mid2.html +++ b/pages/traits/environment/ph_delta_mid2.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000476 is a pH delta - METPO:1000232 - rdfs:subClassOf + METPO:1000232 + rdfs:subClassOf

    pH delta mid2 is a quantitative bin of the pH-delta phenotype.

      @@ -286,7 +287,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • pHd_3_4 RELATED_SYNONYM · metpo.owl
        • +
      • pHd_3_4 RELATED_SYNONYM · metpo.owl
    @@ -302,7 +303,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -527,7 +528,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Microbaculum mangrovi (NCBITaxon:3447298; DOI:10.1099/ijsem.0.006972). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Microbaculum mangrovi (NCBITaxon:3447298; DOI:10.1099/ijsem.0.006972). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -623,7 +624,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -987,12 +997,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-08 03:30 UTC diff --git a/pages/traits/environment/ph_delta_mid3.html b/pages/traits/environment/ph_delta_mid3.html index 1b6ed3d341c..4a52cc77364 100644 --- a/pages/traits/environment/ph_delta_mid3.html +++ b/pages/traits/environment/ph_delta_mid3.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000477 is a pH delta - METPO:1000232 - rdfs:subClassOf + METPO:1000232 + rdfs:subClassOf

    pH delta mid3 is a quantitative bin of the pH-delta phenotype.

      @@ -305,7 +306,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • pHd_4_5 RELATED_SYNONYM · metpo.owl
        • +
      • pHd_4_5 RELATED_SYNONYM · metpo.owl
    @@ -321,7 +322,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -582,7 +583,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Gemmobacter lutimaris (NCBITaxon:2306023; DOI:10.1099/ijsem.0.003375). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Gemmobacter lutimaris (NCBITaxon:2306023; DOI:10.1099/ijsem.0.003375). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -684,7 +685,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -1048,12 +1058,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-08 03:30 UTC diff --git a/pages/traits/environment/ph_delta_very_low.html b/pages/traits/environment/ph_delta_very_low.html index d656baeda83..a547de2e420 100644 --- a/pages/traits/environment/ph_delta_very_low.html +++ b/pages/traits/environment/ph_delta_very_low.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000473 is a pH delta - METPO:1000232 - rdfs:subClassOf + METPO:1000232 + rdfs:subClassOf

    pH delta very low is a quantitative bin of the pH-delta phenotype.

      @@ -267,7 +268,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • pHd_<=1 RELATED_SYNONYM · metpo.owl
        • +
      • pHd_<=1 RELATED_SYNONYM · metpo.owl
    @@ -283,7 +284,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -508,7 +509,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -598,7 +599,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -962,12 +972,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-08 03:30 UTC diff --git a/pages/traits/environment/ph_growth_preference.html b/pages/traits/environment/ph_growth_preference.html index cc7fbc64043..c9be0f1d62d 100644 --- a/pages/traits/environment/ph_growth_preference.html +++ b/pages/traits/environment/ph_growth_preference.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -392,7 +393,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -680,7 +681,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 2 direct source-backed canonical example(s): Picrophilus oshimae (NCBITaxon:46632; DOI:10.1007/s007920050044), Evansella tamaricis (NCBITaxon:2069301; DOI:10.1099/ijsem.0.002543). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 2 direct source-backed canonical example(s): Picrophilus oshimae (NCBITaxon:46632; DOI:10.1007/s007920050044), Evansella tamaricis (NCBITaxon:2069301; DOI:10.1099/ijsem.0.002543). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -713,7 +714,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1077,12 +1087,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/ph_optimum.html b/pages/traits/environment/ph_optimum.html index 510bcc4c856..0b8d5a3862e 100644 --- a/pages/traits/environment/ph_optimum.html +++ b/pages/traits/environment/ph_optimum.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -373,7 +374,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000331 [-2.375, -0.997, -3.355, +0.508, …]
      • +
    • pH optimum METPO:1000331 [-2.375, -0.997, -3.355, +0.508, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -646,7 +647,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Microbaculum mangrovi (NCBITaxon:3447298; DOI:10.1099/ijsem.0.006972). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Microbaculum mangrovi (NCBITaxon:3447298; DOI:10.1099/ijsem.0.006972). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -679,7 +680,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1043,12 +1053,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/ph_optimum_high.html b/pages/traits/environment/ph_optimum_high.html index d5a0425b03a..32be68d2d7e 100644 --- a/pages/traits/environment/ph_optimum_high.html +++ b/pages/traits/environment/ph_optimum_high.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -156,8 +157,8 @@

    Edge evidence

    METPO:1000458 is a pH optimum - METPO:1000331 - rdfs:subClassOf + METPO:1000331 + rdfs:subClassOf

    pH optimum high is a quantitative bin of the pH-optimum phenotype.

      @@ -330,13 +331,13 @@

      Parent traits (1)

      Synonyms (4)

        -
      • Alkali Tolerant EXACT_SYNONYM · metpo.owl
        • +
      • Alkali Tolerant EXACT_SYNONYM · metpo.owl
        • -
      • Alkaliphile EXACT_SYNONYM · metpo.owl
        • +
      • Alkaliphile EXACT_SYNONYM · metpo.owl
        • -
      • Extreme Alkaliphile EXACT_SYNONYM · metpo.owl
        • +
      • Extreme Alkaliphile EXACT_SYNONYM · metpo.owl
        • -
      • pHO_8_to_14 RELATED_SYNONYM · metpo.owl
        • +
      • pHO_8_to_14 RELATED_SYNONYM · metpo.owl
    @@ -352,7 +353,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -658,7 +659,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1022,12 +1032,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/ph_optimum_low.html b/pages/traits/environment/ph_optimum_low.html index 8e06fba4c16..08a06ae3d6b 100644 --- a/pages/traits/environment/ph_optimum_low.html +++ b/pages/traits/environment/ph_optimum_low.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000455 is a pH optimum - METPO:1000331 - rdfs:subClassOf + METPO:1000331 + rdfs:subClassOf

    pH optimum low is a quantitative bin of the pH-optimum phenotype.

      @@ -273,17 +274,17 @@

      Parent traits (1)

      Synonyms (6)

        -
      • Acid Tolerant EXACT_SYNONYM · metpo.owl
        • +
      • Acid Tolerant EXACT_SYNONYM · metpo.owl
        • -
      • Acidophile EXACT_SYNONYM · metpo.owl
        • +
      • Acidophile EXACT_SYNONYM · metpo.owl
        • -
      • Extreme Acidophile EXACT_SYNONYM · metpo.owl
        • +
      • Extreme Acidophile EXACT_SYNONYM · metpo.owl
        • -
      • Facultative acidophile EXACT_SYNONYM · metpo.owl
        • +
      • Facultative acidophile EXACT_SYNONYM · metpo.owl
        • -
      • Obligative acidophile EXACT_SYNONYM · metpo.owl
        • +
      • Obligative acidophile EXACT_SYNONYM · metpo.owl
        • -
      • pHO_0_to_6 RELATED_SYNONYM · metpo.owl
        • +
      • pHO_0_to_6 RELATED_SYNONYM · metpo.owl
    @@ -299,7 +300,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -548,7 +549,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Picrophilus oshimae (NCBITaxon:46632; DOI:10.1007/s007920050044). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Picrophilus oshimae (NCBITaxon:46632; DOI:10.1007/s007920050044). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -581,7 +582,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -945,12 +955,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/ph_optimum_mid1.html b/pages/traits/environment/ph_optimum_mid1.html index 818eda52d37..b8cb11c6643 100644 --- a/pages/traits/environment/ph_optimum_mid1.html +++ b/pages/traits/environment/ph_optimum_mid1.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000456 is a pH optimum - METPO:1000331 - rdfs:subClassOf + METPO:1000331 + rdfs:subClassOf

    pH optimum mid1 is a quantitative bin of the pH-optimum phenotype.

      @@ -305,11 +306,11 @@

      Parent traits (1)

      Synonyms (3)

        -
      • Alkali Tolerant EXACT_SYNONYM · metpo.owl
        • +
      • Alkali Tolerant EXACT_SYNONYM · metpo.owl
        • -
      • Neutrophile EXACT_SYNONYM · metpo.owl
        • +
      • Neutrophile EXACT_SYNONYM · metpo.owl
        • -
      • pHO_6_to_7 RELATED_SYNONYM · metpo.owl
        • +
      • pHO_6_to_7 RELATED_SYNONYM · metpo.owl
    @@ -325,7 +326,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -574,7 +575,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Pseudomonas mangiferae (NCBITaxon:2593654; DOI:10.1099/ijsem.0.003657). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Pseudomonas mangiferae (NCBITaxon:2593654; DOI:10.1099/ijsem.0.003657). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -607,7 +608,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -971,12 +981,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/ph_optimum_mid2.html b/pages/traits/environment/ph_optimum_mid2.html index 0061c98b4a5..1cb8ccc493b 100644 --- a/pages/traits/environment/ph_optimum_mid2.html +++ b/pages/traits/environment/ph_optimum_mid2.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000457 is a pH optimum - METPO:1000331 - rdfs:subClassOf + METPO:1000331 + rdfs:subClassOf

    pH optimum mid2 is a quantitative bin of the pH-optimum phenotype.

      @@ -305,13 +306,13 @@

      Parent traits (1)

      Synonyms (4)

        -
      • Alkali Tolerant EXACT_SYNONYM · metpo.owl
        • +
      • Alkali Tolerant EXACT_SYNONYM · metpo.owl
        • -
      • Alkaliphile EXACT_SYNONYM · metpo.owl
        • +
      • Alkaliphile EXACT_SYNONYM · metpo.owl
        • -
      • Neutrophile EXACT_SYNONYM · metpo.owl
        • +
      • Neutrophile EXACT_SYNONYM · metpo.owl
        • -
      • pHO_7_to_8 RELATED_SYNONYM · metpo.owl
        • +
      • pHO_7_to_8 RELATED_SYNONYM · metpo.owl
    @@ -327,7 +328,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -576,7 +577,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Rubellicoccus peritrichatus (NCBITaxon:3080537; DOI:10.1099/ijsem.0.006325). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Rubellicoccus peritrichatus (NCBITaxon:3080537; DOI:10.1099/ijsem.0.006325). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -615,7 +616,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -979,12 +989,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 06:33 UTC diff --git a/pages/traits/environment/ph_phenotype_with_numerical_limits.html b/pages/traits/environment/ph_phenotype_with_numerical_limits.html index 024aaafafae..99f2a5c3b04 100644 --- a/pages/traits/environment/ph_phenotype_with_numerical_limits.html +++ b/pages/traits/environment/ph_phenotype_with_numerical_limits.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,11 +116,11 @@

    Edge evidence

  • pH optimum - METPO:1000331 + METPO:1000331 is a pH phenotype with numerical limits METPO:1000531 - rdfs:subClassOf + rdfs:subClassOf

    pH optimum is a numerical-limit pH phenotype.

      @@ -134,11 +135,11 @@

      Edge evidence

    • pH range - METPO:1000332 + METPO:1000332 is a pH phenotype with numerical limits METPO:1000531 - rdfs:subClassOf + rdfs:subClassOf

      pH range is a numerical-limit pH phenotype.

        @@ -153,11 +154,11 @@

        Edge evidence

      • pH delta - METPO:1000232 + METPO:1000232 is a pH phenotype with numerical limits METPO:1000531 - rdfs:subClassOf + rdfs:subClassOf

        pH delta is a numerical-limit pH phenotype.

          @@ -426,7 +427,7 @@

          kg-microbe context

          via direct_metpo.

          512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

          @@ -669,7 +670,7 @@

          Curation history

        • · ADD_CANONICAL_EXAMPLES · codex -

          Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli K-12 (NCBITaxon:83333; DOI:10.1371/journal.pone.0018960). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

          +

          Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli K-12 (NCBITaxon:83333; DOI:10.1371/journal.pone.0018960). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

        • @@ -759,7 +760,16 @@

          Identifier

          Term kind
          CLASS
          Status
          -
          REVIEWED
          +
          REVIEWED + + +
          + What this status means +

          Curator has signed off on label / definition / parents.

          +

          Quoted from the schema's status definitions.

          +
          + +
    • @@ -1123,12 +1133,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-07 20:05 UTC diff --git a/pages/traits/environment/ph_range.html b/pages/traits/environment/ph_range.html index f9babca05a7..00d264d0694 100644 --- a/pages/traits/environment/ph_range.html +++ b/pages/traits/environment/ph_range.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -358,7 +359,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000332 [-2.054, -2.222, -3.843, +1.421, …]
      • +
    • pH range METPO:1000332 [-2.054, -2.222, -3.843, +1.421, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -607,7 +608,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -640,7 +641,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1004,12 +1014,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/ph_range_high.html b/pages/traits/environment/ph_range_high.html index 189a37471eb..52d8343aeac 100644 --- a/pages/traits/environment/ph_range_high.html +++ b/pages/traits/environment/ph_range_high.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,8 +119,8 @@

    Edge evidence

    METPO:1000464 is a pH range - METPO:1000332 - rdfs:subClassOf + METPO:1000332 + rdfs:subClassOf

    pH range high is a quantitative bin of the pH-range phenotype.

      @@ -311,13 +312,13 @@

      Parent traits (1)

      Synonyms (4)

        -
      • Alkali Tolerant EXACT_SYNONYM · metpo.owl
        • +
      • Alkali Tolerant EXACT_SYNONYM · metpo.owl
        • -
      • Alkaliphile EXACT_SYNONYM · metpo.owl
        • +
      • Alkaliphile EXACT_SYNONYM · metpo.owl
        • -
      • Extreme Alkaliphile EXACT_SYNONYM · metpo.owl
        • +
      • Extreme Alkaliphile EXACT_SYNONYM · metpo.owl
        • -
      • 10_to_14 RELATED_SYNONYM · metpo.owl
        • +
      • 10_to_14 RELATED_SYNONYM · metpo.owl
    @@ -333,7 +334,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -578,7 +579,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -942,12 +952,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/ph_range_low.html b/pages/traits/environment/ph_range_low.html index a7771180606..a89fa3f282b 100644 --- a/pages/traits/environment/ph_range_low.html +++ b/pages/traits/environment/ph_range_low.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000460 is a pH range - METPO:1000332 - rdfs:subClassOf + METPO:1000332 + rdfs:subClassOf

    pH range low is a quantitative bin of the pH-range phenotype.

      @@ -286,15 +287,15 @@

      Parent traits (1)

      Synonyms (5)

        -
      • Acid Tolerant EXACT_SYNONYM · metpo.owl
        • +
      • Acid Tolerant EXACT_SYNONYM · metpo.owl
        • -
      • Acidophile EXACT_SYNONYM · metpo.owl
        • +
      • Acidophile EXACT_SYNONYM · metpo.owl
        • -
      • Facultative acidophile EXACT_SYNONYM · metpo.owl
        • +
      • Facultative acidophile EXACT_SYNONYM · metpo.owl
        • -
      • Obligative acidophile EXACT_SYNONYM · metpo.owl
        • +
      • Obligative acidophile EXACT_SYNONYM · metpo.owl
        • -
      • pHR_4_to_6 RELATED_SYNONYM · metpo.owl
        • +
      • pHR_4_to_6 RELATED_SYNONYM · metpo.owl
    @@ -310,7 +311,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -592,7 +593,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -956,12 +966,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/ph_range_mid1.html b/pages/traits/environment/ph_range_mid1.html index c76b7a7a268..c5768019b85 100644 --- a/pages/traits/environment/ph_range_mid1.html +++ b/pages/traits/environment/ph_range_mid1.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000461 is a pH range - METPO:1000332 - rdfs:subClassOf + METPO:1000332 + rdfs:subClassOf

    pH range mid1 is a quantitative bin of the pH-range phenotype.

      @@ -286,13 +287,13 @@

      Parent traits (1)

      Synonyms (4)

        -
      • Alkali Tolerant EXACT_SYNONYM · metpo.owl
        • +
      • Alkali Tolerant EXACT_SYNONYM · metpo.owl
        • -
      • Facultative acidophile EXACT_SYNONYM · metpo.owl
        • +
      • Facultative acidophile EXACT_SYNONYM · metpo.owl
        • -
      • Neutrophile EXACT_SYNONYM · metpo.owl
        • +
      • Neutrophile EXACT_SYNONYM · metpo.owl
        • -
      • pHR_6_to_7 RELATED_SYNONYM · metpo.owl
        • +
      • pHR_6_to_7 RELATED_SYNONYM · metpo.owl
    @@ -308,7 +309,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -557,7 +558,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -590,7 +591,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -954,12 +964,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/ph_range_mid2.html b/pages/traits/environment/ph_range_mid2.html index 0e417e0f119..5929c6c20bf 100644 --- a/pages/traits/environment/ph_range_mid2.html +++ b/pages/traits/environment/ph_range_mid2.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000462 is a pH range - METPO:1000332 - rdfs:subClassOf + METPO:1000332 + rdfs:subClassOf

    pH range mid2 is a quantitative bin of the pH-range phenotype.

      @@ -305,15 +306,15 @@

      Parent traits (1)

      Synonyms (5)

        -
      • Alkali Tolerant EXACT_SYNONYM · metpo.owl
        • +
      • Alkali Tolerant EXACT_SYNONYM · metpo.owl
        • -
      • Alkaliphile EXACT_SYNONYM · metpo.owl
        • +
      • Alkaliphile EXACT_SYNONYM · metpo.owl
        • -
      • Facultative acidophile EXACT_SYNONYM · metpo.owl
        • +
      • Facultative acidophile EXACT_SYNONYM · metpo.owl
        • -
      • Neutrophile EXACT_SYNONYM · metpo.owl
        • +
      • Neutrophile EXACT_SYNONYM · metpo.owl
        • -
      • pHR_7_to_8 RELATED_SYNONYM · metpo.owl
        • +
      • pHR_7_to_8 RELATED_SYNONYM · metpo.owl
    @@ -329,7 +330,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -572,7 +573,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Solimonas fluminis (NCBITaxon:2086571; DOI:10.1099/ijsem.0.002865). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Solimonas fluminis (NCBITaxon:2086571; DOI:10.1099/ijsem.0.002865). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -632,7 +633,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -996,12 +1006,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-07 07:24 UTC diff --git a/pages/traits/environment/ph_range_mid3.html b/pages/traits/environment/ph_range_mid3.html index 62ab2b5797a..c72892e7050 100644 --- a/pages/traits/environment/ph_range_mid3.html +++ b/pages/traits/environment/ph_range_mid3.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000463 is a pH range - METPO:1000332 - rdfs:subClassOf + METPO:1000332 + rdfs:subClassOf

    pH range mid3 is a quantitative bin of the pH-range phenotype.

      @@ -305,15 +306,15 @@

      Parent traits (1)

      Synonyms (5)

        -
      • Alkali Tolerant EXACT_SYNONYM · metpo.owl
        • +
      • Alkali Tolerant EXACT_SYNONYM · metpo.owl
        • -
      • Alkaliphile EXACT_SYNONYM · metpo.owl
        • +
      • Alkaliphile EXACT_SYNONYM · metpo.owl
        • -
      • Extreme Alkaliphile EXACT_SYNONYM · metpo.owl
        • +
      • Extreme Alkaliphile EXACT_SYNONYM · metpo.owl
        • -
      • Facultative acidophile EXACT_SYNONYM · metpo.owl
        • +
      • Facultative acidophile EXACT_SYNONYM · metpo.owl
        • -
      • pHR_8_to_10 RELATED_SYNONYM · metpo.owl
        • +
      • pHR_8_to_10 RELATED_SYNONYM · metpo.owl
    @@ -329,7 +330,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -554,7 +555,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Evansella tamaricis (NCBITaxon:2069301; DOI:10.1099/ijsem.0.002543). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Evansella tamaricis (NCBITaxon:2069301; DOI:10.1099/ijsem.0.002543). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -587,7 +588,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -951,12 +961,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/ph_range_very_low.html b/pages/traits/environment/ph_range_very_low.html index f420d5def3a..424e889fdc5 100644 --- a/pages/traits/environment/ph_range_very_low.html +++ b/pages/traits/environment/ph_range_very_low.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000459 is a pH range - METPO:1000332 - rdfs:subClassOf + METPO:1000332 + rdfs:subClassOf

    pH range very low is a quantitative bin of the pH-range phenotype.

      @@ -267,17 +268,17 @@

      Parent traits (1)

      Synonyms (6)

        -
      • Acid Tolerant EXACT_SYNONYM · metpo.owl
        • +
      • Acid Tolerant EXACT_SYNONYM · metpo.owl
        • -
      • Acidophile EXACT_SYNONYM · metpo.owl
        • +
      • Acidophile EXACT_SYNONYM · metpo.owl
        • -
      • Extreme Acidophile EXACT_SYNONYM · metpo.owl
        • +
      • Extreme Acidophile EXACT_SYNONYM · metpo.owl
        • -
      • Facultative acidophile EXACT_SYNONYM · metpo.owl
        • +
      • Facultative acidophile EXACT_SYNONYM · metpo.owl
        • -
      • Obligative acidophile EXACT_SYNONYM · metpo.owl
        • +
      • Obligative acidophile EXACT_SYNONYM · metpo.owl
        • -
      • pHR_0_to_4 RELATED_SYNONYM · metpo.owl
        • +
      • pHR_0_to_4 RELATED_SYNONYM · metpo.owl
    @@ -293,7 +294,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -542,7 +543,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Picrophilus oshimae (NCBITaxon:46632; DOI:10.1007/s007920050044). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Picrophilus oshimae (NCBITaxon:46632; DOI:10.1007/s007920050044). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -575,7 +576,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -939,12 +949,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/piezophilic.html b/pages/traits/environment/piezophilic.html index e53765c4858..98178c19b85 100644 --- a/pages/traits/environment/piezophilic.html +++ b/pages/traits/environment/piezophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    selects for piezophilic - traitmech:000001 + traitmech:000001 METPO:2007401

    HHP habitats favor optimal-at-pressure growth phenotype.

      @@ -137,7 +138,7 @@

      Edge evidence

      confers piezophilic - traitmech:000001 + traitmech:000001 METPO:2007700

      Membrane lipid adaptation enables high-pressure-optimal growth.

        @@ -270,7 +271,7 @@

        Edge evidence

        contributes to piezophilic - traitmech:000001 + traitmech:000001 RO:0002326

        Pressure tolerance via piezolytes contributes to optimal growth at high pressure.

    @@ -357,7 +358,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -470,16 +471,16 @@

    Deep research

    | priority | subject | predicate | object | representative taxon/assay | evidence class | confidence | DOI | |---|---|---|---|---|---|---|---| -| 1 | high hydrostatic pressure (HHP) | induces_via | TorRS-dependent torA expression / TMAO reductase induction | *Vibrio fluvialis* QY27, ΔtorR/ΔtorS mutants and complementation at 30 MPa vs 0.1 MPa (liu2023thetorrstwo pages 1-2, liu2023thetorrstwo pages 8-10) | direct perturbation | high | 10.3389/fmicb.2023.1291578 | -| 1 | TorS alternative transmitter histidine H902 | required_for | HHP-responsive induction of torA | *Vibrio fluvialis* QY27, TorS H902Q complementation abolishes pressure induction at 30 MPa (liu2023thetorrstwo pages 6-8, liu2023thetorrstwo pages 8-10) | direct perturbation | high | 10.3389/fmicb.2023.1291578 | -| 1 | FtsZ N-terminal GTPase domain residues | promotes | Z-ring stability / FtsZ filament stability under HHP | *Shewanella benthica* DB21MT-2 vs *S. oneidensis* MR-1; chimeras and 14 point mutants assayed at 50 MPa (cui2024nterminusgtpasedomain pages 1-2, cui2024nterminusgtpasedomain pages 7-9, cui2024nterminusgtpasedomain pages 9-10) | direct perturbation | high | 10.3389/fmicb.2024.1441398 | -| 2 | HHP | causes | membrane compression with loss of fluidity | cross-taxon membrane physiology synthesis from cultured piezophiles/piezotolerants (tamby2023microbialmembranelipid pages 1-2, malas2024biologicalfunctionsat pages 9-10) | comparative correlation | medium | 10.3389/fmolb.2022.1058381 | -| 2 | membrane compression / reduced fluidity under HHP | selects_for | increased unsaturated and/or branched fatty acid remodeling | multiple taxa including *Photobacterium profundum*, *Shewanella piezotolerans*, *Pseudothermotoga elfii*; lipid comparisons across pressure conditions (tamby2023microbialmembranelipid pages 1-2, tamby2023microbialmembranelipid pages 4-6, scheffer2023themysteryof pages 7-9) | condition-response | medium | 10.3389/fmolb.2022.1058381 | -| 2 | HHP | increases | superoxide dismutase activity / antioxidant defense | *Halomonas titanicae* ANRCS81, transcriptomics and SOD assay at 40 MPa (li2023strategyforthe pages 10-12) | condition-response | medium | 10.1128/aem.01304-22 | -| 2 | HHP | shifts_to | TMAO respiration | *Shewanella eurypsychrophilus* YLB-09, metabolomics/transcriptomics at 23 MPa vs 0.1 MPa (qiu2024metabolicadaptationsof pages 1-2, qiu2024metabolicadaptationsof pages 6-8, qiu2024metabolicadaptationsof pages 11-12) | condition-response | medium | 10.3389/fmicb.2024.1467153 | -| 3 | pfa operon / desaturase functions | increases | PUFA or unsaturated fatty acid content / membrane fluidity maintenance | *Photobacterium profundum* SS9 and piezophilic *Colwellia* comparative genomics/transcriptomics (scheffer2023themysteryof pages 6-7, peoples2020distinctivegeneand pages 9-11) | comparative correlation | medium | 10.3390/microorganisms11071629 | -| 3 | HHP | increases | compatible solute accumulation (e.g., glutamate, betaine, β-hydroxybutyrate) | *Photobacterium profundum*, *Desulfovibrio hydrothermalis*, *D. piezophilus* metabolite responses under pressure (scheffer2023themysteryof pages 9-10, scheffer2023themysteryof pages 7-9) | condition-response | medium | 10.3390/microorganisms11071629 | -| 3 | flagellar biosynthesis genes | supports | growth and motility under HHP | *Desulfovibrio alaskensis* high-pressure growth/motility genetics summarized in review synthesis (scheffer2023themysteryof pages 6-7) | comparative correlation | low-medium | 10.3390/microorganisms11071629 | +| 1 | high hydrostatic pressure (HHP) | induces_via | TorRS-dependent torA expression / TMAO reductase induction | *Vibrio fluvialis* QY27, ΔtorR/ΔtorS mutants and complementation at 30 MPa vs 0.1 MPa (liu2023thetorrstwo pages 1-2, liu2023thetorrstwo pages 8-10) | direct perturbation | high | 10.3389/fmicb.2023.1291578 | +| 1 | TorS alternative transmitter histidine H902 | required_for | HHP-responsive induction of torA | *Vibrio fluvialis* QY27, TorS H902Q complementation abolishes pressure induction at 30 MPa (liu2023thetorrstwo pages 6-8, liu2023thetorrstwo pages 8-10) | direct perturbation | high | 10.3389/fmicb.2023.1291578 | +| 1 | FtsZ N-terminal GTPase domain residues | promotes | Z-ring stability / FtsZ filament stability under HHP | *Shewanella benthica* DB21MT-2 vs *S. oneidensis* MR-1; chimeras and 14 point mutants assayed at 50 MPa (cui2024nterminusgtpasedomain pages 1-2, cui2024nterminusgtpasedomain pages 7-9, cui2024nterminusgtpasedomain pages 9-10) | direct perturbation | high | 10.3389/fmicb.2024.1441398 | +| 2 | HHP | causes | membrane compression with loss of fluidity | cross-taxon membrane physiology synthesis from cultured piezophiles/piezotolerants (tamby2023microbialmembranelipid pages 1-2, malas2024biologicalfunctionsat pages 9-10) | comparative correlation | medium | 10.3389/fmolb.2022.1058381 | +| 2 | membrane compression / reduced fluidity under HHP | selects_for | increased unsaturated and/or branched fatty acid remodeling | multiple taxa including *Photobacterium profundum*, *Shewanella piezotolerans*, *Pseudothermotoga elfii*; lipid comparisons across pressure conditions (tamby2023microbialmembranelipid pages 1-2, tamby2023microbialmembranelipid pages 4-6, scheffer2023themysteryof pages 7-9) | condition-response | medium | 10.3389/fmolb.2022.1058381 | +| 2 | HHP | increases | superoxide dismutase activity / antioxidant defense | *Halomonas titanicae* ANRCS81, transcriptomics and SOD assay at 40 MPa (li2023strategyforthe pages 10-12) | condition-response | medium | 10.1128/aem.01304-22 | +| 2 | HHP | shifts_to | TMAO respiration | *Shewanella eurypsychrophilus* YLB-09, metabolomics/transcriptomics at 23 MPa vs 0.1 MPa (qiu2024metabolicadaptationsof pages 1-2, qiu2024metabolicadaptationsof pages 6-8, qiu2024metabolicadaptationsof pages 11-12) | condition-response | medium | 10.3389/fmicb.2024.1467153 | +| 3 | pfa operon / desaturase functions | increases | PUFA or unsaturated fatty acid content / membrane fluidity maintenance | *Photobacterium profundum* SS9 and piezophilic *Colwellia* comparative genomics/transcriptomics (scheffer2023themysteryof pages 6-7, peoples2020distinctivegeneand pages 9-11) | comparative correlation | medium | 10.3390/microorganisms11071629 | +| 3 | HHP | increases | compatible solute accumulation (e.g., glutamate, betaine, β-hydroxybutyrate) | *Photobacterium profundum*, *Desulfovibrio hydrothermalis*, *D. piezophilus* metabolite responses under pressure (scheffer2023themysteryof pages 9-10, scheffer2023themysteryof pages 7-9) | condition-response | medium | 10.3390/microorganisms11071629 | +| 3 | flagellar biosynthesis genes | supports | growth and motility under HHP | *Desulfovibrio alaskensis* high-pressure growth/motility genetics summarized in review synthesis (scheffer2023themysteryof pages 6-7) | comparative correlation | low-medium | 10.3390/microorganisms11071629 | *Table: This table prioritizes the strongest candidate causal edges for curating a TraitMech graph of piezophily, emphasizing direct perturbation evidence first and broader condition-response or comparative mechanisms second. It helps focus curation on edges most likely to be stable and mechanistically defensible.* @@ -624,7 +625,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -988,12 +998,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/piezotolerant.html b/pages/traits/environment/piezotolerant.html index 49c70348504..55b4365720d 100644 --- a/pages/traits/environment/piezotolerant.html +++ b/pages/traits/environment/piezotolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    confers piezotolerant - traitmech:000003 + traitmech:000003 METPO:2007700

    Membrane adaptation supports growth across the pressure range atmospheric ↔ high.

      @@ -292,7 +293,7 @@

      Parent traits (1)

      Synonyms (1)

    @@ -308,7 +309,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -581,7 +582,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -945,12 +955,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/pressure_delta.html b/pages/traits/environment/pressure_delta.html index 2392ad388f4..c56584d0f80 100644 --- a/pages/traits/environment/pressure_delta.html +++ b/pages/traits/environment/pressure_delta.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    PATO:0001025 defines pressure delta - traitmech:000006 + traitmech:000006 METPO:2007500

    The hydrostatic-pressure axis defines the values whose max minus min yields the delta.

      @@ -115,7 +116,7 @@

      Edge evidence

    • pressure delta - traitmech:000006 + traitmech:000006 associated with pressure-tolerance breadth @@ -276,7 +277,7 @@

      Edge evidence

      defines pressure delta - traitmech:000006 + traitmech:000006 METPO:2007500

      The minimum and maximum growth-pressure limits define the breadth (max minus min) recorded by the delta.

        @@ -343,7 +344,7 @@

        kg-microbe context

        via parent_proxy.

          -
        • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
          • +
        • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

        512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

        @@ -562,7 +563,7 @@

        Curation history

      • · ADD_CANONICAL_EXAMPLES · codex -

        Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Colwellia marinimaniae (NCBITaxon:1513592; DOI:10.1099/ijsem.0.001671). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

        +

        Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Colwellia marinimaniae (NCBITaxon:1513592; DOI:10.1099/ijsem.0.001671). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

        • @@ -595,7 +596,16 @@

        Identifier

        Term kind
        CLASS
        Status
        -
        REVIEWED
        +
        REVIEWED + + +
        + What this status means +

        Curator has signed off on label / definition / parents.

        +

        Quoted from the schema's status definitions.

        +
        + +
    @@ -959,12 +969,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/pressure_optimum.html b/pages/traits/environment/pressure_optimum.html index 95e389e7d4e..26a2a4c4110 100644 --- a/pages/traits/environment/pressure_optimum.html +++ b/pages/traits/environment/pressure_optimum.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    PATO:0001025 defines pressure optimum - traitmech:000004 + traitmech:000004 METPO:2007500

    The hydrostatic-pressure axis defines the value at which growth is fastest.

      @@ -115,7 +116,7 @@

      Edge evidence

    • pressure optimum - traitmech:000004 + traitmech:000004 associated with maximal growth rate @@ -137,7 +138,7 @@

      Edge evidence

      confers pressure optimum - traitmech:000004 + traitmech:000004 METPO:2007700

      Increased membrane unsaturated/PUFA content confers growth at elevated hydrostatic pressure, shaping the pressure optimum.

        @@ -175,7 +176,7 @@

        Edge evidence

        confers high hydrostatic pressure tolerance - traitmech:000003 + traitmech:000003 METPO:2007700

        Elevated intracellular osmotic pressure confers high hydrostatic pressure tolerance.

          @@ -213,7 +214,7 @@

          Edge evidence

          confers high hydrostatic pressure tolerance - traitmech:000003 + traitmech:000003 METPO:2007700

          Compatible-solute (piezolyte) accumulation confers pressure tolerance.

            @@ -280,7 +281,7 @@

            kg-microbe context

            via parent_proxy.

              -
            • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
              • +
            • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

            512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

            @@ -523,7 +524,7 @@

            Curation history

          • · ADD_CANONICAL_EXAMPLES · codex -

            Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Colwellia marinimaniae (NCBITaxon:1513592; DOI:10.1099/ijsem.0.001671). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

            +

            Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Colwellia marinimaniae (NCBITaxon:1513592; DOI:10.1099/ijsem.0.001671). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

            • @@ -556,7 +557,16 @@

            Identifier

            Term kind
            CLASS
            Status
            -
            REVIEWED
            +
            REVIEWED + + +
            + What this status means +

            Curator has signed off on label / definition / parents.

            +

            Quoted from the schema's status definitions.

            +
            + +
    @@ -920,12 +930,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/pressure_range.html b/pages/traits/environment/pressure_range.html index 509bbeaa06a..9f89a39655a 100644 --- a/pages/traits/environment/pressure_range.html +++ b/pages/traits/environment/pressure_range.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    PATO:0001025 defines pressure range - traitmech:000005 + traitmech:000005 METPO:2007500

    The hydrostatic-pressure axis defines the min/max bounds bracketed by the pressure range.

      @@ -115,7 +116,7 @@

      Edge evidence

    • pressure range - traitmech:000005 + traitmech:000005 associated with growth-permissive pressure span @@ -156,7 +157,7 @@

      Edge evidence

      positively regulates pressure range - traitmech:000005 + traitmech:000005 RO:0002213

      Unsaturated membrane lipids support growth across high hydrostatic pressures.

        @@ -175,7 +176,7 @@

        Edge evidence

        expands pressure range - traitmech:000005 + traitmech:000005

        Maintaining membrane fluidity under pressure expands the growth-supporting pressure range.

          @@ -280,7 +281,7 @@

          kg-microbe context

          via parent_proxy.

            -
          • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
            • +
          • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

          512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

          @@ -517,7 +518,7 @@

          Curation history

        • · ADD_CANONICAL_EXAMPLES · codex -

          Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Colwellia marinimaniae (NCBITaxon:1513592; DOI:10.1099/ijsem.0.001671). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

          +

          Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Colwellia marinimaniae (NCBITaxon:1513592; DOI:10.1099/ijsem.0.001671). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

          • @@ -550,7 +551,16 @@

          Identifier

          Term kind
          CLASS
          Status
          -
          REVIEWED
          +
          REVIEWED + + +
          + What this status means +

          Curator has signed off on label / definition / parents.

          +

          Quoted from the schema's status definitions.

          +
          + +
    @@ -914,12 +924,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/psychrophilic.html b/pages/traits/environment/psychrophilic.html index 39bbbf02d76..a6a362bada7 100644 --- a/pages/traits/environment/psychrophilic.html +++ b/pages/traits/environment/psychrophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -356,7 +357,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -680,7 +681,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1044,12 +1054,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/psychrotolerant.html b/pages/traits/environment/psychrotolerant.html index f6eaac77f8a..fb48a10d912 100644 --- a/pages/traits/environment/psychrotolerant.html +++ b/pages/traits/environment/psychrotolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -134,7 +135,7 @@

    Edge evidence

  • cold-shock response - traitmech:000206 + traitmech:000206 confers psychrotolerant METPO:1000618 @@ -299,7 +300,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -650,7 +651,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -1014,12 +1024,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 05:32 UTC diff --git a/pages/traits/environment/radiotolerant.html b/pages/traits/environment/radiotolerant.html index 9f6cf9f8ee5..d581a7eb4ea 100644 --- a/pages/traits/environment/radiotolerant.html +++ b/pages/traits/environment/radiotolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    challenges radiotolerant - traitmech:000007 + traitmech:000007 METPO:2007406

    Radiation exposure is the environmental challenge the trait counters.

      @@ -118,7 +119,7 @@

      Edge evidence

      GO:0006281 confers radiotolerant - traitmech:000007 + traitmech:000007 METPO:2007700

      Efficient repair of radiation-induced DNA lesions enables survival.

        @@ -137,7 +138,7 @@

        Edge evidence

        confers radiotolerant - traitmech:000007 + traitmech:000007 METPO:2007700

        Mn-antioxidant protection of the proteome preserves repair capacity under irradiation.

          @@ -326,8 +327,8 @@

          Protein and taxon examples

    		 - Deinococcus radiodurans R1 -
    NCBITaxon:243230 + Deinococcus radiodurans R1 +
    NCBITaxon:243230         		REVIEWED
    @@ -404,7 +405,7 @@

    Children (2)

    Synonyms (1)

    @@ -420,7 +421,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -693,7 +694,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1057,12 +1067,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/environment/salinity_phenotype_with_numerical_limits.html b/pages/traits/environment/salinity_phenotype_with_numerical_limits.html index edae60a4de0..c1b84837c45 100644 --- a/pages/traits/environment/salinity_phenotype_with_numerical_limits.html +++ b/pages/traits/environment/salinity_phenotype_with_numerical_limits.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,11 +116,11 @@

    Edge evidence

  • NaCl optimum - METPO:1000333 + METPO:1000333 is a salinity phenotype with numerical limits METPO:1000532 - rdfs:subClassOf + rdfs:subClassOf

    NaCl optimum is a numerical-limit salinity phenotype.

      @@ -134,11 +135,11 @@

      Edge evidence

    • NaCl range - METPO:1000334 + METPO:1000334 is a salinity phenotype with numerical limits METPO:1000532 - rdfs:subClassOf + rdfs:subClassOf

      NaCl range is a numerical-limit salinity phenotype.

        @@ -153,11 +154,11 @@

        Edge evidence

      • NaCl delta - METPO:1000335 + METPO:1000335 is a salinity phenotype with numerical limits METPO:1000532 - rdfs:subClassOf + rdfs:subClassOf

        NaCl delta is a numerical-limit salinity phenotype.

          @@ -384,7 +385,7 @@

          kg-microbe context

          via direct_metpo.

          512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

          @@ -633,7 +634,7 @@

          Curation history

        • · ADD_CANONICAL_EXAMPLES · codex -

          Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Natranaerobius thermophilus (NCBITaxon:375929; DOI:10.1128/aem.00145-24). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

          +

          Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Natranaerobius thermophilus (NCBITaxon:375929; DOI:10.1128/aem.00145-24). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

        • @@ -672,7 +673,16 @@

          Identifier

          Term kind
          CLASS
          Status
          -
          REVIEWED
          +
          REVIEWED + + +
          + What this status means +

          Curator has signed off on label / definition / parents.

          +

          Quoted from the schema's status definitions.

          +
          + +
    • @@ -1036,12 +1046,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 17:46 UTC diff --git a/pages/traits/environment/slightly_halophilic.html b/pages/traits/environment/slightly_halophilic.html index 5ed12f0d29b..e1bfef87c1e 100644 --- a/pages/traits/environment/slightly_halophilic.html +++ b/pages/traits/environment/slightly_halophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -312,7 +313,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -615,7 +616,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Paraliobacillus ryukyuensis (NCBITaxon:200904; DOI:10.2323/jgam.48.269). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Paraliobacillus ryukyuensis (NCBITaxon:200904; DOI:10.2323/jgam.48.269). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -648,7 +649,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1012,12 +1022,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/stenohaline.html b/pages/traits/environment/stenohaline.html index 214f0a4b861..b790ce9fad2 100644 --- a/pages/traits/environment/stenohaline.html +++ b/pages/traits/environment/stenohaline.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -445,7 +446,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -754,7 +755,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1118,12 +1128,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 10:04 UTC diff --git a/pages/traits/environment/strictly_anaerobic.html b/pages/traits/environment/strictly_anaerobic.html index e2bd24e3826..a915ee9b198 100644 --- a/pages/traits/environment/strictly_anaerobic.html +++ b/pages/traits/environment/strictly_anaerobic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -273,7 +274,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -289,7 +290,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -571,7 +572,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -935,12 +945,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/temperature_delta.html b/pages/traits/environment/temperature_delta.html index e7e02578517..3ad8faf8b10 100644 --- a/pages/traits/environment/temperature_delta.html +++ b/pages/traits/environment/temperature_delta.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -299,7 +300,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -536,7 +537,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Kushneria aurantia (NCBITaxon:504092; DOI:10.1099/ijs.0.001461-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Kushneria aurantia (NCBITaxon:504092; DOI:10.1099/ijs.0.001461-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -569,7 +570,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -933,12 +943,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/temperature_delta_high.html b/pages/traits/environment/temperature_delta_high.html index 74d2bb3fa4a..48c03a3fc21 100644 --- a/pages/traits/environment/temperature_delta_high.html +++ b/pages/traits/environment/temperature_delta_high.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,8 +119,8 @@

    Edge evidence

    METPO:1000487 is a temperature delta - METPO:1000303 - rdfs:subClassOf + METPO:1000303 + rdfs:subClassOf

    Temperature delta high is a quantitative bin of the temperature-delta phenotype.

      @@ -387,7 +388,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • Td_>30 RELATED_SYNONYM · metpo.owl
        • +
      • Td_>30 RELATED_SYNONYM · metpo.owl
    @@ -403,7 +404,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -736,7 +737,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1100,12 +1110,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 07:07 UTC diff --git a/pages/traits/environment/temperature_delta_low.html b/pages/traits/environment/temperature_delta_low.html index a30c8b85518..80de3c50a4e 100644 --- a/pages/traits/environment/temperature_delta_low.html +++ b/pages/traits/environment/temperature_delta_low.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000484 is a temperature delta - METPO:1000303 - rdfs:subClassOf + METPO:1000303 + rdfs:subClassOf

    Temperature delta low is a quantitative bin of the temperature-delta phenotype.

      @@ -286,7 +287,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • Td_5_10 RELATED_SYNONYM · metpo.owl
        • +
      • Td_5_10 RELATED_SYNONYM · metpo.owl
    @@ -302,7 +303,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -562,7 +563,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -926,12 +936,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 07:07 UTC diff --git a/pages/traits/environment/temperature_delta_mid1.html b/pages/traits/environment/temperature_delta_mid1.html index 8c9f268aab0..85788920921 100644 --- a/pages/traits/environment/temperature_delta_mid1.html +++ b/pages/traits/environment/temperature_delta_mid1.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000485 is a temperature delta - METPO:1000303 - rdfs:subClassOf + METPO:1000303 + rdfs:subClassOf

    Temperature delta mid1 is a quantitative bin of the temperature-delta phenotype.

      @@ -245,8 +246,8 @@

      Edge evidence

      is a temperature delta - METPO:1000303 - rdfs:subClassOf + METPO:1000303 + rdfs:subClassOf

      The Tmin/Tmax-bounded thermal niche is the breadth quantity captured by the temperature-delta phenotype.

        @@ -305,7 +306,7 @@

        Parent traits (1)

        Synonyms (1)

          -
        • Td_10_20 RELATED_SYNONYM · metpo.owl
          • +
        • Td_10_20 RELATED_SYNONYM · metpo.owl
    @@ -321,7 +322,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -552,7 +553,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Pontibacterium sinense (NCBITaxon:2781979; DOI:10.1099/ijsem.0.006018). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Pontibacterium sinense (NCBITaxon:2781979; DOI:10.1099/ijsem.0.006018). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -585,7 +586,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -949,12 +959,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/temperature_delta_mid2.html b/pages/traits/environment/temperature_delta_mid2.html index 4c2ea185586..79cd211df6f 100644 --- a/pages/traits/environment/temperature_delta_mid2.html +++ b/pages/traits/environment/temperature_delta_mid2.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000486 is a temperature delta - METPO:1000303 - rdfs:subClassOf + METPO:1000303 + rdfs:subClassOf

    Temperature delta mid2 is a quantitative bin of the temperature-delta phenotype.

      @@ -286,7 +287,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • Td_20_30 RELATED_SYNONYM · metpo.owl
        • +
      • Td_20_30 RELATED_SYNONYM · metpo.owl
    @@ -302,7 +303,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -539,7 +540,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Pseudomonas mangiferae (NCBITaxon:2593654; DOI:10.1099/ijsem.0.003657). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Pseudomonas mangiferae (NCBITaxon:2593654; DOI:10.1099/ijsem.0.003657). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -587,7 +588,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -951,12 +961,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 07:07 UTC diff --git a/pages/traits/environment/temperature_delta_very_low.html b/pages/traits/environment/temperature_delta_very_low.html index a244896f081..9ad55e268e8 100644 --- a/pages/traits/environment/temperature_delta_very_low.html +++ b/pages/traits/environment/temperature_delta_very_low.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000483 is a temperature delta - METPO:1000303 - rdfs:subClassOf + METPO:1000303 + rdfs:subClassOf

    Temperature delta very low is a quantitative bin of the temperature-delta phenotype.

      @@ -368,7 +369,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • Td_1_5 RELATED_SYNONYM · metpo.owl
        • +
      • Td_1_5 RELATED_SYNONYM · metpo.owl
    @@ -384,7 +385,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -662,7 +663,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1026,12 +1036,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-07 02:20 UTC diff --git a/pages/traits/environment/temperature_optimum.html b/pages/traits/environment/temperature_optimum.html index df74f21f655..4cf389c2bce 100644 --- a/pages/traits/environment/temperature_optimum.html +++ b/pages/traits/environment/temperature_optimum.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -322,7 +323,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -589,7 +590,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -637,7 +638,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -1001,12 +1011,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 07:07 UTC diff --git a/pages/traits/environment/temperature_optimum_high.html b/pages/traits/environment/temperature_optimum_high.html index 84efd2476dc..6293e23a2fd 100644 --- a/pages/traits/environment/temperature_optimum_high.html +++ b/pages/traits/environment/temperature_optimum_high.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -137,8 +138,8 @@

    Edge evidence

    METPO:1000447 is a temperature optimum - METPO:1000304 - rdfs:subClassOf + METPO:1000304 + rdfs:subClassOf

    Temperature optimum high is a quantitative bin of the temperature-optimum phenotype.

      @@ -406,9 +407,9 @@

      Parent traits (1)

      Synonyms (2)

        -
      • Thermophile EXACT_SYNONYM · metpo.owl
        • +
      • Thermophile EXACT_SYNONYM · metpo.owl
        • -
      • TO_>40 RELATED_SYNONYM · metpo.owl
        • +
      • TO_>40 RELATED_SYNONYM · metpo.owl
    @@ -424,7 +425,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -781,7 +782,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1145,12 +1155,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-08 03:30 UTC diff --git a/pages/traits/environment/temperature_optimum_low.html b/pages/traits/environment/temperature_optimum_low.html index 2a7893e592e..122483c89df 100644 --- a/pages/traits/environment/temperature_optimum_low.html +++ b/pages/traits/environment/temperature_optimum_low.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000442 is a temperature optimum - METPO:1000304 - rdfs:subClassOf + METPO:1000304 + rdfs:subClassOf

    Temperature optimum low is a quantitative bin of the temperature-optimum phenotype.

      @@ -324,11 +325,11 @@

      Parent traits (1)

      Synonyms (3)

        -
      • Psychrophile EXACT_SYNONYM · metpo.owl
        • +
      • Psychrophile EXACT_SYNONYM · metpo.owl
        • -
      • Psychrotolerant EXACT_SYNONYM · metpo.owl
        • +
      • Psychrotolerant EXACT_SYNONYM · metpo.owl
        • -
      • TO_10_to_22 RELATED_SYNONYM · metpo.owl
        • +
      • TO_10_to_22 RELATED_SYNONYM · metpo.owl
    @@ -344,7 +345,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -629,7 +630,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -993,12 +1003,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/temperature_optimum_mid1.html b/pages/traits/environment/temperature_optimum_mid1.html index 70fe680799e..605901e2531 100644 --- a/pages/traits/environment/temperature_optimum_mid1.html +++ b/pages/traits/environment/temperature_optimum_mid1.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000443 is a temperature optimum - METPO:1000304 - rdfs:subClassOf + METPO:1000304 + rdfs:subClassOf

    Temperature optimum mid1 is a quantitative bin of the temperature-optimum phenotype.

      @@ -305,11 +306,11 @@

      Parent traits (1)

      Synonyms (3)

        -
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • +
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • -
      • TO_22_to_27 RELATED_SYNONYM · metpo.owl
        • +
      • TO_22_to_27 RELATED_SYNONYM · metpo.owl
        • -
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
        • +
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
    @@ -325,7 +326,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -568,7 +569,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Rubellicoccus peritrichatus (NCBITaxon:3080537; DOI:10.1099/ijsem.0.006325). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Rubellicoccus peritrichatus (NCBITaxon:3080537; DOI:10.1099/ijsem.0.006325). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -616,7 +617,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -980,12 +990,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 07:07 UTC diff --git a/pages/traits/environment/temperature_optimum_mid2.html b/pages/traits/environment/temperature_optimum_mid2.html index 45a38e7d052..ec153fb5957 100644 --- a/pages/traits/environment/temperature_optimum_mid2.html +++ b/pages/traits/environment/temperature_optimum_mid2.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000444 is a temperature optimum - METPO:1000304 - rdfs:subClassOf + METPO:1000304 + rdfs:subClassOf

    Temperature optimum mid2 is a quantitative bin of the temperature-optimum phenotype.

      @@ -286,11 +287,11 @@

      Parent traits (1)

      Synonyms (3)

        -
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • +
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • -
      • TO_27_to_30 RELATED_SYNONYM · metpo.owl
        • +
      • TO_27_to_30 RELATED_SYNONYM · metpo.owl
        • -
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
        • +
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
    @@ -306,7 +307,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -555,7 +556,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Pontibacterium sinense (NCBITaxon:2781979; DOI:10.1099/ijsem.0.006018). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Pontibacterium sinense (NCBITaxon:2781979; DOI:10.1099/ijsem.0.006018). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -588,7 +589,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -952,12 +962,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/temperature_optimum_mid3.html b/pages/traits/environment/temperature_optimum_mid3.html index 9cfc3dc2009..3929a440941 100644 --- a/pages/traits/environment/temperature_optimum_mid3.html +++ b/pages/traits/environment/temperature_optimum_mid3.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000445 is a temperature optimum - METPO:1000304 - rdfs:subClassOf + METPO:1000304 + rdfs:subClassOf

    Temperature optimum mid3 is a quantitative bin of the temperature-optimum phenotype.

      @@ -267,11 +268,11 @@

      Parent traits (1)

      Synonyms (3)

        -
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • +
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • -
      • TO_30_to_34 RELATED_SYNONYM · metpo.owl
        • +
      • TO_30_to_34 RELATED_SYNONYM · metpo.owl
        • -
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
        • +
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
    @@ -287,7 +288,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -530,7 +531,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Mucor circinelloides (NCBITaxon:36080; DOI:10.1016/j.heliyon.2024.e30812). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Mucor circinelloides (NCBITaxon:36080; DOI:10.1016/j.heliyon.2024.e30812). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -578,7 +579,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -942,12 +952,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 07:08 UTC diff --git a/pages/traits/environment/temperature_optimum_mid4.html b/pages/traits/environment/temperature_optimum_mid4.html index 930b6e7fa99..548a5060657 100644 --- a/pages/traits/environment/temperature_optimum_mid4.html +++ b/pages/traits/environment/temperature_optimum_mid4.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000446 is a temperature optimum - METPO:1000304 - rdfs:subClassOf + METPO:1000304 + rdfs:subClassOf

    Temperature optimum mid4 is a quantitative bin of the temperature-optimum phenotype.

      @@ -343,11 +344,11 @@

      Parent traits (1)

      Synonyms (3)

        -
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • +
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • -
      • TO_34_to_40 RELATED_SYNONYM · metpo.owl
        • +
      • TO_34_to_40 RELATED_SYNONYM · metpo.owl
        • -
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
        • +
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
    @@ -363,7 +364,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -612,7 +613,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli K-12 (NCBITaxon:83333; DOI:10.1128/AEM.05773-11). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli K-12 (NCBITaxon:83333; DOI:10.1128/AEM.05773-11). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -645,7 +646,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1009,12 +1019,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/temperature_optimum_very_low.html b/pages/traits/environment/temperature_optimum_very_low.html index 6c26e5c9622..b8385eb0cb5 100644 --- a/pages/traits/environment/temperature_optimum_very_low.html +++ b/pages/traits/environment/temperature_optimum_very_low.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000441 is a temperature optimum - METPO:1000304 - rdfs:subClassOf + METPO:1000304 + rdfs:subClassOf

    Temperature optimum very low is a quantitative bin of the temperature-optimum phenotype.

      @@ -425,9 +426,9 @@

      Parent traits (1)

      Synonyms (2)

        -
      • Psychrophile EXACT_SYNONYM · metpo.owl
        • +
      • Psychrophile EXACT_SYNONYM · metpo.owl
        • -
      • TO_<=10 RELATED_SYNONYM · metpo.owl
        • +
      • TO_<=10 RELATED_SYNONYM · metpo.owl
    @@ -443,7 +444,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -692,7 +693,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Clostridium psychrophilum (NCBITaxon:132926; DOI:10.1016/j.bbalip.2013.02.004). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Clostridium psychrophilum (NCBITaxon:132926; DOI:10.1016/j.bbalip.2013.02.004). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -776,7 +777,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -1140,12 +1150,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-08 03:25 UTC diff --git a/pages/traits/environment/temperature_phenotype_with_numerical_limits.html b/pages/traits/environment/temperature_phenotype_with_numerical_limits.html index b422d23964c..564e8004646 100644 --- a/pages/traits/environment/temperature_phenotype_with_numerical_limits.html +++ b/pages/traits/environment/temperature_phenotype_with_numerical_limits.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,11 +116,11 @@

    Edge evidence

  • temperature optimum - METPO:1000304 + METPO:1000304 is a temperature phenotype with numerical limits METPO:1000533 - rdfs:subClassOf + rdfs:subClassOf

    Temperature optimum is a numerical-limit temperature phenotype.

      @@ -134,11 +135,11 @@

      Edge evidence

    • temperature range - METPO:1000306 + METPO:1000306 is a temperature phenotype with numerical limits METPO:1000533 - rdfs:subClassOf + rdfs:subClassOf

      Temperature range is a numerical-limit temperature phenotype.

        @@ -153,11 +154,11 @@

        Edge evidence

      • temperature delta - METPO:1000303 + METPO:1000303 is a temperature phenotype with numerical limits METPO:1000533 - rdfs:subClassOf + rdfs:subClassOf

        Temperature delta is a numerical-limit temperature phenotype.

          @@ -331,7 +332,7 @@

          kg-microbe context

          via direct_metpo.

          512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

          @@ -562,7 +563,7 @@

          Curation history

        • · ADD_CANONICAL_EXAMPLES · codex -

          Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Thermoanaerobacter kivui (NCBITaxon:2325; DOI:10.3389/fmicb.2023.1265216). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

          +

          Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Thermoanaerobacter kivui (NCBITaxon:2325; DOI:10.3389/fmicb.2023.1265216). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

          • @@ -595,7 +596,16 @@

          Identifier

          Term kind
          CLASS
          Status
          -
          REVIEWED
          +
          REVIEWED + + +
          + What this status means +

          Curator has signed off on label / definition / parents.

          +

          Quoted from the schema's status definitions.

          +
          + +
    • @@ -959,12 +969,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/temperature_preference.html b/pages/traits/environment/temperature_preference.html index d9629737b56..187b27972c1 100644 --- a/pages/traits/environment/temperature_preference.html +++ b/pages/traits/environment/temperature_preference.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -385,9 +386,9 @@

    Children (8)

    Synonyms (2)

      -
    • Physiology and metabolism.culture temp.temperature RELATED_SYNONYM · metpo.owl
      • +
    • Physiology and metabolism.culture temp.temperature RELATED_SYNONYM · metpo.owl
      • -
    • range_tmp RELATED_SYNONYM · metpo.owl
      • +
    • range_tmp RELATED_SYNONYM · metpo.owl
    @@ -403,7 +404,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -709,7 +710,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 2 direct source-backed canonical example(s): Clostridium psychrophilum (NCBITaxon:132926; DOI:10.1016/j.bbalip.2013.02.004), Thermoanaerobacter kivui (NCBITaxon:2325; DOI:10.3389/fmicb.2023.1265216). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 2 direct source-backed canonical example(s): Clostridium psychrophilum (NCBITaxon:132926; DOI:10.1016/j.bbalip.2013.02.004), Thermoanaerobacter kivui (NCBITaxon:2325; DOI:10.3389/fmicb.2023.1265216). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -742,7 +743,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1106,12 +1116,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/temperature_range.html b/pages/traits/environment/temperature_range.html index 0c358928c86..d49fc8af8de 100644 --- a/pages/traits/environment/temperature_range.html +++ b/pages/traits/environment/temperature_range.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -398,7 +399,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -481,7 +482,7 @@

    Deep research

    **Target trait:** `METPO:1000306` (**temperature range**; ENVIRONMENT; CLASS; REVIEWED). -The trait should represent the **closed or operationally estimated interval of ambient temperatures supporting net microbial population growth under specified conditions**, conventionally bounded by minimum and maximum cardinal growth temperatures, *T*min and *T*max. In cardinal-temperature models, growth rate is zero below *T*min and above *T*max, while *T*opt is the temperature producing the maximum growth rate; therefore, *T*opt is a related parameter but is not the range itself. Rosso et al. explicitly model growth as zero for *T* < *T*min or *T* > *T*max. [DOI, published February 1995](https://doi.org/10.1128/aem.61.2.610-616.1995) (rosso1995convenientmodelto pages 1-2) +The trait should represent the **closed or operationally estimated interval of ambient temperatures supporting net microbial population growth under specified conditions**, conventionally bounded by minimum and maximum cardinal growth temperatures, *T*min and *T*max. In cardinal-temperature models, growth rate is zero below *T*min and above *T*max, while *T*opt is the temperature producing the maximum growth rate; therefore, *T*opt is a related parameter but is not the range itself. Rosso et al. explicitly model growth as zero for *T* < *T*min or *T* > *T*max. [DOI, published February 1995](https://doi.org/10.1128/aem.61.2.610-616.1995) (rosso1995convenientmodelto pages 1-2) ### Included @@ -492,8 +493,8 @@

    Deep research

    ### Boundary cases and exclusions -1. **Not optimal growth temperature.** A change in *T*opt does not necessarily change range width or either boundary. In *Thermoanaerobacter kivui*, approximately 180 generations at 45°C shifted *T*opt from 66°C to 60°C, but the molecular basis and effects on the complete growth range remained unresolved. [DOI, published October 2023](https://doi.org/10.3389/fmicb.2023.1265216) (lehmann2023adaptivelaboratoryevolution pages 6-7, lehmann2023adaptivelaboratoryevolution pages 7-8) -2. **Not acute thermal survival.** Heat-shock resistance can be mechanistically opposed to growth at high temperature. Loss of `dnaJ` increased acute survival by 1,000–100,000-fold yet prevented sustained growth above 43°C in *Salmonella Typhimurium* and above 41°C in *E. coli*. [DOI, published 13 February 2024](https://doi.org/10.1128/mbio.03105-23) (berdejo2024evolutionarytradeoffbetween pages 8-10, berdejo2024evolutionarytradeoffbetween pages 1-2) +1. **Not optimal growth temperature.** A change in *T*opt does not necessarily change range width or either boundary. In *Thermoanaerobacter kivui*, approximately 180 generations at 45°C shifted *T*opt from 66°C to 60°C, but the molecular basis and effects on the complete growth range remained unresolved. [DOI, published October 2023](https://doi.org/10.3389/fmicb.2023.1265216) (lehmann2023adaptivelaboratoryevolution pages 6-7, lehmann2023adaptivelaboratoryevolution pages 7-8) +2. **Not acute thermal survival.** Heat-shock resistance can be mechanistically opposed to growth at high temperature. Loss of `dnaJ` increased acute survival by 1,000–100,000-fold yet prevented sustained growth above 43°C in *Salmonella Typhimurium* and above 41°C in *E. coli*. [DOI, published 13 February 2024](https://doi.org/10.1128/mbio.03105-23) (berdejo2024evolutionarytradeoffbetween pages 8-10, berdejo2024evolutionarytradeoffbetween pages 1-2) 3. **Not dormancy or persistence.** A persister-like cell surviving heat without division does not establish that the organism grows at that temperature. 4. **Not metabolic activity alone.** Maintenance metabolism, substrate turnover, transcription, or viability without net population increase should be modeled separately. 5. **Not habitat temperature or isolation source.** Recovery from a hot spring, permafrost, or heated process is ecological evidence, not a measured growth range. @@ -503,13 +504,13 @@

    Deep research

    ## 2. Current mechanistic synthesis -Temperature range is an emergent systems phenotype. At the cold boundary, reduced reaction rates, membrane rigidification, impaired transport, stable inhibitory RNA structures, slow transcription/translation, protein folding defects, and possible ice formation jointly constrain growth. At the hot boundary, excess membrane fluidity/permeability, protein unfolding and aggregation, RNA/translation damage, redox imbalance, and loss of bioenergetic coupling become limiting. The authoritative psychrophile review lists “reduced enzyme activity,” “decreased membrane fluidity,” altered nutrient/waste transport, reduced transcription/translation/cell division, protein cold denaturation, inappropriate folding, and intracellular ice as cold-growth barriers. [DOI, published April 2006](https://doi.org/10.1038/sj.embor.7400662) (damico2006psychrophilicmicroorganismschallenges pages 1-2) +Temperature range is an emergent systems phenotype. At the cold boundary, reduced reaction rates, membrane rigidification, impaired transport, stable inhibitory RNA structures, slow transcription/translation, protein folding defects, and possible ice formation jointly constrain growth. At the hot boundary, excess membrane fluidity/permeability, protein unfolding and aggregation, RNA/translation damage, redox imbalance, and loss of bioenergetic coupling become limiting. The authoritative psychrophile review lists “reduced enzyme activity,” “decreased membrane fluidity,” altered nutrient/waste transport, reduced transcription/translation/cell division, protein cold denaturation, inappropriate folding, and intracellular ice as cold-growth barriers. [DOI, published April 2006](https://doi.org/10.1038/sj.embor.7400662) (damico2006psychrophilicmicroorganismschallenges pages 1-2) The strongest current graph architecture is therefore: **ambient temperature → physicochemical damage/constraint → compensatory homeostasis module → retained cellular function → growth near boundary → temperature range.** -Recent research reinforces that no single universal mechanism determines the range. In 2024, a comparison of 2,739 thermal-performance datasets fitted to 83 models found no universal best mathematical model across traits and taxa, supporting explicit assay and taxon annotation rather than a universal curve assumption. [DOI, published October 2024](https://doi.org/10.1038/s41467-024-53046-2) +Recent research reinforces that no single universal mechanism determines the range. In 2024, a comparison of 2,739 thermal-performance datasets fitted to 83 models found no universal best mathematical model across traits and taxa, supporting explicit assay and taxon annotation rather than a universal curve assumption. [DOI, published October 2024](https://doi.org/10.1038/s41467-024-53046-2) ## 3. Candidate nodes grouped by type @@ -641,7 +642,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Lederbergia graminis (NCBITaxon:735518; DOI:10.1099/ijs.0.023820-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Lederbergia graminis (NCBITaxon:735518; DOI:10.1099/ijs.0.023820-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -674,7 +675,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1038,12 +1048,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/temperature_range_high.html b/pages/traits/environment/temperature_range_high.html index af6615efd38..11bea652ee1 100644 --- a/pages/traits/environment/temperature_range_high.html +++ b/pages/traits/environment/temperature_range_high.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,8 +119,8 @@

    Edge evidence

    METPO:1000454 is a temperature range - METPO:1000306 - rdfs:subClassOf + METPO:1000306 + rdfs:subClassOf

    Temperature range high is a quantitative bin of the temperature-range phenotype.

      @@ -311,9 +312,9 @@

      Parent traits (1)

      Synonyms (2)

        -
      • Thermophile EXACT_SYNONYM · metpo.owl
        • +
      • Thermophile EXACT_SYNONYM · metpo.owl
        • -
      • TR_>40 RELATED_SYNONYM · metpo.owl
        • +
      • TR_>40 RELATED_SYNONYM · metpo.owl
    @@ -329,7 +330,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -647,7 +648,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1011,12 +1021,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/temperature_range_low.html b/pages/traits/environment/temperature_range_low.html index 36f11edf8c3..fc760a37b30 100644 --- a/pages/traits/environment/temperature_range_low.html +++ b/pages/traits/environment/temperature_range_low.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000449 is a temperature range - METPO:1000306 - rdfs:subClassOf + METPO:1000306 + rdfs:subClassOf

    Temperature range low is a quantitative bin of the temperature-range phenotype.

      @@ -286,11 +287,11 @@

      Parent traits (1)

      Synonyms (3)

        -
      • Psychrophile EXACT_SYNONYM · metpo.owl
        • +
      • Psychrophile EXACT_SYNONYM · metpo.owl
        • -
      • Psychrotolerant EXACT_SYNONYM · metpo.owl
        • +
      • Psychrotolerant EXACT_SYNONYM · metpo.owl
        • -
      • TR_10_to_22 RELATED_SYNONYM · metpo.owl
        • +
      • TR_10_to_22 RELATED_SYNONYM · metpo.owl
    @@ -306,7 +307,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -537,7 +538,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Aestuariibius violaceus (NCBITaxon:3234132; DOI:10.1099/ijsem.0.006834). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Aestuariibius violaceus (NCBITaxon:3234132; DOI:10.1099/ijsem.0.006834). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -570,7 +571,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -934,12 +944,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/temperature_range_mid1.html b/pages/traits/environment/temperature_range_mid1.html index 50d94137c49..9b4cd558e54 100644 --- a/pages/traits/environment/temperature_range_mid1.html +++ b/pages/traits/environment/temperature_range_mid1.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000450 is a temperature range - METPO:1000306 - rdfs:subClassOf + METPO:1000306 + rdfs:subClassOf

    Temperature range mid1 is a quantitative bin of the temperature-range phenotype.

      @@ -286,11 +287,11 @@

      Parent traits (1)

      Synonyms (3)

        -
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • +
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • -
      • TR_22_to_27 RELATED_SYNONYM · metpo.owl
        • +
      • TR_22_to_27 RELATED_SYNONYM · metpo.owl
        • -
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
        • +
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
    @@ -306,7 +307,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -549,7 +550,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Nakamurella aerolata (NCBITaxon:1656892; DOI:10.1007/s00284-020-02274-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Nakamurella aerolata (NCBITaxon:1656892; DOI:10.1007/s00284-020-02274-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -582,7 +583,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -946,12 +956,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/environment/temperature_range_mid2.html b/pages/traits/environment/temperature_range_mid2.html index 700a3d4922f..fb0905f1bcd 100644 --- a/pages/traits/environment/temperature_range_mid2.html +++ b/pages/traits/environment/temperature_range_mid2.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000451 is a temperature range - METPO:1000306 - rdfs:subClassOf + METPO:1000306 + rdfs:subClassOf

    Temperature range mid2 is a quantitative bin of the temperature-range phenotype.

      @@ -324,11 +325,11 @@

      Parent traits (1)

      Synonyms (3)

        -
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • +
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • -
      • TR_27_to_30 RELATED_SYNONYM · metpo.owl
        • +
      • TR_27_to_30 RELATED_SYNONYM · metpo.owl
        • -
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
        • +
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
    @@ -344,7 +345,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -581,7 +582,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Pseudomonas mangiferae (NCBITaxon:2593654; DOI:10.1099/ijsem.0.003657). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Pseudomonas mangiferae (NCBITaxon:2593654; DOI:10.1099/ijsem.0.003657). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -629,7 +630,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -993,12 +1003,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 07:08 UTC diff --git a/pages/traits/environment/temperature_range_mid3.html b/pages/traits/environment/temperature_range_mid3.html index d7d71732f1c..edc487ff759 100644 --- a/pages/traits/environment/temperature_range_mid3.html +++ b/pages/traits/environment/temperature_range_mid3.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000452 is a temperature range - METPO:1000306 - rdfs:subClassOf + METPO:1000306 + rdfs:subClassOf

    Temperature range mid3 is a quantitative bin of the temperature-range phenotype.

      @@ -324,11 +325,11 @@

      Parent traits (1)

      Synonyms (3)

        -
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • +
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • -
      • TR_30_to_34 RELATED_SYNONYM · metpo.owl
        • +
      • TR_30_to_34 RELATED_SYNONYM · metpo.owl
        • -
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
        • +
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
    @@ -344,7 +345,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -593,7 +594,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Bacillus nakamurai (NCBITaxon:1793963; DOI:10.1099/ijsem.0.001135). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Bacillus nakamurai (NCBITaxon:1793963; DOI:10.1099/ijsem.0.001135). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -695,7 +696,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -1059,12 +1069,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 07:08 UTC diff --git a/pages/traits/environment/temperature_range_mid4.html b/pages/traits/environment/temperature_range_mid4.html index 8a476b443d0..d2f180e7117 100644 --- a/pages/traits/environment/temperature_range_mid4.html +++ b/pages/traits/environment/temperature_range_mid4.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000453 is a temperature range - METPO:1000306 - rdfs:subClassOf + METPO:1000306 + rdfs:subClassOf

    Temperature range mid4 is a quantitative bin of the temperature-range phenotype.

      @@ -343,11 +344,11 @@

      Parent traits (1)

      Synonyms (3)

        -
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • +
      • Mesophilie EXACT_SYNONYM · metpo.owl
        • -
      • TR_34_to_40 RELATED_SYNONYM · metpo.owl
        • +
      • TR_34_to_40 RELATED_SYNONYM · metpo.owl
        • -
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
        • +
      • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl
    @@ -363,7 +364,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -600,7 +601,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -676,7 +677,7 @@

    Recorded curation sessions

  • · codex
    • REVIEW — Repair PR 664 warm-mesophile snippet -

      Addressed adversarial review issue #667 by dropping the weak protein-damage snippet from the protein_unfolding_aggregation to mesophile_growth_impairment edge while preserving its DOI:10.1186/s12864-023-09266-9 reference and review notes; the focused replay tests verify the patched script and curated YAML stay in sync.

    +

    Addressed adversarial review issue #667 by dropping the weak protein-damage snippet from the protein_unfolding_aggregation to mesophile_growth_impairment edge while preserving its DOI:10.1186/s12864-023-09266-9 reference and review notes; the focused replay tests verify the patched script and curated YAML stay in sync.

    • Read this curation session
  • @@ -720,7 +721,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -1084,12 +1094,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 07:08 UTC diff --git a/pages/traits/environment/temperature_range_very_low.html b/pages/traits/environment/temperature_range_very_low.html index 8b32bed4b43..d7918835aab 100644 --- a/pages/traits/environment/temperature_range_very_low.html +++ b/pages/traits/environment/temperature_range_very_low.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000448 is a temperature range - METPO:1000306 - rdfs:subClassOf + METPO:1000306 + rdfs:subClassOf

    Temperature range very low is a quantitative bin of the temperature-range phenotype.

      @@ -400,9 +401,9 @@

      Parent traits (1)

      Synonyms (2)

        -
      • Psychrophile EXACT_SYNONYM · metpo.owl
        • +
      • Psychrophile EXACT_SYNONYM · metpo.owl
        • -
      • TR_<=10 RELATED_SYNONYM · metpo.owl
        • +
      • TR_<=10 RELATED_SYNONYM · metpo.owl
    @@ -418,7 +419,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -649,7 +650,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Psychromonas ingrahamii (NCBITaxon:357794; DOI:10.1099/ijs.0.64068-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Psychromonas ingrahamii (NCBITaxon:357794; DOI:10.1099/ijs.0.64068-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -715,7 +716,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -1079,12 +1089,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-06 17:10 UTC diff --git a/pages/traits/environment/thermophilic.html b/pages/traits/environment/thermophilic.html index e169135a81d..1c424879885 100644 --- a/pages/traits/environment/thermophilic.html +++ b/pages/traits/environment/thermophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -337,7 +338,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -655,7 +656,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1019,12 +1029,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/thermotolerant.html b/pages/traits/environment/thermotolerant.html index 2005fd5e106..7407f553833 100644 --- a/pages/traits/environment/thermotolerant.html +++ b/pages/traits/environment/thermotolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    causes heat-shock response - traitmech:000205 + traitmech:000205 biolink:causes

    Elevated temperature triggers heat-shock chaperone induction.

      @@ -175,7 +176,7 @@

      Edge evidence

      enables heat-shock response - traitmech:000205 + traitmech:000205 RO:0002327

      Induced chaperone/disaggregase gene expression enables the protective heat-shock response.

        @@ -318,7 +319,7 @@

        kg-microbe context

        via direct_metpo.

        512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

        @@ -645,7 +646,16 @@

        Identifier

        Term kind
        CLASS
        Status
        -
        REVIEWED
        +
        REVIEWED + + +
        + What this status means +

        Curator has signed off on label / definition / parents.

        +

        Quoted from the schema's status definitions.

        +
        + +
    @@ -1009,12 +1019,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 04:58 UTC diff --git a/pages/traits/environment/uv_radiation_tolerant.html b/pages/traits/environment/uv_radiation_tolerant.html index 58d9f1b8448..6178d47cd89 100644 --- a/pages/traits/environment/uv_radiation_tolerant.html +++ b/pages/traits/environment/uv_radiation_tolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    ENVO:21001216 challenges UV radiation tolerant - traitmech:000009 + traitmech:000009 METPO:2007406

    UV exposure is the environmental challenge the trait counters.

      @@ -118,7 +119,7 @@

      Edge evidence

      GO:0006289 confers UV radiation tolerant - traitmech:000009 + traitmech:000009 METPO:2007700

      NER removes UV-induced cyclobutane pyrimidine dimers and 6-4 photoproducts.

        @@ -137,7 +138,7 @@

        Edge evidence

        confers UV radiation tolerant - traitmech:000009 + traitmech:000009 METPO:2007700

        Photolyase-mediated dimer reversal complements excision repair.

          @@ -311,7 +312,7 @@

          Parent traits (1)

          Synonyms (1)

    @@ -327,7 +328,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -618,7 +619,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -982,12 +992,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/environment/xerophilic.html b/pages/traits/environment/xerophilic.html index 86652357305..2aae1b2a51d 100644 --- a/pages/traits/environment/xerophilic.html +++ b/pages/traits/environment/xerophilic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    selects for xerophilic - traitmech:000011 + traitmech:000011 METPO:2007401

    Persistent low-aw habitats favor organisms with active xerophilic growth.

      @@ -115,7 +116,7 @@

      Edge evidence

    • xerophilic - traitmech:000011 + traitmech:000011 enables response to osmotic stress GO:0006970 @@ -273,7 +274,7 @@

      Parent traits (1)

      Synonyms (1)

    @@ -289,7 +290,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -559,7 +560,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -923,12 +933,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 10:32 UTC diff --git a/pages/traits/environment/zinc_tolerant.html b/pages/traits/environment/zinc_tolerant.html index 6bc5d4fbf83..4296f531529 100644 --- a/pages/traits/environment/zinc_tolerant.html +++ b/pages/traits/environment/zinc_tolerant.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -105,7 +106,7 @@

    Edge evidence

    CHEBI:29105 challenges zinc tolerant - traitmech:000014 + traitmech:000014 METPO:2007406

    Cytoplasmic zinc excess is the challenge the trait counters.

      @@ -181,7 +182,7 @@

      Edge evidence

      promotes zinc tolerant - traitmech:000014 + traitmech:000014 RO:0002213

      ZntA-mediated efflux is causal for zinc resistance.

        @@ -351,8 +352,8 @@

        Protein and taxon examples

    		 - Cupriavidus metallidurans CH34 -
    NCBITaxon:266264 + Cupriavidus metallidurans CH34 +
    NCBITaxon:266264         		UNREVIEWED
    @@ -425,7 +426,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -683,7 +684,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added PMID:12829273 (Nies 2003) with verified verbatim snippet to record-level evidence to match definition_source (Stage 5 remediation of F-DEF-SRC-ZINC-004 in group G-STAGE4-RECORD-LEVEL-DEFINITION-SOURCE, issue #1981).

    +

    Added PMID:12829273 (Nies 2003) with verified verbatim snippet to record-level evidence to match definition_source (Stage 5 remediation of F-DEF-SRC-ZINC-004 in group G-STAGE4-RECORD-LEVEL-DEFINITION-SOURCE, issue #1981).

    • @@ -716,7 +717,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1080,12 +1090,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 05:20 UTC diff --git a/pages/traits/genomics/abi2_system.html b/pages/traits/genomics/abi2_system.html index 3f17741e53d..8c8ac06c9a7 100644 --- a/pages/traits/genomics/abi2_system.html +++ b/pages/traits/genomics/abi2_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -172,7 +173,7 @@

    Edge evidence

    confers Abi2 system - traitmech:000338 + traitmech:000338 METPO:2007700

    Restriction of phage propagation realizes the Abi2 abortive-infection system possession trait.

    @@ -283,7 +284,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -442,7 +443,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -806,12 +816,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 14:56 UTC diff --git a/pages/traits/genomics/abia_system.html b/pages/traits/genomics/abia_system.html index b5a5b58f7b4..174a913f1f8 100644 --- a/pages/traits/genomics/abia_system.html +++ b/pages/traits/genomics/abia_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -221,7 +222,7 @@

    Edge evidence

    confers AbiA system - traitmech:000344 + traitmech:000344 METPO:2007700

    AbiA-mediated reduction of lactococcal phage propagation realizes the AbiA system trait.

    @@ -328,7 +329,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -571,7 +572,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -935,12 +945,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 20:46 UTC diff --git a/pages/traits/genomics/abialpha_system.html b/pages/traits/genomics/abialpha_system.html index 322055db610..4cfdd693a51 100644 --- a/pages/traits/genomics/abialpha_system.html +++ b/pages/traits/genomics/abialpha_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -210,7 +211,7 @@

    Edge evidence

    contributes to AbiAlpha system - traitmech:000322 + traitmech:000322 RO:0002326

    Perturbation of Idefix lytic-cycle progression contributes to the AbiAlpha system trait.

    @@ -330,7 +331,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -494,7 +495,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add AbiAlpha system trait -

      Added traitmech:000322 AbiAlpha system as a DOI-backed GENOMICS TraitRecord under abortive infection system. DOI:10.3390/v11010048 and PMID:30634666 identify the Enterococcus faecalis V583 prophage 6 AbiAlpha determinant, connect ef2833 with the abortive mechanism, map the system to DUF4393/PF14337, and link AbiAlpha to perturbed Idefix lytic-cycle timing plus premature infected-cell lysis. Pinned DefenseFinder article and HMM registries map AbiAlpha to the AbiAlpha__AbiAlpha model namespace. Reserved METPO:1027600 in proposals/metpo_traitmech_v199 for the upstream replacement ID.

    +

    Added traitmech:000322 AbiAlpha system as a DOI-backed GENOMICS TraitRecord under abortive infection system. DOI:10.3390/v11010048 and PMID:30634666 identify the Enterococcus faecalis V583 prophage 6 AbiAlpha determinant, connect ef2833 with the abortive mechanism, map the system to DUF4393/PF14337, and link AbiAlpha to perturbed Idefix lytic-cycle timing plus premature infected-cell lysis. Pinned DefenseFinder article and HMM registries map AbiAlpha to the AbiAlpha__AbiAlpha model namespace. Reserved METPO:1027600 in proposals/metpo_traitmech_v199 for the upstream replacement ID.

    • Read this curation session
  • @@ -538,7 +539,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -902,12 +912,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 00:55 UTC diff --git a/pages/traits/genomics/abib_system.html b/pages/traits/genomics/abib_system.html index efcf3ad6724..1f789d57349 100644 --- a/pages/traits/genomics/abib_system.html +++ b/pages/traits/genomics/abib_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -204,7 +205,7 @@

    Edge evidence

    confers AbiB system - traitmech:000319 + traitmech:000319 METPO:2007700

    Arrest of sensitive lactococcal phage development realizes the AbiB abortive-infection trait.

      @@ -226,11 +227,11 @@

      Edge evidence

    • AbiB system - traitmech:000319 + traitmech:000319 is a abortive infection system - traitmech:000214 - rdfs:subClassOf + traitmech:000214 + rdfs:subClassOf

      AbiB system possession is an abortive-infection-system trait.

    @@ -305,7 +306,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -457,7 +458,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add AbiB system trait -

      Added traitmech:000319 AbiB system as a DOI-backed GENOMICS TraitRecord under abortive infection system. PMID:8825768 identifies AbiB as an abortive-infection determinant in Lactococcus lactis strain IL1403, reports that it prevents growth of sensitive bIL170 phage, and links AbiB activity to rapid degradation of sensitive phage transcripts and likely arrest of sensitive phage development. Pinned DefenseFinder article, rules, and HMM registries map AbiB to the AbiB__AbiB one-profile model namespace. Reserved METPO:1027300 in proposals/metpo_traitmech_v196 for the upstream replacement ID.

    +

    Added traitmech:000319 AbiB system as a DOI-backed GENOMICS TraitRecord under abortive infection system. PMID:8825768 identifies AbiB as an abortive-infection determinant in Lactococcus lactis strain IL1403, reports that it prevents growth of sensitive bIL170 phage, and links AbiB activity to rapid degradation of sensitive phage transcripts and likely arrest of sensitive phage development. Pinned DefenseFinder article, rules, and HMM registries map AbiB to the AbiB__AbiB one-profile model namespace. Reserved METPO:1027300 in proposals/metpo_traitmech_v196 for the upstream replacement ID.

    • Read this curation session @@ -489,7 +490,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -853,12 +863,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 21:21 UTC diff --git a/pages/traits/genomics/abic_system.html b/pages/traits/genomics/abic_system.html index 7823b3bba51..a65a8eba4f2 100644 --- a/pages/traits/genomics/abic_system.html +++ b/pages/traits/genomics/abic_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -222,7 +223,7 @@

    Edge evidence

    confers AbiC system - traitmech:000320 + traitmech:000320 METPO:2007700

    Reduced p2 phage propagation realizes the AbiC abortive-infection trait.

    @@ -329,7 +330,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -481,7 +482,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add AbiC system trait -

      Added traitmech:000320 AbiC system as a DOI-backed GENOMICS TraitRecord under abortive infection system. PMID:1429469 subclones the pTN20 Prf determinant from Lactococcus lactis subsp. lactis ME2, names the abiC structural gene, shows abiC expression confers Prf-positive activity, and links Prf to reduced p2 plaquing, plaque size, burst size, and infected-cell death. Pinned DefenseFinder article, rules, and HMM registries map AbiC to the AbiC__AbiC one-profile model namespace. Reserved METPO:1027400 in proposals/metpo_traitmech_v197 for the upstream replacement ID.

    +

    Added traitmech:000320 AbiC system as a DOI-backed GENOMICS TraitRecord under abortive infection system. PMID:1429469 subclones the pTN20 Prf determinant from Lactococcus lactis subsp. lactis ME2, names the abiC structural gene, shows abiC expression confers Prf-positive activity, and links Prf to reduced p2 plaquing, plaque size, burst size, and infected-cell death. Pinned DefenseFinder article, rules, and HMM registries map AbiC to the AbiC__AbiC one-profile model namespace. Reserved METPO:1027400 in proposals/metpo_traitmech_v197 for the upstream replacement ID.

    • Read this curation session @@ -513,7 +514,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -877,12 +887,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 22:01 UTC diff --git a/pages/traits/genomics/abid_system.html b/pages/traits/genomics/abid_system.html index 2f6c83243b3..7096e9bdfc4 100644 --- a/pages/traits/genomics/abid_system.html +++ b/pages/traits/genomics/abid_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -185,7 +186,7 @@

    Edge evidence

    confers AbiD system - traitmech:000318 + traitmech:000318 METPO:2007700

    Restriction of lactococcal phage propagation realizes the AbiD abortive-infection trait.

    @@ -286,7 +287,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -438,7 +439,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add AbiD system trait -

      Added traitmech:000318 AbiD system as a DOI-backed GENOMICS TraitRecord under abortive infection system. PMID:7646042 identifies the pBF61 determinant from Lactococcus lactis subsp. lactis KR5, reports an abortive phage infection phenotype with reduced sk1 and c2 plating or plaque size and reduced c2 burst size, and verifies that abiD is required for the Abi+ phenotype. Pinned DefenseFinder article, rules, and HMM registries map AbiD to the AbiD__AbiD one-profile model namespace. Reserved METPO:1027200 in proposals/metpo_traitmech_v195 for the upstream replacement ID.

    +

    Added traitmech:000318 AbiD system as a DOI-backed GENOMICS TraitRecord under abortive infection system. PMID:7646042 identifies the pBF61 determinant from Lactococcus lactis subsp. lactis KR5, reports an abortive phage infection phenotype with reduced sk1 and c2 plating or plaque size and reduced c2 burst size, and verifies that abiD is required for the Abi+ phenotype. Pinned DefenseFinder article, rules, and HMM registries map AbiD to the AbiD__AbiD one-profile model namespace. Reserved METPO:1027200 in proposals/metpo_traitmech_v195 for the upstream replacement ID.

    • Read this curation session @@ -470,7 +471,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -834,12 +844,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 20:30 UTC diff --git a/pages/traits/genomics/abie_system.html b/pages/traits/genomics/abie_system.html index f47f3c6d19d..cd1ec5a87c2 100644 --- a/pages/traits/genomics/abie_system.html +++ b/pages/traits/genomics/abie_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -180,7 +181,7 @@

    Edge evidence

    confers AbiE system - traitmech:000227 + traitmech:000227 METPO:2007700

    Restriction of phage propagation realizes the AbiE abortive-infection defense trait.

      @@ -196,11 +197,11 @@

      Edge evidence

    • AbiE system - traitmech:000227 + traitmech:000227 is a abortive infection system - traitmech:000214 - rdfs:subClassOf + traitmech:000214 + rdfs:subClassOf

      AbiE system possession is an abortive-infection-system trait.

        @@ -266,7 +267,7 @@

        kg-microbe context

        via parent_proxy.

          -
        • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
          • +
        • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

        512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

        @@ -413,7 +414,16 @@

        Identifier

        Term kind
        CLASS
        Status
        -
        PROPOSED
        +
        PROPOSED + + +
        + What this status means +

        Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

        +

        Quoted from the schema's status definitions.

        +
        + +
    @@ -777,12 +787,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 19:46 UTC diff --git a/pages/traits/genomics/abif_system.html b/pages/traits/genomics/abif_system.html index fab0c5f7989..8d56d2584be 100644 --- a/pages/traits/genomics/abif_system.html +++ b/pages/traits/genomics/abif_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -167,7 +168,7 @@

    Edge evidence

    confers AbiF system - traitmech:000504 + traitmech:000504 METPO:2007700

    Restricted phage propagation realizes the AbiF abortive-infection system possession trait.

      @@ -189,11 +190,11 @@

      Edge evidence

    • AbiF system - traitmech:000504 + traitmech:000504 is a abortive infection system - traitmech:000214 - rdfs:subClassOf + traitmech:000214 + rdfs:subClassOf

      AbiF system possession is an abortive-infection-system trait.

        @@ -265,7 +266,7 @@

        kg-microbe context

        via parent_proxy.

          -
        • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
          • +
        • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

        512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

        @@ -481,7 +482,16 @@

        Identifier

        Term kind
        CLASS
        Status
        -
        PROPOSED
        +
        PROPOSED + + +
        + What this status means +

        Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

        +

        Quoted from the schema's status definitions.

        +
        + +
    @@ -845,12 +855,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 03:14 UTC diff --git a/pages/traits/genomics/abig_system.html b/pages/traits/genomics/abig_system.html index d8cf794cde0..4e5e9b26f54 100644 --- a/pages/traits/genomics/abig_system.html +++ b/pages/traits/genomics/abig_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -234,7 +235,7 @@

    Edge evidence

    confers AbiG system - traitmech:000306 + traitmech:000306 METPO:2007700

    Restriction of lactococcal phage propagation realizes the AbiG abortive-infection trait.

      @@ -256,11 +257,11 @@

      Edge evidence

    • AbiG system - traitmech:000306 + traitmech:000306 is a abortive infection system - traitmech:000214 - rdfs:subClassOf + traitmech:000214 + rdfs:subClassOf

      AbiG system possession is an abortive-infection-system trait.

        @@ -319,7 +320,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -335,7 +336,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -543,7 +544,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -907,12 +917,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 10:19 UTC diff --git a/pages/traits/genomics/abih_system.html b/pages/traits/genomics/abih_system.html index e07c7f8eedc..38f3096fb71 100644 --- a/pages/traits/genomics/abih_system.html +++ b/pages/traits/genomics/abih_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -198,7 +199,7 @@

    Edge evidence

    confers AbiH system - traitmech:000304 + traitmech:000304 METPO:2007700

    Restriction of lactococcal phage propagation realizes the AbiH abortive-infection trait.

    @@ -299,7 +300,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -483,7 +484,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -847,12 +857,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 08:14 UTC diff --git a/pages/traits/genomics/abii_system.html b/pages/traits/genomics/abii_system.html index f4309191eb3..5cb409c58cc 100644 --- a/pages/traits/genomics/abii_system.html +++ b/pages/traits/genomics/abii_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -209,7 +210,7 @@

    Edge evidence

    confers AbiI system - traitmech:000316 + traitmech:000316 METPO:2007700

    Restriction of lactococcal phage propagation realizes the AbiI abortive-infection trait.

    @@ -310,7 +311,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -474,7 +475,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add AbiI system trait -

      Added traitmech:000316 AbiI system as a DOI-backed GENOMICS TraitRecord under abortive infection system. PMID:9195753 identifies the Lactococcus lactis M138 pND852 phage-resistance locus, localizes its abortive-infection phenotype to a 2.6 kb pND817 fragment, and shows that the single abiI open reading frame is required for phage resistance. Pinned DefenseFinder article, rules, and HMM registries map AbiI to the AbiI__AbiI one-profile model namespace. Reserved METPO:1027000 in proposals/metpo_traitmech_v193 for the upstream replacement ID.

    +

    Added traitmech:000316 AbiI system as a DOI-backed GENOMICS TraitRecord under abortive infection system. PMID:9195753 identifies the Lactococcus lactis M138 pND852 phage-resistance locus, localizes its abortive-infection phenotype to a 2.6 kb pND817 fragment, and shows that the single abiI open reading frame is required for phage resistance. Pinned DefenseFinder article, rules, and HMM registries map AbiI to the AbiI__AbiI one-profile model namespace. Reserved METPO:1027000 in proposals/metpo_traitmech_v193 for the upstream replacement ID.

    • Read this curation session @@ -506,7 +507,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -870,12 +880,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 18:33 UTC diff --git a/pages/traits/genomics/abij_system.html b/pages/traits/genomics/abij_system.html index 1733ee34bea..9e84b8837af 100644 --- a/pages/traits/genomics/abij_system.html +++ b/pages/traits/genomics/abij_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (9)

    DOI:10.1111/j.1574-6968.1997.tb10185.x
    A novel plasmid-encoded phage abortive infection system from Lactococcus lactis biovar. diacetylactis
    -

    Europe PMC metadata verifies the Deng et al. 1997 AbiJ primary paper title and PMID:8997719; the DOI landing page was Cloudflare-blocked and Europe PMC exposed no abstract or full text, so this record cites Deng et al. for the primary AbiJ identity and uses later accessible sources for snippet-backed system details.

    +

    Europe PMC metadata verifies the Deng et al. 1997 AbiJ primary paper title and PMID:8997719; the DOI landing page was Cloudflare-blocked and Europe PMC exposed no abstract or full text, so this record cites Deng et al. for the primary AbiJ identity and uses later accessible sources for snippet-backed system details.

  • @@ -172,7 +173,7 @@

    Edge evidence

    confers AbiJ system - traitmech:000339 + traitmech:000339 METPO:2007700

    Restriction of phage propagation realizes the AbiJ abortive-infection system possession trait.

    • @@ -283,7 +284,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -467,7 +468,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -831,12 +841,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 16:48 UTC diff --git a/pages/traits/genomics/abik_system.html b/pages/traits/genomics/abik_system.html index 20bbd4a321f..ea91826254d 100644 --- a/pages/traits/genomics/abik_system.html +++ b/pages/traits/genomics/abik_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -211,7 +212,7 @@

    Edge evidence

    confers AbiK system - traitmech:000229 + traitmech:000229 METPO:2007700

    Restriction of 936/P335 phage propagation realizes the AbiK abortive-infection defense trait.

      @@ -227,11 +228,11 @@

      Edge evidence

    • AbiK system - traitmech:000229 + traitmech:000229 is a abortive infection system - traitmech:000214 - rdfs:subClassOf + traitmech:000214 + rdfs:subClassOf

      AbiK system possession is an abortive-infection-system trait.

        @@ -297,7 +298,7 @@

        kg-microbe context

        via parent_proxy.

          -
        • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
          • +
        • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

        512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

        @@ -444,7 +445,16 @@

        Identifier

        Term kind
        CLASS
        Status
        -
        PROPOSED
        +
        PROPOSED + + +
        + What this status means +

        Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

        +

        Quoted from the schema's status definitions.

        +
        + +
    @@ -808,12 +818,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 21:30 UTC diff --git a/pages/traits/genomics/abil_system.html b/pages/traits/genomics/abil_system.html index bcbc7da599d..19b3c727119 100644 --- a/pages/traits/genomics/abil_system.html +++ b/pages/traits/genomics/abil_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -166,7 +167,7 @@

    Edge evidence

    confers AbiL system - traitmech:000340 + traitmech:000340 METPO:2007700

    Restriction of phage propagation realizes the AbiL abortive-infection system possession trait.

    @@ -277,7 +278,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -469,7 +470,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -833,12 +843,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 17:20 UTC diff --git a/pages/traits/genomics/abin_system.html b/pages/traits/genomics/abin_system.html index d1a98465d98..013b03bb854 100644 --- a/pages/traits/genomics/abin_system.html +++ b/pages/traits/genomics/abin_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers AbiN system - traitmech:000341 + traitmech:000341 METPO:2007700

    Restriction of phage propagation realizes the AbiN abortive-infection system possession trait.

    @@ -263,7 +264,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -455,7 +456,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -819,12 +829,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 17:59 UTC diff --git a/pages/traits/genomics/abio_system.html b/pages/traits/genomics/abio_system.html index 6a5491b8aee..0c2c17514d8 100644 --- a/pages/traits/genomics/abio_system.html +++ b/pages/traits/genomics/abio_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers AbiO system - traitmech:000342 + traitmech:000342 METPO:2007700

    Restriction of phage propagation realizes the AbiO abortive-infection system possession trait.

    @@ -269,7 +270,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -468,7 +469,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -832,12 +842,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 18:34 UTC diff --git a/pages/traits/genomics/abip2_system.html b/pages/traits/genomics/abip2_system.html index 3a7aade256f..98e1efe5480 100644 --- a/pages/traits/genomics/abip2_system.html +++ b/pages/traits/genomics/abip2_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers AbiP2 system - traitmech:000343 + traitmech:000343 METPO:2007700

    Restriction of phage propagation realizes the AbiP2 abortive-infection system possession trait.

    @@ -263,7 +264,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -523,7 +524,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -887,12 +897,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 19:57 UTC diff --git a/pages/traits/genomics/abiq_system.html b/pages/traits/genomics/abiq_system.html index 31db48d99ef..6e7fe59d5bc 100644 --- a/pages/traits/genomics/abiq_system.html +++ b/pages/traits/genomics/abiq_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -180,7 +181,7 @@

    Edge evidence

    confers AbiQ system - traitmech:000225 + traitmech:000225 METPO:2007700

    Restriction of phage propagation realizes the AbiQ antiphage defense trait.

      @@ -196,11 +197,11 @@

      Edge evidence

    • AbiQ system - traitmech:000225 + traitmech:000225 is a abortive infection system - traitmech:000214 - rdfs:subClassOf + traitmech:000214 + rdfs:subClassOf

      AbiQ system possession is an abortive-infection-system trait.

        @@ -266,7 +267,7 @@

        kg-microbe context

        via parent_proxy.

          -
        • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
          • +
        • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

        512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

        @@ -413,7 +414,16 @@

        Identifier

        Term kind
        CLASS
        Status
        -
        PROPOSED
        +
        PROPOSED + + +
        + What this status means +

        Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

        +

        Quoted from the schema's status definitions.

        +
        + +
    @@ -777,12 +787,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 18:45 UTC diff --git a/pages/traits/genomics/abir_system.html b/pages/traits/genomics/abir_system.html index 5fd241e2f0d..7fde0a206c3 100644 --- a/pages/traits/genomics/abir_system.html +++ b/pages/traits/genomics/abir_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -228,7 +229,7 @@

    Edge evidence

    confers AbiR system - traitmech:000317 + traitmech:000317 METPO:2007700

    Restriction of lactococcal phage propagation realizes the AbiR abortive-infection trait.

      @@ -250,11 +251,11 @@

      Edge evidence

    • AbiR system - traitmech:000317 + traitmech:000317 is a abortive infection system - traitmech:000214 - rdfs:subClassOf + traitmech:000214 + rdfs:subClassOf

      AbiR system possession is an abortive-infection-system trait.

        @@ -313,7 +314,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -329,7 +330,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -499,7 +500,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add AbiR system trait -

      Added traitmech:000317 AbiR system as a DOI-backed GENOMICS TraitRecord under abortive infection system. PMID:10831451 identifies pKR223 from Lactococcus lactis subsp. lactis KR2 as encoding AbiR, demonstrates that AbiR is encoded by two separated genetic loci, and reports heat-sensitive early abortive-infection activity that impedes phage DNA replication. Pinned DefenseFinder article, rules, and HMM registries map AbiR to the AbiR__AbiRa, AbiR__AbiRb, and AbiR__AbiRc three-profile model namespace. Reserved METPO:1027100 in proposals/metpo_traitmech_v194 for the upstream replacement ID.

    +

    Added traitmech:000317 AbiR system as a DOI-backed GENOMICS TraitRecord under abortive infection system. PMID:10831451 identifies pKR223 from Lactococcus lactis subsp. lactis KR2 as encoding AbiR, demonstrates that AbiR is encoded by two separated genetic loci, and reports heat-sensitive early abortive-infection activity that impedes phage DNA replication. Pinned DefenseFinder article, rules, and HMM registries map AbiR to the AbiR__AbiRa, AbiR__AbiRb, and AbiR__AbiRc three-profile model namespace. Reserved METPO:1027100 in proposals/metpo_traitmech_v194 for the upstream replacement ID.

    • Read this curation session
  • @@ -537,7 +538,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -901,12 +911,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 20:02 UTC diff --git a/pages/traits/genomics/abit_system.html b/pages/traits/genomics/abit_system.html index 436b4b188bf..d6c3a05033c 100644 --- a/pages/traits/genomics/abit_system.html +++ b/pages/traits/genomics/abit_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -198,7 +199,7 @@

    Edge evidence

    confers AbiT system - traitmech:000230 + traitmech:000230 METPO:2007700

    Restriction of 936/P335 phage propagation realizes the AbiT abortive-infection defense trait.

      @@ -214,11 +215,11 @@

      Edge evidence

    • AbiT system - traitmech:000230 + traitmech:000230 is a abortive infection system - traitmech:000214 - rdfs:subClassOf + traitmech:000214 + rdfs:subClassOf

      AbiT system possession is an abortive-infection-system trait.

        @@ -284,7 +285,7 @@

        kg-microbe context

        via parent_proxy.

          -
        • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
          • +
        • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

        512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

        @@ -431,7 +432,16 @@

        Identifier

        Term kind
        CLASS
        Status
        -
        PROPOSED
        +
        PROPOSED + + +
        + What this status means +

        Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

        +

        Quoted from the schema's status definitions.

        +
        + +
    @@ -795,12 +805,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 22:05 UTC diff --git a/pages/traits/genomics/abiu_system.html b/pages/traits/genomics/abiu_system.html index 35d45021532..604524258f0 100644 --- a/pages/traits/genomics/abiu_system.html +++ b/pages/traits/genomics/abiu_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -222,7 +223,7 @@

    Edge evidence

    confers AbiU system - traitmech:000321 + traitmech:000321 METPO:2007700

    Reduced c2/936/P335 lactococcal phage plaquing realizes the AbiU abortive-infection trait.

      @@ -253,7 +254,7 @@

      Edge evidence

      contributes to AbiU system - traitmech:000321 + traitmech:000321 RO:0002326

      Delayed 712/c2 phage transcription contributes to the AbiU abortive-infection trait.

        @@ -269,11 +270,11 @@

        Edge evidence

      • AbiU system - traitmech:000321 + traitmech:000321 is a abortive infection system - traitmech:000214 - rdfs:subClassOf + traitmech:000214 + rdfs:subClassOf

        AbiU system possession is an abortive-infection-system trait.

    @@ -348,7 +349,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -500,7 +501,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add AbiU system trait -

      Added traitmech:000321 AbiU system as a DOI-backed GENOMICS TraitRecord under abortive infection system. DOI:10.1128/AEM.67.11.5225-5232.2001 and PMID:11679349 identify AbiU from Lactococcus lactis LL51-1, report that AbiU confers resistance to c2, 936, and P335 lactococcal phages, name the abiU1 and abiU2 open reading frames, and link AbiU to delayed phage 712 and c2 transcription. Pinned DefenseFinder article, rules, and HMM registries map AbiU to the AbiU__AbiU one-profile model namespace. Reserved METPO:1027500 in proposals/metpo_traitmech_v198 for the upstream replacement ID.

    +

    Added traitmech:000321 AbiU system as a DOI-backed GENOMICS TraitRecord under abortive infection system. DOI:10.1128/AEM.67.11.5225-5232.2001 and PMID:11679349 identify AbiU from Lactococcus lactis LL51-1, report that AbiU confers resistance to c2, 936, and P335 lactococcal phages, name the abiU1 and abiU2 open reading frames, and link AbiU to delayed phage 712 and c2 transcription. Pinned DefenseFinder article, rules, and HMM registries map AbiU to the AbiU__AbiU one-profile model namespace. Reserved METPO:1027500 in proposals/metpo_traitmech_v198 for the upstream replacement ID.

    • Read this curation session @@ -532,7 +533,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -896,12 +906,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 22:50 UTC diff --git a/pages/traits/genomics/abiv_system.html b/pages/traits/genomics/abiv_system.html index c28bed9f516..5b9f43eea82 100644 --- a/pages/traits/genomics/abiv_system.html +++ b/pages/traits/genomics/abiv_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -335,7 +336,7 @@

    Edge evidence

    confers AbiV system - traitmech:000300 + traitmech:000300 METPO:2007700

    Restriction of 936-like or c2-like phage propagation realizes the AbiV abortive-infection defense trait.

      @@ -357,11 +358,11 @@

      Edge evidence

    • AbiV system - traitmech:000300 + traitmech:000300 is a abortive infection system - traitmech:000214 - rdfs:subClassOf + traitmech:000214 + rdfs:subClassOf

      AbiV system possession is an abortive-infection-system trait.

        @@ -427,7 +428,7 @@

        kg-microbe context

        via parent_proxy.

          -
        • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
          • +
        • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

        512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

        @@ -629,7 +630,16 @@

        Identifier

        Term kind
        CLASS
        Status
        -
        PROPOSED
        +
        PROPOSED + + +
        + What this status means +

        Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

        +

        Quoted from the schema's status definitions.

        +
        + +
    @@ -993,12 +1003,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 04:10 UTC diff --git a/pages/traits/genomics/abiz_system.html b/pages/traits/genomics/abiz_system.html index 835bd308201..e2f4d6d4778 100644 --- a/pages/traits/genomics/abiz_system.html +++ b/pages/traits/genomics/abiz_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -186,7 +187,7 @@

    Edge evidence

    confers AbiZ system - traitmech:000228 + traitmech:000228 METPO:2007700

    Restriction of P335 phage propagation realizes the AbiZ abortive-infection defense trait.

      @@ -202,11 +203,11 @@

      Edge evidence

    • AbiZ system - traitmech:000228 + traitmech:000228 is a abortive infection system - traitmech:000214 - rdfs:subClassOf + traitmech:000214 + rdfs:subClassOf

      AbiZ system possession is an abortive-infection-system trait.

        @@ -272,7 +273,7 @@

        kg-microbe context

        via parent_proxy.

          -
        • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
          • +
        • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

        512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

        @@ -431,7 +432,16 @@

        Identifier

        Term kind
        CLASS
        Status
        -
        PROPOSED
        +
        PROPOSED + + +
        + What this status means +

        Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

        +

        Quoted from the schema's status definitions.

        +
        + +
    @@ -795,12 +805,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 21:04 UTC diff --git a/pages/traits/genomics/abortive_infection_system.html b/pages/traits/genomics/abortive_infection_system.html index defe58fdf64..1be8688734c 100644 --- a/pages/traits/genomics/abortive_infection_system.html +++ b/pages/traits/genomics/abortive_infection_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -193,7 +194,7 @@

    Edge evidence

    confers abortive infection system - traitmech:000214 + traitmech:000214 METPO:2007700

    Phage-triggered infected-host arrest or death realizes the abortive-infection defense phenotype.

      @@ -209,11 +210,11 @@

      Edge evidence

    • abortive infection system - traitmech:000214 + traitmech:000214 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Abortive-infection-system possession is a phage-defense-system trait.

        @@ -345,7 +346,7 @@

        Children (33)

        Synonyms (1)

    @@ -361,7 +362,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -654,7 +655,7 @@

    Curation history

  • · ADDRESS_PR_REVIEW · codex -

    Corrected the CmdTAC split-gap source attribution from Goesswein et al. to Vassallo et al. after verifying DOI:10.1038/s41586-024-08102-8 against Crossref and Europe PMC metadata.

    +

    Corrected the CmdTAC split-gap source attribution from Goesswein et al. to Vassallo et al. after verifying DOI:10.1038/s41586-024-08102-8 against Crossref and Europe PMC metadata.

  • @@ -856,7 +857,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Correct CmdTAC source attribution -

      Corrected the abortive-infection split-gap discussion to attribute the CmdTAC source paper to Vassallo et al. after Crossref and Europe PMC metadata confirmed Vassallo, Doering, and Laub as the authors of DOI:10.1038/s41586-024-08102-8.

    +

    Corrected the abortive-infection split-gap discussion to attribute the CmdTAC source paper to Vassallo et al. after Crossref and Europe PMC metadata confirmed Vassallo, Doering, and Laub as the authors of DOI:10.1038/s41586-024-08102-8.

    • Read this curation session
  • @@ -900,7 +901,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -1264,12 +1274,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 03:14 UTC diff --git a/pages/traits/genomics/aditi_system.html b/pages/traits/genomics/aditi_system.html index 5a2a0cc086e..24783122b23 100644 --- a/pages/traits/genomics/aditi_system.html +++ b/pages/traits/genomics/aditi_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers Aditi system - traitmech:000247 + traitmech:000247 METPO:2007700

    Aditi-mediated phage restriction realizes the Aditi system trait.

    @@ -255,7 +256,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -414,7 +415,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -778,12 +788,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 18:47 UTC diff --git a/pages/traits/genomics/ambrosia_system.html b/pages/traits/genomics/ambrosia_system.html index 72fb352ba01..7cd40445483 100644 --- a/pages/traits/genomics/ambrosia_system.html +++ b/pages/traits/genomics/ambrosia_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers Ambrosia system - traitmech:000329 + traitmech:000329 METPO:2007700

    Ambrosia-mediated phage restriction realizes the Ambrosia system trait.

      @@ -170,11 +171,11 @@

      Edge evidence

    • Ambrosia system - traitmech:000329 + traitmech:000329 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Ambrosia system possession is a phage-defense-system trait.

        @@ -239,7 +240,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -255,7 +256,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -414,7 +415,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -778,12 +788,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 06:39 UTC diff --git a/pages/traits/genomics/apsab_system.html b/pages/traits/genomics/apsab_system.html index cac59b41011..590690d1cef 100644 --- a/pages/traits/genomics/apsab_system.html +++ b/pages/traits/genomics/apsab_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers ApsAB system - traitmech:000328 + traitmech:000328 METPO:2007700

    ApsAB-mediated plasmid destabilization realizes the ApsAB system trait.

    @@ -232,7 +233,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -384,7 +385,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add ApsAB system trait -

      Added traitmech:000328 ApsAB system as a DOI-backed GENOMICS TraitRecord under the quality root. DOI:10.1038/s41467-024-48219-y names ApsAB as an anti-plasmid system, shows that the F3141-F3140 locus was renamed apsAB, reports that ApsAB targets high- and low-copy-number plasmids, and supports a nuclease/helicase plus Argonaute-like two-component architecture. The pinned DefenseFinder article registry maps ApsAB to the Zongo et al. Escherichia coli anti-plasmid-system paper. Reserved METPO:1028200 in proposals/metpo_traitmech_v205 for the upstream replacement ID.

    +

    Added traitmech:000328 ApsAB system as a DOI-backed GENOMICS TraitRecord under the quality root. DOI:10.1038/s41467-024-48219-y names ApsAB as an anti-plasmid system, shows that the F3141-F3140 locus was renamed apsAB, reports that ApsAB targets high- and low-copy-number plasmids, and supports a nuclease/helicase plus Argonaute-like two-component architecture. The pinned DefenseFinder article registry maps ApsAB to the Zongo et al. Escherichia coli anti-plasmid-system paper. Reserved METPO:1028200 in proposals/metpo_traitmech_v205 for the upstream replacement ID.

    • Read this curation session @@ -416,7 +417,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -780,12 +790,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 05:47 UTC diff --git a/pages/traits/genomics/aristaios_system.html b/pages/traits/genomics/aristaios_system.html index d1566f8387d..c118211b04d 100644 --- a/pages/traits/genomics/aristaios_system.html +++ b/pages/traits/genomics/aristaios_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Aristaios system - traitmech:000313 + traitmech:000313 METPO:2007700

    Aristaios-mediated phage restriction realizes the Aristaios system trait.

      @@ -158,11 +159,11 @@

      Edge evidence

    • Aristaios system - traitmech:000313 + traitmech:000313 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Aristaios system possession is a phage-defense-system trait.

        @@ -221,7 +222,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -237,7 +238,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -364,7 +365,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Aristaios system phage-defense trait -

      Added traitmech:000313 Aristaios system as a DOI-backed GENOMICS TraitRecord under phage defense system. DOI:10.1093/nar/gkae671 names Aristaios among newly described lactococcal antiphage systems, DOI:10.1128/aem.01120-24 characterizes Aristaios among three plasmid-encoded lactococcal antiphage systems, and the pinned DefenseFinder article registry maps Aristaios to the Grafakou et al. discovery paper. Reserved METPO:1026700 in proposals/metpo_traitmech_v190 for the upstream replacement ID.

    +

    Added traitmech:000313 Aristaios system as a DOI-backed GENOMICS TraitRecord under phage defense system. DOI:10.1093/nar/gkae671 names Aristaios among newly described lactococcal antiphage systems, DOI:10.1128/aem.01120-24 characterizes Aristaios among three plasmid-encoded lactococcal antiphage systems, and the pinned DefenseFinder article registry maps Aristaios to the Grafakou et al. discovery paper. Reserved METPO:1026700 in proposals/metpo_traitmech_v190 for the upstream replacement ID.

    • Read this curation session @@ -396,7 +397,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -760,12 +770,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 15:58 UTC diff --git a/pages/traits/genomics/armada_system.html b/pages/traits/genomics/armada_system.html index 3c1758ce03c..2644fe3cd6a 100644 --- a/pages/traits/genomics/armada_system.html +++ b/pages/traits/genomics/armada_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers ARMADA system - traitmech:000477 + traitmech:000477 METPO:2007700

    Broad phage protection realizes the ARMADA system possession trait.

    @@ -265,7 +266,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -496,7 +497,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -860,12 +870,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 00:02 UTC diff --git a/pages/traits/genomics/audmula_system.html b/pages/traits/genomics/audmula_system.html index f6af008a6c9..040a94ea27e 100644 --- a/pages/traits/genomics/audmula_system.html +++ b/pages/traits/genomics/audmula_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Audmula system - traitmech:000312 + traitmech:000312 METPO:2007700

    Audmula-mediated phage restriction realizes the Audmula system trait.

      @@ -152,11 +153,11 @@

      Edge evidence

    • Audmula system - traitmech:000312 + traitmech:000312 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Audmula system possession is a phage-defense-system trait.

        @@ -215,7 +216,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -231,7 +232,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -358,7 +359,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Audmula system trait -

      Added traitmech:000312 Audmula system as a DOI-backed GENOMICS TraitRecord under phage defense system. DOI:10.1093/nar/gkae671 names Audmula among newly described lactococcal antiphage systems, DOI:10.1073/pnas.2426508122 treats Audmula as a plasmid-encoded lactococcal phage-resistance system in an escape-mutant screen, and the pinned DefenseFinder article registry maps Audmula to the Grafakou et al. lactococcal plasmidome discovery paper. Reserved METPO:1026600 in proposals/metpo_traitmech_v189 for the upstream replacement ID.

    +

    Added traitmech:000312 Audmula system as a DOI-backed GENOMICS TraitRecord under phage defense system. DOI:10.1093/nar/gkae671 names Audmula among newly described lactococcal antiphage systems, DOI:10.1073/pnas.2426508122 treats Audmula as a plasmid-encoded lactococcal phage-resistance system in an escape-mutant screen, and the pinned DefenseFinder article registry maps Audmula to the Grafakou et al. lactococcal plasmidome discovery paper. Reserved METPO:1026600 in proposals/metpo_traitmech_v189 for the upstream replacement ID.

    • Read this curation session @@ -390,7 +391,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -754,12 +764,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 15:18 UTC diff --git a/pages/traits/genomics/avast_system.html b/pages/traits/genomics/avast_system.html index f9f7b43a0d3..a899ef110e2 100644 --- a/pages/traits/genomics/avast_system.html +++ b/pages/traits/genomics/avast_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -180,7 +181,7 @@

    Edge evidence

    confers AVAST system - traitmech:000239 + traitmech:000239 METPO:2007700

    Activated AVAST effector outputs realize the AVAST phage-defense-system trait.

      @@ -196,11 +197,11 @@

      Edge evidence

    • AVAST system - traitmech:000239 + traitmech:000239 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      AVAST system possession is a phage-defense-system trait.

        @@ -276,9 +277,9 @@

        Children (5)

        Synonyms (2)

          -
        • antiviral ATPase/NTPase of the STAND superfamily system EXACT_SYNONYM · DOI:10.1126/science.aba0372
          • +
        • antiviral ATPase/NTPase of the STAND superfamily system EXACT_SYNONYM · DOI:10.1126/science.aba0372
          • -
        • antiviral STAND system EXACT_SYNONYM · DOI:10.1126/science.aba0372
          • +
        • antiviral STAND system EXACT_SYNONYM · DOI:10.1126/science.aba0372
    @@ -294,7 +295,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -479,7 +480,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -843,12 +853,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 10:48 UTC diff --git a/pages/traits/genomics/avs_i_system.html b/pages/traits/genomics/avs_i_system.html index 5979693dd6b..360e4a9aaa0 100644 --- a/pages/traits/genomics/avs_i_system.html +++ b/pages/traits/genomics/avs_i_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -172,7 +173,7 @@

    Edge evidence

    confers Avs I system - traitmech:000534 + traitmech:000534 METPO:2007700

    The first-pass Avs I system trait is realized by Avs1 target recognition and downstream antiviral activity.

    @@ -297,7 +298,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -509,7 +510,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -873,12 +883,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 04:42 UTC diff --git a/pages/traits/genomics/avs_ii_system.html b/pages/traits/genomics/avs_ii_system.html index 7826f1404be..0f75add34db 100644 --- a/pages/traits/genomics/avs_ii_system.html +++ b/pages/traits/genomics/avs_ii_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers Avs II system - traitmech:000535 + traitmech:000535 METPO:2007700

    The first-pass Avs II system trait is realized by Avs2 target recognition and downstream antiviral activity.

    @@ -269,7 +270,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -467,7 +468,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -831,12 +841,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 05:02 UTC diff --git a/pages/traits/genomics/avs_iii_system.html b/pages/traits/genomics/avs_iii_system.html index 0a5d88437ac..119676362d2 100644 --- a/pages/traits/genomics/avs_iii_system.html +++ b/pages/traits/genomics/avs_iii_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers Avs III system - traitmech:000536 + traitmech:000536 METPO:2007700

    The first-pass Avs III system trait is realized by Avs3 target recognition and downstream antiviral activity.

    @@ -283,7 +284,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -488,7 +489,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -852,12 +862,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 05:46 UTC diff --git a/pages/traits/genomics/avs_iv_system.html b/pages/traits/genomics/avs_iv_system.html index 7afc72b5bea..91eac223585 100644 --- a/pages/traits/genomics/avs_iv_system.html +++ b/pages/traits/genomics/avs_iv_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers Avs IV system - traitmech:000537 + traitmech:000537 METPO:2007700

    The first-pass Avs IV system trait is realized by Avs4 target recognition and downstream antiviral activity.

    @@ -269,7 +270,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -467,7 +468,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -831,12 +841,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 06:36 UTC diff --git a/pages/traits/genomics/avs_v_system.html b/pages/traits/genomics/avs_v_system.html index 19b7ec7404d..ecd48e8e0a2 100644 --- a/pages/traits/genomics/avs_v_system.html +++ b/pages/traits/genomics/avs_v_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers Avs V system - traitmech:000538 + traitmech:000538 METPO:2007700

    The first-pass Avs V system trait is realized by Avs5 phage recognition, Sir2-like effector activation, and conserved immunity against jumbo phages.

    @@ -269,7 +270,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -467,7 +468,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -831,12 +841,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 07:21 UTC diff --git a/pages/traits/genomics/azaca_system.html b/pages/traits/genomics/azaca_system.html index b2ebe5d040e..adb9d921918 100644 --- a/pages/traits/genomics/azaca_system.html +++ b/pages/traits/genomics/azaca_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers Azaca system - traitmech:000251 + traitmech:000251 METPO:2007700

    Azaca-mediated phage restriction realizes the Azaca system trait.

    @@ -261,7 +262,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -420,7 +421,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -784,12 +794,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 21:23 UTC diff --git a/pages/traits/genomics/belenos_system.html b/pages/traits/genomics/belenos_system.html index f37f066da8d..bd565c6b0ef 100644 --- a/pages/traits/genomics/belenos_system.html +++ b/pages/traits/genomics/belenos_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Belenos system - traitmech:000268 + traitmech:000268 METPO:2007700

    Belenos-mediated phage restriction realizes the Belenos system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -392,7 +393,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -756,12 +766,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 06:35 UTC diff --git a/pages/traits/genomics/belisama_system.html b/pages/traits/genomics/belisama_system.html index 9d3f3d8b0d2..e0a32cd165c 100644 --- a/pages/traits/genomics/belisama_system.html +++ b/pages/traits/genomics/belisama_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Belisama system - traitmech:000269 + traitmech:000269 METPO:2007700

    Belisama-mediated phage restriction realizes the Belisama system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -392,7 +393,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -756,12 +766,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 07:03 UTC diff --git a/pages/traits/genomics/bil_system.html b/pages/traits/genomics/bil_system.html index c7da4bdb4a5..cd8d546328b 100644 --- a/pages/traits/genomics/bil_system.html +++ b/pages/traits/genomics/bil_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -198,7 +199,7 @@

    Edge evidence

    confers Bil system - traitmech:000369 + traitmech:000369 METPO:2007700

    Bil-mediated impairment of phage infectivity realizes the Bil system trait.

    @@ -301,7 +302,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -478,7 +479,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -842,12 +852,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-25 03:03 UTC diff --git a/pages/traits/genomics/borvo_system.html b/pages/traits/genomics/borvo_system.html index 57c9672f36c..d5404ef217d 100644 --- a/pages/traits/genomics/borvo_system.html +++ b/pages/traits/genomics/borvo_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers Borvo system - traitmech:000249 + traitmech:000249 METPO:2007700

    Borvo-mediated phage restriction realizes the Borvo system trait.

    @@ -255,7 +256,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -414,7 +415,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -778,12 +788,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 20:04 UTC diff --git a/pages/traits/genomics/brc113_system.html b/pages/traits/genomics/brc113_system.html index aa64d1c41ab..c58381e3bf9 100644 --- a/pages/traits/genomics/brc113_system.html +++ b/pages/traits/genomics/brc113_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -156,7 +157,7 @@

    Edge evidence

    confers Brc113 system - traitmech:000522 + traitmech:000522 METPO:2007700

    Brc113-linked phage resistance realizes the Brc113 system possession trait.

      @@ -178,11 +179,11 @@

      Edge evidence

    • Brc113 system - traitmech:000522 + traitmech:000522 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Brc113 system possession is a phage-defense-system trait.

        @@ -252,9 +253,9 @@

        Parent traits (1)

        Synonyms (2)

    @@ -270,7 +271,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -476,7 +477,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Brc113 system -

      Minted traitmech:000522 for the Brc113 phage-defense system with DOI:10.1126/science.ads0915 phage-panel and construct evidence, recorded the absence of exact pinned DefenseFinder article/HMM/rules rows as a knowledge gap, and reserved METPO:1047600 in proposals/metpo_traitmech_v399.

    +

    Minted traitmech:000522 for the Brc113 phage-defense system with DOI:10.1126/science.ads0915 phage-panel and construct evidence, recorded the absence of exact pinned DefenseFinder article/HMM/rules rows as a knowledge gap, and reserved METPO:1047600 in proposals/metpo_traitmech_v399.

    • Read this curation session @@ -508,7 +509,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -872,12 +882,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 18:36 UTC diff --git a/pages/traits/genomics/brc142_system.html b/pages/traits/genomics/brc142_system.html index 10bf1e760c6..7c0828af869 100644 --- a/pages/traits/genomics/brc142_system.html +++ b/pages/traits/genomics/brc142_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -168,7 +169,7 @@

    Edge evidence

    confers Brc142 system - traitmech:000515 + traitmech:000515 METPO:2007700

    Brc142-linked phage resistance realizes the Brc142 system possession trait.

    @@ -277,7 +278,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -499,7 +500,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -863,12 +873,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 12:41 UTC diff --git a/pages/traits/genomics/brc167_system.html b/pages/traits/genomics/brc167_system.html index 672834b2ae6..c1f10c64747 100644 --- a/pages/traits/genomics/brc167_system.html +++ b/pages/traits/genomics/brc167_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers Brc167 system - traitmech:000517 + traitmech:000517 METPO:2007700

    Brc167-linked phage resistance realizes the Brc167 system possession trait.

    @@ -275,7 +276,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -511,7 +512,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -875,12 +885,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 15:19 UTC diff --git a/pages/traits/genomics/brc217_system.html b/pages/traits/genomics/brc217_system.html index cce6e4a987f..d6c4dcb5e81 100644 --- a/pages/traits/genomics/brc217_system.html +++ b/pages/traits/genomics/brc217_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -159,7 +160,7 @@

    Edge evidence

    confers Brc217 system - traitmech:000521 + traitmech:000521 METPO:2007700

    Brc217-linked phage resistance realizes the Brc217 system possession trait.

      @@ -187,11 +188,11 @@

      Edge evidence

    • Brc217 system - traitmech:000521 + traitmech:000521 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Brc217 system possession is a phage-defense-system trait.

        @@ -261,9 +262,9 @@

        Parent traits (1)

        Synonyms (2)

    @@ -279,7 +280,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -482,7 +483,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Brc217 system -

      Minted traitmech:000521 for the Brc217 phage-defense system with DOI:10.1126/science.ads0915 phage-panel and construct evidence, recorded the absence of exact pinned DefenseFinder article/HMM/rules rows as a knowledge gap, and reserved METPO:1047500 in proposals/metpo_traitmech_v398.

    +

    Minted traitmech:000521 for the Brc217 phage-defense system with DOI:10.1126/science.ads0915 phage-panel and construct evidence, recorded the absence of exact pinned DefenseFinder article/HMM/rules rows as a knowledge gap, and reserved METPO:1047500 in proposals/metpo_traitmech_v398.

    • Read this curation session @@ -514,7 +515,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -878,12 +888,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 17:56 UTC diff --git a/pages/traits/genomics/brc22_system.html b/pages/traits/genomics/brc22_system.html index ebb3ad59fbc..ebd7dea80a4 100644 --- a/pages/traits/genomics/brc22_system.html +++ b/pages/traits/genomics/brc22_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -158,7 +159,7 @@

    Edge evidence

    confers Brc22 system - traitmech:000523 + traitmech:000523 METPO:2007700

    Brc22-linked phage resistance realizes the Brc22 system possession trait.

      @@ -180,11 +181,11 @@

      Edge evidence

    • Brc22 system - traitmech:000523 + traitmech:000523 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Brc22 system possession is a phage-defense-system trait.

        @@ -254,9 +255,9 @@

        Parent traits (1)

        Synonyms (2)

    @@ -272,7 +273,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -490,7 +491,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Brc22 system -

      Minted traitmech:000523 for the Brc22 phage-defense system with DOI:10.1126/science.ads0915 BRiC and construct evidence, recorded the absence of exact pinned DefenseFinder article/HMM/rules rows as a knowledge gap, and reserved METPO:1047700 in proposals/metpo_traitmech_v400.

    +

    Minted traitmech:000523 for the Brc22 phage-defense system with DOI:10.1126/science.ads0915 BRiC and construct evidence, recorded the absence of exact pinned DefenseFinder article/HMM/rules rows as a knowledge gap, and reserved METPO:1047700 in proposals/metpo_traitmech_v400.

    • Read this curation session @@ -522,7 +523,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -886,12 +896,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 19:21 UTC diff --git a/pages/traits/genomics/brc233_system.html b/pages/traits/genomics/brc233_system.html index c8fcb32f8cd..5fe487a222e 100644 --- a/pages/traits/genomics/brc233_system.html +++ b/pages/traits/genomics/brc233_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -152,7 +153,7 @@

    Edge evidence

    confers Brc233 system - traitmech:000518 + traitmech:000518 METPO:2007700

    Brc233-linked phage resistance realizes the Brc233 system possession trait.

    @@ -267,7 +268,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -488,7 +489,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -852,12 +862,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 15:36 UTC diff --git a/pages/traits/genomics/brc23_system.html b/pages/traits/genomics/brc23_system.html index e1ee9df7083..be98206f351 100644 --- a/pages/traits/genomics/brc23_system.html +++ b/pages/traits/genomics/brc23_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -152,7 +153,7 @@

    Edge evidence

    confers Brc23 system - traitmech:000524 + traitmech:000524 METPO:2007700

    Brc23-linked phage resistance realizes the Brc23 system possession trait.

      @@ -174,11 +175,11 @@

      Edge evidence

    • Brc23 system - traitmech:000524 + traitmech:000524 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Brc23 system possession is a phage-defense-system trait.

        @@ -248,9 +249,9 @@

        Parent traits (1)

        Synonyms (2)

    @@ -266,7 +267,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -477,7 +478,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Brc23 system -

      Minted traitmech:000524 for the Brc23 phage-defense system with DOI:10.1126/science.ads0915 BRiC and construct evidence, recorded the absence of exact pinned DefenseFinder article/HMM/rules rows as a knowledge gap, and reserved METPO:1047800 in proposals/metpo_traitmech_v401.

    +

    Minted traitmech:000524 for the Brc23 phage-defense system with DOI:10.1126/science.ads0915 BRiC and construct evidence, recorded the absence of exact pinned DefenseFinder article/HMM/rules rows as a knowledge gap, and reserved METPO:1047800 in proposals/metpo_traitmech_v401.

    • Read this curation session @@ -509,7 +510,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -873,12 +883,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 20:08 UTC diff --git a/pages/traits/genomics/brc24_system.html b/pages/traits/genomics/brc24_system.html index 83162f7ff83..b93a101a943 100644 --- a/pages/traits/genomics/brc24_system.html +++ b/pages/traits/genomics/brc24_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -168,7 +169,7 @@

    Edge evidence

    confers Brc24 system - traitmech:000516 + traitmech:000516 METPO:2007700

    Brc24-linked phage resistance realizes the Brc24 system possession trait.

    @@ -277,7 +278,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -499,7 +500,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -863,12 +873,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 13:36 UTC diff --git a/pages/traits/genomics/brc59_system.html b/pages/traits/genomics/brc59_system.html index e6a621a0e33..eae535b1588 100644 --- a/pages/traits/genomics/brc59_system.html +++ b/pages/traits/genomics/brc59_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -159,7 +160,7 @@

    Edge evidence

    confers Brc59 system - traitmech:000525 + traitmech:000525 METPO:2007700

    Brc59-linked phage resistance realizes the Brc59 system possession trait.

      @@ -187,11 +188,11 @@

      Edge evidence

    • Brc59 system - traitmech:000525 + traitmech:000525 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Brc59 system possession is a phage-defense-system trait.

        @@ -261,7 +262,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -277,7 +278,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -489,7 +490,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Brc59 system -

      Minted traitmech:000525 for the Brc59 phage-defense system with DOI:10.1126/science.ads0915 BRiC heatmap and construct evidence, recorded the absence of exact pinned DefenseFinder article/HMM/rules rows as a knowledge gap, and reserved METPO:1047900 in proposals/metpo_traitmech_v402.

    +

    Minted traitmech:000525 for the Brc59 phage-defense system with DOI:10.1126/science.ads0915 BRiC heatmap and construct evidence, recorded the absence of exact pinned DefenseFinder article/HMM/rules rows as a knowledge gap, and reserved METPO:1047900 in proposals/metpo_traitmech_v402.

    • Read this curation session @@ -521,7 +522,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -885,12 +895,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 20:30 UTC diff --git a/pages/traits/genomics/brc76_system.html b/pages/traits/genomics/brc76_system.html index 912ccd60d6e..b0c787baa91 100644 --- a/pages/traits/genomics/brc76_system.html +++ b/pages/traits/genomics/brc76_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -164,7 +165,7 @@

    Edge evidence

    confers Brc76 system - traitmech:000519 + traitmech:000519 METPO:2007700

    Brc76-linked phage resistance realizes the Brc76 system possession trait.

    @@ -290,7 +291,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -492,7 +493,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Brc76 system trait -

      Minted traitmech:000519 for the Brc76 phage-defense system with DOI:10.1126/science.ads0915, the pinned DefenseFinder gcu76 article row, sparse Supplementary Fig. S2 heatmap evidence, Supplementary Fig. S4 attC context, and the pMBA brc76 E. coli IJ1862 and Klebsiella pneumoniae KP5 construct rows; left canonical_examples empty because the public evidence supports heterologous assays but not a directly validated endogenous native isolate.

    +

    Minted traitmech:000519 for the Brc76 phage-defense system with DOI:10.1126/science.ads0915, the pinned DefenseFinder gcu76 article row, sparse Supplementary Fig. S2 heatmap evidence, Supplementary Fig. S4 attC context, and the pMBA brc76 E. coli IJ1862 and Klebsiella pneumoniae KP5 construct rows; left canonical_examples empty because the public evidence supports heterologous assays but not a directly validated endogenous native isolate.

    • Read this curation session @@ -524,7 +525,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -888,12 +898,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 16:20 UTC diff --git a/pages/traits/genomics/brcwgs21_system.html b/pages/traits/genomics/brcwgs21_system.html index eef700a1e8a..06923559790 100644 --- a/pages/traits/genomics/brcwgs21_system.html +++ b/pages/traits/genomics/brcwgs21_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -165,7 +166,7 @@

    Edge evidence

    confers BrcWGS21 system - traitmech:000520 + traitmech:000520 METPO:2007700

    BrcWGS21-linked phage resistance realizes the BrcWGS21 system possession trait.

    @@ -291,7 +292,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -494,7 +495,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Added BrcWGS21 system genomics trait -

      Added traitmech:000520 for BrcWGS21 system with DOI:10.1126/science.ads0915 phage-panel, attC, and construct evidence plus the pinned DefenseFinder gcuWGS21 article row; left canonical_examples empty because the supporting BRiC assays are heterologous rather than direct native isolate exemplars; kept the causal graph at a nonmechanistic integron-cassette level because the pinned DefenseFinder HMM inventory and rules table have no exact WGS21 model rows; reserved METPO:1047400 in proposals/metpo_traitmech_v397.

    +

    Added traitmech:000520 for BrcWGS21 system with DOI:10.1126/science.ads0915 phage-panel, attC, and construct evidence plus the pinned DefenseFinder gcuWGS21 article row; left canonical_examples empty because the supporting BRiC assays are heterologous rather than direct native isolate exemplars; kept the causal graph at a nonmechanistic integron-cassette level because the pinned DefenseFinder HMM inventory and rules table have no exact WGS21 model rows; reserved METPO:1047400 in proposals/metpo_traitmech_v397.

    • Read this curation session @@ -526,7 +527,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -890,12 +900,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 17:12 UTC diff --git a/pages/traits/genomics/brex_system.html b/pages/traits/genomics/brex_system.html index 859e6598e60..a01db757c40 100644 --- a/pages/traits/genomics/brex_system.html +++ b/pages/traits/genomics/brex_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -174,7 +175,7 @@

    Edge evidence

    confers BREX system - traitmech:000210 + traitmech:000210 METPO:2007700

    Methylation-guided self/non-self discrimination realizes the BREX defense trait.

      @@ -209,11 +210,11 @@

      Edge evidence

    • BREX system - traitmech:000210 + traitmech:000210 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      BREX possession is a methylation-based phage-defense system.

        @@ -249,8 +250,8 @@

        Protein and taxon examples

    		 - Lacticaseibacillus casei str. Zhang -
    NCBITaxon:498216 + Lacticaseibacillus casei str. Zhang +
    NCBITaxon:498216         		REVIEWED
    @@ -316,9 +317,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • bacteriophage exclusion EXACT_SYNONYM · DOI:10.15252/embj.201489455
      • +
    • bacteriophage exclusion EXACT_SYNONYM · DOI:10.15252/embj.201489455
      • -
    • bacteriophage exclusion system EXACT_SYNONYM · DOI:10.1128/AEM.01001-19
      • +
    • bacteriophage exclusion system EXACT_SYNONYM · DOI:10.1128/AEM.01001-19
    @@ -334,7 +335,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -519,7 +520,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -883,12 +893,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 08:46 UTC diff --git a/pages/traits/genomics/brig1_system.html b/pages/traits/genomics/brig1_system.html index 0540a5934cb..1a4cbb4570b 100644 --- a/pages/traits/genomics/brig1_system.html +++ b/pages/traits/genomics/brig1_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -185,7 +186,7 @@

    Edge evidence

    confers Brig1 system - traitmech:000307 + traitmech:000307 METPO:2007700

    Restriction of T-even phage propagation realizes the Brig1 system trait.

      @@ -207,11 +208,11 @@

      Edge evidence

    • Brig1 system - traitmech:000307 + traitmech:000307 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Brig1 system possession is a phage-defense-system trait.

        @@ -270,9 +271,9 @@

        Parent traits (1)

        Synonyms (2)

          -
        • Brig1 RELATED_SYNONYM · DOI:10.1038/s41586-024-07329-9
          • +
        • Brig1 RELATED_SYNONYM · DOI:10.1038/s41586-024-07329-9
          • -
        • bacteriophage replication inhibition DNA glycosylase 1 RELATED_SYNONYM · DOI:10.1038/s41586-024-07329-9
          • +
        • bacteriophage replication inhibition DNA glycosylase 1 RELATED_SYNONYM · DOI:10.1038/s41586-024-07329-9
    @@ -288,7 +289,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -472,7 +473,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -836,12 +846,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 11:12 UTC diff --git a/pages/traits/genomics/brigantia_system.html b/pages/traits/genomics/brigantia_system.html index ca238ebf185..e696ac609c0 100644 --- a/pages/traits/genomics/brigantia_system.html +++ b/pages/traits/genomics/brigantia_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Brigantia system - traitmech:000270 + traitmech:000270 METPO:2007700

    Brigantia-mediated phage restriction realizes the Brigantia system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -392,7 +393,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -756,12 +766,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 07:32 UTC diff --git a/pages/traits/genomics/bsta_system.html b/pages/traits/genomics/bsta_system.html index f7502edd767..703fbcecdc1 100644 --- a/pages/traits/genomics/bsta_system.html +++ b/pages/traits/genomics/bsta_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -235,7 +236,7 @@

    Edge evidence

    confers BstA system - traitmech:000301 + traitmech:000301 METPO:2007700

    BstA-mediated suppression of lytic-phage DNA replication realizes BstA-system abortive-infection defense.

    @@ -336,7 +337,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -506,7 +507,7 @@

    Recorded curation sessions

  • · claude-code
    • CREATE — Add BstA system genomics trait -

      Minted traitmech:000301 for BstA system as a DOI-backed GENOMICS abortive-infection-system possession trait after an ignored-and-hidden duplicate review found no live BstA TraitMech record, METPO class, or prior proposal. The record uses Owen et al. DOI:10.1016/j.chom.2021.09.002 for BstA phage-defense, DNA-replication-suppression, and aba self-immunity evidence, carries pinned DefenseFinder registry, HMM inventory, and rule snippets for BstA, updates the abortive-infection parent split-gap discussion, and reserves METPO:1025500 in proposals/metpo_traitmech_v178 for upstream migration.

    +

    Minted traitmech:000301 for BstA system as a DOI-backed GENOMICS abortive-infection-system possession trait after an ignored-and-hidden duplicate review found no live BstA TraitMech record, METPO class, or prior proposal. The record uses Owen et al. DOI:10.1016/j.chom.2021.09.002 for BstA phage-defense, DNA-replication-suppression, and aba self-immunity evidence, carries pinned DefenseFinder registry, HMM inventory, and rule snippets for BstA, updates the abortive-infection parent split-gap discussion, and reserves METPO:1025500 in proposals/metpo_traitmech_v178 for upstream migration.

    • Read this curation session
  • @@ -556,7 +557,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -920,12 +930,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 05:42 UTC diff --git a/pages/traits/genomics/bunzi_system.html b/pages/traits/genomics/bunzi_system.html index 42ea05dfbcb..75116162d80 100644 --- a/pages/traits/genomics/bunzi_system.html +++ b/pages/traits/genomics/bunzi_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers Bunzi system - traitmech:000248 + traitmech:000248 METPO:2007700

    Bunzi-mediated phage restriction realizes the Bunzi system trait.

    @@ -255,7 +256,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -414,7 +415,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -778,12 +788,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 19:27 UTC diff --git a/pages/traits/genomics/butters_gp30_gp31_system.html b/pages/traits/genomics/butters_gp30_gp31_system.html index e2d0dcbee92..471ecb1c92b 100644 --- a/pages/traits/genomics/butters_gp30_gp31_system.html +++ b/pages/traits/genomics/butters_gp30_gp31_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -166,7 +167,7 @@

    Edge evidence

    confers Butters gp30-gp31 system - traitmech:000298 + traitmech:000298 METPO:2007700

    Butters-gp30-gp31-associated restriction of phage propagation realizes the Butters gp30-gp31 system trait.

    @@ -267,7 +268,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -394,7 +395,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Butters gp30-gp31 system genomics trait -

      Minted traitmech:000298 for Butters gp30-gp31 system as a DOI-backed GENOMICS phage-defense-system possession trait after an ignored-and-hidden duplicate review found no live Butters gp30-gp31 TraitMech record, METPO class, or prior proposal. The record uses Mageeney et al. DOI:10.1128/mSystems.00534-20 for central-gene and genes 30/31 defense evidence, carries pinned DefenseFinder registry, HMM inventory, and rule snippets for Butters_gp30_gp31, and reserves METPO:1025200 in proposals/metpo_traitmech_v175 for upstream migration.

    +

    Minted traitmech:000298 for Butters gp30-gp31 system as a DOI-backed GENOMICS phage-defense-system possession trait after an ignored-and-hidden duplicate review found no live Butters gp30-gp31 TraitMech record, METPO class, or prior proposal. The record uses Mageeney et al. DOI:10.1128/mSystems.00534-20 for central-gene and genes 30/31 defense evidence, carries pinned DefenseFinder registry, HMM inventory, and rule snippets for Butters_gp30_gp31, and reserves METPO:1025200 in proposals/metpo_traitmech_v175 for upstream migration.

    • Read this curation session @@ -426,7 +427,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -790,12 +800,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 01:36 UTC diff --git a/pages/traits/genomics/butters_gp57r_system.html b/pages/traits/genomics/butters_gp57r_system.html index 3fd4171dddc..f1d85357b9b 100644 --- a/pages/traits/genomics/butters_gp57r_system.html +++ b/pages/traits/genomics/butters_gp57r_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers Butters gp57r system - traitmech:000299 + traitmech:000299 METPO:2007700

    Butters-gp57r-associated restriction of phage propagation realizes the Butters gp57r system trait.

    @@ -261,7 +262,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -388,7 +389,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Butters gp57r system genomics trait -

      Minted traitmech:000299 for Butters gp57r system as a DOI-backed GENOMICS phage-defense-system possession trait after an ignored-and-hidden duplicate review found no live Butters gp57r TraitMech record, METPO class, or prior proposal. The record uses Mohammed et al. DOI:10.1101/2023.01.03.522681 for Butters gene 57r sufficiency and heterotypic-phage defense evidence, carries pinned DefenseFinder registry, HMM inventory, and rule snippets for Butters_gp57r, and reserves METPO:1025300 in proposals/metpo_traitmech_v176 for upstream migration.

    +

    Minted traitmech:000299 for Butters gp57r system as a DOI-backed GENOMICS phage-defense-system possession trait after an ignored-and-hidden duplicate review found no live Butters gp57r TraitMech record, METPO class, or prior proposal. The record uses Mohammed et al. DOI:10.1101/2023.01.03.522681 for Butters gene 57r sufficiency and heterotypic-phage defense evidence, carries pinned DefenseFinder registry, HMM inventory, and rule snippets for Butters_gp57r, and reserves METPO:1025300 in proposals/metpo_traitmech_v176 for upstream migration.

    • Read this curation session @@ -420,7 +421,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -784,12 +794,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 02:23 UTC diff --git a/pages/traits/genomics/caprel_system.html b/pages/traits/genomics/caprel_system.html index 4e93041f7e0..7dbd13bd872 100644 --- a/pages/traits/genomics/caprel_system.html +++ b/pages/traits/genomics/caprel_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -224,7 +225,7 @@

    Edge evidence

    confers CapRel system - traitmech:000244 + traitmech:000244 METPO:2007700

    CapRel-dependent restriction of phage propagation realizes the CapRel system trait.

      @@ -240,11 +241,11 @@

      Edge evidence

    • CapRel system - traitmech:000244 + traitmech:000244 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      CapRel system possession is a phage-defense-system trait.

        @@ -303,9 +304,9 @@

        Parent traits (1)

        Synonyms (2)

          -
        • CapRel toxin-antitoxin system EXACT_SYNONYM · DOI:10.1038/s41586-022-05444-z
          • +
        • CapRel toxin-antitoxin system EXACT_SYNONYM · DOI:10.1038/s41586-022-05444-z
          • -
        • fused CapRel system EXACT_SYNONYM · DOI:10.1038/s41586-022-05444-z
          • +
        • fused CapRel system EXACT_SYNONYM · DOI:10.1038/s41586-022-05444-z
    @@ -321,7 +322,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -493,7 +494,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -857,12 +867,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 15:43 UTC diff --git a/pages/traits/genomics/card_nlr_endonuclease_system.html b/pages/traits/genomics/card_nlr_endonuclease_system.html index 04db00f77d8..acbce23c316 100644 --- a/pages/traits/genomics/card_nlr_endonuclease_system.html +++ b/pages/traits/genomics/card_nlr_endonuclease_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers CARD-NLR endonuclease system - traitmech:000550 + traitmech:000550 METPO:2007700

    The first-pass CARD-NLR endonuclease system trait is realized by a DefenseFinder CARD_NLR_Endonuclease subtype locus.

    @@ -251,7 +252,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -442,7 +443,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -806,12 +816,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 16:58 UTC diff --git a/pages/traits/genomics/card_nlr_gasdermin_system.html b/pages/traits/genomics/card_nlr_gasdermin_system.html index 586ebeb9352..9da62ccb733 100644 --- a/pages/traits/genomics/card_nlr_gasdermin_system.html +++ b/pages/traits/genomics/card_nlr_gasdermin_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -142,7 +143,7 @@

    Edge evidence

    confers CARD-NLR GasderMIN system - traitmech:000555 + traitmech:000555 METPO:2007700

    The first-pass CARD-NLR GasderMIN system trait is realized by a DefenseFinder CARD_NLR_GasderMIN subtype locus.

    @@ -263,7 +264,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -454,7 +455,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -818,12 +828,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 21:05 UTC diff --git a/pages/traits/genomics/card_nlr_like_system.html b/pages/traits/genomics/card_nlr_like_system.html index 677159e2ed6..6dd159af3f5 100644 --- a/pages/traits/genomics/card_nlr_like_system.html +++ b/pages/traits/genomics/card_nlr_like_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -149,7 +150,7 @@

    Edge evidence

    confers CARD-NLR-like system - traitmech:000559 + traitmech:000559 METPO:2007700

    The first-pass CARD-NLR-like system trait is realized by a DefenseFinder CARD_NLR_like subtype locus.

    @@ -268,7 +269,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -480,7 +481,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -844,12 +854,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 00:04 UTC diff --git a/pages/traits/genomics/card_nlr_phospho_system.html b/pages/traits/genomics/card_nlr_phospho_system.html index 8de178c53c6..04f51e00395 100644 --- a/pages/traits/genomics/card_nlr_phospho_system.html +++ b/pages/traits/genomics/card_nlr_phospho_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers CARD-NLR phospho system - traitmech:000551 + traitmech:000551 METPO:2007700

    The first-pass CARD-NLR phospho system trait is realized by a DefenseFinder CARD_NLR_Phospho subtype locus.

    @@ -251,7 +252,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -442,7 +443,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -806,12 +816,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 17:23 UTC diff --git a/pages/traits/genomics/card_nlr_subtilase_system.html b/pages/traits/genomics/card_nlr_subtilase_system.html index ef0e7831abb..15d0ac2a1f2 100644 --- a/pages/traits/genomics/card_nlr_subtilase_system.html +++ b/pages/traits/genomics/card_nlr_subtilase_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,7 +132,7 @@

    Edge evidence

    confers CARD-NLR subtilase system - traitmech:000553 + traitmech:000553 METPO:2007700

    The first-pass CARD-NLR subtilase system trait is realized by a DefenseFinder CARD_NLR_Subtilase subtype locus.

    @@ -246,7 +247,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -438,7 +439,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -802,12 +812,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 19:23 UTC diff --git a/pages/traits/genomics/card_nlr_system.html b/pages/traits/genomics/card_nlr_system.html index a12e73b21ba..cc5569f40ea 100644 --- a/pages/traits/genomics/card_nlr_system.html +++ b/pages/traits/genomics/card_nlr_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -264,7 +265,7 @@

    Edge evidence

    confers CARD-NLR system - traitmech:000337 + traitmech:000337 METPO:2007700

    CARD-like effector-associated cell death realizes the CARD-NLR phage-defense-system output.

    @@ -392,7 +393,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -537,7 +538,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add CARD-NLR phage-defense trait -

      Minted traitmech:000337 for the DOI- and stable-URL-backed CARD-NLR bacterial phage-defense system under the phage defense system parent, added Wein et al. CARD-like anti-phage defense evidence from DOI:10.1101/2023.05.28.542683 and a stable Europe PMC abstract page, added pinned DefenseFinder registry/profile/rules evidence for CARD_NLR subtypes, and recorded a knowledge gap for CARD-NLR subtype triggers, effectors, and natural-host examples.

    +

    Minted traitmech:000337 for the DOI- and stable-URL-backed CARD-NLR bacterial phage-defense system under the phage defense system parent, added Wein et al. CARD-like anti-phage defense evidence from DOI:10.1101/2023.05.28.542683 and a stable Europe PMC abstract page, added pinned DefenseFinder registry/profile/rules evidence for CARD_NLR subtypes, and recorded a knowledge gap for CARD-NLR subtype triggers, effectors, and natural-host examples.

    • Read this curation session
  • @@ -587,7 +588,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -951,12 +961,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 00:04 UTC diff --git a/pages/traits/genomics/cbass_system.html b/pages/traits/genomics/cbass_system.html index 7292633a0b4..55942cffdec 100644 --- a/pages/traits/genomics/cbass_system.html +++ b/pages/traits/genomics/cbass_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -187,7 +188,7 @@

    Edge evidence

    confers CBASS system - traitmech:000212 + traitmech:000212 METPO:2007700

    CBASS effector-induced abortive cell death realizes CBASS-mediated antiphage defense.

      @@ -203,11 +204,11 @@

      Edge evidence

    • CBASS system - traitmech:000212 + traitmech:000212 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      CBASS possession is a cyclic-oligonucleotide-mediated phage-defense-system trait.

        @@ -266,9 +267,9 @@

        Parent traits (1)

        Synonyms (2)

          -
        • cyclic-oligonucleotide-based anti-phage signalling system EXACT_SYNONYM · DOI:10.1038/s41564-020-0777-y
          • +
        • cyclic-oligonucleotide-based anti-phage signalling system EXACT_SYNONYM · DOI:10.1038/s41564-020-0777-y
          • -
        • cyclic-oligonucleotide-based anti-phage signaling system EXACT_SYNONYM · DOI:10.1038/s41564-020-0777-y
          • +
        • cyclic-oligonucleotide-based anti-phage signaling system EXACT_SYNONYM · DOI:10.1038/s41564-020-0777-y
    @@ -284,7 +285,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -469,7 +470,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -833,12 +843,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 10:20 UTC diff --git a/pages/traits/genomics/ceres_system.html b/pages/traits/genomics/ceres_system.html index 47d588f1140..2698cfb826c 100644 --- a/pages/traits/genomics/ceres_system.html +++ b/pages/traits/genomics/ceres_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers Ceres system - traitmech:000288 + traitmech:000288 METPO:2007700

    Ceres-mediated phage restriction realizes the Ceres system trait.

    @@ -259,7 +260,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -418,7 +419,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -782,12 +792,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 18:24 UTC diff --git a/pages/traits/genomics/cernunnos_system.html b/pages/traits/genomics/cernunnos_system.html index 5aa4fa9c98b..07d3df7aff2 100644 --- a/pages/traits/genomics/cernunnos_system.html +++ b/pages/traits/genomics/cernunnos_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Cernunnos system - traitmech:000271 + traitmech:000271 METPO:2007700

    Cernunnos-mediated phage restriction realizes the Cernunnos system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -392,7 +393,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -756,12 +766,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 08:00 UTC diff --git a/pages/traits/genomics/charlie_gp32_system.html b/pages/traits/genomics/charlie_gp32_system.html index 3bce5e2baed..b26336de215 100644 --- a/pages/traits/genomics/charlie_gp32_system.html +++ b/pages/traits/genomics/charlie_gp32_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -161,7 +162,7 @@

    Edge evidence

    confers Charlie gp32 system - traitmech:000295 + traitmech:000295 METPO:2007700

    Charlie-gp32-mediated Che9c exclusion realizes the Charlie gp32 system trait.

    @@ -264,7 +265,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -435,7 +436,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -799,12 +809,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 23:11 UTC diff --git a/pages/traits/genomics/clover_system.html b/pages/traits/genomics/clover_system.html index ac67a9c3c47..6b38e80a15b 100644 --- a/pages/traits/genomics/clover_system.html +++ b/pages/traits/genomics/clover_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -180,7 +181,7 @@

    Edge evidence

    confers Clover system - traitmech:000415 + traitmech:000415 METPO:2007700

    Regulated CloA effector activity realizes Clover antiviral immunity.

      @@ -202,11 +203,11 @@

      Edge evidence

    • Clover system - traitmech:000415 + traitmech:000415 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Clover system possession is a phage-defense-system trait.

        @@ -271,7 +272,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -287,7 +288,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -485,7 +486,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -849,12 +859,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 19:36 UTC diff --git a/pages/traits/genomics/cmdtac_system.html b/pages/traits/genomics/cmdtac_system.html index a05f87aac2e..b09bc209566 100644 --- a/pages/traits/genomics/cmdtac_system.html +++ b/pages/traits/genomics/cmdtac_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -243,7 +244,7 @@

    Edge evidence

    confers CmdTAC system - traitmech:000335 + traitmech:000335 METPO:2007700

    Translation arrest and viral-replication inhibition realize the CmdTAC system trait.

    @@ -344,7 +345,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -550,13 +551,13 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add CmdTAC abortive-infection trait -

      Minted traitmech:000335 for the DOI-backed CmdTAC system under abortive infection system, added CmdTAC evidence from DOI:10.1038/s41586-024-08102-8 and stable PMC full text, recorded the pinned DefenseFinder article-registry row, and left an open model-coverage knowledge gap because the pinned HMM and rules registries do not yet list CmdTAC.

    +

    Minted traitmech:000335 for the DOI-backed CmdTAC system under abortive infection system, added CmdTAC evidence from DOI:10.1038/s41586-024-08102-8 and stable PMC full text, recorded the pinned DefenseFinder article-registry row, and left an open model-coverage knowledge gap because the pinned HMM and rules registries do not yet list CmdTAC.

    • Read this curation session
  • · codex
    • EDIT — Address CmdTAC review findings -

      Corrected DOI:10.1038/s41586-024-08102-8 source attribution from Goesswein et al. to Vassallo et al., rewrote the definition so mRNA modification is attributed to CmdT rather than the CmdC chaperone, added the proposal-only cmdTAC locus label as a related synonym, and kept the DefenseFinder article-registry row as record-level evidence only.

    +

    Corrected DOI:10.1038/s41586-024-08102-8 source attribution from Goesswein et al. to Vassallo et al., rewrote the definition so mRNA modification is attributed to CmdT rather than the CmdC chaperone, added the proposal-only cmdTAC locus label as a related synonym, and kept the DefenseFinder article-registry row as record-level evidence only.

    • Read this curation session
  • @@ -594,7 +595,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -958,12 +968,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 21:53 UTC diff --git a/pages/traits/genomics/coconut_system.html b/pages/traits/genomics/coconut_system.html index 10c575a786e..37409d5d08a 100644 --- a/pages/traits/genomics/coconut_system.html +++ b/pages/traits/genomics/coconut_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -132,11 +133,11 @@

    Edge evidence

  • CoCoNuT system - traitmech:000422 + traitmech:000422 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

    CoCoNuT system possession is treated as a phage-defense-system trait.

    • @@ -225,7 +226,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -412,7 +413,7 @@

    Recorded curation sessions

  • · claude-code
    • CREATE — Add CoCoNuT system trait -

      Minted traitmech:000422 for the DOI-backed CoCoNuT system under phage defense system. DOI:10.7554/eLife.94800.3 supports CoCoNuTs as a predicted RNA-targeting McrBC Type IV restriction-system branch, and the pinned DefenseFinder article and HMM inventories map CoCoNut to representative CoCoNut-I, CoCoNut-II, and CoCoNut-III custom profiles while the pinned rules table has no CoCoNut row, so the graph stays nonmechanistic at system-family level and the record keeps profile-to-protein boundaries, pseudo-CoCoNuT scope, native host breadth, phage range, and substrate-level mechanism unresolved. Reserved METPO:1037600 in proposals/metpo_traitmech_v299.

    +

    Minted traitmech:000422 for the DOI-backed CoCoNuT system under phage defense system. DOI:10.7554/eLife.94800.3 supports CoCoNuTs as a predicted RNA-targeting McrBC Type IV restriction-system branch, and the pinned DefenseFinder article and HMM inventories map CoCoNut to representative CoCoNut-I, CoCoNut-II, and CoCoNut-III custom profiles while the pinned rules table has no CoCoNut row, so the graph stays nonmechanistic at system-family level and the record keeps profile-to-protein boundaries, pseudo-CoCoNuT scope, native host breadth, phage range, and substrate-level mechanism unresolved. Reserved METPO:1037600 in proposals/metpo_traitmech_v299.

    • Read this curation session @@ -444,7 +445,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -808,12 +818,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 01:08 UTC diff --git a/pages/traits/genomics/codon_usage_bias.html b/pages/traits/genomics/codon_usage_bias.html index 4a274fd34d8..ca3b0714d9b 100644 --- a/pages/traits/genomics/codon_usage_bias.html +++ b/pages/traits/genomics/codon_usage_bias.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • codon usage bias - traitmech:000096 + traitmech:000096 regulates translation GO:0006412 @@ -115,7 +116,7 @@

    Edge evidence

  • codon usage bias - traitmech:000096 + traitmech:000096 associated with gene expression level @@ -137,7 +138,7 @@

    Edge evidence

    strengthens selection for codon usage bias - traitmech:000096 + traitmech:000096

    Selection on synonymous codons scales with protein production; highly expressed genes show stronger codon preferences.

      @@ -162,7 +163,7 @@

      Edge evidence

      influences codon usage bias - traitmech:000096 + traitmech:000096

      Synonymous codons decoded by more abundant tRNAs tend to be more adapted and often preferred.

        @@ -260,7 +261,7 @@

        Parent traits (1)

        Synonyms (1)

          -
        • codon bias RELATED_SYNONYM · DOI:10.1038/nrg2899
          • +
        • codon bias RELATED_SYNONYM · DOI:10.1038/nrg2899
    • @@ -276,7 +277,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -522,7 +523,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -886,12 +896,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/genomics/crispr_cas_system.html b/pages/traits/genomics/crispr_cas_system.html index fd77fd326b3..980d0a31790 100644 --- a/pages/traits/genomics/crispr_cas_system.html +++ b/pages/traits/genomics/crispr_cas_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    InterPro:IPR028629 confers CRISPR-Cas system - traitmech:000094 + traitmech:000094 METPO:2007700

    Cas9 together with CRISPR-derived guide RNAs realizes the type II adaptive immune interference system.

      @@ -115,7 +116,7 @@

      Edge evidence

    • CRISPR-Cas system - traitmech:000094 + traitmech:000094 participates in defense response to virus GO:0051607 @@ -213,7 +214,7 @@

      Edge evidence

      selects for CRISPR-Cas system - traitmech:000094 + traitmech:000094 METPO:2007401

      Selective pressure from invading phages and plasmids favors maintenance of CRISPR-Cas immunity.

        @@ -232,7 +233,7 @@

        Edge evidence

        contributes to CRISPR-Cas system - traitmech:000094 + traitmech:000094 RO:0002326

        crRNA-guided interference by the effector complex realizes the adaptive-defense trait.

          @@ -251,7 +252,7 @@

          Edge evidence

          confers CRISPR-Cas system - traitmech:000094 + traitmech:000094 METPO:2007700

          Cas1-Cas2 spacer acquisition realizes the adaptation branch of CRISPR-Cas immunity.

            @@ -288,8 +289,8 @@

            Protein and taxon examples

    		 - Streptococcus pyogenes serotype M1 -
    NCBITaxon:301447 + Streptococcus pyogenes serotype M1 +
    NCBITaxon:301447         		REVIEWED
    @@ -318,8 +319,8 @@

    Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -348,8 +349,8 @@

    Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -415,7 +416,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -431,7 +432,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -683,7 +684,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Added reviewed E. coli K-12 subunit protein_examples UniProtKB:Q46896 (Cas1/ygbT, v154) and UniProtKB:P45956 (Cas2/ygbF, v145) on cas1_cas2_complex (DOI:10.1038/nsmb.2820), updated scope_notes for component-level subunit scope, and refreshed UniProtKB:Q99ZW2 entry_version 147 -> 148 on cas9_effector.

    +

    Added reviewed E. coli K-12 subunit protein_examples UniProtKB:Q46896 (Cas1/ygbT, v154) and UniProtKB:P45956 (Cas2/ygbF, v145) on cas1_cas2_complex (DOI:10.1038/nsmb.2820), updated scope_notes for component-level subunit scope, and refreshed UniProtKB:Q99ZW2 entry_version 147 -> 148 on cas9_effector.

    • @@ -731,7 +732,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1095,12 +1105,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/genomics/crouga_system.html b/pages/traits/genomics/crouga_system.html index 66a3d3f330b..a130ce8dde6 100644 --- a/pages/traits/genomics/crouga_system.html +++ b/pages/traits/genomics/crouga_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Crouga system - traitmech:000500 + traitmech:000500 METPO:2007700

    Crouga-mediated phage protection realizes the Crouga system trait.

      @@ -152,11 +153,11 @@

      Edge evidence

    • Crouga system - traitmech:000500 + traitmech:000500 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Crouga system possession is a phage-defense-system trait.

        @@ -215,7 +216,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -231,7 +232,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -429,7 +430,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -793,12 +803,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 20:57 UTC diff --git a/pages/traits/genomics/dag_system.html b/pages/traits/genomics/dag_system.html index acad4819544..581aef99535 100644 --- a/pages/traits/genomics/dag_system.html +++ b/pages/traits/genomics/dag_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -142,7 +143,7 @@

    Edge evidence

    confers Dag system - traitmech:000507 + traitmech:000507 METPO:2007700

    Modified-guanine phage targeting realizes the organism-level Dag system possession trait.

    @@ -253,7 +254,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -458,7 +459,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -822,12 +832,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 05:07 UTC diff --git a/pages/traits/genomics/damona_system.html b/pages/traits/genomics/damona_system.html index 865b9f0844b..eedca48b6aa 100644 --- a/pages/traits/genomics/damona_system.html +++ b/pages/traits/genomics/damona_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Damona system - traitmech:000272 + traitmech:000272 METPO:2007700

    Damona-mediated phage restriction realizes the Damona system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -392,7 +393,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -756,12 +766,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 08:24 UTC diff --git a/pages/traits/genomics/darna_system.html b/pages/traits/genomics/darna_system.html index 0aab7e68eaa..7414894d5d4 100644 --- a/pages/traits/genomics/darna_system.html +++ b/pages/traits/genomics/darna_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -168,7 +169,7 @@

    Edge evidence

    confers DARNA system - traitmech:000273 + traitmech:000273 METPO:2007700

    DARNA-mediated phage-propagation inhibition realizes the DARNA system trait.

      @@ -184,11 +185,11 @@

      Edge evidence

    • DARNA system - traitmech:000273 + traitmech:000273 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      DARNA system possession is a phage-defense-system trait.

        @@ -247,7 +248,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -263,7 +264,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -422,7 +423,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -786,12 +796,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 08:56 UTC diff --git a/pages/traits/genomics/dartg_system.html b/pages/traits/genomics/dartg_system.html index 1c26a62ca5c..39b1964d843 100644 --- a/pages/traits/genomics/dartg_system.html +++ b/pages/traits/genomics/dartg_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -211,7 +212,7 @@

    Edge evidence

    confers DarTG system - traitmech:000243 + traitmech:000243 METPO:2007700

    The DarTG system trait is realized by inhibition of phage replication and propagation.

      @@ -227,11 +228,11 @@

      Edge evidence

    • DarTG system - traitmech:000243 + traitmech:000243 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      DarTG system possession is a phage-defense-system trait.

        @@ -290,7 +291,7 @@

        Parent traits (1)

        Synonyms (1)

          -
        • DarTG toxin-antitoxin system EXACT_SYNONYM · DOI:10.1038/s41564-022-01153-5
          • +
        • DarTG toxin-antitoxin system EXACT_SYNONYM · DOI:10.1038/s41564-022-01153-5
    @@ -306,7 +307,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -453,7 +454,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -817,12 +827,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 14:20 UTC diff --git a/pages/traits/genomics/dazbog_system.html b/pages/traits/genomics/dazbog_system.html index a218385bfce..0dabbc56fe8 100644 --- a/pages/traits/genomics/dazbog_system.html +++ b/pages/traits/genomics/dazbog_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -142,7 +143,7 @@

    Edge evidence

    confers Dazbog system - traitmech:000245 + traitmech:000245 METPO:2007700

    Dazbog-mediated phage restriction realizes the Dazbog system trait.

    @@ -243,7 +244,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -403,7 +404,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -767,12 +777,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 16:14 UTC diff --git a/pages/traits/genomics/dctpdeaminase_system.html b/pages/traits/genomics/dctpdeaminase_system.html index 560d1b85a9d..5f59e1357d8 100644 --- a/pages/traits/genomics/dctpdeaminase_system.html +++ b/pages/traits/genomics/dctpdeaminase_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -224,7 +225,7 @@

    Edge evidence

    confers dCTPdeaminase system - traitmech:000274 + traitmech:000274 METPO:2007700

    dCTPdeaminase-mediated arrest of phage replication realizes the dCTPdeaminase system trait.

    @@ -319,7 +320,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -478,7 +479,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -842,12 +852,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 09:26 UTC diff --git a/pages/traits/genomics/ddmde_system.html b/pages/traits/genomics/ddmde_system.html index 2a42cde70a0..e5207eeab31 100644 --- a/pages/traits/genomics/ddmde_system.html +++ b/pages/traits/genomics/ddmde_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -192,7 +193,7 @@

    Edge evidence

    confers DdmDE system - traitmech:000275 + traitmech:000275 METPO:2007700

    DdmDE-mediated clearance of small multicopy plasmids realizes the DdmDE system trait.

    @@ -268,7 +269,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -476,7 +477,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -840,12 +850,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 22:12 UTC diff --git a/pages/traits/genomics/detocs_system.html b/pages/traits/genomics/detocs_system.html index 6d1cb1c2ce5..fd97730f6dc 100644 --- a/pages/traits/genomics/detocs_system.html +++ b/pages/traits/genomics/detocs_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -203,7 +204,7 @@

    Edge evidence

    confers Detocs system - traitmech:000302 + traitmech:000302 METPO:2007700

    Detocs-associated ATP and dATP depletion realizes the Detocs system trait.

    @@ -316,7 +317,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -499,7 +500,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -863,12 +873,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 07:11 UTC diff --git a/pages/traits/genomics/dgtpase_system.html b/pages/traits/genomics/dgtpase_system.html index 26cdd5cba52..71fc5ab00bb 100644 --- a/pages/traits/genomics/dgtpase_system.html +++ b/pages/traits/genomics/dgtpase_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -211,7 +212,7 @@

    Edge evidence

    confers dGTPase system - traitmech:000276 + traitmech:000276 METPO:2007700

    dGTPase-mediated arrest of phage replication realizes the dGTPase system trait.

    @@ -306,7 +307,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -465,7 +466,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -829,12 +839,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 10:47 UTC diff --git a/pages/traits/genomics/dionysus_system.html b/pages/traits/genomics/dionysus_system.html index e603c56cc1d..7f6610b650e 100644 --- a/pages/traits/genomics/dionysus_system.html +++ b/pages/traits/genomics/dionysus_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers Dionysus system - traitmech:000330 + traitmech:000330 METPO:2007700

    Dionysus-mediated phage restriction realizes the Dionysus system trait.

      @@ -170,11 +171,11 @@

      Edge evidence

    • Dionysus system - traitmech:000330 + traitmech:000330 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Dionysus system possession is a phage-defense-system trait.

        @@ -239,7 +240,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -255,7 +256,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -414,7 +415,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -778,12 +788,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 07:22 UTC diff --git a/pages/traits/genomics/disarm1_system.html b/pages/traits/genomics/disarm1_system.html index 4736edadb13..7118f3e0c1c 100644 --- a/pages/traits/genomics/disarm1_system.html +++ b/pages/traits/genomics/disarm1_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -144,7 +145,7 @@

    Edge evidence

    confers DISARM1 system - traitmech:000548 + traitmech:000548 METPO:2007700

    The first-pass DISARM1 system trait is realized by a DefenseFinder DISARM_1 subtype locus within the methyltransferase-associated DISARM family.

    @@ -265,7 +266,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -460,7 +461,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -824,12 +834,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 15:20 UTC diff --git a/pages/traits/genomics/disarm2_system.html b/pages/traits/genomics/disarm2_system.html index cde3777a229..d5bcc694014 100644 --- a/pages/traits/genomics/disarm2_system.html +++ b/pages/traits/genomics/disarm2_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -144,7 +145,7 @@

    Edge evidence

    confers DISARM2 system - traitmech:000549 + traitmech:000549 METPO:2007700

    The first-pass DISARM2 system trait is realized by a DefenseFinder DISARM_2 subtype locus within the methyltransferase-associated DISARM family.

    @@ -265,7 +266,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -460,7 +461,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -824,12 +834,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 16:05 UTC diff --git a/pages/traits/genomics/disarm_system.html b/pages/traits/genomics/disarm_system.html index db10ff706fc..da5a26ee18e 100644 --- a/pages/traits/genomics/disarm_system.html +++ b/pages/traits/genomics/disarm_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -187,7 +188,7 @@

    Edge evidence

    confers DISARM system - traitmech:000211 + traitmech:000211 METPO:2007700

    DrmAB activation realizes DISARM-mediated anti-phage defense.

      @@ -203,11 +204,11 @@

      Edge evidence

    • DISARM system - traitmech:000211 + traitmech:000211 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      DISARM possession is a methyltransferase-associated phage-defense-system trait.

        @@ -243,8 +244,8 @@

        Protein and taxon examples

    		 - Bacillus paralicheniformis ATCC 9945a -
    NCBITaxon:766760 + Bacillus paralicheniformis ATCC 9945a +
    NCBITaxon:766760         		REVIEWED
    @@ -273,8 +274,8 @@

    Protein and taxon examples

    		 - Bacillus paralicheniformis ATCC 9945a -
    NCBITaxon:766760 + Bacillus paralicheniformis ATCC 9945a +
    NCBITaxon:766760         		REVIEWED
    @@ -351,9 +352,9 @@

    Children (2)

    Synonyms (2)

      -
    • Defense Island System Associated with Restriction-Modification EXACT_SYNONYM · DOI:10.1038/s41467-022-30673-1
      • +
    • Defense Island System Associated with Restriction-Modification EXACT_SYNONYM · DOI:10.1038/s41467-022-30673-1
      • -
    • Defense Island System Associated with Restriction Modification EXACT_SYNONYM · DOI:10.1038/s41467-022-30673-1
      • +
    • Defense Island System Associated with Restriction Modification EXACT_SYNONYM · DOI:10.1038/s41467-022-30673-1
    @@ -369,7 +370,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -554,7 +555,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -918,12 +928,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 09:40 UTC diff --git a/pages/traits/genomics/divona_system.html b/pages/traits/genomics/divona_system.html index 542832f0a77..858f393d9df 100644 --- a/pages/traits/genomics/divona_system.html +++ b/pages/traits/genomics/divona_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Divona system - traitmech:000277 + traitmech:000277 METPO:2007700

    Divona-mediated phage restriction realizes the Divona system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -392,7 +393,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -756,12 +766,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 11:16 UTC diff --git a/pages/traits/genomics/dnd_system.html b/pages/traits/genomics/dnd_system.html index cc759af86b0..c51e0541985 100644 --- a/pages/traits/genomics/dnd_system.html +++ b/pages/traits/genomics/dnd_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -218,7 +219,7 @@

    Edge evidence

    confers Dnd system - traitmech:000221 + traitmech:000221 METPO:2007700

    PT-guided foreign-DNA nicking realizes the Dnd restriction-modification system trait.

      @@ -234,11 +235,11 @@

      Edge evidence

    • Dnd system - traitmech:000221 + traitmech:000221 is a phosphorothioate defense system - traitmech:000213 - rdfs:subClassOf + traitmech:000213 + rdfs:subClassOf

      Dnd system possession is a phosphorothioate-defense-system trait.

        @@ -297,11 +298,11 @@

        Parent traits (1)

        Synonyms (3)

          -
        • Dnd R-M system EXACT_SYNONYM · DOI:10.1128/mbio.00933-23
          • +
        • Dnd R-M system EXACT_SYNONYM · DOI:10.1128/mbio.00933-23
          • -
        • Dnd-related R-M system EXACT_SYNONYM · DOI:10.1128/mbio.00933-23
          • +
        • Dnd-related R-M system EXACT_SYNONYM · DOI:10.1128/mbio.00933-23
          • -
        • Dnd-related restriction and modification system EXACT_SYNONYM · DOI:10.1128/mbio.00933-23
          • +
        • Dnd-related restriction and modification system EXACT_SYNONYM · DOI:10.1128/mbio.00933-23
    @@ -317,7 +318,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -464,7 +465,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -828,12 +838,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 16:03 UTC diff --git a/pages/traits/genomics/dndcdea_pbeabcd_system.html b/pages/traits/genomics/dndcdea_pbeabcd_system.html index ea2f8127358..cc4e0ca6807 100644 --- a/pages/traits/genomics/dndcdea_pbeabcd_system.html +++ b/pages/traits/genomics/dndcdea_pbeabcd_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -211,7 +212,7 @@

    Edge evidence

    confers DndCDEA-PbeABCD system - traitmech:000224 + traitmech:000224 METPO:2007700

    PT-dependent PbeABCD antiviral activity realizes the DndCDEA-PbeABCD defense trait.

      @@ -227,11 +228,11 @@

      Edge evidence

    • DndCDEA-PbeABCD system - traitmech:000224 + traitmech:000224 is a phosphorothioate defense system - traitmech:000213 - rdfs:subClassOf + traitmech:000213 + rdfs:subClassOf

      DndCDEA-PbeABCD possession is a phosphorothioate-defense-system trait.

        @@ -290,7 +291,7 @@

        Parent traits (1)

        Synonyms (1)

          -
        • PbeABCD-mediated PT defence system EXACT_SYNONYM · DOI:10.1038/s41467-019-09390-9
          • +
        • PbeABCD-mediated PT defence system EXACT_SYNONYM · DOI:10.1038/s41467-019-09390-9
    @@ -306,7 +307,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -453,7 +454,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -817,12 +827,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 17:42 UTC diff --git a/pages/traits/genomics/dodola_system.html b/pages/traits/genomics/dodola_system.html index eb11ff9b75b..40ca66686fa 100644 --- a/pages/traits/genomics/dodola_system.html +++ b/pages/traits/genomics/dodola_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers Dodola system - traitmech:000252 + traitmech:000252 METPO:2007700

    Dodola-mediated phage restriction realizes the Dodola system trait.

    @@ -255,7 +256,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -414,7 +415,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -778,12 +788,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 21:39 UTC diff --git a/pages/traits/genomics/dpd_system.html b/pages/traits/genomics/dpd_system.html index 6a893be2744..7017d2f74e9 100644 --- a/pages/traits/genomics/dpd_system.html +++ b/pages/traits/genomics/dpd_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -173,7 +174,7 @@

    Edge evidence

    confers Dpd system - traitmech:000278 + traitmech:000278 METPO:2007700

    DefenseFinder models Dpd as a multi-profile defense system rooted in DpdA-K DNA modification.

    @@ -270,7 +271,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -429,7 +430,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -793,12 +803,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 18:31 UTC diff --git a/pages/traits/genomics/drt1_system.html b/pages/traits/genomics/drt1_system.html index 6e466e59334..a5cee5d2d3d 100644 --- a/pages/traits/genomics/drt1_system.html +++ b/pages/traits/genomics/drt1_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -150,7 +151,7 @@

    Edge evidence

    confers DRT1 system - traitmech:000543 + traitmech:000543 METPO:2007700

    The first-pass DRT1 system trait is realized by a DefenseFinder DRT_1 subtype locus within the reverse-transcriptase-dependent DRT family.

    @@ -267,7 +268,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -466,7 +467,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -830,12 +840,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 11:06 UTC diff --git a/pages/traits/genomics/drt2_system.html b/pages/traits/genomics/drt2_system.html index 21ca73b353b..390be697d27 100644 --- a/pages/traits/genomics/drt2_system.html +++ b/pages/traits/genomics/drt2_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers DRT2 system - traitmech:000544 + traitmech:000544 METPO:2007700

    The first-pass DRT2 system trait is realized by a DefenseFinder DRT_2 subtype locus within the reverse-transcriptase-dependent DRT family.

    @@ -263,7 +264,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -461,7 +462,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -825,12 +835,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 11:52 UTC diff --git a/pages/traits/genomics/drt3_system.html b/pages/traits/genomics/drt3_system.html index f92beaf1a22..90ca07031b7 100644 --- a/pages/traits/genomics/drt3_system.html +++ b/pages/traits/genomics/drt3_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -157,7 +158,7 @@

    Edge evidence

    confers DRT3 system - traitmech:000545 + traitmech:000545 METPO:2007700

    The first-pass DRT3 system trait is realized by a DefenseFinder DRT_3 subtype locus within the reverse-transcriptase-dependent DRT family.

    @@ -280,7 +281,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -487,7 +488,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -851,12 +861,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 12:43 UTC diff --git a/pages/traits/genomics/drt4_system.html b/pages/traits/genomics/drt4_system.html index 54d3eb62f95..00a4c9cb5bc 100644 --- a/pages/traits/genomics/drt4_system.html +++ b/pages/traits/genomics/drt4_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers DRT4 system - traitmech:000546 + traitmech:000546 METPO:2007700

    The first-pass DRT4 system trait is realized by a DefenseFinder DRT_4 subtype locus within the reverse-transcriptase-dependent DRT family.

    @@ -263,7 +264,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -461,7 +462,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -825,12 +835,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 13:42 UTC diff --git a/pages/traits/genomics/drt5_system.html b/pages/traits/genomics/drt5_system.html index aecd3c70174..043864af119 100644 --- a/pages/traits/genomics/drt5_system.html +++ b/pages/traits/genomics/drt5_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers DRT5 system - traitmech:000547 + traitmech:000547 METPO:2007700

    The first-pass DRT5 system trait is realized by a DefenseFinder DRT_5 subtype locus within the reverse-transcriptase-dependent DRT family.

    @@ -263,7 +264,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -461,7 +462,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -825,12 +835,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 14:34 UTC diff --git a/pages/traits/genomics/drt6_system.html b/pages/traits/genomics/drt6_system.html index 59c45836e8b..163fb5124b9 100644 --- a/pages/traits/genomics/drt6_system.html +++ b/pages/traits/genomics/drt6_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers DRT6 system - traitmech:000539 + traitmech:000539 METPO:2007700

    The first-pass DRT6 system trait is realized by a DefenseFinder DRT6 subtype locus within the reverse-transcriptase-dependent DRT family.

    @@ -263,7 +264,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -461,7 +462,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -825,12 +835,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 08:13 UTC diff --git a/pages/traits/genomics/drt7_system.html b/pages/traits/genomics/drt7_system.html index d4638d524d7..c6d754b7993 100644 --- a/pages/traits/genomics/drt7_system.html +++ b/pages/traits/genomics/drt7_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -150,7 +151,7 @@

    Edge evidence

    confers DRT7 system - traitmech:000540 + traitmech:000540 METPO:2007700

    The first-pass DRT7 system trait is realized by a DefenseFinder DRT7 subtype locus within the reverse-transcriptase-dependent DRT family.

    @@ -267,7 +268,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -466,7 +467,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -830,12 +840,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 09:21 UTC diff --git a/pages/traits/genomics/drt8_system.html b/pages/traits/genomics/drt8_system.html index 6849bf61c40..fa708ad28f0 100644 --- a/pages/traits/genomics/drt8_system.html +++ b/pages/traits/genomics/drt8_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -152,7 +153,7 @@

    Edge evidence

    confers DRT8 system - traitmech:000541 + traitmech:000541 METPO:2007700

    The first-pass DRT8 system trait is realized by a DefenseFinder DRT8 subtype locus within the reverse-transcriptase-dependent DRT family.

    @@ -269,7 +270,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -469,7 +470,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -833,12 +843,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 09:39 UTC diff --git a/pages/traits/genomics/drt9_system.html b/pages/traits/genomics/drt9_system.html index 944b09be631..458b31d1527 100644 --- a/pages/traits/genomics/drt9_system.html +++ b/pages/traits/genomics/drt9_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -150,7 +151,7 @@

    Edge evidence

    confers DRT9 system - traitmech:000542 + traitmech:000542 METPO:2007700

    The first-pass DRT9 system trait is realized by a DefenseFinder DRT9 subtype locus within the reverse-transcriptase-dependent DRT family.

    @@ -265,7 +266,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -464,7 +465,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -828,12 +838,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 10:19 UTC diff --git a/pages/traits/genomics/drt_system.html b/pages/traits/genomics/drt_system.html index 7b02f8c4311..66b13a75a81 100644 --- a/pages/traits/genomics/drt_system.html +++ b/pages/traits/genomics/drt_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -204,7 +205,7 @@

    Edge evidence

    confers DRT system - traitmech:000279 + traitmech:000279 METPO:2007700

    DefenseFinder models DRT as a phage-defense system with subtype models such as DRT_1.

    @@ -328,7 +329,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -487,7 +488,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -851,12 +861,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 12:30 UTC diff --git a/pages/traits/genomics/druantia_iii_system.html b/pages/traits/genomics/druantia_iii_system.html index 36b19456ab6..93d511643b1 100644 --- a/pages/traits/genomics/druantia_iii_system.html +++ b/pages/traits/genomics/druantia_iii_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -166,7 +167,7 @@

    Edge evidence

    confers Druantia III system - traitmech:000560 + traitmech:000560 METPO:2007700

    The first-pass Druantia III system trait is realized by a DruE/DruH locus whose late defense uses DruE helicase-nuclease effector activity.

    @@ -273,7 +274,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -496,7 +497,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -860,12 +870,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 01:24 UTC diff --git a/pages/traits/genomics/druantia_system.html b/pages/traits/genomics/druantia_system.html index 4ff31dc3c63..e6fa49738d7 100644 --- a/pages/traits/genomics/druantia_system.html +++ b/pages/traits/genomics/druantia_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -151,7 +152,7 @@

    Children (4)

    Synonyms (1)

    @@ -167,7 +168,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -288,7 +289,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    Doron et al. separated Type I DruABCDE, Type II DruMFGE, and Type III DruHE architectures and validated one Type I locus, while Wu et al. define a Type III mechanism in which DruH likely senses infection and DruE engages ssDNA-containing intermediates. Druantia III system now captures the DruE/DruH Type III branch from the pinned Druantia_III DefenseFinder row, but the parent record remains at the DruE-core family level until separate review resolves Type I and Type II partner functions, Type IV partner functions represented by the pinned Druantia_IV HMM rows, exact phage triggers, native host breadth, and Zorya-coupled versus standalone outputs across Druantia loci. Druantia type IV system (traitmech:000577) now captures the DruE/F/L architecture described by Payne et al. (DOI:10.1093/nar/gkab883), without the type-II DruM/G components. This resolves the architectural child, not type-IV experimental defense or partner chemistry. The family definition no longer requires universal helicase-nuclease DNA processing. Wu et al.'s family-wide conservation claim is a hypothesis in a type-III preprint. The overgeneralized parent graph is removed; the characterized III branch remains at traitmech:000560. New proposal v454 replaces the unminted v111 family row without changing the local family identifier or historical TSV. Type I architecture is now represented by traitmech:000578 Druantia type I system: DruB/C/D/E with optional DruA. Doron's optional DUF4338 component and the Ralstonia study's mapping of that domain to DruA qualify the earlier five-gene shorthand. The five-profile PADLOC rule and three-match DefenseFinder threshold are detection criteria, not identical biological definitions. This resolves the type-I architecture lead, not its partner functions or native-host mechanism. Type II architecture is now represented by traitmech:000579 Druantia type II system, defined by DruM/F/G/E possession using DOI:10.1093/nar/gkab883. Hou et al. version 2 (DOI:10.65215/LTSpreprints.2026.06.18.000273, 2026-07-08 preprint) adds Pf-5 DruE biochemistry and a limited heterologous assay, not full-system or native-host phage-defense validation. The architectural lead is resolved; accessory roles and the transition from DNA unwinding to phage restriction remain open.

    +

    Doron et al. separated Type I DruABCDE, Type II DruMFGE, and Type III DruHE architectures and validated one Type I locus, while Wu et al. define a Type III mechanism in which DruH likely senses infection and DruE engages ssDNA-containing intermediates. Druantia III system now captures the DruE/DruH Type III branch from the pinned Druantia_III DefenseFinder row, but the parent record remains at the DruE-core family level until separate review resolves Type I and Type II partner functions, Type IV partner functions represented by the pinned Druantia_IV HMM rows, exact phage triggers, native host breadth, and Zorya-coupled versus standalone outputs across Druantia loci. Druantia type IV system (traitmech:000577) now captures the DruE/F/L architecture described by Payne et al. (DOI:10.1093/nar/gkab883), without the type-II DruM/G components. This resolves the architectural child, not type-IV experimental defense or partner chemistry. The family definition no longer requires universal helicase-nuclease DNA processing. Wu et al.'s family-wide conservation claim is a hypothesis in a type-III preprint. The overgeneralized parent graph is removed; the characterized III branch remains at traitmech:000560. New proposal v454 replaces the unminted v111 family row without changing the local family identifier or historical TSV. Type I architecture is now represented by traitmech:000578 Druantia type I system: DruB/C/D/E with optional DruA. Doron's optional DUF4338 component and the Ralstonia study's mapping of that domain to DruA qualify the earlier five-gene shorthand. The five-profile PADLOC rule and three-match DefenseFinder threshold are detection criteria, not identical biological definitions. This resolves the type-I architecture lead, not its partner functions or native-host mechanism. Type II architecture is now represented by traitmech:000579 Druantia type II system, defined by DruM/F/G/E possession using DOI:10.1093/nar/gkab883. Hou et al. version 2 (DOI:10.65215/LTSpreprints.2026.06.18.000273, 2026-07-08 preprint) adds Pf-5 DruE biochemistry and a limited heterologous assay, not full-system or native-host phage-defense validation. The architectural lead is resolved; accessory roles and the transition from DNA unwinding to phage restriction remain open.

    @@ -342,13 +343,13 @@

    Curation history

  • · TRACK_DRUANTIA_TYPE_I_CLASS · codex -

    Linked traitmech:000578 using DOI:10.1126/science.aar4120 and DOI:10.3389/fmicb.2020.00961. Resolved the type-I architecture lead with optional DruA and distinct detector thresholds. Kept family identity, definition, hierarchy, evidence and example unchanged; type-I functions and the type-II lead remain open.

    +

    Linked traitmech:000578 using DOI:10.1126/science.aar4120 and DOI:10.3389/fmicb.2020.00961. Resolved the type-I architecture lead with optional DruA and distinct detector thresholds. Kept family identity, definition, hierarchy, evidence and example unchanged; type-I functions and the type-II lead remain open.

  • · TRACK_NARROWER_RECORD · codex -

    Linked traitmech:000579 Druantia II possession using DOI:10.1093/nar/gkab883 and the July 8 version of DOI:10.65215/LTSpreprints.2026.06.18.000273. Resolved the architecture lead while preserving full-system mechanism uncertainty. Family identity, evidence and example are unchanged.

    +

    Linked traitmech:000579 Druantia II possession using DOI:10.1093/nar/gkab883 and the July 8 version of DOI:10.65215/LTSpreprints.2026.06.18.000273. Resolved the architecture lead while preserving full-system mechanism uncertainty. Family identity, evidence and example are unchanged.

    • @@ -370,13 +371,13 @@

    Recorded curation sessions

  • · codex
    • EDIT — Restrict Druantia family to shared architecture -

      Addressed #1635 by removing universal helicase-nuclease DNA processing from the Druantia family definition and removing its overgeneralized family graph. The characterized type-III child remains unchanged. Preserved existing evidence and canonical example, identified Wu et al. DOI:10.64898/2026.05.12.724681 as a preprint and the universal mechanism as a hypothesis, and added Payne et al. DOI:10.1093/nar/gkab883 architecture evidence. Linked type-IV traitmech:000577 without resolving its functional gaps. Proposal v454 replaces the unminted v111 family placeholder while retaining its TSV and stable traitmech:000234 identity.

    +

    Addressed #1635 by removing universal helicase-nuclease DNA processing from the Druantia family definition and removing its overgeneralized family graph. The characterized type-III child remains unchanged. Preserved existing evidence and canonical example, identified Wu et al. DOI:10.64898/2026.05.12.724681 as a preprint and the universal mechanism as a hypothesis, and added Payne et al. DOI:10.1093/nar/gkab883 architecture evidence. Linked type-IV traitmech:000577 without resolving its functional gaps. Proposal v454 replaces the unminted v111 family placeholder while retaining its TSV and stable traitmech:000234 identity.

    • Read this curation session
  • · codex
    • EDIT — Resolve Druantia type-I architecture lead -

      Replaced the open type-I architecture lead with a link to traitmech:000578 and explained optional DruA versus detector thresholds, citing DOI:10.1126/science.aar4120 and DOI:10.3389/fmicb.2020.00961. Type-I partner mechanisms and the type-II lead remain open. Guarded writer preserves the family definition, identity, hierarchy, evidence and canonical example; adds one curation-history event. No protected record or existing III/IV child was edited.

    +

    Replaced the open type-I architecture lead with a link to traitmech:000578 and explained optional DruA versus detector thresholds, citing DOI:10.1126/science.aar4120 and DOI:10.3389/fmicb.2020.00961. Type-I partner mechanisms and the type-II lead remain open. Guarded writer preserves the family definition, identity, hierarchy, evidence and canonical example; adds one curation-history event. No protected record or existing III/IV child was edited.

    • Read this curation session
  • @@ -414,7 +415,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -443,12 +453,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 21:25 UTC diff --git a/pages/traits/genomics/druantia_type_i_system.html b/pages/traits/genomics/druantia_type_i_system.html index 2685e94fa0f..04d38ca7b33 100644 --- a/pages/traits/genomics/druantia_type_i_system.html +++ b/pages/traits/genomics/druantia_type_i_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -123,7 +124,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Type I Druantia system EXACT_SYNONYM · DOI:10.3389/fmicb.2020.00961
      • +
    • Type I Druantia system EXACT_SYNONYM · DOI:10.3389/fmicb.2020.00961
    @@ -139,7 +140,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -292,7 +293,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add literature-defined Druantia type I possession -

      Added traitmech:000578 and proposal v455 METPO:1053200 under the corrected v454 family parent. Doron DOI:10.1126/science.aar4120 and the Ralstonia comparative-genomics study DOI:10.3389/fmicb.2020.00961 support DruB/C/D/E with optional DruA. Four evidence snippets include two pinned executable models with different thresholds. Natural UMEA 4076-1 possession is distinguished from the engineered MG1655 assay; NCBITaxon:562 was resolved at NCBI. No type-III mechanism is transferred. Whole-repository novelty and allocation searches included ignored and hidden files. Guarded writer passes 17 focused tests; full validation follows before PR submission.

    +

    Added traitmech:000578 and proposal v455 METPO:1053200 under the corrected v454 family parent. Doron DOI:10.1126/science.aar4120 and the Ralstonia comparative-genomics study DOI:10.3389/fmicb.2020.00961 support DruB/C/D/E with optional DruA. Four evidence snippets include two pinned executable models with different thresholds. Natural UMEA 4076-1 possession is distinguished from the engineered MG1655 assay; NCBITaxon:562 was resolved at NCBI. No type-III mechanism is transferred. Whole-repository novelty and allocation searches included ignored and hidden files. Guarded writer passes 17 focused tests; full validation follows before PR submission.

    • Read this curation session @@ -324,7 +325,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -353,12 +363,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 20:26 UTC diff --git a/pages/traits/genomics/druantia_type_ii_system.html b/pages/traits/genomics/druantia_type_ii_system.html index 8aa6b48f62d..acbf5d40cfe 100644 --- a/pages/traits/genomics/druantia_type_ii_system.html +++ b/pages/traits/genomics/druantia_type_ii_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -61,7 +62,7 @@

    Trait evidence (4)

    DOI:10.65215/LTSpreprints.2026.06.18.000273
    DruE alone confers limited protection against a subset of coliphages in heterologous expression
    -

    Hou et al., version 2 posted 2026-07-08, not peer reviewed; PDF https://langtaosha.org.cn/lts/en/preprint/download/273/1236, pages 5-6 and 18, Figure 1 and supplementary Figure S2. The Pf-5 druMFGE locus is the source. Purified DruE is an ATP-dependent 3-prime-to-5-prime helicase preferring 3-prime overhangs and forks, with an asymmetric homodimer. Standalone DruE in E. coli BL21 gave limited T7/T1 protection; R1241A reduced protection. Insoluble DruF/G prevented full-system reconstitution. Native-host phage defense and the link from unwinding to restriction remain untested or unresolved. Pf-5 deletion assays under mitomycin C suggest accessory control of toxicity, not a demonstrated defense trigger.

    +

    Hou et al., version 2 posted 2026-07-08, not peer reviewed; PDF https://langtaosha.org.cn/lts/en/preprint/download/273/1236, pages 5-6 and 18, Figure 1 and supplementary Figure S2. The Pf-5 druMFGE locus is the source. Purified DruE is an ATP-dependent 3-prime-to-5-prime helicase preferring 3-prime overhangs and forks, with an asymmetric homodimer. Standalone DruE in E. coli BL21 gave limited T7/T1 protection; R1241A reduced protection. Insoluble DruF/G prevented full-system reconstitution. Native-host phage defense and the link from unwinding to restriction remain untested or unresolved. Pf-5 deletion assays under mitomycin C suggest accessory control of toxicity, not a demonstrated defense trigger.

  • @@ -122,7 +123,7 @@

    Parent traits (1)

    Synonyms (1)

    • @@ -138,7 +139,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -287,7 +288,7 @@

    Curation history

  • · CORRECT_EVIDENCE_LOCATOR · codex -

    Corrected the Payne evidence subsection locator to Results: Identification of new defence system variants after checking primary PMC8565338 XML; the snippet, architecture claim and Figure 2C locator are unchanged. Addresses issue #1639.

    +

    Corrected the Payne evidence subsection locator to Results: Identification of new defence system variants after checking primary PMC8565338 XML; the snippet, architecture claim and Figure 2C locator are unchanged. Addresses issue #1639.

    • @@ -297,13 +298,13 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Druantia II possession with bounded DruE evidence -

      Created traitmech:000579 under Druantia family traitmech:000234 using DOI:10.1093/nar/gkab883, version 2 of DOI:10.65215/LTSpreprints.2026.06.18.000273 and commit-pinned executable DefenseFinder/PADLOC models. Four snippets were checked against primary text and structured model files. Pf-5 natural locus possession is distinct from isolated DruE assays in engineered E. coli; NCBITaxon:220664 resolved at NCBI. No full-system graph or trait xref was inferred from protein evidence. Whole-repository ignored-and-hidden novelty and allocation searches found no exact record or METPO term. Reserved METPO:1053300 in proposal v456; guarded writer and controlled-fixture tests cover dry-run, replay, preservation and preimage drift.

    +

    Created traitmech:000579 under Druantia family traitmech:000234 using DOI:10.1093/nar/gkab883, version 2 of DOI:10.65215/LTSpreprints.2026.06.18.000273 and commit-pinned executable DefenseFinder/PADLOC models. Four snippets were checked against primary text and structured model files. Pf-5 natural locus possession is distinct from isolated DruE assays in engineered E. coli; NCBITaxon:220664 resolved at NCBI. No full-system graph or trait xref was inferred from protein evidence. Whole-repository ignored-and-hidden novelty and allocation searches found no exact record or METPO term. Reserved METPO:1053300 in proposal v456; guarded writer and controlled-fixture tests cover dry-run, replay, preservation and preimage drift.

    • Read this curation session
  • · codex
    • EDIT — Correct the Payne primary-source subsection locator -

      Issue #1639: the author-side adversarial review found that Discovery of new Doron system types was not an actual section title. Corrected the evidence note to the Results subsection Identification of new defence system variants after parsing primary PMC8565338 XML. The exact snippet, biological architecture and Figure 2C locator are unchanged. Preserved original curation history and appended CORRECT_EVIDENCE_LOCATOR using the validated writer. Added a regression assertion that failed on the old locator.

    +

    Issue #1639: the author-side adversarial review found that Discovery of new Doron system types was not an actual section title. Corrected the evidence note to the Results subsection Identification of new defence system variants after parsing primary PMC8565338 XML. The exact snippet, biological architecture and Figure 2C locator are unchanged. Preserved original curation history and appended CORRECT_EVIDENCE_LOCATOR using the validated writer. Added a regression assertion that failed on the old locator.

    • Read this curation session @@ -335,7 +336,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -364,12 +374,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 21:32 UTC diff --git a/pages/traits/genomics/druantia_type_iv_system.html b/pages/traits/genomics/druantia_type_iv_system.html index cbcc7cfe48a..ae1648e630a 100644 --- a/pages/traits/genomics/druantia_type_iv_system.html +++ b/pages/traits/genomics/druantia_type_iv_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -117,7 +118,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Druantia type IV EXACT_SYNONYM · DOI:10.1093/nar/gkab883
      • +
    • Druantia type IV EXACT_SYNONYM · DOI:10.1093/nar/gkab883
    @@ -133,7 +134,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -261,7 +262,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add literature-defined Druantia type IV possession -

      Added traitmech:000577 as a PROPOSED GENOMICS class for the DruE/F/L locus architecture without type-II DruM/G. DOI:10.1093/nar/gkab883 and immutable DefenseFinder/PADLOC models support the class, with three exact source snippets. Neither detector forbids DruM/G and the original paper did not assay Druantia IV; no resistance claim, causal graph, unverified xref or canonical taxon is added. Whole-repository searches included ignored and hidden files. METPO v454 reserves 1053101 below the corrected family placeholder 1053100. Used a fail-closed validated writer and controlled-fixture tests.

    +

    Added traitmech:000577 as a PROPOSED GENOMICS class for the DruE/F/L locus architecture without type-II DruM/G. DOI:10.1093/nar/gkab883 and immutable DefenseFinder/PADLOC models support the class, with three exact source snippets. Neither detector forbids DruM/G and the original paper did not assay Druantia IV; no resistance claim, causal graph, unverified xref or canonical taxon is added. Whole-repository searches included ignored and hidden files. METPO v454 reserves 1053101 below the corrected family placeholder 1053100. Used a fail-closed validated writer and controlled-fixture tests.

    • Read this curation session @@ -293,7 +294,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -322,12 +332,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 19:45 UTC diff --git a/pages/traits/genomics/ds_10_system.html b/pages/traits/genomics/ds_10_system.html index f7f99b31d42..c613893728c 100644 --- a/pages/traits/genomics/ds_10_system.html +++ b/pages/traits/genomics/ds_10_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers DS-10 system - traitmech:000434 + traitmech:000434 METPO:2007700

    DS-10-mediated phage plaquing reduction realizes the DS-10 system trait.

    @@ -265,7 +266,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -484,7 +485,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -848,12 +858,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 12:48 UTC diff --git a/pages/traits/genomics/ds_11_system.html b/pages/traits/genomics/ds_11_system.html index 38b5a820b7d..2d7dea604b5 100644 --- a/pages/traits/genomics/ds_11_system.html +++ b/pages/traits/genomics/ds_11_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -179,7 +180,7 @@

    Edge evidence

    confers DS-11 system - traitmech:000435 + traitmech:000435 METPO:2007700

    DS-11-mediated phage plaquing reduction realizes the DS-11 system trait.

    @@ -296,7 +297,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -557,7 +558,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -921,12 +931,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 14:33 UTC diff --git a/pages/traits/genomics/ds_12_system.html b/pages/traits/genomics/ds_12_system.html index 54879ea0284..1c50ad0125a 100644 --- a/pages/traits/genomics/ds_12_system.html +++ b/pages/traits/genomics/ds_12_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -172,7 +173,7 @@

    Edge evidence

    confers DS-12 system - traitmech:000436 + traitmech:000436 METPO:2007700

    DS-12-mediated phage plaquing reduction realizes the DS-12 system trait.

    @@ -289,7 +290,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -536,7 +537,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -900,12 +910,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 15:22 UTC diff --git a/pages/traits/genomics/ds_13_system.html b/pages/traits/genomics/ds_13_system.html index 05178b65cde..6227df42d90 100644 --- a/pages/traits/genomics/ds_13_system.html +++ b/pages/traits/genomics/ds_13_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -123,7 +124,7 @@

    Edge evidence

    contributes to DS-13 system - traitmech:000437 + traitmech:000437 RO:0002326

    DefenseFinder links the DS-13 source key to the DefensePredictor preprint and represents DS-13 in the HMM inventory with DS-13A and DS-13B custom profiles.

    @@ -240,7 +241,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -459,7 +460,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -823,12 +833,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 16:08 UTC diff --git a/pages/traits/genomics/ds_14_system.html b/pages/traits/genomics/ds_14_system.html index 767f81e3d5f..5da7a67f1b8 100644 --- a/pages/traits/genomics/ds_14_system.html +++ b/pages/traits/genomics/ds_14_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -178,7 +179,7 @@

    Edge evidence

    confers DS-14 system - traitmech:000429 + traitmech:000429 METPO:2007700

    DS-14-mediated phage plaquing reduction realizes the DS-14 system trait.

    @@ -295,7 +296,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -535,7 +536,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -899,12 +909,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 08:12 UTC diff --git a/pages/traits/genomics/ds_15_system.html b/pages/traits/genomics/ds_15_system.html index ea4f4e68bc7..a801388c105 100644 --- a/pages/traits/genomics/ds_15_system.html +++ b/pages/traits/genomics/ds_15_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -202,7 +203,7 @@

    Edge evidence

    confers DS-15 system - traitmech:000438 + traitmech:000438 METPO:2007700

    DS-15-mediated phage plaquing reduction realizes the DS-15 system trait.

    @@ -323,7 +324,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -577,7 +578,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -941,12 +951,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 16:51 UTC diff --git a/pages/traits/genomics/ds_16_system.html b/pages/traits/genomics/ds_16_system.html index bfb3da68475..a013839ab82 100644 --- a/pages/traits/genomics/ds_16_system.html +++ b/pages/traits/genomics/ds_16_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -208,7 +209,7 @@

    Edge evidence

    confers DS-16 system - traitmech:000439 + traitmech:000439 METPO:2007700

    DS-16-mediated phage plaquing reduction realizes the DS-16 system trait.

    @@ -333,7 +334,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -580,7 +581,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -944,12 +954,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 17:26 UTC diff --git a/pages/traits/genomics/ds_17_system.html b/pages/traits/genomics/ds_17_system.html index aea8038ca2f..5cf96f2bf3f 100644 --- a/pages/traits/genomics/ds_17_system.html +++ b/pages/traits/genomics/ds_17_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -178,7 +179,7 @@

    Edge evidence

    confers DS-17 system - traitmech:000440 + traitmech:000440 METPO:2007700

    DS-17-mediated phage plaquing reduction realizes the DS-17 system trait.

    @@ -295,7 +296,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -521,7 +522,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -885,12 +895,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 18:14 UTC diff --git a/pages/traits/genomics/ds_18_system.html b/pages/traits/genomics/ds_18_system.html index 15572b2749e..9ef8e9b18d2 100644 --- a/pages/traits/genomics/ds_18_system.html +++ b/pages/traits/genomics/ds_18_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -178,7 +179,7 @@

    Edge evidence

    confers DS-18 system - traitmech:000441 + traitmech:000441 METPO:2007700

    DS-18-mediated phage plaquing reduction realizes the DS-18 system trait.

    @@ -295,7 +296,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -521,7 +522,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -885,12 +895,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 18:55 UTC diff --git a/pages/traits/genomics/ds_19_system.html b/pages/traits/genomics/ds_19_system.html index 033513acdbf..0f6ca9f83ea 100644 --- a/pages/traits/genomics/ds_19_system.html +++ b/pages/traits/genomics/ds_19_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -178,7 +179,7 @@

    Edge evidence

    confers DS-19 system - traitmech:000444 + traitmech:000444 METPO:2007700

    DS-19-mediated phage plaquing reduction realizes the DS-19 system trait.

    @@ -295,7 +296,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -521,7 +522,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -885,12 +895,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 21:10 UTC diff --git a/pages/traits/genomics/ds_1_system.html b/pages/traits/genomics/ds_1_system.html index 9a61f2c79db..d1a55b80358 100644 --- a/pages/traits/genomics/ds_1_system.html +++ b/pages/traits/genomics/ds_1_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -178,7 +179,7 @@

    Edge evidence

    confers DS-1 system - traitmech:000424 + traitmech:000424 METPO:2007700

    DS-1-mediated phage plaquing reduction realizes the DS-1 system trait.

    @@ -297,7 +298,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -504,7 +505,7 @@

    Recorded curation sessions

  • · claude-code
    • CREATE — Add DS-1 system trait -

      Minted traitmech:000424 for the DOI-backed DS-1 system under phage defense system. DOI:10.1126/science.adv7924 and the final Science supplementary tables support DS-1 as the DefensePredictor-discovered system corresponding to the two-gene D390 transcriptional unit that reduces bacteriophage plaquing when cloned in E. coli MG1655; the pinned DefenseFinder article and HMM inventories map DS-1 to the DS-1A and DS-1B custom profiles while the pinned rules table has no DS-1 row, so the graph stays nonmechanistic at cloned-transcriptional-unit level and the record keeps profile-to-component mapping, native host breadth, phage range, and direct molecular output unresolved. Reserved METPO:1037800 in proposals/metpo_traitmech_v301.

    +

    Minted traitmech:000424 for the DOI-backed DS-1 system under phage defense system. DOI:10.1126/science.adv7924 and the final Science supplementary tables support DS-1 as the DefensePredictor-discovered system corresponding to the two-gene D390 transcriptional unit that reduces bacteriophage plaquing when cloned in E. coli MG1655; the pinned DefenseFinder article and HMM inventories map DS-1 to the DS-1A and DS-1B custom profiles while the pinned rules table has no DS-1 row, so the graph stays nonmechanistic at cloned-transcriptional-unit level and the record keeps profile-to-component mapping, native host breadth, phage range, and direct molecular output unresolved. Reserved METPO:1037800 in proposals/metpo_traitmech_v301.

    • Read this curation session
  • @@ -542,7 +543,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -906,12 +916,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 03:20 UTC diff --git a/pages/traits/genomics/ds_20_system.html b/pages/traits/genomics/ds_20_system.html index 13bbaba7857..95c923b3c08 100644 --- a/pages/traits/genomics/ds_20_system.html +++ b/pages/traits/genomics/ds_20_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -178,7 +179,7 @@

    Edge evidence

    confers DS-20 system - traitmech:000445 + traitmech:000445 METPO:2007700

    DS-20-mediated phage plaquing reduction realizes the DS-20 system trait.

    @@ -295,7 +296,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -521,7 +522,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -885,12 +895,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 21:46 UTC diff --git a/pages/traits/genomics/ds_21_system.html b/pages/traits/genomics/ds_21_system.html index d3fcce61524..5af5ab42593 100644 --- a/pages/traits/genomics/ds_21_system.html +++ b/pages/traits/genomics/ds_21_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -182,7 +183,7 @@

    Edge evidence

    confers DS-21 system - traitmech:000446 + traitmech:000446 METPO:2007700

    DS-21-mediated phage plaquing reduction realizes the DS-21 system trait.

    @@ -303,7 +304,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -531,7 +532,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -895,12 +905,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 22:17 UTC diff --git a/pages/traits/genomics/ds_22_system.html b/pages/traits/genomics/ds_22_system.html index 40f844418d1..a9d46864959 100644 --- a/pages/traits/genomics/ds_22_system.html +++ b/pages/traits/genomics/ds_22_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -184,7 +185,7 @@

    Edge evidence

    confers DS-22 system - traitmech:000447 + traitmech:000447 METPO:2007700

    DS-22-mediated phage plaquing reduction realizes the DS-22 system trait.

    @@ -301,7 +302,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -558,7 +559,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -922,12 +932,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 00:35 UTC diff --git a/pages/traits/genomics/ds_23_system.html b/pages/traits/genomics/ds_23_system.html index 64773ad74c6..9d877711299 100644 --- a/pages/traits/genomics/ds_23_system.html +++ b/pages/traits/genomics/ds_23_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -184,7 +185,7 @@

    Edge evidence

    confers DS-23 system - traitmech:000448 + traitmech:000448 METPO:2007700

    DS-23-mediated phage plaquing reduction realizes the DS-23 system trait.

    @@ -301,7 +302,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -534,7 +535,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -898,12 +908,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 00:59 UTC diff --git a/pages/traits/genomics/ds_24_system.html b/pages/traits/genomics/ds_24_system.html index a951333289b..2d3bf4fa953 100644 --- a/pages/traits/genomics/ds_24_system.html +++ b/pages/traits/genomics/ds_24_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -178,7 +179,7 @@

    Edge evidence

    confers DS-24 system - traitmech:000449 + traitmech:000449 METPO:2007700

    DS-24-mediated phage plaquing reduction realizes the DS-24 system trait.

    @@ -295,7 +296,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -521,7 +522,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -885,12 +895,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 01:45 UTC diff --git a/pages/traits/genomics/ds_25_system.html b/pages/traits/genomics/ds_25_system.html index 524d9c30bec..c5e2326cacd 100644 --- a/pages/traits/genomics/ds_25_system.html +++ b/pages/traits/genomics/ds_25_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -123,7 +124,7 @@

    Edge evidence

    contributes to DS-25 system - traitmech:000473 + traitmech:000473 RO:0002326

    DefenseFinder links the DS-25 source key to the DefensePredictor preprint and represents DS-25 in the HMM inventory with DS-25A and DS-25B custom profiles.

    @@ -240,7 +241,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -459,7 +460,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -823,12 +833,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 20:22 UTC diff --git a/pages/traits/genomics/ds_26_system.html b/pages/traits/genomics/ds_26_system.html index a9b001d019f..076fcd42f94 100644 --- a/pages/traits/genomics/ds_26_system.html +++ b/pages/traits/genomics/ds_26_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -178,7 +179,7 @@

    Edge evidence

    confers DS-26 system - traitmech:000472 + traitmech:000472 METPO:2007700

    DS-26-mediated phage plaquing reduction realizes the DS-26 system trait.

    @@ -293,7 +294,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -526,7 +527,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -890,12 +900,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 19:30 UTC diff --git a/pages/traits/genomics/ds_27_system.html b/pages/traits/genomics/ds_27_system.html index c0cce56d0b2..05618e5779f 100644 --- a/pages/traits/genomics/ds_27_system.html +++ b/pages/traits/genomics/ds_27_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -172,7 +173,7 @@

    Edge evidence

    confers DS-27 system - traitmech:000451 + traitmech:000451 METPO:2007700

    DS-27-mediated phage plaquing reduction realizes the DS-27 system trait.

    @@ -289,7 +290,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -508,7 +509,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -872,12 +882,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 04:13 UTC diff --git a/pages/traits/genomics/ds_28_system.html b/pages/traits/genomics/ds_28_system.html index 96789fa8160..8aeaa2abb1a 100644 --- a/pages/traits/genomics/ds_28_system.html +++ b/pages/traits/genomics/ds_28_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -208,7 +209,7 @@

    Edge evidence

    confers DS-28 system - traitmech:000452 + traitmech:000452 METPO:2007700

    DS-28-mediated phage plaquing reduction realizes the DS-28 system trait.

    @@ -327,7 +328,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -567,7 +568,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -931,12 +941,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 04:59 UTC diff --git a/pages/traits/genomics/ds_29_system.html b/pages/traits/genomics/ds_29_system.html index b9f1a55ea79..f35f6e60ad6 100644 --- a/pages/traits/genomics/ds_29_system.html +++ b/pages/traits/genomics/ds_29_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -184,7 +185,7 @@

    Edge evidence

    confers DS-29 system - traitmech:000453 + traitmech:000453 METPO:2007700

    DS-29-mediated phage plaquing reduction realizes the DS-29 system trait.

    @@ -301,7 +302,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -527,7 +528,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -891,12 +901,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 05:50 UTC diff --git a/pages/traits/genomics/ds_2_system.html b/pages/traits/genomics/ds_2_system.html index dfd4f652b2a..6b1130c2003 100644 --- a/pages/traits/genomics/ds_2_system.html +++ b/pages/traits/genomics/ds_2_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -166,7 +167,7 @@

    Edge evidence

    confers DS-2 system - traitmech:000425 + traitmech:000425 METPO:2007700

    DS-2-mediated phage plaquing reduction realizes the DS-2 system trait.

    @@ -283,7 +284,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -477,7 +478,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add DS-2 system trait -

      Minted traitmech:000425 for the DOI-backed DS-2 system under phage defense system. DOI:10.1126/science.adv7924 and the final Science supplementary tables support DS-2 as the DefensePredictor-discovered system corresponding to the three-gene DISA transcriptional unit that reduces bacteriophage plaquing when cloned in E. coli MG1655; the pinned DefenseFinder article and HMM inventories map DS-2 to the DS-2C custom profile while the pinned rules table has no DS-2 row, so the graph stays nonmechanistic at cloned-transcriptional-unit level and the record keeps profile-to-component mapping, native host breadth, phage range, and direct molecular output unresolved. Reserved METPO:1037900 in proposals/metpo_traitmech_v302.

    +

    Minted traitmech:000425 for the DOI-backed DS-2 system under phage defense system. DOI:10.1126/science.adv7924 and the final Science supplementary tables support DS-2 as the DefensePredictor-discovered system corresponding to the three-gene DISA transcriptional unit that reduces bacteriophage plaquing when cloned in E. coli MG1655; the pinned DefenseFinder article and HMM inventories map DS-2 to the DS-2C custom profile while the pinned rules table has no DS-2 row, so the graph stays nonmechanistic at cloned-transcriptional-unit level and the record keeps profile-to-component mapping, native host breadth, phage range, and direct molecular output unresolved. Reserved METPO:1037900 in proposals/metpo_traitmech_v302.

    • Read this curation session @@ -509,7 +510,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -873,12 +883,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 04:14 UTC diff --git a/pages/traits/genomics/ds_30_system.html b/pages/traits/genomics/ds_30_system.html index 81e45a33874..a2219279758 100644 --- a/pages/traits/genomics/ds_30_system.html +++ b/pages/traits/genomics/ds_30_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -202,7 +203,7 @@

    Edge evidence

    confers DS-30 system - traitmech:000470 + traitmech:000470 METPO:2007700

    DS-30-mediated phage plaquing reduction realizes the DS-30 system trait.

    @@ -343,7 +344,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -604,7 +605,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -968,12 +978,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 18:01 UTC diff --git a/pages/traits/genomics/ds_31_system.html b/pages/traits/genomics/ds_31_system.html index fe4d2ae645c..c584209ed02 100644 --- a/pages/traits/genomics/ds_31_system.html +++ b/pages/traits/genomics/ds_31_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -184,7 +185,7 @@

    Edge evidence

    confers DS-31 system - traitmech:000454 + traitmech:000454 METPO:2007700

    DS-31-mediated phage plaquing reduction realizes the DS-31 system trait.

    @@ -301,7 +302,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -527,7 +528,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -891,12 +901,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 06:40 UTC diff --git a/pages/traits/genomics/ds_32_system.html b/pages/traits/genomics/ds_32_system.html index f6424cdac25..62919d52ed7 100644 --- a/pages/traits/genomics/ds_32_system.html +++ b/pages/traits/genomics/ds_32_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -220,7 +221,7 @@

    Edge evidence

    confers DS-32 system - traitmech:000455 + traitmech:000455 METPO:2007700

    DS-32-mediated phage plaquing reduction realizes the DS-32 system trait.

    @@ -339,7 +340,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -586,7 +587,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -950,12 +960,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 07:26 UTC diff --git a/pages/traits/genomics/ds_33_system.html b/pages/traits/genomics/ds_33_system.html index b800eb85aea..f226bed13d9 100644 --- a/pages/traits/genomics/ds_33_system.html +++ b/pages/traits/genomics/ds_33_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -196,7 +197,7 @@

    Edge evidence

    confers DS-33 system - traitmech:000456 + traitmech:000456 METPO:2007700

    DS-33-mediated phage plaquing reduction realizes the DS-33 system trait.

    @@ -313,7 +314,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -546,7 +547,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -910,12 +920,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 08:05 UTC diff --git a/pages/traits/genomics/ds_34_system.html b/pages/traits/genomics/ds_34_system.html index ea5c69e46b1..2bcbb9a36ea 100644 --- a/pages/traits/genomics/ds_34_system.html +++ b/pages/traits/genomics/ds_34_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -208,7 +209,7 @@

    Edge evidence

    confers DS-34 system - traitmech:000457 + traitmech:000457 METPO:2007700

    DS-34-mediated phage plaquing reduction realizes the DS-34 system trait.

    @@ -327,7 +328,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -567,7 +568,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -931,12 +941,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 08:41 UTC diff --git a/pages/traits/genomics/ds_35_system.html b/pages/traits/genomics/ds_35_system.html index d636aa48116..a4f911b7954 100644 --- a/pages/traits/genomics/ds_35_system.html +++ b/pages/traits/genomics/ds_35_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -196,7 +197,7 @@

    Edge evidence

    confers DS-35 system - traitmech:000458 + traitmech:000458 METPO:2007700

    DS-35-mediated phage plaquing reduction realizes the DS-35 system trait.

    @@ -319,7 +320,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -552,7 +553,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -916,12 +926,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 09:13 UTC diff --git a/pages/traits/genomics/ds_36_system.html b/pages/traits/genomics/ds_36_system.html index 8a458955b68..90d9d757abb 100644 --- a/pages/traits/genomics/ds_36_system.html +++ b/pages/traits/genomics/ds_36_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -117,7 +118,7 @@

    Edge evidence

    contributes to DS-36 system - traitmech:000474 + traitmech:000474 RO:0002326

    DefenseFinder links the DS-36 source key to the DefensePredictor preprint and represents DS-36 in the HMM inventory with a DS-36 custom profile.

    @@ -226,7 +227,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -438,7 +439,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -802,12 +812,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 21:06 UTC diff --git a/pages/traits/genomics/ds_37_system.html b/pages/traits/genomics/ds_37_system.html index ba5a535b68b..394bc03666d 100644 --- a/pages/traits/genomics/ds_37_system.html +++ b/pages/traits/genomics/ds_37_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -190,7 +191,7 @@

    Edge evidence

    confers DS-37 system - traitmech:000459 + traitmech:000459 METPO:2007700

    DS-37-mediated phage plaquing reduction realizes the DS-37 system trait.

    @@ -313,7 +314,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -546,7 +547,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -910,12 +920,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 10:28 UTC diff --git a/pages/traits/genomics/ds_38_system.html b/pages/traits/genomics/ds_38_system.html index 894242a8e6b..4e604a6e663 100644 --- a/pages/traits/genomics/ds_38_system.html +++ b/pages/traits/genomics/ds_38_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -208,7 +209,7 @@

    Edge evidence

    confers DS-38 system - traitmech:000460 + traitmech:000460 METPO:2007700

    DS-38-mediated phage plaquing reduction realizes the DS-38 system trait.

    @@ -331,7 +332,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -571,7 +572,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -935,12 +945,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 11:00 UTC diff --git a/pages/traits/genomics/ds_39_system.html b/pages/traits/genomics/ds_39_system.html index 9efedebf268..cf3f31c2654 100644 --- a/pages/traits/genomics/ds_39_system.html +++ b/pages/traits/genomics/ds_39_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -220,7 +221,7 @@

    Edge evidence

    confers DS-39 system - traitmech:000461 + traitmech:000461 METPO:2007700

    DS-39-mediated phage plaquing reduction realizes the DS-39 system trait.

    @@ -343,7 +344,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -590,7 +591,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -954,12 +964,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 11:35 UTC diff --git a/pages/traits/genomics/ds_3_system.html b/pages/traits/genomics/ds_3_system.html index 4679f8aec11..edd28c13151 100644 --- a/pages/traits/genomics/ds_3_system.html +++ b/pages/traits/genomics/ds_3_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -184,7 +185,7 @@

    Edge evidence

    confers DS-3 system - traitmech:000426 + traitmech:000426 METPO:2007700

    DS-3-mediated phage plaquing reduction realizes the DS-3 system trait.

    @@ -301,7 +302,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -502,7 +503,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add DS-3 system trait -

      Minted traitmech:000426 for the DOI-backed DS-3 system under phage defense system. DOI:10.1126/science.adv7924 and the final Science supplementary tables support DS-3 as the DefensePredictor-discovered system corresponding to the one-gene PIN8 transcriptional unit that reduces bacteriophage plaquing when cloned in E. coli MG1655; the pinned DefenseFinder article and HMM inventories map DS-3 to a custom DS-3 profile while the pinned rules table has no DS-3 row, so the graph stays nonmechanistic at cloned-transcriptional-unit level and the record keeps profile-to-protein mapping, native host breadth, phage range, and direct molecular output unresolved. Reserved METPO:1038000 in proposals/metpo_traitmech_v303.

    +

    Minted traitmech:000426 for the DOI-backed DS-3 system under phage defense system. DOI:10.1126/science.adv7924 and the final Science supplementary tables support DS-3 as the DefensePredictor-discovered system corresponding to the one-gene PIN8 transcriptional unit that reduces bacteriophage plaquing when cloned in E. coli MG1655; the pinned DefenseFinder article and HMM inventories map DS-3 to a custom DS-3 profile while the pinned rules table has no DS-3 row, so the graph stays nonmechanistic at cloned-transcriptional-unit level and the record keeps profile-to-protein mapping, native host breadth, phage range, and direct molecular output unresolved. Reserved METPO:1038000 in proposals/metpo_traitmech_v303.

    • Read this curation session @@ -534,7 +535,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -898,12 +908,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 05:06 UTC diff --git a/pages/traits/genomics/ds_40_system.html b/pages/traits/genomics/ds_40_system.html index 335b1c03e80..e2d813ae588 100644 --- a/pages/traits/genomics/ds_40_system.html +++ b/pages/traits/genomics/ds_40_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -184,7 +185,7 @@

    Edge evidence

    confers DS-40 system - traitmech:000462 + traitmech:000462 METPO:2007700

    DS-40-mediated phage plaquing reduction realizes the DS-40 system trait.

    @@ -301,7 +302,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -527,7 +528,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -891,12 +901,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 12:03 UTC diff --git a/pages/traits/genomics/ds_41_system.html b/pages/traits/genomics/ds_41_system.html index 0e971721fc3..7fdc430a06c 100644 --- a/pages/traits/genomics/ds_41_system.html +++ b/pages/traits/genomics/ds_41_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -196,7 +197,7 @@

    Edge evidence

    confers DS-41 system - traitmech:000463 + traitmech:000463 METPO:2007700

    DS-41-mediated phage plaquing reduction realizes the DS-41 system trait.

    @@ -319,7 +320,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -552,7 +553,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -916,12 +926,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 12:50 UTC diff --git a/pages/traits/genomics/ds_42_system.html b/pages/traits/genomics/ds_42_system.html index 551e36f9d2e..b15d4d72b69 100644 --- a/pages/traits/genomics/ds_42_system.html +++ b/pages/traits/genomics/ds_42_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -220,7 +221,7 @@

    Edge evidence

    confers DS-42 system - traitmech:000464 + traitmech:000464 METPO:2007700

    DS-42-mediated phage plaquing reduction realizes the DS-42 system trait.

    @@ -341,7 +342,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -588,7 +589,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -952,12 +962,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 13:32 UTC diff --git a/pages/traits/genomics/ds_43_system.html b/pages/traits/genomics/ds_43_system.html index 3ab44a40d8f..66e0b890d09 100644 --- a/pages/traits/genomics/ds_43_system.html +++ b/pages/traits/genomics/ds_43_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -184,7 +185,7 @@

    Edge evidence

    confers DS-43 system - traitmech:000468 + traitmech:000468 METPO:2007700

    DS-43-mediated phage plaquing reduction realizes the DS-43 system trait.

    @@ -307,7 +308,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -533,7 +534,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -897,12 +907,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 16:06 UTC diff --git a/pages/traits/genomics/ds_44_system.html b/pages/traits/genomics/ds_44_system.html index c9b5fe5a688..4d99c5a17a0 100644 --- a/pages/traits/genomics/ds_44_system.html +++ b/pages/traits/genomics/ds_44_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -117,7 +118,7 @@

    Edge evidence

    contributes to DS-44 system - traitmech:000475 + traitmech:000475 RO:0002326

    DefenseFinder links the DS-44 source key to the DefensePredictor preprint and represents DS-44 in the HMM inventory with a DS-44 custom profile.

    @@ -226,7 +227,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -438,7 +439,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -802,12 +812,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 21:52 UTC diff --git a/pages/traits/genomics/ds_45_system.html b/pages/traits/genomics/ds_45_system.html index 2ac2b7068c9..8ef1a49228a 100644 --- a/pages/traits/genomics/ds_45_system.html +++ b/pages/traits/genomics/ds_45_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -184,7 +185,7 @@

    Edge evidence

    confers DS-45 system - traitmech:000469 + traitmech:000469 METPO:2007700

    DS-45-mediated phage plaquing reduction realizes the DS-45 system trait.

    @@ -307,7 +308,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -533,7 +534,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -897,12 +907,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 17:02 UTC diff --git a/pages/traits/genomics/ds_46_system.html b/pages/traits/genomics/ds_46_system.html index 7a0990d49fa..e70230411c0 100644 --- a/pages/traits/genomics/ds_46_system.html +++ b/pages/traits/genomics/ds_46_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -130,7 +131,7 @@

    Edge evidence

    confers DS-46 system - traitmech:000471 + traitmech:000471 METPO:2007700

    DS-46-mediated phage plaquing reduction realizes the DS-46 system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -452,7 +453,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -816,12 +826,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 18:47 UTC diff --git a/pages/traits/genomics/ds_4_system.html b/pages/traits/genomics/ds_4_system.html index 936a4dc73fe..e23976187fa 100644 --- a/pages/traits/genomics/ds_4_system.html +++ b/pages/traits/genomics/ds_4_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -214,7 +215,7 @@

    Edge evidence

    confers DS-4 system - traitmech:000427 + traitmech:000427 METPO:2007700

    DS-4-mediated phage plaquing reduction realizes the DS-4 system trait.

    @@ -339,7 +340,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -561,7 +562,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add DS-4 system trait -

      Minted traitmech:000427 for the DOI-backed DS-4 system under phage defense system. DOI:10.1126/science.adv7924 and the final Science supplementary tables support DS-4 as the DefensePredictor-discovered system corresponding to the five-gene NTTI transcriptional unit that reduces bacteriophage plaquing when cloned in E. coli MG1655; the pinned DefenseFinder article and HMM inventories map DS-4 to five custom profile rows while the pinned rules table has no DS-4 row, so the graph stays nonmechanistic at cloned-transcriptional-unit level and leaves native host breadth, component activities, profile-to-protein mapping, phage target breadth, and direct molecular output unresolved. Reserved METPO:1038100 in proposals/metpo_traitmech_v304.

    +

    Minted traitmech:000427 for the DOI-backed DS-4 system under phage defense system. DOI:10.1126/science.adv7924 and the final Science supplementary tables support DS-4 as the DefensePredictor-discovered system corresponding to the five-gene NTTI transcriptional unit that reduces bacteriophage plaquing when cloned in E. coli MG1655; the pinned DefenseFinder article and HMM inventories map DS-4 to five custom profile rows while the pinned rules table has no DS-4 row, so the graph stays nonmechanistic at cloned-transcriptional-unit level and leaves native host breadth, component activities, profile-to-protein mapping, phage target breadth, and direct molecular output unresolved. Reserved METPO:1038100 in proposals/metpo_traitmech_v304.

    • Read this curation session @@ -593,7 +594,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -957,12 +967,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 06:13 UTC diff --git a/pages/traits/genomics/ds_5_system.html b/pages/traits/genomics/ds_5_system.html index 12f982771f0..be946c0b1df 100644 --- a/pages/traits/genomics/ds_5_system.html +++ b/pages/traits/genomics/ds_5_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -196,7 +197,7 @@

    Edge evidence

    confers DS-5 system - traitmech:000428 + traitmech:000428 METPO:2007700

    DS-5-mediated phage plaquing reduction realizes the DS-5 system trait.

    @@ -315,7 +316,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -568,7 +569,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -932,12 +942,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 07:38 UTC diff --git a/pages/traits/genomics/ds_6_system.html b/pages/traits/genomics/ds_6_system.html index c1c16b74a31..85d73556abd 100644 --- a/pages/traits/genomics/ds_6_system.html +++ b/pages/traits/genomics/ds_6_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -230,7 +231,7 @@

    Edge evidence

    confers DS-6 system - traitmech:000430 + traitmech:000430 METPO:2007700

    DS-6-mediated phage plaquing reduction realizes the DS-6 system trait.

    @@ -351,7 +352,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -635,7 +636,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -999,12 +1009,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 09:22 UTC diff --git a/pages/traits/genomics/ds_7_system.html b/pages/traits/genomics/ds_7_system.html index b7f27172511..24a11f94f75 100644 --- a/pages/traits/genomics/ds_7_system.html +++ b/pages/traits/genomics/ds_7_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -200,7 +201,7 @@

    Edge evidence

    confers DS-7 system - traitmech:000431 + traitmech:000431 METPO:2007700

    DS-7-mediated phage plaquing reduction realizes the DS-7 system trait.

    @@ -317,7 +318,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -573,7 +574,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -937,12 +947,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 09:58 UTC diff --git a/pages/traits/genomics/ds_8_system.html b/pages/traits/genomics/ds_8_system.html index 177cd602b7c..33c803b7070 100644 --- a/pages/traits/genomics/ds_8_system.html +++ b/pages/traits/genomics/ds_8_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -190,7 +191,7 @@

    Edge evidence

    confers DS-8 system - traitmech:000432 + traitmech:000432 METPO:2007700

    DS-8-mediated phage plaquing reduction realizes the DS-8 system trait.

    @@ -307,7 +308,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -582,7 +583,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -946,12 +956,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 11:24 UTC diff --git a/pages/traits/genomics/ds_9_system.html b/pages/traits/genomics/ds_9_system.html index f8be9a7742c..d9810cfd845 100644 --- a/pages/traits/genomics/ds_9_system.html +++ b/pages/traits/genomics/ds_9_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -196,7 +197,7 @@

    Edge evidence

    confers DS-9 system - traitmech:000433 + traitmech:000433 METPO:2007700

    DS-9-mediated phage plaquing reduction realizes the DS-9 system trait.

    @@ -315,7 +316,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -590,7 +591,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -954,12 +964,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 12:06 UTC diff --git a/pages/traits/genomics/dsr_system.html b/pages/traits/genomics/dsr_system.html index 66400a5a490..0e7b61530d0 100644 --- a/pages/traits/genomics/dsr_system.html +++ b/pages/traits/genomics/dsr_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -222,7 +223,7 @@

    Edge evidence

    confers Dsr system - traitmech:000280 + traitmech:000280 METPO:2007700

    DefenseFinder represents Dsr as Dsr_I and Dsr_II subtypes within its Dsr system models.

    @@ -325,7 +326,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -484,7 +485,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -848,12 +858,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 13:00 UTC diff --git a/pages/traits/genomics/duf262_schlafen_system.html b/pages/traits/genomics/duf262_schlafen_system.html index 96db244cda2..8a02422eb67 100644 --- a/pages/traits/genomics/duf262_schlafen_system.html +++ b/pages/traits/genomics/duf262_schlafen_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -124,7 +125,7 @@

    Edge evidence

    confers DUF262 Schlafen system - traitmech:000530 + traitmech:000530 METPO:2007700

    Prokaryotic Schlafen antiviral effector activity realizes the organism-level DUF262 Schlafen system trait.

    @@ -231,7 +232,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -436,7 +437,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -800,12 +810,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 01:00 UTC diff --git a/pages/traits/genomics/ecokmcra_system.html b/pages/traits/genomics/ecokmcra_system.html index 5a6b639a56b..3894d5eab61 100644 --- a/pages/traits/genomics/ecokmcra_system.html +++ b/pages/traits/genomics/ecokmcra_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -167,7 +168,7 @@

    Edge evidence

    confers EcoKMcrA system - traitmech:000509 + traitmech:000509 METPO:2007700

    EcoKMcrA-dependent Type IV restriction realizes the organism-level EcoKMcrA system possession trait.

      @@ -189,11 +190,11 @@

      Edge evidence

    • EcoKMcrA system - traitmech:000509 + traitmech:000509 is a type IV modification-dependent restriction system - traitmech:000496 - rdfs:subClassOf + traitmech:000496 + rdfs:subClassOf

      EcoKMcrA system possession is a Type IV modification-dependent restriction system trait.

        @@ -258,7 +259,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -274,7 +275,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -479,7 +480,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -843,12 +853,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 07:11 UTC diff --git a/pages/traits/genomics/eleos_system.html b/pages/traits/genomics/eleos_system.html index 1426c37d80d..5e6cd49590c 100644 --- a/pages/traits/genomics/eleos_system.html +++ b/pages/traits/genomics/eleos_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -172,7 +173,7 @@

    Edge evidence

    confers Eleos system - traitmech:000250 + traitmech:000250 METPO:2007700

    Eleos-mediated phage restriction realizes the Eleos system trait.

    @@ -273,7 +274,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -432,7 +433,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -796,12 +806,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 20:41 UTC diff --git a/pages/traits/genomics/endpacf1_system.html b/pages/traits/genomics/endpacf1_system.html index 28ef1f147a4..7816e51055b 100644 --- a/pages/traits/genomics/endpacf1_system.html +++ b/pages/traits/genomics/endpacf1_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -204,7 +205,7 @@

    Edge evidence

    confers ENDPaCF1 system - traitmech:000503 + traitmech:000503 METPO:2007700

    ENDPaCF1-family targeting of hypermodified phage DNA realizes the ENDPaCF1 system trait.

    @@ -305,7 +306,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -555,7 +556,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -919,12 +929,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 00:24 UTC diff --git a/pages/traits/genomics/epona_system.html b/pages/traits/genomics/epona_system.html index 89846b1f747..12f08ecc78d 100644 --- a/pages/traits/genomics/epona_system.html +++ b/pages/traits/genomics/epona_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Epona system - traitmech:000281 + traitmech:000281 METPO:2007700

    Epona-mediated phage restriction realizes the Epona system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -392,7 +393,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -756,12 +766,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 14:03 UTC diff --git a/pages/traits/genomics/erebus_system.html b/pages/traits/genomics/erebus_system.html index ac19ff9ed80..a7100901998 100644 --- a/pages/traits/genomics/erebus_system.html +++ b/pages/traits/genomics/erebus_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -142,7 +143,7 @@

    Edge evidence

    confers Erebus system - traitmech:000308 + traitmech:000308 METPO:2007700

    Erebus-mediated phage restriction realizes the Erebus system trait.

    @@ -239,7 +240,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -404,7 +405,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -768,12 +778,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 12:25 UTC diff --git a/pages/traits/genomics/esos_system.html b/pages/traits/genomics/esos_system.html index 314c1c948cf..fd55a6cf73e 100644 --- a/pages/traits/genomics/esos_system.html +++ b/pages/traits/genomics/esos_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Esos system - traitmech:000282 + traitmech:000282 METPO:2007700

    Esos-mediated phage restriction realizes the Esos system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -392,7 +393,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -756,12 +766,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 14:36 UTC diff --git a/pages/traits/genomics/fliodhais_system.html b/pages/traits/genomics/fliodhais_system.html index 939fbd0ba24..fe453fd669f 100644 --- a/pages/traits/genomics/fliodhais_system.html +++ b/pages/traits/genomics/fliodhais_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers Fliodhais system - traitmech:000326 + traitmech:000326 METPO:2007700

    Fliodhais-mediated phage restriction realizes the Fliodhais system trait.

      @@ -164,11 +165,11 @@

      Edge evidence

    • Fliodhais system - traitmech:000326 + traitmech:000326 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Fliodhais system possession is a phage-defense-system trait.

        @@ -227,7 +228,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -243,7 +244,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -370,7 +371,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Fliodhais system trait -

      Added traitmech:000326 Fliodhais system as a DOI-backed GENOMICS TraitRecord under phage defense system. DOI:10.1093/nar/gkae671 names Fliodhais among newly described lactococcal antiphage systems, reports that both Fliodhais genetic components are necessary for the observed activity, and describes Fliodhais-associated phage c2 plaque-size reduction. The pinned DefenseFinder article registry maps Fliodhais to the Grafakou et al. lactococcal plasmidome discovery paper. Reserved METPO:1028000 in proposals/metpo_traitmech_v203 for the upstream replacement ID.

    +

    Added traitmech:000326 Fliodhais system as a DOI-backed GENOMICS TraitRecord under phage defense system. DOI:10.1093/nar/gkae671 names Fliodhais among newly described lactococcal antiphage systems, reports that both Fliodhais genetic components are necessary for the observed activity, and describes Fliodhais-associated phage c2 plaque-size reduction. The pinned DefenseFinder article registry maps Fliodhais to the Grafakou et al. lactococcal plasmidome discovery paper. Reserved METPO:1028000 in proposals/metpo_traitmech_v203 for the upstream replacement ID.

    • Read this curation session @@ -402,7 +403,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -766,12 +776,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 04:19 UTC diff --git a/pages/traits/genomics/fs_giy_yig_system.html b/pages/traits/genomics/fs_giy_yig_system.html index 81543b2b48d..8e137aa31c3 100644 --- a/pages/traits/genomics/fs_giy_yig_system.html +++ b/pages/traits/genomics/fs_giy_yig_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers FS-GIY-YIG system - traitmech:000346 + traitmech:000346 METPO:2007700

    FS_GIY_YIG-associated mobile-element defense realizes the FS-GIY-YIG system trait.

    @@ -257,7 +258,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -416,7 +417,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -780,12 +790,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 21:36 UTC diff --git a/pages/traits/genomics/fs_hepn_tm_system.html b/pages/traits/genomics/fs_hepn_tm_system.html index 9506fbdcbab..d7d6d0b892b 100644 --- a/pages/traits/genomics/fs_hepn_tm_system.html +++ b/pages/traits/genomics/fs_hepn_tm_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -166,7 +167,7 @@

    Edge evidence

    confers FS-HEPN-TM system - traitmech:000347 + traitmech:000347 METPO:2007700

    FS_HEPN_TM-associated mobile-element defense realizes the FS-HEPN-TM system trait.

    @@ -271,7 +272,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -430,7 +431,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -794,12 +804,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 22:22 UTC diff --git a/pages/traits/genomics/fs_hp_sdh_sah_system.html b/pages/traits/genomics/fs_hp_sdh_sah_system.html index 86bf67f38db..c33b41114a3 100644 --- a/pages/traits/genomics/fs_hp_sdh_sah_system.html +++ b/pages/traits/genomics/fs_hp_sdh_sah_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -166,7 +167,7 @@

    Edge evidence

    confers FS-HP-SDH-sah system - traitmech:000349 + traitmech:000349 METPO:2007700

    FS_HP_SDH_sah-associated mobile-element defense realizes the FS-HP-SDH-sah system trait.

    @@ -271,7 +272,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -430,7 +431,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -794,12 +804,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 23:29 UTC diff --git a/pages/traits/genomics/fs_hp_system.html b/pages/traits/genomics/fs_hp_system.html index eff70d91ce1..b9d28b2e973 100644 --- a/pages/traits/genomics/fs_hp_system.html +++ b/pages/traits/genomics/fs_hp_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers FS-HP system - traitmech:000348 + traitmech:000348 METPO:2007700

    FS_HP-associated mobile-element defense realizes the FS-HP system trait.

    @@ -257,7 +258,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -416,7 +417,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -780,12 +790,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 22:51 UTC diff --git a/pages/traits/genomics/fs_hsdr_like_system.html b/pages/traits/genomics/fs_hsdr_like_system.html index 95fb0bf0bba..4df1b173019 100644 --- a/pages/traits/genomics/fs_hsdr_like_system.html +++ b/pages/traits/genomics/fs_hsdr_like_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -178,7 +179,7 @@

    Edge evidence

    confers FS-HsdR-like system - traitmech:000350 + traitmech:000350 METPO:2007700

    FS_HsdR_like-associated mobile-element defense realizes the FS-HsdR-like system trait.

    @@ -285,7 +286,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -444,7 +445,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -808,12 +818,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-22 00:00 UTC diff --git a/pages/traits/genomics/fs_sma_system.html b/pages/traits/genomics/fs_sma_system.html index 650ece535bd..d4c868691d8 100644 --- a/pages/traits/genomics/fs_sma_system.html +++ b/pages/traits/genomics/fs_sma_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers FS-Sma system - traitmech:000351 + traitmech:000351 METPO:2007700

    FS_Sma-associated mobile-element defense realizes the FS-Sma system trait.

    @@ -257,7 +258,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -416,7 +417,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -780,12 +790,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-22 00:54 UTC diff --git a/pages/traits/genomics/gabija_system.html b/pages/traits/genomics/gabija_system.html index e87faaec425..044e12dc570 100644 --- a/pages/traits/genomics/gabija_system.html +++ b/pages/traits/genomics/gabija_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -212,7 +213,7 @@

    Edge evidence

    confers Gabija system - traitmech:000215 + traitmech:000215 METPO:2007700

    GajAB DNA cleavage is part of the antiviral output that realizes the Gabija system defense phenotype.

      @@ -228,11 +229,11 @@

      Edge evidence

    • Gabija system - traitmech:000215 + traitmech:000215 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Gabija system possession is a phage-defense-system trait.

        @@ -291,9 +292,9 @@

        Parent traits (1)

        Synonyms (2)

          -
        • Gabija anti-phage defense system EXACT_SYNONYM · DOI:10.1093/nar/gkad951
          • +
        • Gabija anti-phage defense system EXACT_SYNONYM · DOI:10.1093/nar/gkad951
          • -
        • Gabija anti-phage defence system EXACT_SYNONYM · DOI:10.1038/s41586-023-06855-2
          • +
        • Gabija anti-phage defence system EXACT_SYNONYM · DOI:10.1038/s41586-023-06855-2
    @@ -309,7 +310,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -494,7 +495,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -858,12 +868,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 12:39 UTC diff --git a/pages/traits/genomics/gao_ape_system.html b/pages/traits/genomics/gao_ape_system.html index e9c9eb2647c..6a30906cc8e 100644 --- a/pages/traits/genomics/gao_ape_system.html +++ b/pages/traits/genomics/gao_ape_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -240,7 +241,7 @@

    Edge evidence

    confers ApeA system - traitmech:000334 + traitmech:000334 METPO:2007700

    ApeA low-MOI protection and abortive infection realize the ApeA system possession trait.

    @@ -406,7 +407,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -551,7 +552,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Broadened ApeA system mechanism scope -

      Addressed issue #1191 from the PR #1190 adversarial review by making ApeA system mechanism-neutral at the root, adding DOI:10.64898/2026.03.20.713152 RNA-phage evidence, splitting host-tRNA abortive infection from phage-genomic-RNA non-abortive restriction in the causal graph, and preserving the canonical-example evidence gap.

    +

    Addressed issue #1191 from the PR #1190 adversarial review by making ApeA system mechanism-neutral at the root, adding DOI:10.64898/2026.03.20.713152 RNA-phage evidence, splitting host-tRNA abortive infection from phage-genomic-RNA non-abortive restriction in the causal graph, and preserving the canonical-example evidence gap.

    • Read this curation session @@ -583,7 +584,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -947,12 +957,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 11:21 UTC diff --git a/pages/traits/genomics/gao_her_duf_system.html b/pages/traits/genomics/gao_her_duf_system.html index 30cb7137ed1..443066f1403 100644 --- a/pages/traits/genomics/gao_her_duf_system.html +++ b/pages/traits/genomics/gao_her_duf_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (5)

    DOI:10.1126/science.aba0372
    By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.
    -

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

    +

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

  • @@ -160,7 +161,7 @@

    Edge evidence

    confers Gao-Her-DUF system - traitmech:000361 + traitmech:000361 METPO:2007700

    Gao_Her_DUF-associated antiviral cassette defense realizes the Gao-Her-DUF system trait.

    • @@ -259,7 +260,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -394,7 +395,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 5 Stage 5 remediation of F-C5S4-DEF-SRC-001 in group G-C5S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 5 Stage 5 remediation of F-C5S4-DEF-SRC-001 in group G-C5S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -442,7 +443,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -806,12 +816,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 21:40 UTC diff --git a/pages/traits/genomics/gao_her_sir_system.html b/pages/traits/genomics/gao_her_sir_system.html index 9064642c8e7..b0e98e70577 100644 --- a/pages/traits/genomics/gao_her_sir_system.html +++ b/pages/traits/genomics/gao_her_sir_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (5)

    DOI:10.1126/science.aba0372
    By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.
    -

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

    +

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

  • @@ -160,7 +161,7 @@

    Edge evidence

    confers Gao-Her-SIR system - traitmech:000362 + traitmech:000362 METPO:2007700

    Gao_Her_SIR-associated antiviral cassette defense realizes the Gao-Her-SIR system trait.

    • @@ -259,7 +260,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -394,7 +395,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 5 Stage 5 remediation of F-C5S4-DEF-SRC-002 in group G-C5S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 5 Stage 5 remediation of F-C5S4-DEF-SRC-002 in group G-C5S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -442,7 +443,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -806,12 +816,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 21:40 UTC diff --git a/pages/traits/genomics/gao_her_system.html b/pages/traits/genomics/gao_her_system.html index d33a615ddab..e4ac08e77f3 100644 --- a/pages/traits/genomics/gao_her_system.html +++ b/pages/traits/genomics/gao_her_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (4)

    DOI:10.1126/science.aba0372
    By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.
    -

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

    +

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

  • @@ -148,7 +149,7 @@

    Edge evidence

    confers Gao-Her system - traitmech:000409 + traitmech:000409 METPO:2007700

    Gao_Her-associated antiviral cassette defense realizes the Gao-Her system trait.

    • @@ -266,7 +267,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -395,7 +396,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-009 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-009 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -437,7 +438,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -801,12 +811,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/genomics/gao_hhe_system.html b/pages/traits/genomics/gao_hhe_system.html index 8f94995f42c..71807caec85 100644 --- a/pages/traits/genomics/gao_hhe_system.html +++ b/pages/traits/genomics/gao_hhe_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (4)

    DOI:10.1126/science.aba0372
    By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.
    -

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

    +

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

  • @@ -148,7 +149,7 @@

    Edge evidence

    confers Gao-Hhe system - traitmech:000353 + traitmech:000353 METPO:2007700

    Gao_Hhe-associated antiviral cassette defense realizes the Gao-Hhe system trait.

    • @@ -251,7 +252,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -374,7 +375,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-010 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-010 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -416,7 +417,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -780,12 +790,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/genomics/gao_iet_system.html b/pages/traits/genomics/gao_iet_system.html index 987228bd7a4..84aeb1daf64 100644 --- a/pages/traits/genomics/gao_iet_system.html +++ b/pages/traits/genomics/gao_iet_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (5)

    DOI:10.1126/science.aba0372
    By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.
    -

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

    +

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

  • @@ -160,7 +161,7 @@

    Edge evidence

    confers Gao-Iet system - traitmech:000354 + traitmech:000354 METPO:2007700

    Gao_Iet-associated antiviral cassette defense realizes the Gao-Iet system trait.

    • @@ -265,7 +266,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -388,7 +389,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-011 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-011 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -430,7 +431,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -794,12 +804,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/genomics/gao_mza_system.html b/pages/traits/genomics/gao_mza_system.html index 8bb9bb35d46..37bd30c10ec 100644 --- a/pages/traits/genomics/gao_mza_system.html +++ b/pages/traits/genomics/gao_mza_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (8)

    DOI:10.1126/science.aba0372
    By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.
    -

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

    +

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

  • @@ -196,7 +197,7 @@

    Edge evidence

    confers Gao-Mza system - traitmech:000355 + traitmech:000355 METPO:2007700

    Gao_Mza-associated antiviral cassette defense realizes the Gao-Mza system trait.

    • @@ -307,7 +308,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -430,7 +431,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-012 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-012 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -472,7 +473,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -836,12 +846,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/genomics/gao_ppl_system.html b/pages/traits/genomics/gao_ppl_system.html index 287b6e22cfe..c4d79121498 100644 --- a/pages/traits/genomics/gao_ppl_system.html +++ b/pages/traits/genomics/gao_ppl_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (4)

    DOI:10.1126/science.aba0372
    By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.
    -

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

    +

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

  • @@ -148,7 +149,7 @@

    Edge evidence

    confers Gao-Ppl system - traitmech:000356 + traitmech:000356 METPO:2007700

    Gao_Ppl-associated antiviral cassette defense realizes the Gao-Ppl system trait.

    • @@ -251,7 +252,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -374,7 +375,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-013 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-013 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -416,7 +417,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -780,12 +790,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/genomics/gao_qat_system.html b/pages/traits/genomics/gao_qat_system.html index 3b51d46e4bd..336ceb5a3a5 100644 --- a/pages/traits/genomics/gao_qat_system.html +++ b/pages/traits/genomics/gao_qat_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (7)

    DOI:10.1126/science.aba0372
    By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.
    -

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

    +

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

  • @@ -184,7 +185,7 @@

    Edge evidence

    confers Gao-Qat system - traitmech:000359 + traitmech:000359 METPO:2007700

    Gao_Qat-associated antiviral cassette defense realizes the Gao-Qat system trait.

    • @@ -293,7 +294,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -416,7 +417,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-014 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-014 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -458,7 +459,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -822,12 +832,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/genomics/gao_rl_system.html b/pages/traits/genomics/gao_rl_system.html index 2fef248e2b1..c786551ce53 100644 --- a/pages/traits/genomics/gao_rl_system.html +++ b/pages/traits/genomics/gao_rl_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (7)

    DOI:10.1126/science.aba0372
    By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.
    -

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

    +

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

  • @@ -184,7 +185,7 @@

    Edge evidence

    confers Gao-RL system - traitmech:000352 + traitmech:000352 METPO:2007700

    Gao_RL-associated antiviral cassette defense realizes the Gao-RL system trait.

    • @@ -293,7 +294,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -416,7 +417,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-015 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-015 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -458,7 +459,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -822,12 +832,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/genomics/gao_tery_system.html b/pages/traits/genomics/gao_tery_system.html index 8e586c23044..52abd8e0d85 100644 --- a/pages/traits/genomics/gao_tery_system.html +++ b/pages/traits/genomics/gao_tery_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (6)

    DOI:10.1126/science.aba0372
    By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.
    -

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

    +

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

  • @@ -172,7 +173,7 @@

    Edge evidence

    confers Gao-TerY system - traitmech:000360 + traitmech:000360 METPO:2007700

    Gao_TerY-associated antiviral cassette defense realizes the Gao-TerY system trait.

    • @@ -279,7 +280,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -402,7 +403,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-016 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-016 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -444,7 +445,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -808,12 +818,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/genomics/gao_tmn_system.html b/pages/traits/genomics/gao_tmn_system.html index 56717418e80..d28c6d1fb38 100644 --- a/pages/traits/genomics/gao_tmn_system.html +++ b/pages/traits/genomics/gao_tmn_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (4)

    DOI:10.1126/science.aba0372
    By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.
    -

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

    +

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

  • @@ -148,7 +149,7 @@

    Edge evidence

    confers Gao-Tmn system - traitmech:000357 + traitmech:000357 METPO:2007700

    Gao_Tmn-associated antiviral cassette defense realizes the Gao-Tmn system trait.

    • @@ -251,7 +252,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -374,7 +375,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-017 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-017 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -416,7 +417,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -780,12 +790,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/genomics/gao_upx_system.html b/pages/traits/genomics/gao_upx_system.html index 1d3745b6500..cfb91ef2ef1 100644 --- a/pages/traits/genomics/gao_upx_system.html +++ b/pages/traits/genomics/gao_upx_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (4)

    DOI:10.1126/science.aba0372
    By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.
    -

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

    +

    Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes (PMID:32855333 / DOI:10.1126/science.aba0372).

  • @@ -148,7 +149,7 @@

    Edge evidence

    confers Gao-Upx system - traitmech:000358 + traitmech:000358 METPO:2007700

    Gao_Upx-associated antiviral cassette defense realizes the Gao-Upx system trait.

    • @@ -251,7 +252,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -374,7 +375,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-018 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Aligned record-level evidence[0].reference from PMID:32855333 to DOI:10.1126/science.aba0372 (same Gao et al. 2020 publication) to match definition_source while preserving the verified verbatim snippet and PMID cross-reference in notes (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-018 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -416,7 +417,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -780,12 +790,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/genomics/gaps1_system.html b/pages/traits/genomics/gaps1_system.html index d6fab7dee4c..3c337071302 100644 --- a/pages/traits/genomics/gaps1_system.html +++ b/pages/traits/genomics/gaps1_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -123,7 +124,7 @@

    Edge evidence

    contributes to GAPS1 system - traitmech:000371 + traitmech:000371 RO:0002326

    DefenseFinder records GAPS1 as a named system and models it as a single-profile GAPS1__GAPS1 rule.

    @@ -257,7 +258,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -453,7 +454,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -817,12 +827,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 11:58 UTC diff --git a/pages/traits/genomics/gaps2_system.html b/pages/traits/genomics/gaps2_system.html index 74a0ae369a0..f8c3e531f9a 100644 --- a/pages/traits/genomics/gaps2_system.html +++ b/pages/traits/genomics/gaps2_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -60,13 +61,13 @@

    Trait evidence (10) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md -
    The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the "GMT-encoded Anti-Phage System" acronym.
    +
    The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the "GMT-encoded Anti-Phage System" acronym.

    The DefenseFinder wiki describes GAPS2 as a single-protein GMT-encoded system cloned from Vibrio into E. coli K-12.

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md -
    GAPS2 is composed of a single protein with a DNA BRCT domains :ref{doi=10.4161/cc.10.15.16312}.
    +
    GAPS2 is composed of a single protein with a DNA BRCT domains :ref{doi=10.4161/cc.10.15.16312}.

    The DefenseFinder wiki reports a DNA BRCT domain in the single GAPS2 protein.

    • @@ -84,9 +85,9 @@

    Trait evidence (10) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md -
    Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 +
    Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus -<a href='https://ncbi.nlm.nih.gov/protein/WP_174208646.1'>WP_174208646.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/WP_174208646.1'>WP_174208646.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> P1-vir & Lambda-vir

    The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS2 source locus expressed in E. coli against P1-vir and Lambda-vir.

    @@ -159,15 +160,15 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md - The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the "GMT-encoded Anti-Phage System" acronym. + The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the "GMT-encoded Anti-Phage System" acronym. The DefenseFinder wiki describes GAPS2 as a single-protein GMT-encoded system cloned from Vibrio into E. coli K-12.
  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md - Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 + Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus -<a href='https://ncbi.nlm.nih.gov/protein/WP_174208646.1'>WP_174208646.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/WP_174208646.1'>WP_174208646.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> P1-vir & Lambda-vir The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS2 source locus expressed in E. coli against P1-vir and Lambda-vir.
    • @@ -200,16 +201,16 @@

    Edge evidence

    confers GAPS2 system - traitmech:000380 + traitmech:000380 METPO:2007700

    Protection against P1-vir and lambda-vir realizes the GAPS2 system trait.

    @@ -320,7 +321,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -426,14 +427,14 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md -
    The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the "GMT-encoded Anti-Phage System" acronym.
    +
    The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the "GMT-encoded Anti-Phage System" acronym.
  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md -
    GAPS2 is composed of a single protein with a DNA BRCT domains :ref{doi=10.4161/cc.10.15.16312}.
    +
    GAPS2 is composed of a single protein with a DNA BRCT domains :ref{doi=10.4161/cc.10.15.16312}.
    • @@ -447,9 +448,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md -
    Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 +
    Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus -<a href='https://ncbi.nlm.nih.gov/protein/WP_174208646.1'>WP_174208646.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/WP_174208646.1'>WP_174208646.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> P1-vir & Lambda-vir
    • @@ -535,7 +536,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -899,12 +909,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 11:30 UTC diff --git a/pages/traits/genomics/gaps4_system.html b/pages/traits/genomics/gaps4_system.html index 67481fc6ac5..2d38b1f5f12 100644 --- a/pages/traits/genomics/gaps4_system.html +++ b/pages/traits/genomics/gaps4_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -66,13 +67,13 @@

    Trait evidence (11) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md -
    GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.
    +
    GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.

    The DefenseFinder wiki summarizes GAPS4 activity against T4, P1-vir, lambda-vir, and T7 plaque lysis in an E. coli assay.

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md -
    GAPS4a is a nuclease containing a domain from the PDDEXK clan (CL0236) suggesting that the GAPS4 defense system is acting via DNA degradation. Both genes are required for phage defense and were predicted to form a heterodimer. It was shown that the system causes host DNA degradation upon infection by lambda-vir only, which would suggest that GAPS4 is an abortive infection system :ref{doi=10.1101/2023.03.28.534373}.
    +
    GAPS4a is a nuclease containing a domain from the PDDEXK clan (CL0236) suggesting that the GAPS4 defense system is acting via DNA degradation. Both genes are required for phage defense and were predicted to form a heterodimer. It was shown that the system causes host DNA degradation upon infection by lambda-vir only, which would suggest that GAPS4 is an abortive infection system :ref{doi=10.1101/2023.03.28.534373}.

    The DefenseFinder wiki summarizes evidence for PDDEXK-domain GAPS4a, dual-gene requirement, and lambda-vir-associated host DNA degradation.

    • @@ -84,9 +85,9 @@

    Trait evidence (11) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md -
    Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 +
    Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus -<a href='https://ncbi.nlm.nih.gov/protein/WP_055466293.1'>WP_055466293.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/WP_055466293.1'>WP_055466293.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir

    The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS4 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir.

    @@ -173,15 +174,15 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md - GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}. + GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}. The DefenseFinder wiki summarizes GAPS4 activity against T4, P1-vir, lambda-vir, and T7 plaque lysis in an E. coli assay.
  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md - Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 + Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus -<a href='https://ncbi.nlm.nih.gov/protein/WP_055466293.1'>WP_055466293.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/WP_055466293.1'>WP_055466293.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS4 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir.
    • @@ -222,22 +223,22 @@

    Edge evidence

    confers GAPS4 system - traitmech:000379 + traitmech:000379 METPO:2007700

    Protection against T7, T4, P1-vir, and lambda-vir realizes the GAPS4 system trait.

    @@ -352,7 +353,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -458,23 +459,23 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md -
    GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.
    +
    GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.
  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md -
    GAPS4a is a nuclease containing a domain from the PDDEXK clan (CL0236) suggesting that the GAPS4 defense system is acting via DNA degradation. Both genes are required for phage defense and were predicted to form a heterodimer. It was shown that the system causes host DNA degradation upon infection by lambda-vir only, which would suggest that GAPS4 is an abortive infection system :ref{doi=10.1101/2023.03.28.534373}.
    +
    GAPS4a is a nuclease containing a domain from the PDDEXK clan (CL0236) suggesting that the GAPS4 defense system is acting via DNA degradation. Both genes are required for phage defense and were predicted to form a heterodimer. It was shown that the system causes host DNA degradation upon infection by lambda-vir only, which would suggest that GAPS4 is an abortive infection system :ref{doi=10.1101/2023.03.28.534373}.
  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md -
    Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 +
    Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus -<a href='https://ncbi.nlm.nih.gov/protein/WP_055466293.1'>WP_055466293.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/WP_055466293.1'>WP_055466293.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir
    • @@ -567,7 +568,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -931,12 +941,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 10:48 UTC diff --git a/pages/traits/genomics/gaps6_system.html b/pages/traits/genomics/gaps6_system.html index 0f839d15adf..a135fada3f3 100644 --- a/pages/traits/genomics/gaps6_system.html +++ b/pages/traits/genomics/gaps6_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -60,7 +61,7 @@

    Trait evidence (10) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md -
    GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/) and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These two proteins are encoded together in diverse Gram-negative bacteria.
    +
    GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/) and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These two proteins are encoded together in diverse Gram-negative bacteria.

    The DefenseFinder wiki describes GAPS6 as a two-protein system with GAPS6a and GAPS6b encoded together.

    @@ -72,7 +73,7 @@

    Trait evidence (10) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md -
    GAPS6b is composed of TPR repeats at the N-terminus, possibly allowing ligand binding and a predicted RNAse domain (PINc, PF08745.14) at the C-terminus. PINc domains have been implicated as toxins in bacterial toxin-antitoxin modules :ref{doi=10.1093/protein/gzq081}. The PINc domain is required for the anti-phage defense activity of GAPS6.
    +
    GAPS6b is composed of TPR repeats at the N-terminus, possibly allowing ligand binding and a predicted RNAse domain (PINc, PF08745.14) at the C-terminus. PINc domains have been implicated as toxins in bacterial toxin-antitoxin modules :ref{doi=10.1093/protein/gzq081}. The PINc domain is required for the anti-phage defense activity of GAPS6.

    The DefenseFinder wiki reports that GAPS6b carries TPR repeats and a PINc domain required for GAPS6 anti-phage activity.

    @@ -84,9 +85,9 @@

    Trait evidence (10) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md -
    Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 +
    Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus -<a href='https://ncbi.nlm.nih.gov/protein/WP_248387294.1'>WP_248387294.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/WP_248387294.1'>WP_248387294.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir

    The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS6 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir.

    @@ -157,15 +158,15 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md - GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/) and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These two proteins are encoded together in diverse Gram-negative bacteria. + GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/) and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These two proteins are encoded together in diverse Gram-negative bacteria. The DefenseFinder wiki describes GAPS6 as a two-protein system with GAPS6a and GAPS6b encoded together.
  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md - Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 + Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus -<a href='https://ncbi.nlm.nih.gov/protein/WP_248387294.1'>WP_248387294.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/WP_248387294.1'>WP_248387294.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS6 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir.
    • @@ -196,16 +197,16 @@

    Edge evidence

    confers GAPS6 system - traitmech:000381 + traitmech:000381 METPO:2007700

    Protection against T7, T4, P1-vir, and lambda-vir realizes the GAPS6 system trait.

    @@ -310,7 +311,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -416,7 +417,7 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md -
    GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/) and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These two proteins are encoded together in diverse Gram-negative bacteria.
    +
    GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/) and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These two proteins are encoded together in diverse Gram-negative bacteria.
    • @@ -430,16 +431,16 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md -
    GAPS6b is composed of TPR repeats at the N-terminus, possibly allowing ligand binding and a predicted RNAse domain (PINc, PF08745.14) at the C-terminus. PINc domains have been implicated as toxins in bacterial toxin-antitoxin modules :ref{doi=10.1093/protein/gzq081}. The PINc domain is required for the anti-phage defense activity of GAPS6.
    +
    GAPS6b is composed of TPR repeats at the N-terminus, possibly allowing ligand binding and a predicted RNAse domain (PINc, PF08745.14) at the C-terminus. PINc domains have been implicated as toxins in bacterial toxin-antitoxin modules :ref{doi=10.1093/protein/gzq081}. The PINc domain is required for the anti-phage defense activity of GAPS6.
  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md -
    Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 +
    Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus -<a href='https://ncbi.nlm.nih.gov/protein/WP_248387294.1'>WP_248387294.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/WP_248387294.1'>WP_248387294.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir
    • @@ -532,7 +533,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -896,12 +906,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 11:59 UTC diff --git a/pages/traits/genomics/gasdermin_system.html b/pages/traits/genomics/gasdermin_system.html index 8d9cd4bf8f6..abf102b6e76 100644 --- a/pages/traits/genomics/gasdermin_system.html +++ b/pages/traits/genomics/gasdermin_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -91,7 +92,7 @@

    Trait evidence (10) https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    GasderMIN | 10\.1101/2021\.06\.07\.447441 | Bacterial gasdermins reveal an ancient mechanism of cell death
    -

    The DefenseFinder article registry maps the GasderMIN model namespace to the Johnson et al. bacterial gasdermin preprint, later published under DOI:10.1126/science.abj8432.

    +

    The DefenseFinder article registry maps the GasderMIN model namespace to the Johnson et al. bacterial gasdermin preprint, later published under DOI:10.1126/science.abj8432.

  • @@ -235,7 +236,7 @@

    Edge evidence

    contributes to GasderMIN system - traitmech:000336 + traitmech:000336 RO:0002326

    The GasderMIN DefenseFinder model identifies a GasderMIN__bGSDM profile, and Johnson et al. show that deleting a bGSDM gene can abolish phage protection by a gasdermin operon.

    • @@ -375,7 +376,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -527,7 +528,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add GasderMIN phage-defense trait -

      Minted traitmech:000336 for the DOI-backed GasderMIN bacterial gasdermin phage-defense system under the phage defense system parent, added Johnson et al. evidence from DOI:10.1126/science.abj8432 and stable PMC full text, added pinned DefenseFinder registry/profile/rules evidence for GasderMIN__bGSDM, added a Lysobacter enzymogenes canonical example, and recorded a knowledge gap for CARD-NLR-associated gasdermins and family breadth.

    +

    Minted traitmech:000336 for the DOI-backed GasderMIN bacterial gasdermin phage-defense system under the phage defense system parent, added Johnson et al. evidence from DOI:10.1126/science.abj8432 and stable PMC full text, added pinned DefenseFinder registry/profile/rules evidence for GasderMIN__bGSDM, added a Lysobacter enzymogenes canonical example, and recorded a knowledge gap for CARD-NLR-associated gasdermins and family breadth.

    • Read this curation session @@ -559,7 +560,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -923,12 +933,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 13:10 UTC diff --git a/pages/traits/genomics/gc_content.html b/pages/traits/genomics/gc_content.html index 3a303c41032..5715918b22a 100644 --- a/pages/traits/genomics/gc_content.html +++ b/pages/traits/genomics/gc_content.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -172,11 +173,11 @@

    Edge evidence

  • GC high - METPO:1000432 + METPO:1000432 is a GC content METPO:1000127 - rdfs:subClassOf + rdfs:subClassOf

    GC high is a quantitative bin of the GC-content phenotype.

      @@ -191,11 +192,11 @@

      Edge evidence

    • GC low - METPO:1000429 + METPO:1000429 is a GC content METPO:1000127 - rdfs:subClassOf + rdfs:subClassOf

      GC low is a quantitative bin of the GC-content phenotype.

        @@ -210,11 +211,11 @@

        Edge evidence

      • GC mid1 - METPO:1000430 + METPO:1000430 is a GC content METPO:1000127 - rdfs:subClassOf + rdfs:subClassOf

        GC mid1 is a quantitative bin of the GC-content phenotype.

          @@ -229,11 +230,11 @@

          Edge evidence

        • GC mid2 - METPO:1000431 + METPO:1000431 is a GC content METPO:1000127 - rdfs:subClassOf + rdfs:subClassOf

          GC mid2 is a quantitative bin of the GC-content phenotype.

            @@ -390,7 +391,7 @@

            kg-microbe context

            via direct_metpo.

              -
            • METPO:1000127 [-0.539, -1.149, -2.445, +1.588, …]
              • +
            • GC content METPO:1000127 [-0.539, -1.149, -2.445, +1.588, …]

            512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

            @@ -627,7 +628,7 @@

            Curation history

          • · ADD_CANONICAL_EXAMPLES · codex -

            Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; PMID:9278503). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

            +

            Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; PMID:9278503). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

            • @@ -660,7 +661,16 @@

            Identifier

            Term kind
            CLASS
            Status
            -
            REVIEWED
            +
            REVIEWED + + +
            + What this status means +

            Curator has signed off on label / definition / parents.

            +

            Quoted from the schema's status definitions.

            +
            + +
    • @@ -1024,12 +1034,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/genomics/gc_high.html b/pages/traits/genomics/gc_high.html index d3b496a1ccc..e86c2441969 100644 --- a/pages/traits/genomics/gc_high.html +++ b/pages/traits/genomics/gc_high.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000432 is a GC content - METPO:1000127 - rdfs:subClassOf + METPO:1000127 + rdfs:subClassOf

    GC high is a quantitative bin of the GC-content phenotype.

      @@ -305,7 +306,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • GC_<=42.65 RELATED_SYNONYM · metpo.owl
        • +
      • GC_<=42.65 RELATED_SYNONYM · metpo.owl
    @@ -321,7 +322,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000432 [+0.921, +1.707, +0.625, +3.297, …]
      • +
    • GC high METPO:1000432 [+0.921, +1.707, +0.625, +3.297, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -546,7 +547,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Mycoplasmoides genitalium G37 (NCBITaxon:243273; DOI:10.1126/science.270.5235.397). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Mycoplasmoides genitalium G37 (NCBITaxon:243273; DOI:10.1126/science.270.5235.397). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -579,7 +580,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -943,12 +953,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/genomics/gc_low.html b/pages/traits/genomics/gc_low.html index f2d13530c37..fdbf63be997 100644 --- a/pages/traits/genomics/gc_low.html +++ b/pages/traits/genomics/gc_low.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -93,7 +94,7 @@

    Edge evidence

    contributes to GC content - METPO:1000127 + METPO:1000127 RO:0002326

    Moderate mutation-bias balance contributes to continuous genome-wide GC composition.

      @@ -112,8 +113,8 @@

      Edge evidence

      METPO:1000429 is a GC content - METPO:1000127 - rdfs:subClassOf + METPO:1000127 + rdfs:subClassOf

      GC low is a quantitative bin of the GC-content phenotype.

        @@ -169,7 +170,7 @@

        Edge evidence

        associated with GC content - METPO:1000127 + METPO:1000127 biolink:associated_with

        AT-enriching C>A/T and depleted C>G mutation spectra are associated with continuous genome-wide G+C content.

          @@ -188,7 +189,7 @@

          Edge evidence

          contributes to GC content - METPO:1000127 + METPO:1000127 RO:0002326

          Biases of DNA replication/repair enzymes and inter-nucleotide mutation rates contribute to genomic GC percent.

            @@ -208,7 +209,7 @@

            Edge evidence

            is a mutational spectrum - rdfs:subClassOf + rdfs:subClassOf

            The AT-enriching C>A/T spectrum is a mutational-spectrum context connecting cytosine-deamination bias to bacterial DNA-repair mutational signatures.

              @@ -267,7 +268,7 @@

              Parent traits (1)

              Synonyms (1)

                -
              • GC_42.65_57.0 RELATED_SYNONYM · metpo.owl
                • +
              • GC_42.65_57.0 RELATED_SYNONYM · metpo.owl
    @@ -283,7 +284,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000429 [-2.626, -2.012, +2.413, +3.679, …]
      • +
    • GC low METPO:1000429 [-2.626, -2.012, +2.413, +3.679, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -508,7 +509,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Bacillus nakamurai (NCBITaxon:1793963; DOI:10.1099/ijsem.0.001135). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Bacillus nakamurai (NCBITaxon:1793963; DOI:10.1099/ijsem.0.001135). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -586,7 +587,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -950,12 +960,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-06 17:10 UTC diff --git a/pages/traits/genomics/gc_mid1.html b/pages/traits/genomics/gc_mid1.html index a3151f258ba..c41043dcdca 100644 --- a/pages/traits/genomics/gc_mid1.html +++ b/pages/traits/genomics/gc_mid1.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000430 is a GC content - METPO:1000127 - rdfs:subClassOf + METPO:1000127 + rdfs:subClassOf

    GC mid1 is a quantitative bin of the GC-content phenotype.

      @@ -248,7 +249,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • GC_>66.3 RELATED_SYNONYM · metpo.owl
        • +
      • GC_>66.3 RELATED_SYNONYM · metpo.owl
    @@ -264,7 +265,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000430 [-2.804, -2.753, -0.396, +5.171, …]
      • +
    • GC mid1 METPO:1000430 [-2.804, -2.753, -0.396, +5.171, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -489,7 +490,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Streptomyces coelicolor A3(2) (NCBITaxon:100226; DOI:10.1038/417141a). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Streptomyces coelicolor A3(2) (NCBITaxon:100226; DOI:10.1038/417141a). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -522,7 +523,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -886,12 +896,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/genomics/gc_mid2.html b/pages/traits/genomics/gc_mid2.html index fb9dfe446b3..45e9b0f7475 100644 --- a/pages/traits/genomics/gc_mid2.html +++ b/pages/traits/genomics/gc_mid2.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,8 +113,8 @@

    Edge evidence

    METPO:1000431 is a GC content - METPO:1000127 - rdfs:subClassOf + METPO:1000127 + rdfs:subClassOf

    GC mid2 is a quantitative bin of the GC-content phenotype.

      @@ -286,7 +287,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • GC_57.0_66.3 RELATED_SYNONYM · metpo.owl
        • +
      • GC_57.0_66.3 RELATED_SYNONYM · metpo.owl
    @@ -302,7 +303,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000431 [-0.166, -0.334, -3.408, +1.036, …]
      • +
    • GC mid2 METPO:1000431 [-0.166, -0.334, -3.408, +1.036, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -527,7 +528,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -560,7 +561,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -924,12 +934,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/genomics/gc_skew.html b/pages/traits/genomics/gc_skew.html index 3fd362b845a..2953a7aa6c8 100644 --- a/pages/traits/genomics/gc_skew.html +++ b/pages/traits/genomics/gc_skew.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    GO:0006260 causes GC skew - traitmech:000097 + traitmech:000097 biolink:causes

    Asymmetric mutation between leading and lagging strands during replication produces strand-specific G/C bias.

      @@ -115,7 +116,7 @@

      Edge evidence

    • GC skew - traitmech:000097 + traitmech:000097 associated with replication origin / terminus @@ -156,7 +157,7 @@

      Edge evidence

      contributes to GC skew - traitmech:000097 + traitmech:000097 RO:0002326

      Cytosine deamination at the replication fork generates strand-specific G/C bias.

        @@ -175,7 +176,7 @@

        Edge evidence

        contributes to GC skew - traitmech:000097 + traitmech:000097 RO:0002326

        Biased gene density on leading versus lagging strands contributes to skew.

          @@ -194,7 +195,7 @@

          Edge evidence

          contributes to GC skew - traitmech:000097 + traitmech:000097 RO:0002326

          Translational selection and genetic-code constraints shape asymmetric G/C distributions.

            @@ -213,7 +214,7 @@

            Edge evidence

            contributes to GC skew - traitmech:000097 + traitmech:000097 RO:0002326

            Mutational bias at the degenerate third codon position contributes to strand compositional asymmetry.

              @@ -232,7 +233,7 @@

              Edge evidence

              contributes to GC skew - traitmech:000097 + traitmech:000097 RO:0002326

              Strand-specific MMR and transcription-coupled NER contribute to strand compositional asymmetry.

                @@ -292,7 +293,7 @@

                Parent traits (1)

                Synonyms (1)

                  -
                • strand compositional asymmetry RELATED_SYNONYM · DOI:10.1016/S0378-1119(99)00297-8
                  • +
                • strand compositional asymmetry RELATED_SYNONYM · DOI:10.1016/S0378-1119(99)00297-8
    @@ -308,7 +309,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -521,7 +522,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; PMID:9278503). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; PMID:9278503). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -554,7 +555,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -918,12 +928,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/genomics/geb_system.html b/pages/traits/genomics/geb_system.html index 43904b3865a..51f1cec157d 100644 --- a/pages/traits/genomics/geb_system.html +++ b/pages/traits/genomics/geb_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers Geb system - traitmech:000287 + traitmech:000287 METPO:2007700

    Geb-mediated phage restriction realizes the Geb system trait.

    @@ -259,7 +260,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -442,7 +443,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -806,12 +816,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 18:00 UTC diff --git a/pages/traits/genomics/genome_size.html b/pages/traits/genomics/genome_size.html index 62b9c364d99..2da2b0ef25d 100644 --- a/pages/traits/genomics/genome_size.html +++ b/pages/traits/genomics/genome_size.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    METPO:1007721 causes genome size - traitmech:000098 + traitmech:000098 biolink:causes

    Reductive evolution sets the observed genome length.

      @@ -137,7 +138,7 @@

      Edge evidence

      positively associated with genome size - traitmech:000098 + traitmech:000098

      Average genome size of marine communities increases with ocean depth.

        @@ -156,7 +157,7 @@

        Edge evidence

        ENVO:09200010 negatively associated with genome size - traitmech:000098 + traitmech:000098

        Low-pH soils host communities with larger average genomes.

          @@ -175,7 +176,7 @@

          Edge evidence

          GO:0009292 increases genome size - traitmech:000098 + traitmech:000098 RO:0002213

          HGT is a driving force behind genome expansion, adding accessory gene content.

            @@ -213,7 +214,7 @@

            Edge evidence

            decreases genome size - traitmech:000098 + traitmech:000098 RO:0002212

            Loss of protein-coding genes reduces genome length.

              @@ -232,7 +233,7 @@

              Edge evidence

              positively associated with genome size - traitmech:000098 + traitmech:000098

              Greater metabolic versatility is correlated with larger genomes.

                @@ -292,7 +293,7 @@

                Parent traits (1)

                Synonyms (1)

                  -
                • genome length RELATED_SYNONYM · DOI:10.1038/nrmicro3331
                  • +
                • genome length RELATED_SYNONYM · DOI:10.1038/nrmicro3331
    @@ -308,7 +309,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -539,7 +540,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Mycoplasmoides genitalium G37 (NCBITaxon:243273; DOI:10.1126/science.270.5235.397). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Mycoplasmoides genitalium G37 (NCBITaxon:243273; DOI:10.1126/science.270.5235.397). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -572,7 +573,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -936,12 +946,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/genomics/genome_streamlining.html b/pages/traits/genomics/genome_streamlining.html index 54920d6581e..9228b17fc44 100644 --- a/pages/traits/genomics/genome_streamlining.html +++ b/pages/traits/genomics/genome_streamlining.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    selects for genome streamlining - traitmech:000099 + traitmech:000099 METPO:2007401

    Resource limitation and large Ne favor minimizing cellular cost via genome reduction.

      @@ -118,7 +119,7 @@

      Edge evidence

      METPO:1007721 causes genome streamlining - traitmech:000099 + traitmech:000099 biolink:causes

      Reductive evolution is the population-genetic process realizing the streamlined-genome phenotype.

        @@ -153,7 +154,7 @@

        Edge evidence

      • genome streamlining - traitmech:000099 + traitmech:000099 associated with depletion of metabolic genes @@ -172,7 +173,7 @@

        Edge evidence

      • genome streamlining - traitmech:000099 + traitmech:000099 promotes metabolic cross-feeding @@ -210,7 +211,7 @@

        Edge evidence

      • genome streamlining - traitmech:000099 + traitmech:000099 associated with dependence on exogenous B-vitamin precursors @@ -279,7 +280,7 @@

        Parent traits (1)

        Synonyms (1)

          -
        • streamlined genome RELATED_SYNONYM · DOI:10.1038/ismej.2014.60
          • +
        • streamlined genome RELATED_SYNONYM · DOI:10.1038/ismej.2014.60
    @@ -295,7 +296,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -520,7 +521,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1038/ismej.2014.60 (already present on oligotrophic.yaml causal_graphs[0].edges[2].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 5 Stage 5 remediation of F-C5S4-DEF-SRC-003 in group G-C5S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.1038/ismej.2014.60 (already present on oligotrophic.yaml causal_graphs[0].edges[2].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 5 Stage 5 remediation of F-C5S4-DEF-SRC-003 in group G-C5S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -562,7 +563,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -926,12 +936,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 21:40 UTC diff --git a/pages/traits/genomics/genomic_island.html b/pages/traits/genomics/genomic_island.html index 5f53bde3d2c..1dee148ec9a 100644 --- a/pages/traits/genomics/genomic_island.html +++ b/pages/traits/genomics/genomic_island.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    GO:0009292 causes genomic island - traitmech:000093 + traitmech:000093 biolink:causes

    Genomic islands are integrated into host chromosomes via HGT.

      @@ -115,7 +116,7 @@

      Edge evidence

    • genomic island - traitmech:000093 + traitmech:000093 contributes to accessory function @@ -134,7 +135,7 @@

      Edge evidence

    • genomic island - traitmech:000093 + traitmech:000093 includes integrase/recombinase/transposase mobility module @@ -153,7 +154,7 @@

      Edge evidence

    • integrative conjugative element - traitmech:000410 + traitmech:000410 enables conjugation GO:0009291 @@ -210,11 +211,11 @@

      Edge evidence

    • integrative conjugative element - traitmech:000410 + traitmech:000410 is a genomic island - traitmech:000093 - rdfs:subClassOf + traitmech:000093 + rdfs:subClassOf

      Integrative-conjugative-element possession is a genomic-island possession trait.

        @@ -282,7 +283,7 @@

        Children (1)

        Synonyms (1)

          -
        • pathogenicity island NARROW_SYNONYM · DOI:10.1038/nrmicro884
          • +
        • pathogenicity island NARROW_SYNONYM · DOI:10.1038/nrmicro884
    @@ -298,7 +299,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -604,7 +605,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -968,12 +978,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 14:44 UTC diff --git a/pages/traits/genomics/gmrsd_system.html b/pages/traits/genomics/gmrsd_system.html index e0ef4fd8147..9f3137a2f93 100644 --- a/pages/traits/genomics/gmrsd_system.html +++ b/pages/traits/genomics/gmrsd_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -179,7 +180,7 @@

    Edge evidence

    confers GmrSD system - traitmech:000506 + traitmech:000506 METPO:2007700

    GmrSD-dependent Type IV restriction realizes the organism-level GmrSD system possession trait.

    @@ -288,7 +289,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -514,7 +515,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -878,12 +888,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 04:21 UTC diff --git a/pages/traits/genomics/hachiman_system.html b/pages/traits/genomics/hachiman_system.html index b50c900048b..9b602f66007 100644 --- a/pages/traits/genomics/hachiman_system.html +++ b/pages/traits/genomics/hachiman_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -198,7 +199,7 @@

    Edge evidence

    confers Hachiman system - traitmech:000219 + traitmech:000219 METPO:2007700

    HamAB-mediated DNA cleavage is the antiviral output that realizes the Hachiman system trait.

      @@ -214,11 +215,11 @@

      Edge evidence

    • Hachiman system - traitmech:000219 + traitmech:000219 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Hachiman system possession is a phage-defense-system trait.

        @@ -288,9 +289,9 @@

        Children (2)

        Synonyms (2)

          -
        • Hachiman antiphage defense system EXACT_SYNONYM · DOI:10.1016/j.cell.2024.09.020
          • +
        • Hachiman antiphage defense system EXACT_SYNONYM · DOI:10.1016/j.cell.2024.09.020
          • -
        • Hachiman defense system EXACT_SYNONYM · DOI:10.1038/s41467-025-57851-1
          • +
        • Hachiman defense system EXACT_SYNONYM · DOI:10.1038/s41467-025-57851-1
    @@ -306,7 +307,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -427,7 +428,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    Tuck et al. support DNA-damage-triggered type I-A HamAB activation and Cui et al. support type I-B HamAB ATPase and DNA-cleavage activity, but Hachiman variants need separate review before TraitMech asserts one universal triggering DNA substrate, HamA catalytic domain, HamC accessory role, Cap4 fusion architecture, phage range, or abortive-infection output. Hachiman type II system (traitmech:000574) now resolves the HamABC architecture defined by Payne et al. (DOI:10.1093/nar/gkab883) and retained by Cui et al. The DSM 14551 locus has heterologous antiphage evidence, but HamC function and type-II mechanism remain open. The family definition no longer requires universal DNA cleavage; this graph and its evidence remain restricted to characterized type-I systems. Proposal v451 replaces v96's overgeneralized family definition while preserving the stable local family identifier. Type I remains a separate architecture-class discovery lead. That architecture-class lead is now represented by traitmech:000575 Hachiman type I system for HamAB loci without HamC. The component definition follows Payne and Cui, not a failed detector hit or a type-II knockout. The existing graph still describes characterized I-A/I-B mechanisms, not all type-I subtypes. Subtype-specific mechanisms and native-locus activity remain open; no graph, example or hierarchy is changed.

    +

    Tuck et al. support DNA-damage-triggered type I-A HamAB activation and Cui et al. support type I-B HamAB ATPase and DNA-cleavage activity, but Hachiman variants need separate review before TraitMech asserts one universal triggering DNA substrate, HamA catalytic domain, HamC accessory role, Cap4 fusion architecture, phage range, or abortive-infection output. Hachiman type II system (traitmech:000574) now resolves the HamABC architecture defined by Payne et al. (DOI:10.1093/nar/gkab883) and retained by Cui et al. The DSM 14551 locus has heterologous antiphage evidence, but HamC function and type-II mechanism remain open. The family definition no longer requires universal DNA cleavage; this graph and its evidence remain restricted to characterized type-I systems. Proposal v451 replaces v96's overgeneralized family definition while preserving the stable local family identifier. Type I remains a separate architecture-class discovery lead. That architecture-class lead is now represented by traitmech:000575 Hachiman type I system for HamAB loci without HamC. The component definition follows Payne and Cui, not a failed detector hit or a type-II knockout. The existing graph still describes characterized I-A/I-B mechanisms, not all type-I subtypes. Subtype-specific mechanisms and native-locus activity remain open; no graph, example or hierarchy is changed.

    @@ -461,7 +462,7 @@

    Curation history

  • · TRACK_HACHIMAN_TYPE_I_CLASS · codex -

    Linked traitmech:000575 Hachiman type I system using the component classification in DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57851-1. Kept definitions, hierarchy, examples, evidence and graphs unchanged; mechanism questions remain open. No absence assertion is inferred from detector output.

    +

    Linked traitmech:000575 Hachiman type I system using the component classification in DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57851-1. Kept definitions, hierarchy, examples, evidence and graphs unchanged; mechanism questions remain open. No absence assertion is inferred from detector output.

    • @@ -515,7 +516,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -879,12 +889,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 18:41 UTC diff --git a/pages/traits/genomics/hachiman_type_i_system.html b/pages/traits/genomics/hachiman_type_i_system.html index 97ecbba1e5e..3c167a4bb94 100644 --- a/pages/traits/genomics/hachiman_type_i_system.html +++ b/pages/traits/genomics/hachiman_type_i_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -119,7 +120,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Hachiman type I EXACT_SYNONYM · DOI:10.1093/nar/gkab883
      • +
    • Hachiman type I EXACT_SYNONYM · DOI:10.1093/nar/gkab883
    @@ -135,7 +136,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -288,7 +289,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add literature-defined HamC-lacking Hachiman type I -

      Added traitmech:000575 from DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57851-1 with exact full-text snippets, pinned PADLOC and DefenseFinder rules and NCBITaxon:511145 MG1655 source locus U00096.3:2761204-2765368. Distinguished biological absence from detector misses and engineered complementation from unmodified native-locus activity. Whole-repository ignored-and-hidden novelty and allocation checks plus a fresh 399-record seed preceded minting. Proposal v452 reserves METPO:1052900 under the corrected v451 parent. Guarded writer defaults to dry run and prevalidates all three records.

    +

    Added traitmech:000575 from DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57851-1 with exact full-text snippets, pinned PADLOC and DefenseFinder rules and NCBITaxon:511145 MG1655 source locus U00096.3:2761204-2765368. Distinguished biological absence from detector misses and engineered complementation from unmodified native-locus activity. Whole-repository ignored-and-hidden novelty and allocation checks plus a fresh 399-record seed preceded minting. Proposal v452 reserves METPO:1052900 under the corrected v451 parent. Guarded writer defaults to dry run and prevalidates all three records.

    • Read this curation session @@ -320,7 +321,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -349,12 +359,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 18:41 UTC diff --git a/pages/traits/genomics/hachiman_type_ii_system.html b/pages/traits/genomics/hachiman_type_ii_system.html index e5eeae002b7..80b1914c678 100644 --- a/pages/traits/genomics/hachiman_type_ii_system.html +++ b/pages/traits/genomics/hachiman_type_ii_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -123,7 +124,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Hachiman type II EXACT_SYNONYM · DOI:10.1093/nar/gkab883
      • +
    • Hachiman type II EXACT_SYNONYM · DOI:10.1093/nar/gkab883
    @@ -139,7 +140,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -288,7 +289,7 @@

    Curation history

  • · TRACK_HACHIMAN_TYPE_I_CLASS · codex -

    Linked traitmech:000575 Hachiman type I system using the component classification in DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57851-1. Kept definitions, hierarchy, examples, evidence and graphs unchanged; mechanism questions remain open. No absence assertion is inferred from detector output.

    +

    Linked traitmech:000575 Hachiman type I system using the component classification in DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57851-1. Kept definitions, hierarchy, examples, evidence and graphs unchanged; mechanism questions remain open. No absence assertion is inferred from detector output.

    • @@ -298,7 +299,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add HamABC Hachiman type II possession trait -

      Added traitmech:000574 from DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57851-1, with exact full-text snippets, pinned DefenseFinder and PADLOC rules, and NCBITaxon:173675 DSM 14551 source locus NZ_NISJ01000011.1. Kept heterologous defense separate from native activity and type-I mechanisms. Whole-repository ignored-and-hidden novelty and allocation checks plus fresh 399-record seeder review preceded minting. Proposal v451 reserves METPO:1052801 below corrected family placeholder METPO:1052800. Writer prevalidates both records and defaults to dry run.

    +

    Added traitmech:000574 from DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57851-1, with exact full-text snippets, pinned DefenseFinder and PADLOC rules, and NCBITaxon:173675 DSM 14551 source locus NZ_NISJ01000011.1. Kept heterologous defense separate from native activity and type-I mechanisms. Whole-repository ignored-and-hidden novelty and allocation checks plus fresh 399-record seeder review preceded minting. Proposal v451 reserves METPO:1052801 below corrected family placeholder METPO:1052800. Writer prevalidates both records and defaults to dry run.

    • Read this curation session
  • @@ -336,7 +337,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -365,12 +375,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 18:41 UTC diff --git a/pages/traits/genomics/hailong_system.html b/pages/traits/genomics/hailong_system.html index f42af994f39..40b772b6ff5 100644 --- a/pages/traits/genomics/hailong_system.html +++ b/pages/traits/genomics/hailong_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -230,7 +231,7 @@

    Edge evidence

    confers Hailong system - traitmech:000242 + traitmech:000242 METPO:2007700

    Hailong-mediated host growth arrest is the phage-defense output that realizes the Hailong system trait.

      @@ -246,11 +247,11 @@

      Edge evidence

    • Hailong system - traitmech:000242 + traitmech:000242 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Hailong system possession is a phage-defense-system trait.

        @@ -309,7 +310,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -325,7 +326,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -510,7 +511,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -874,12 +884,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 13:30 UTC diff --git a/pages/traits/genomics/hec_02_system.html b/pages/traits/genomics/hec_02_system.html index 1e3d323db37..154bfa734e8 100644 --- a/pages/traits/genomics/hec_02_system.html +++ b/pages/traits/genomics/hec_02_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers HEC-02 system - traitmech:000417 + traitmech:000417 METPO:2007700

    HEC-02-mediated plaquing reduction realizes the HEC-02 system trait.

      @@ -182,11 +183,11 @@

      Edge evidence

    • HEC-02 system - traitmech:000417 + traitmech:000417 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      HEC-02 system possession is a phage-defense-system trait.

        @@ -245,7 +246,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -261,7 +262,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -473,7 +474,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -837,12 +847,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 20:53 UTC diff --git a/pages/traits/genomics/hec_03_system.html b/pages/traits/genomics/hec_03_system.html index 0eea1138d2b..fb9f2bc5dbf 100644 --- a/pages/traits/genomics/hec_03_system.html +++ b/pages/traits/genomics/hec_03_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers HEC-03 system - traitmech:000418 + traitmech:000418 METPO:2007700

    HEC-03-mediated plaquing reduction realizes the HEC-03 system trait.

      @@ -182,11 +183,11 @@

      Edge evidence

    • HEC-03 system - traitmech:000418 + traitmech:000418 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      HEC-03 system possession is a phage-defense-system trait.

        @@ -245,7 +246,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -261,7 +262,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -473,7 +474,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -837,12 +847,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 21:24 UTC diff --git a/pages/traits/genomics/hec_04_system.html b/pages/traits/genomics/hec_04_system.html index 23542f0617e..f8aee3d00c0 100644 --- a/pages/traits/genomics/hec_04_system.html +++ b/pages/traits/genomics/hec_04_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers HEC-04 system - traitmech:000465 + traitmech:000465 METPO:2007700

    HEC-04-mediated plaquing reduction realizes the HEC-04 system trait.

    @@ -251,7 +252,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -456,7 +457,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -820,12 +830,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 14:18 UTC diff --git a/pages/traits/genomics/hec_05_system.html b/pages/traits/genomics/hec_05_system.html index 0dc0d09a36d..34eca3177a2 100644 --- a/pages/traits/genomics/hec_05_system.html +++ b/pages/traits/genomics/hec_05_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers HEC-05 system - traitmech:000466 + traitmech:000466 METPO:2007700

    HEC-05-mediated plaquing reduction realizes the HEC-05 system trait.

    @@ -245,7 +246,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -450,7 +451,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -814,12 +824,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 16:05 UTC diff --git a/pages/traits/genomics/hec_06_system.html b/pages/traits/genomics/hec_06_system.html index 965d634d5f3..09d97262360 100644 --- a/pages/traits/genomics/hec_06_system.html +++ b/pages/traits/genomics/hec_06_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers HEC-06 system - traitmech:000467 + traitmech:000467 METPO:2007700

    HEC-06-mediated plaquing reduction realizes the HEC-06 system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -431,7 +432,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -795,12 +805,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 15:29 UTC diff --git a/pages/traits/genomics/hec_07_system.html b/pages/traits/genomics/hec_07_system.html index 775aaf3ec99..4b870e91666 100644 --- a/pages/traits/genomics/hec_07_system.html +++ b/pages/traits/genomics/hec_07_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers HEC-07 system - traitmech:000478 + traitmech:000478 METPO:2007700

    HEC-07-mediated plaquing reduction realizes the HEC-07 system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -431,7 +432,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -795,12 +805,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 00:50 UTC diff --git a/pages/traits/genomics/hec_08_system.html b/pages/traits/genomics/hec_08_system.html index 621cf09328d..2a840950b9e 100644 --- a/pages/traits/genomics/hec_08_system.html +++ b/pages/traits/genomics/hec_08_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers HEC-08 system - traitmech:000479 + traitmech:000479 METPO:2007700

    HEC-08-mediated plaquing reduction realizes the HEC-08 system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -431,7 +432,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -795,12 +805,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 01:36 UTC diff --git a/pages/traits/genomics/hesat_system.html b/pages/traits/genomics/hesat_system.html index a75fd600e6e..9fffedaf485 100644 --- a/pages/traits/genomics/hesat_system.html +++ b/pages/traits/genomics/hesat_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers Hesat system - traitmech:000327 + traitmech:000327 METPO:2007700

    Hesat-mediated phage restriction realizes the Hesat system trait.

      @@ -164,11 +165,11 @@

      Edge evidence

    • Hesat system - traitmech:000327 + traitmech:000327 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Hesat system possession is a phage-defense-system trait.

        @@ -227,7 +228,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -243,7 +244,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -370,7 +371,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Hesat system trait -

      Added traitmech:000327 Hesat system as a DOI-backed GENOMICS TraitRecord under phage defense system. DOI:10.1093/nar/gkae671 names Hesat among newly described lactococcal antiphage systems, identifies Hesat as a single-gene antiphage system, and proposes a colicin-D-like translation-blocking activity upon phage infection. The pinned DefenseFinder article registry maps Hesat to the Grafakou et al. lactococcal plasmidome discovery paper. Reserved METPO:1028100 in proposals/metpo_traitmech_v204 for the upstream replacement ID.

    +

    Added traitmech:000327 Hesat system as a DOI-backed GENOMICS TraitRecord under phage defense system. DOI:10.1093/nar/gkae671 names Hesat among newly described lactococcal antiphage systems, identifies Hesat as a single-gene antiphage system, and proposes a colicin-D-like translation-blocking activity upon phage infection. The pinned DefenseFinder article registry maps Hesat to the Grafakou et al. lactococcal plasmidome discovery paper. Reserved METPO:1028100 in proposals/metpo_traitmech_v204 for the upstream replacement ID.

    • Read this curation session @@ -402,7 +403,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -766,12 +776,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 04:57 UTC diff --git a/pages/traits/genomics/heterokaryosis.html b/pages/traits/genomics/heterokaryosis.html index 0fd11977e14..ec90126abfb 100644 --- a/pages/traits/genomics/heterokaryosis.html +++ b/pages/traits/genomics/heterokaryosis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1098/rspb.2022.0971
    Heterokaryosis is a system in which genetically distinct nuclei coexist within the same cytoplasm.
    -

    2022 primary study, PMID:35946150. Exact span of the directly retrieved Europe PMC abstract. Introduction, Methods, Results and Discussion were read in the PMC9363985 full-text XML; actual figures and supplements were not inspected. Neurospora tetrasperma lineages L1, L6 and L10 were reconstituted from homokaryotic components, with DNA-ratio validation. Developmental stage and lineage affect expression; global transcription does not diagnose heterokaryosis by itself. L10 heterokaryons can remain largely sterile despite containing both mating types. Expression correlations do not establish a protein-resolved regulatory mechanism.

    +

    2022 primary study, PMID:35946150. Exact span of the directly retrieved Europe PMC abstract. Introduction, Methods, Results and Discussion were read in the PMC9363985 full-text XML; actual figures and supplements were not inspected. Neurospora tetrasperma lineages L1, L6 and L10 were reconstituted from homokaryotic components, with DNA-ratio validation. Developmental stage and lineage affect expression; global transcription does not diagnose heterokaryosis by itself. L10 heterokaryons can remain largely sterile despite containing both mating types. Expression correlations do not establish a protein-resolved regulatory mechanism.

  • DOI:10.1098/rspb.2014.0084
    A heterokaryon is a tissue type composed of cells containing genetically different nuclei.
    -

    Samils et al. (2014), PMID:24850920. Exact span of the directly retrieved Europe PMC abstract. Main-text Methods, Results and Discussion were read at PMC4046401; actual figures and supplements were not visually inspected. The study assays natural N. tetrasperma heterokaryons from lineages L1, L6 and L7 with multiple mating-type-linked SNPs. Bulk DNA ratios and RNA expression are different readouts; they do not count nuclei in every cell. The snippet names the tissue, whereas this record denotes the phenotype.

    +

    Samils et al. (2014), PMID:24850920. Exact span of the directly retrieved Europe PMC abstract. Main-text Methods, Results and Discussion were read at PMC4046401; actual figures and supplements were not visually inspected. The study assays natural N. tetrasperma heterokaryons from lineages L1, L6 and L7 with multiple mating-type-linked SNPs. Bulk DNA ratios and RNA expression are different readouts; they do not count nuclei in every cell. The snippet names the tissue, whereas this record denotes the phenotype.

  • DOI:10.1016/j.fgb.2018.01.005
    Shifts in fungicide sensitivity and microsatellite genotypes indicated that heterokaryons could adapt to changes in fungicide pressure.
    -

    Kessler et al. (2018), PMID:29331685. Exact span of the directly retrieved Europe PMC abstract. Methods and relevant Results and Discussion were read in the author-hosted PDF at https://researchmap.jp/umassturfpathology/published_papers/2317022/attachment_file.pdf; actual Figures 5-6 were inspected, but other figures and supplements remain uninspected. Sclerotinia homoeocarpa field isolates were paired in vitro; fluorescent nuclear imaging used engineered derivatives. Tagged histones can move through shared cytoplasm into other nuclei, so dual fluorescence alone does not establish nuclear fusion or genotype. Microsatellite and SNP assays provide complementary evidence, with detection-limit qualifications. Fungicide responses are condition-specific, not defining properties of every heterokaryon; parasexuality was suspected, not demonstrated.

    +

    Kessler et al. (2018), PMID:29331685. Exact span of the directly retrieved Europe PMC abstract. Methods and relevant Results and Discussion were read in the author-hosted PDF at https://researchmap.jp/umassturfpathology/published_papers/2317022/attachment_file.pdf; actual Figures 5-6 were inspected, but other figures and supplements remain uninspected. Sclerotinia homoeocarpa field isolates were paired in vitro; fluorescent nuclear imaging used engineered derivatives. Tagged histones can move through shared cytoplasm into other nuclei, so dual fluorescence alone does not establish nuclear fusion or genotype. Microsatellite and SNP assays provide complementary evidence, with detection-limit qualifications. Fungicide responses are condition-specific, not defining properties of every heterokaryon; parasexuality was suspected, not demonstrated.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1098/rspb.2014.0084 - Qualified example: natural heterokaryon P581 (lineage L6), Lihue, Hawaii. Primary provenance is Methods 2a and Table 1 at https://pmc.ncbi.nlm.nih.gov/articles/PMC4046401/. FGSC 2508 and 2509 are its homokaryotic components, not identifiers for the heterokaryon. The study measures cultured mycelial and sexual tissues at 25 C, not an in-situ nuclear census. This does not assert that all isolates or life stages are heterokaryotic. NCBI taxonomy 40127 resolves to the active species name on 2026-10-04. + Qualified example: natural heterokaryon P581 (lineage L6), Lihue, Hawaii. Primary provenance is Methods 2a and Table 1 at https://pmc.ncbi.nlm.nih.gov/articles/PMC4046401/. FGSC 2508 and 2509 are its homokaryotic components, not identifiers for the heterokaryon. The study measures cultured mycelial and sexual tissues at 25 C, not an in-situ nuclear census. This does not assert that all isolates or life stages are heterokaryotic. NCBI taxonomy 40127 resolves to the active species name on 2026-10-04. @@ -340,7 +341,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -369,12 +379,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 00:36 UTC diff --git a/pages/traits/genomics/hma_system.html b/pages/traits/genomics/hma_system.html index 084eb3101cb..a165358d690 100644 --- a/pages/traits/genomics/hma_system.html +++ b/pages/traits/genomics/hma_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -166,7 +167,7 @@

    Edge evidence

    confers Hma system - traitmech:000533 + traitmech:000533 METPO:2007700

    HmaA-dependent anti-phage activity realizes the first-pass organism-level Hma system trait.

    @@ -285,7 +286,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -504,7 +505,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -868,12 +878,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 03:38 UTC diff --git a/pages/traits/genomics/hna_system.html b/pages/traits/genomics/hna_system.html index b20632f62d1..48ce49b121f 100644 --- a/pages/traits/genomics/hna_system.html +++ b/pages/traits/genomics/hna_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -192,7 +193,7 @@

    Edge evidence

    confers Hna system - traitmech:000241 + traitmech:000241 METPO:2007700

    Hna-mediated abortive infection is the phage-defense output that realizes the Hna system trait.

      @@ -208,11 +209,11 @@

      Edge evidence

    • Hna system - traitmech:000241 + traitmech:000241 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Hna system possession is a phage-defense-system trait.

        @@ -271,7 +272,7 @@

        Parent traits (1)

        Synonyms (1)

          -
        • Hna anti-phage defense system EXACT_SYNONYM · DOI:10.1038/s41467-026-73157-2
          • +
        • Hna anti-phage defense system EXACT_SYNONYM · DOI:10.1038/s41467-026-73157-2
    @@ -287,7 +288,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -472,7 +473,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -836,12 +846,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 12:46 UTC diff --git a/pages/traits/genomics/hypnos_system.html b/pages/traits/genomics/hypnos_system.html index c966b9f5abb..b5821a7f557 100644 --- a/pages/traits/genomics/hypnos_system.html +++ b/pages/traits/genomics/hypnos_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -142,7 +143,7 @@

    Edge evidence

    confers Hypnos system - traitmech:000309 + traitmech:000309 METPO:2007700

    Hypnos-mediated phage restriction realizes the Hypnos system trait.

    @@ -239,7 +240,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -398,7 +399,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -762,12 +772,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 13:11 UTC diff --git a/pages/traits/genomics/ig_like_schlafen_system.html b/pages/traits/genomics/ig_like_schlafen_system.html index 417c8de39e3..cff67f51050 100644 --- a/pages/traits/genomics/ig_like_schlafen_system.html +++ b/pages/traits/genomics/ig_like_schlafen_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -167,7 +168,7 @@

    Edge evidence

    confers Ig-like Schlafen system - traitmech:000508 + traitmech:000508 METPO:2007700

    Schlafen tRNase activity restricts T5 phage and realizes the organism-level Ig-like Schlafen system trait.

    @@ -276,7 +277,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -488,7 +489,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -852,12 +862,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 06:21 UTC diff --git a/pages/traits/genomics/integrative_conjugative_element.html b/pages/traits/genomics/integrative_conjugative_element.html index d7366af1416..20681a95024 100644 --- a/pages/traits/genomics/integrative_conjugative_element.html +++ b/pages/traits/genomics/integrative_conjugative_element.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -175,7 +176,7 @@

    Edge evidence

    confers integrative conjugative element - traitmech:000410 + traitmech:000410 METPO:2007700

    Recipient-chromosome integration completes possession of an integrated conjugative element.

      @@ -191,11 +192,11 @@

      Edge evidence

    • integrative conjugative element - traitmech:000410 + traitmech:000410 is a genomic island - traitmech:000093 - rdfs:subClassOf + traitmech:000093 + rdfs:subClassOf

      Integrative-conjugative-element possession is a genomic-island possession trait.

    @@ -270,7 +271,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -469,7 +470,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -833,12 +843,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 14:44 UTC diff --git a/pages/traits/genomics/jukab_system.html b/pages/traits/genomics/jukab_system.html index 2fcfc47f7ce..cfd7d8598a8 100644 --- a/pages/traits/genomics/jukab_system.html +++ b/pages/traits/genomics/jukab_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -223,7 +224,7 @@

    Edge evidence

    confers JukAB system - traitmech:000305 + traitmech:000305 METPO:2007700

    JukB-associated EPI-vesicle destabilization realizes the JukAB defense trait.

    @@ -320,7 +321,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -504,7 +505,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -868,12 +878,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 08:55 UTC diff --git a/pages/traits/genomics/kamadhenu_system.html b/pages/traits/genomics/kamadhenu_system.html index 407ca8dc4db..1475a1eb7c1 100644 --- a/pages/traits/genomics/kamadhenu_system.html +++ b/pages/traits/genomics/kamadhenu_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Kamadhenu system - traitmech:000310 + traitmech:000310 METPO:2007700

    Kamadhenu-mediated phage restriction realizes the Kamadhenu system trait.

      @@ -152,11 +153,11 @@

      Edge evidence

    • Kamadhenu system - traitmech:000310 + traitmech:000310 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Kamadhenu system possession is a phage-defense-system trait.

        @@ -215,7 +216,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -231,7 +232,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -364,7 +365,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Kamadhenu system trait -

      Added traitmech:000310 Kamadhenu system as a DOI-backed GENOMICS TraitRecord under phage defense system. DOI:10.1093/nar/gkae671 names Kamadhenu among newly described lactococcal antiphage systems, DOI:10.1073/pnas.2426508122 treats Kamadhenu as a plasmid-encoded lactococcal phage-resistance system in an escape-mutant screen, and the pinned DefenseFinder article registry maps Kamadhenu to the Grafakou et al. lactococcal plasmidome discovery paper. Reserved METPO:1026400 in proposals/metpo_traitmech_v187 for the upstream replacement ID.

    +

    Added traitmech:000310 Kamadhenu system as a DOI-backed GENOMICS TraitRecord under phage defense system. DOI:10.1093/nar/gkae671 names Kamadhenu among newly described lactococcal antiphage systems, DOI:10.1073/pnas.2426508122 treats Kamadhenu as a plasmid-encoded lactococcal phage-resistance system in an escape-mutant screen, and the pinned DefenseFinder article registry maps Kamadhenu to the Grafakou et al. lactococcal plasmidome discovery paper. Reserved METPO:1026400 in proposals/metpo_traitmech_v187 for the upstream replacement ID.

    • Read this curation session
  • @@ -402,7 +403,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -766,12 +776,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 14:22 UTC diff --git a/pages/traits/genomics/kiwa_system.html b/pages/traits/genomics/kiwa_system.html index 1b1586d83c9..211e0dfad4f 100644 --- a/pages/traits/genomics/kiwa_system.html +++ b/pages/traits/genomics/kiwa_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -180,7 +181,7 @@

    Edge evidence

    confers Kiwa system - traitmech:000231 + traitmech:000231 METPO:2007700

    Spatially coordinated membrane-associated phage sensing and effector DNA binding realizes the Kiwa antiphage-defense phenotype.

      @@ -196,11 +197,11 @@

      Edge evidence

    • Kiwa system - traitmech:000231 + traitmech:000231 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Kiwa system possession is a phage-defense-system trait.

        @@ -259,7 +260,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -275,7 +276,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -460,7 +461,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -824,12 +834,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 22:47 UTC diff --git a/pages/traits/genomics/kongming_system.html b/pages/traits/genomics/kongming_system.html index ce5d8063bb6..c815a1cfded 100644 --- a/pages/traits/genomics/kongming_system.html +++ b/pages/traits/genomics/kongming_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -216,7 +217,7 @@

    Edge evidence

    confers Kongming system - traitmech:000501 + traitmech:000501 METPO:2007700

    dITP-triggered NAD depletion and infected-cell death realize the Kongming system trait.

    @@ -327,7 +328,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -539,7 +540,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -903,12 +913,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 22:05 UTC diff --git a/pages/traits/genomics/lamassu_amidase_system.html b/pages/traits/genomics/lamassu_amidase_system.html index d06224b5369..98cf040c956 100644 --- a/pages/traits/genomics/lamassu_amidase_system.html +++ b/pages/traits/genomics/lamassu_amidase_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers Lamassu-Amidase system - traitmech:000556 + traitmech:000556 METPO:2007700

    The first-pass Lamassu-Amidase system trait is realized by a DefenseFinder Lamassu-Amidase subtype locus.

    @@ -273,7 +274,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -464,7 +465,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -828,12 +838,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 21:45 UTC diff --git a/pages/traits/genomics/lamassu_cap4_nuclease_system.html b/pages/traits/genomics/lamassu_cap4_nuclease_system.html index e5b03102e1e..34a6b606245 100644 --- a/pages/traits/genomics/lamassu_cap4_nuclease_system.html +++ b/pages/traits/genomics/lamassu_cap4_nuclease_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers Lamassu-Cap4 nuclease system - traitmech:000557 + traitmech:000557 METPO:2007700

    The first-pass Lamassu-Cap4 nuclease system trait is realized by a DefenseFinder Lamassu-Cap4_nuclease subtype locus.

    @@ -273,7 +274,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -464,7 +465,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -828,12 +838,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 22:16 UTC diff --git a/pages/traits/genomics/lamassu_fmo_system.html b/pages/traits/genomics/lamassu_fmo_system.html index 36fddee587f..d74238e02d1 100644 --- a/pages/traits/genomics/lamassu_fmo_system.html +++ b/pages/traits/genomics/lamassu_fmo_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -132,11 +133,11 @@

    Edge evidence

  • Lamassu-FMO system - traitmech:000558 + traitmech:000558 is a Lamassu system - traitmech:000232 - rdfs:subClassOf + traitmech:000232 + rdfs:subClassOf

    Lamassu-FMO system possession is a Lamassu-system trait.

    • @@ -219,7 +220,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -424,7 +425,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -788,12 +798,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 23:13 UTC diff --git a/pages/traits/genomics/lamassu_hnh_system.html b/pages/traits/genomics/lamassu_hnh_system.html index 9571feb44e1..68251640086 100644 --- a/pages/traits/genomics/lamassu_hnh_system.html +++ b/pages/traits/genomics/lamassu_hnh_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -150,9 +151,9 @@

    Parent traits (2)

    Synonyms (2)

    @@ -168,7 +169,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -323,7 +324,7 @@

    Curation history

  • · ADD_TYPE_II_PARENT · codex -

    Linked traitmech:000572 Lamassu type II system using the LmuC-containing classification in DOI:10.1093/nar/gkab883. Preserved biological definitions, evidence, examples and length-family distinctions. Historical proposal parent axioms remain true; v449 documents the additional subclass relations for upstream minting. This is not new experimental validation.

    +

    Linked traitmech:000572 Lamassu type II system using the LmuC-containing classification in DOI:10.1093/nar/gkab883. Preserved biological definitions, evidence, examples and length-family distinctions. Historical proposal parent axioms remain true; v449 documents the additional subclass relations for upstream minting. This is not new experimental validation.

    • @@ -333,7 +334,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add literature-supported short-Lamassu HNH architecture -

      Added traitmech:000568 and proposal v445 METPO:1052200 using Haudiquet et al. DOI:10.1073/pnas.2519643122, pinned executable DefenseFinder XML, Dataset S1 and NCBI assembly identity. Exact-matched all eight snippets to source XML, raw spreadsheet cells or JSON. All 281 dataset HNH calls use short LmuB; the model also accepts long LmuB and is only a related synonym. AN59 GCF_009892245.1 is explicitly a computational genomic example, not experimental antiviral validation. Ignored-and-hidden searches found no exact record or METPO class. No molecular causal graph or exact protein xref asserted. Writer tests cover dry run, idempotency, preimage drift and proposal round trip.

    +

    Added traitmech:000568 and proposal v445 METPO:1052200 using Haudiquet et al. DOI:10.1073/pnas.2519643122, pinned executable DefenseFinder XML, Dataset S1 and NCBI assembly identity. Exact-matched all eight snippets to source XML, raw spreadsheet cells or JSON. All 281 dataset HNH calls use short LmuB; the model also accepts long LmuB and is only a related synonym. AN59 GCF_009892245.1 is explicitly a computational genomic example, not experimental antiviral validation. Ignored-and-hidden searches found no exact record or METPO class. No molecular causal graph or exact protein xref asserted. Writer tests cover dry run, idempotency, preimage drift and proposal round trip.

    • Read this curation session
  • @@ -345,7 +346,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Classify the existing architecture under Lamassu type II -

      Added traitmech:000572 as a second direct parent while retaining traitmech:000570 short Lamassu. The existing definition independently requires LmuC and short LmuB. Preserved the broader detector-scope caveat, computational AN59 example and unresolved experimental function. This is a definition-based inference using DOI:10.1093/nar/gkab883, not new functional validation. The writer guards identity, definition, old parents and discussion preimage, appends curation history, and preserves unrelated fields. Historical METPO proposal IDs and broader axioms remain intact; v449 documents the new subclass relation for upstream integration.

    +

    Added traitmech:000572 as a second direct parent while retaining traitmech:000570 short Lamassu. The existing definition independently requires LmuC and short LmuB. Preserved the broader detector-scope caveat, computational AN59 example and unresolved experimental function. This is a definition-based inference using DOI:10.1093/nar/gkab883, not new functional validation. The writer guards identity, definition, old parents and discussion preimage, appends curation history, and preserves unrelated fields. Historical METPO proposal IDs and broader axioms remain intact; v449 documents the new subclass relation for upstream integration.

    • Read this curation session @@ -377,7 +378,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -406,12 +416,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 15:20 UTC diff --git a/pages/traits/genomics/lamassu_hydrolase_protease_system.html b/pages/traits/genomics/lamassu_hydrolase_protease_system.html index b0fef49f4de..2f25afcdc81 100644 --- a/pages/traits/genomics/lamassu_hydrolase_protease_system.html +++ b/pages/traits/genomics/lamassu_hydrolase_protease_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -142,9 +143,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -160,7 +161,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -309,7 +310,7 @@

    Curation history

  • · ADD_TYPE_II_PARENT · codex -

    Linked traitmech:000572 Lamassu type II system using the LmuC-containing classification in DOI:10.1093/nar/gkab883. Preserved biological definitions, evidence, examples and length-family distinctions. Historical proposal parent axioms remain true; v449 documents the additional subclass relations for upstream minting. This is not new experimental validation.

    +

    Linked traitmech:000572 Lamassu type II system using the LmuC-containing classification in DOI:10.1093/nar/gkab883. Preserved biological definitions, evidence, examples and length-family distinctions. Historical proposal parent axioms remain true; v449 documents the additional subclass relations for upstream minting. This is not new experimental validation.

    • @@ -319,13 +320,13 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add paired Lamassu Hydrolase-Protease system -

      Added traitmech:000567 using DOI:10.1073/pnas.2519643122, DOI:10.1016/j.chom.2022.09.017 and the executable DefenseFinder model at afb0e5a8b466be53586b13266f5d38d98c3ac268. Verified XML and full-text snippets, recorded four-component versus three-component summary drift, and tied the canonical example to B. cereus B4077 using NCBITaxon:1396. Reserved METPO:1052100 in v444. Duplicate searches included ignored and hidden files. Mechanism and accession-level proteins remain unresolved.

    +

    Added traitmech:000567 using DOI:10.1073/pnas.2519643122, DOI:10.1016/j.chom.2022.09.017 and the executable DefenseFinder model at afb0e5a8b466be53586b13266f5d38d98c3ac268. Verified XML and full-text snippets, recorded four-component versus three-component summary drift, and tied the canonical example to B. cereus B4077 using NCBITaxon:1396. Reserved METPO:1052100 in v444. Duplicate searches included ignored and hidden files. Mechanism and accession-level proteins remain unresolved.

    • Read this curation session
  • · codex
    • EDIT — Classify the existing architecture under Lamassu type II -

      Refined the existing LmuC-containing paired effector architecture below traitmech:000572. The definition is unchanged and illustrates why type II is not an exact three-gene bin. Preserved the long/short-family breadth, model-summary discrepancy, evidence and example. This is a definition-based inference using DOI:10.1093/nar/gkab883, not new functional validation. The writer guards identity, definition, old parents and discussion preimage, appends curation history, and preserves unrelated fields. Historical METPO proposal IDs and broader axioms remain intact; v449 documents the new subclass relation for upstream integration.

    +

    Refined the existing LmuC-containing paired effector architecture below traitmech:000572. The definition is unchanged and illustrates why type II is not an exact three-gene bin. Preserved the long/short-family breadth, model-summary discrepancy, evidence and example. This is a definition-based inference using DOI:10.1093/nar/gkab883, not new functional validation. The writer guards identity, definition, old parents and discussion preimage, appends curation history, and preserves unrelated fields. Historical METPO proposal IDs and broader axioms remain intact; v449 documents the new subclass relation for upstream integration.

    • Read this curation session @@ -357,7 +358,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -386,12 +396,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 15:19 UTC diff --git a/pages/traits/genomics/lamassu_hydrolase_system.html b/pages/traits/genomics/lamassu_hydrolase_system.html index a72f3590628..23c33b997c4 100644 --- a/pages/traits/genomics/lamassu_hydrolase_system.html +++ b/pages/traits/genomics/lamassu_hydrolase_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -120,11 +121,11 @@

    Edge evidence

  • Lamassu-Hydrolase system - traitmech:000561 + traitmech:000561 is a Lamassu system - traitmech:000232 - rdfs:subClassOf + traitmech:000232 + rdfs:subClassOf

    Lamassu-Hydrolase system possession is a Lamassu-system trait.

    • @@ -207,7 +208,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -405,7 +406,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -769,12 +779,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 03:10 UTC diff --git a/pages/traits/genomics/lamassu_lipase_system.html b/pages/traits/genomics/lamassu_lipase_system.html index 33bcbe7a6b2..6b309d63fa6 100644 --- a/pages/traits/genomics/lamassu_lipase_system.html +++ b/pages/traits/genomics/lamassu_lipase_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -126,11 +127,11 @@

    Edge evidence

  • Lamassu-Lipase system - traitmech:000562 + traitmech:000562 is a Lamassu system - traitmech:000232 - rdfs:subClassOf + traitmech:000232 + rdfs:subClassOf

    Lamassu-Lipase system possession is a Lamassu-system trait.

    • @@ -213,7 +214,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -418,7 +419,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -782,12 +792,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 03:49 UTC diff --git a/pages/traits/genomics/lamassu_mrr_system.html b/pages/traits/genomics/lamassu_mrr_system.html index 89f857ad2be..1ec52d8380d 100644 --- a/pages/traits/genomics/lamassu_mrr_system.html +++ b/pages/traits/genomics/lamassu_mrr_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -132,11 +133,11 @@

    Edge evidence

  • Lamassu-Mrr system - traitmech:000563 + traitmech:000563 is a Lamassu system - traitmech:000232 - rdfs:subClassOf + traitmech:000232 + rdfs:subClassOf

    Lamassu-Mrr system possession is a Lamassu-system trait.

    • @@ -219,7 +220,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -424,7 +425,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -788,12 +798,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 04:28 UTC diff --git a/pages/traits/genomics/lamassu_pddexk_system.html b/pages/traits/genomics/lamassu_pddexk_system.html index 6c06bbdde08..098a02410dd 100644 --- a/pages/traits/genomics/lamassu_pddexk_system.html +++ b/pages/traits/genomics/lamassu_pddexk_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -132,11 +133,11 @@

    Edge evidence

  • Lamassu-PDDEXK system - traitmech:000564 + traitmech:000564 is a Lamassu system - traitmech:000232 - rdfs:subClassOf + traitmech:000232 + rdfs:subClassOf

    Lamassu-PDDEXK system possession is a Lamassu-system trait.

    • @@ -219,7 +220,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -424,7 +425,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -788,12 +798,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 05:06 UTC diff --git a/pages/traits/genomics/lamassu_protease_system.html b/pages/traits/genomics/lamassu_protease_system.html index b956d6778ee..5d942228928 100644 --- a/pages/traits/genomics/lamassu_protease_system.html +++ b/pages/traits/genomics/lamassu_protease_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -120,11 +121,11 @@

    Edge evidence

  • Lamassu-Protease system - traitmech:000565 + traitmech:000565 is a Lamassu system - traitmech:000232 - rdfs:subClassOf + traitmech:000232 + rdfs:subClassOf

    Lamassu-Protease system possession is a Lamassu-system trait.

    • @@ -207,7 +208,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -398,7 +399,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -762,12 +772,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 05:48 UTC diff --git a/pages/traits/genomics/lamassu_sir2_system.html b/pages/traits/genomics/lamassu_sir2_system.html index 5954155401c..7e735b2a346 100644 --- a/pages/traits/genomics/lamassu_sir2_system.html +++ b/pages/traits/genomics/lamassu_sir2_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -132,11 +133,11 @@

    Edge evidence

  • Lamassu-Sir2 system - traitmech:000566 + traitmech:000566 is a Lamassu system - traitmech:000232 - rdfs:subClassOf + traitmech:000232 + rdfs:subClassOf

    Lamassu-Sir2 system possession is a Lamassu-system trait.

    • @@ -219,7 +220,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -436,7 +437,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -800,12 +810,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 06:56 UTC diff --git a/pages/traits/genomics/lamassu_smek_system.html b/pages/traits/genomics/lamassu_smek_system.html index 532a3fba17b..b79e2ee97c6 100644 --- a/pages/traits/genomics/lamassu_smek_system.html +++ b/pages/traits/genomics/lamassu_smek_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -157,9 +158,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -175,7 +176,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -324,7 +325,7 @@

    Curation history

  • · ADD_TYPE_II_PARENT · codex -

    Linked traitmech:000572 Lamassu type II system using the LmuC-containing classification in DOI:10.1093/nar/gkab883. Preserved biological definitions, evidence, examples and length-family distinctions. Historical proposal parent axioms remain true; v449 documents the additional subclass relations for upstream minting. This is not new experimental validation.

    +

    Linked traitmech:000572 Lamassu type II system using the LmuC-containing classification in DOI:10.1093/nar/gkab883. Preserved biological definitions, evidence, examples and length-family distinctions. Historical proposal parent axioms remain true; v449 documents the additional subclass relations for upstream minting. This is not new experimental validation.

    • @@ -334,13 +335,13 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Lamassu-SMEK architecture with qualified genomic evidence -

      Added traitmech:000569 and proposal v446 METPO:1052300 using DOI:10.1073/pnas.2519643122, pinned executable DefenseFinder XML, published Dataset S1 and NCBI assembly identity. Exact-matched nine snippets to source XML, raw spreadsheet cells or JSON. Counted 125 unique SMEK calls: 124 short-profile and one long-profile call, rather than treating 377 component rows as systems. The definition has no length restriction and records the long-profile exception for review. WCO-9 GCF_021491935.1 is computational genomic possession, not experimental activity. Distinguished the single-gene DS-27 SMEK label; no chemistry, acronym expansion or causal graph asserted. Ignored-and-hidden novelty and ID searches included METPO, proposals, research and history.

    +

    Added traitmech:000569 and proposal v446 METPO:1052300 using DOI:10.1073/pnas.2519643122, pinned executable DefenseFinder XML, published Dataset S1 and NCBI assembly identity. Exact-matched nine snippets to source XML, raw spreadsheet cells or JSON. Counted 125 unique SMEK calls: 124 short-profile and one long-profile call, rather than treating 377 component rows as systems. The definition has no length restriction and records the long-profile exception for review. WCO-9 GCF_021491935.1 is computational genomic possession, not experimental activity. Distinguished the single-gene DS-27 SMEK label; no chemistry, acronym expansion or causal graph asserted. Ignored-and-hidden novelty and ID searches included METPO, proposals, research and history.

    • Read this curation session
  • · codex
    • EDIT — Classify the existing architecture under Lamassu type II -

      Refined the existing LmuC-containing architecture below traitmech:000572 without assigning a short/long family. Preserved the long-profile exception, computational WCO-9 example, definition, evidence and unresolved experimental function. This is a definition-based inference using DOI:10.1093/nar/gkab883, not new functional validation. The writer guards identity, definition, old parents and discussion preimage, appends curation history, and preserves unrelated fields. Historical METPO proposal IDs and broader axioms remain intact; v449 documents the new subclass relation for upstream integration.

    +

    Refined the existing LmuC-containing architecture below traitmech:000572 without assigning a short/long family. Preserved the long-profile exception, computational WCO-9 example, definition, evidence and unresolved experimental function. This is a definition-based inference using DOI:10.1093/nar/gkab883, not new functional validation. The writer guards identity, definition, old parents and discussion preimage, appends curation history, and preserves unrelated fields. Historical METPO proposal IDs and broader axioms remain intact; v449 documents the new subclass relation for upstream integration.

    • Read this curation session @@ -372,7 +373,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -401,12 +411,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 15:20 UTC diff --git a/pages/traits/genomics/lamassu_system.html b/pages/traits/genomics/lamassu_system.html index 65c79c9edf2..3e71d638e56 100644 --- a/pages/traits/genomics/lamassu_system.html +++ b/pages/traits/genomics/lamassu_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -199,7 +200,7 @@

    Edge evidence

    confers Lamassu system - traitmech:000232 + traitmech:000232 METPO:2007700

    Viral-DNA-triggered LmuA effector activation realizes the Lamassu system trait.

      @@ -215,11 +216,11 @@

      Edge evidence

    • Lamassu system - traitmech:000232 + traitmech:000232 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Lamassu system possession is a phage-defense-system trait.

        @@ -313,7 +314,7 @@

        Children (14)

        Synonyms (1)

    @@ -329,7 +330,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -450,7 +451,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    Haudiquet et al. support a structurally characterized Vibrio cholerae Lamassu Vc-Cap4 system with LmuABC DNA-end sensing and LmuA Cap4 nuclease activation, and the pinned DefenseFinder tables model Lamassu-Amidase, Lamassu-Cap4_nuclease, Lamassu-FMO, Lamassu-Hydrolase, Lamassu-Lipase, Lamassu-Mrr, Lamassu-PDDEXK, Lamassu-Protease, Lamassu-Sir2, and other Lamassu-Fam subtypes as rule-row variants. Lamassu-Amidase, Lamassu-Cap4 nuclease, Lamassu-FMO, Lamassu-Hydrolase, Lamassu-Lipase, Lamassu-Mrr, Lamassu-PDDEXK, Lamassu-Protease, and Lamassu-Sir2 now capture nine DefenseFinder rule-row subtypes, but long-versus-short LmuB clades, LmuC-independent subfamilies, the Lamassu-Fam base, Lamassu-Hydrolase_Protease, and Lamassu-Hypothetical rule rows, viral-DNA triggers, exact LmuA effector substrates, FMO acronym expansion, the Lamassu-FMO rule row's relationship to FMO-scoped LmuB/LmuC HMM rows, the Lamassu-Lipase rule row's relationship to its Lipase-scoped LmuB HMM row, the Lamassu-Mrr rule row's relationship to Mrr-scoped LmuB/LmuC HMM rows, the Lamassu-PDDEXK rule row's relationship to PDDEXK-scoped LmuB/LmuC HMM rows, the Lamassu-Sir2 rule row's relationship to Sir2-scoped LmuB/LmuC HMM rows, and cell-death outputs across Lamassu loci remain unresolved. Lamassu Hydrolase-Protease system (traitmech:000567) now captures the literature-supported paired architecture with LmuB and LmuC. Its pinned executable XML requires four components, whereas the summary TSV requires three matches and calls LmuC accessory. The existing table-defined Lamassu-Hydrolase and Lamassu-Protease siblings each forbid the other's effector profile and are not exact matches to this paired architecture. Reconciling the legacy table-based sibling definitions with executable models remains open; do not interpret the summary's profile labels as current executable model requirements. Lamassu-HNH system (traitmech:000568) now captures the literature-supported short-LmuB architecture with HNH-domain LmuA and LmuC. The published dataset supplies complete computational genome calls, not HNH-specific functional validation. The pinned executable HNH model accepts either long or short LmuB, whereas all HNH calls in that dataset use short LmuB; its software key is therefore not an exact synonym for this biological scope. HNH-specific activity, substrates, and activation remain unresolved. Lamassu-SMEK system (traitmech:000569) now captures a locus with SMEK-domain LmuA, LmuB, and LmuC. The paper describes SMEK as short-specific, but its dataset contains 124 short-profile system calls and one long-profile call; the latter requires reconciliation before asserting a biological long-LmuB subtype. The definition therefore does not impose a LmuB-length restriction. The three-component architecture is not equivalent to the single-gene DS-27 system that also uses SMEK as a working label. SMEK-specific functional validation and chemistry remain unresolved. Short Lamassu system (traitmech:000570) now captures the short-LmuB phylogenetic and structural family, not a fixed protein-length bin or an effector-specific detector. Lamassu-HNH is placed below it because its existing definition explicitly requires short-form LmuB. SMEK remains directly under the broader Lamassu parent because of its unresolved long-profile exception. The short family permits the reported LmuC-loss and effector-domain-loss architectures; type I is not an exact synonym for the whole short family. The Lamassu-Hypothetical registry label is not accepted as a separate biological trait here: unknown annotation does not establish effector-domain loss, and its relationship to the paper's clade O still needs explicit mapping. The long family and component-number subtypes remain separate discovery leads. Long Lamassu system (traitmech:000571) now captures the complementary long-LmuB phylogenetic and structural family, not an 800-residue cutoff or a particular effector model. The paper assigns the B. cereus B4077 Hydrolase-Protease system to this family, but that effector architecture also occurs in short Lamassu, so the whole Hydrolase-Protease trait is not reparented. The legacy table-defined FMO trait still needs model and biological-scope reconciliation before assigning the entire record to the long family. SMEK's exception remains unresolved. Raw detection gene_name hits must not be confused with exchangeable hit_gene_ref model slots, and ambiguous loci need phylogenetic classification. Component-number type I/II traits remain separate discovery leads. Lamassu type II system (traitmech:000572) now captures the LmuC-containing component architecture defined by Payne et al. (DOI:10.1093/nar/gkab883) and independently used by Li et al. (DOI:10.1038/s41589-025-02102-z). HNH, SMEK and Hydrolase-Protease already require LmuC in their definitions and now have this parent; HNH retains its short-family parent too. This does not assert a three-gene count, universal LmuC essentiality, or new antiviral validation of those children. Long/short families and legacy detector rows are not equivalent to this component class. Type I and family-wide mechanisms remain open discovery and curation questions. Lamassu type I system (traitmech:000573) now resolves the component-class discovery lead: Haudiquet et al. explicitly identify the LmuC-loss architecture as type I, and Li et al. independently study a type-I LmuA/LmuB complex. This is not equivalent to all short Lamassu or proof that every failed LmuC hit is biological absence. No existing effector-defined child is reparented. Family-wide mechanisms, legacy model reconciliation and native-host activity remain open.

    +

    Haudiquet et al. support a structurally characterized Vibrio cholerae Lamassu Vc-Cap4 system with LmuABC DNA-end sensing and LmuA Cap4 nuclease activation, and the pinned DefenseFinder tables model Lamassu-Amidase, Lamassu-Cap4_nuclease, Lamassu-FMO, Lamassu-Hydrolase, Lamassu-Lipase, Lamassu-Mrr, Lamassu-PDDEXK, Lamassu-Protease, Lamassu-Sir2, and other Lamassu-Fam subtypes as rule-row variants. Lamassu-Amidase, Lamassu-Cap4 nuclease, Lamassu-FMO, Lamassu-Hydrolase, Lamassu-Lipase, Lamassu-Mrr, Lamassu-PDDEXK, Lamassu-Protease, and Lamassu-Sir2 now capture nine DefenseFinder rule-row subtypes, but long-versus-short LmuB clades, LmuC-independent subfamilies, the Lamassu-Fam base, Lamassu-Hydrolase_Protease, and Lamassu-Hypothetical rule rows, viral-DNA triggers, exact LmuA effector substrates, FMO acronym expansion, the Lamassu-FMO rule row's relationship to FMO-scoped LmuB/LmuC HMM rows, the Lamassu-Lipase rule row's relationship to its Lipase-scoped LmuB HMM row, the Lamassu-Mrr rule row's relationship to Mrr-scoped LmuB/LmuC HMM rows, the Lamassu-PDDEXK rule row's relationship to PDDEXK-scoped LmuB/LmuC HMM rows, the Lamassu-Sir2 rule row's relationship to Sir2-scoped LmuB/LmuC HMM rows, and cell-death outputs across Lamassu loci remain unresolved. Lamassu Hydrolase-Protease system (traitmech:000567) now captures the literature-supported paired architecture with LmuB and LmuC. Its pinned executable XML requires four components, whereas the summary TSV requires three matches and calls LmuC accessory. The existing table-defined Lamassu-Hydrolase and Lamassu-Protease siblings each forbid the other's effector profile and are not exact matches to this paired architecture. Reconciling the legacy table-based sibling definitions with executable models remains open; do not interpret the summary's profile labels as current executable model requirements. Lamassu-HNH system (traitmech:000568) now captures the literature-supported short-LmuB architecture with HNH-domain LmuA and LmuC. The published dataset supplies complete computational genome calls, not HNH-specific functional validation. The pinned executable HNH model accepts either long or short LmuB, whereas all HNH calls in that dataset use short LmuB; its software key is therefore not an exact synonym for this biological scope. HNH-specific activity, substrates, and activation remain unresolved. Lamassu-SMEK system (traitmech:000569) now captures a locus with SMEK-domain LmuA, LmuB, and LmuC. The paper describes SMEK as short-specific, but its dataset contains 124 short-profile system calls and one long-profile call; the latter requires reconciliation before asserting a biological long-LmuB subtype. The definition therefore does not impose a LmuB-length restriction. The three-component architecture is not equivalent to the single-gene DS-27 system that also uses SMEK as a working label. SMEK-specific functional validation and chemistry remain unresolved. Short Lamassu system (traitmech:000570) now captures the short-LmuB phylogenetic and structural family, not a fixed protein-length bin or an effector-specific detector. Lamassu-HNH is placed below it because its existing definition explicitly requires short-form LmuB. SMEK remains directly under the broader Lamassu parent because of its unresolved long-profile exception. The short family permits the reported LmuC-loss and effector-domain-loss architectures; type I is not an exact synonym for the whole short family. The Lamassu-Hypothetical registry label is not accepted as a separate biological trait here: unknown annotation does not establish effector-domain loss, and its relationship to the paper's clade O still needs explicit mapping. The long family and component-number subtypes remain separate discovery leads. Long Lamassu system (traitmech:000571) now captures the complementary long-LmuB phylogenetic and structural family, not an 800-residue cutoff or a particular effector model. The paper assigns the B. cereus B4077 Hydrolase-Protease system to this family, but that effector architecture also occurs in short Lamassu, so the whole Hydrolase-Protease trait is not reparented. The legacy table-defined FMO trait still needs model and biological-scope reconciliation before assigning the entire record to the long family. SMEK's exception remains unresolved. Raw detection gene_name hits must not be confused with exchangeable hit_gene_ref model slots, and ambiguous loci need phylogenetic classification. Component-number type I/II traits remain separate discovery leads. Lamassu type II system (traitmech:000572) now captures the LmuC-containing component architecture defined by Payne et al. (DOI:10.1093/nar/gkab883) and independently used by Li et al. (DOI:10.1038/s41589-025-02102-z). HNH, SMEK and Hydrolase-Protease already require LmuC in their definitions and now have this parent; HNH retains its short-family parent too. This does not assert a three-gene count, universal LmuC essentiality, or new antiviral validation of those children. Long/short families and legacy detector rows are not equivalent to this component class. Type I and family-wide mechanisms remain open discovery and curation questions. Lamassu type I system (traitmech:000573) now resolves the component-class discovery lead: Haudiquet et al. explicitly identify the LmuC-loss architecture as type I, and Li et al. independently study a type-I LmuA/LmuB complex. This is not equivalent to all short Lamassu or proof that every failed LmuC hit is biological absence. No existing effector-defined child is reparented. Family-wide mechanisms, legacy model reconciliation and native-host activity remain open.

    @@ -562,13 +563,13 @@

    Curation history

  • · TRACK_TYPE_II_CLASS · codex -

    Linked traitmech:000572 Lamassu type II system using the LmuC-containing classification in DOI:10.1093/nar/gkab883. Preserved biological definitions, evidence, examples and length-family distinctions. Historical proposal parent axioms remain true; v449 documents the additional subclass relations for upstream minting. This is not new experimental validation.

    +

    Linked traitmech:000572 Lamassu type II system using the LmuC-containing classification in DOI:10.1093/nar/gkab883. Preserved biological definitions, evidence, examples and length-family distinctions. Historical proposal parent axioms remain true; v449 documents the additional subclass relations for upstream minting. This is not new experimental validation.

  • · TRACK_TYPE_I_CLASS · codex -

    Linked traitmech:000573 Lamassu type I system to the existing component-architecture discussion using DOI:10.1073/pnas.2519643122 and DOI:10.1038/s41589-025-02102-z. Preserved all definitions, parents, evidence, examples and prior history. Component absence, LmuB-length family and experimental activity remain separate claims.

    +

    Linked traitmech:000573 Lamassu type I system to the existing component-architecture discussion using DOI:10.1073/pnas.2519643122 and DOI:10.1038/s41589-025-02102-z. Preserved all definitions, parents, evidence, examples and prior history. Component absence, LmuB-length family and experimental activity remain separate claims.

    • @@ -656,7 +657,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Track the short Lamassu family and remaining classification gaps -

      Appended a guarded discussion update for new traitmech:000570 and its HNH child. Kept SMEK directly under Lamassu because its published long-profile exception remains unresolved. Rejected equating the Hypothetical registry label with the article effector-domain-loss clade without explicit mapping; retained long-family and component-number classes as discovery leads. The primary source is DOI:10.1073/pnas.2519643122. Preserved all earlier rationale and evidence. Production preimage hash guards and 24 focused writer tests protect unrelated curation.

    +

    Appended a guarded discussion update for new traitmech:000570 and its HNH child. Kept SMEK directly under Lamassu because its published long-profile exception remains unresolved. Rejected equating the Hypothetical registry label with the article effector-domain-loss clade without explicit mapping; retained long-family and component-number classes as discovery leads. The primary source is DOI:10.1073/pnas.2519643122. Preserved all earlier rationale and evidence. Production preimage hash guards and 24 focused writer tests protect unrelated curation.

    • Read this curation session
  • @@ -706,7 +707,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -1070,12 +1080,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 16:01 UTC diff --git a/pages/traits/genomics/lamassu_type_i_system.html b/pages/traits/genomics/lamassu_type_i_system.html index d11ffe0690c..36391e2308a 100644 --- a/pages/traits/genomics/lamassu_type_i_system.html +++ b/pages/traits/genomics/lamassu_type_i_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -67,7 +68,7 @@

    Trait evidence (4)

    https://rest.uniprot.org/uniprotkb/P0DW44.json
    Component of antiviral defense system Lamassu type I, composed of LmuA and LmuB.
    -

    Reviewed P0DW44, entry version 8, retrieved 2026-10-03: the FUNCTION annotation identifies the LmuA/LmuB system in the NIO-1130 source strain (taxon 1761765), citing PMID:29371424. Its protection assays were heterologous expression in B. subtilis BEST7003, not native-host assays. The source organism and expression host are not interchangeable.

    +

    Reviewed P0DW44, entry version 8, retrieved 2026-10-03: the FUNCTION annotation identifies the LmuA/LmuB system in the NIO-1130 source strain (taxon 1761765), citing PMID:29371424. Its protection assays were heterologous expression in B. subtilis BEST7003, not native-host assays. The source organism and expression host are not interchangeable.

  • @@ -118,7 +119,7 @@

    Parent traits (1)

    Synonyms (1)

    • @@ -134,7 +135,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -287,7 +288,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add the LmuC-lacking Lamassu type-I possession trait -

      Added traitmech:000573 with primary DOI sources 10.1073/pnas.2519643122 and 10.1038/s41589-025-02102-z, four directly verified contiguous snippets, reviewed UniProt P0DW44 and PDB 9UX7 source metadata, and NCBITaxon:1761765 Bacillus sp. nio-1130. Distinguished source possession from heterologous activity, component absence from missing hits, and composition from length families. Ignored-and-hidden searches established novelty and allocation. Reserved METPO:1052700 in v450; validate the guarded writer, proposal, histories and regenerated artifacts.

    +

    Added traitmech:000573 with primary DOI sources 10.1073/pnas.2519643122 and 10.1038/s41589-025-02102-z, four directly verified contiguous snippets, reviewed UniProt P0DW44 and PDB 9UX7 source metadata, and NCBITaxon:1761765 Bacillus sp. nio-1130. Distinguished source possession from heterologous activity, component absence from missing hits, and composition from length families. Ignored-and-hidden searches established novelty and allocation. Reserved METPO:1052700 in v450; validate the guarded writer, proposal, histories and regenerated artifacts.

    • Read this curation session @@ -319,7 +320,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -348,12 +358,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 16:01 UTC diff --git a/pages/traits/genomics/lamassu_type_ii_system.html b/pages/traits/genomics/lamassu_type_ii_system.html index 2ce59b3ceb1..752745a4076 100644 --- a/pages/traits/genomics/lamassu_type_ii_system.html +++ b/pages/traits/genomics/lamassu_type_ii_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -119,7 +120,7 @@

    Children (3)

    Synonyms (1)

      -
    • Lamassu type II EXACT_SYNONYM · DOI:10.1093/nar/gkab883
      • +
    • Lamassu type II EXACT_SYNONYM · DOI:10.1093/nar/gkab883
    @@ -135,7 +136,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -284,7 +285,7 @@

    Curation history

  • · TRACK_TYPE_I_CLASS · codex -

    Linked traitmech:000573 Lamassu type I system to the existing component-architecture discussion using DOI:10.1073/pnas.2519643122 and DOI:10.1038/s41589-025-02102-z. Preserved all definitions, parents, evidence, examples and prior history. Component absence, LmuB-length family and experimental activity remain separate claims.

    +

    Linked traitmech:000573 Lamassu type I system to the existing component-architecture discussion using DOI:10.1073/pnas.2519643122 and DOI:10.1038/s41589-025-02102-z. Preserved all definitions, parents, evidence, examples and prior history. Component absence, LmuB-length family and experimental activity remain separate claims.

    • @@ -294,7 +295,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add the LmuC-containing Lamassu type II class -

      Added traitmech:000572 using independent primary studies DOI:10.1093/nar/gkab883 and DOI:10.1038/s41589-025-02102-z. Exact full-text and abstract snippets were checked directly. NCBI Nuccore resolved the source-reported NZ_HG322949.1 locus accession to DSM 9628 and NCBITaxon:1349767; Taxonomy independently confirmed the strain label. Distinguished source-strain possession from heterologous E. coli BL21-AI activity, component classification from long/short families, and LmuC presence from universal essentiality or a fixed three-gene count. No causal mechanism graph or protein accession was invented. Whole-repository ignored-and-hidden searches found no exact trait or METPO term; fresh seed comparison confirmed 55 previously classified duplicate/supporting-field leads. Reserved METPO:1052600 in v449 and refined three existing LmuC-containing child hierarchies. Broader trait discovery remains open.

    +

    Added traitmech:000572 using independent primary studies DOI:10.1093/nar/gkab883 and DOI:10.1038/s41589-025-02102-z. Exact full-text and abstract snippets were checked directly. NCBI Nuccore resolved the source-reported NZ_HG322949.1 locus accession to DSM 9628 and NCBITaxon:1349767; Taxonomy independently confirmed the strain label. Distinguished source-strain possession from heterologous E. coli BL21-AI activity, component classification from long/short families, and LmuC presence from universal essentiality or a fixed three-gene count. No causal mechanism graph or protein accession was invented. Whole-repository ignored-and-hidden searches found no exact trait or METPO term; fresh seed comparison confirmed 55 previously classified duplicate/supporting-field leads. Reserved METPO:1052600 in v449 and refined three existing LmuC-containing child hierarchies. Broader trait discovery remains open.

    • Read this curation session
  • @@ -332,7 +333,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -361,12 +371,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 16:01 UTC diff --git a/pages/traits/genomics/lanthivirin_system.html b/pages/traits/genomics/lanthivirin_system.html index c7f85d77231..a2ff7138dce 100644 --- a/pages/traits/genomics/lanthivirin_system.html +++ b/pages/traits/genomics/lanthivirin_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -173,7 +174,7 @@

    Edge evidence

    confers lanthivirin system - traitmech:000416 + traitmech:000416 METPO:2007700

    Lanthivirin maturation realizes the anti-phage activity of the lanthivirin system.

    @@ -270,7 +271,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -489,7 +490,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -853,12 +863,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 20:06 UTC diff --git a/pages/traits/genomics/lit_system.html b/pages/traits/genomics/lit_system.html index e7e6cde8dae..82a579088ca 100644 --- a/pages/traits/genomics/lit_system.html +++ b/pages/traits/genomics/lit_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers Lit system - traitmech:000363 + traitmech:000363 METPO:2007700

    T4 Gol-Lit phage exclusion realizes the Lit system trait.

    @@ -265,7 +266,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -424,7 +425,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -788,12 +798,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-22 10:39 UTC diff --git a/pages/traits/genomics/long_lamassu_system.html b/pages/traits/genomics/long_lamassu_system.html index 26fed243030..8bc96e37f24 100644 --- a/pages/traits/genomics/long_lamassu_system.html +++ b/pages/traits/genomics/long_lamassu_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -114,7 +115,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -130,7 +131,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -283,7 +284,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add the literature-defined long Lamassu family -

      Minted traitmech:000571 from DOI:10.1073/pnas.2519643122 after ignored-and-hidden whole-repository searches and a fresh METPO seed comparison found no exact primary term. Reserved METPO:1052500 in v448. Two paper spans and the exact Dataset S1 A58:C60 cells support the structural family, B4077 source-organism example and a separate computational long-profile locus. Actual gene_name hits are distinguished from exchangeable hit_gene_ref model slots. The two cited artifacts belong to the same study, not independent experiments. NCBITaxon:1396 was independently resolved; no species-wide possession, genome assembly, numerical cutoff, universal effector mechanism or automatic sibling reparenting is asserted. The original Millman PDF could not be retrieved and is not newly quoted. A dry-run-first validated writer and controlled-fixture drift/idempotence tests cover this addition.

    +

    Minted traitmech:000571 from DOI:10.1073/pnas.2519643122 after ignored-and-hidden whole-repository searches and a fresh METPO seed comparison found no exact primary term. Reserved METPO:1052500 in v448. Two paper spans and the exact Dataset S1 A58:C60 cells support the structural family, B4077 source-organism example and a separate computational long-profile locus. Actual gene_name hits are distinguished from exchangeable hit_gene_ref model slots. The two cited artifacts belong to the same study, not independent experiments. NCBITaxon:1396 was independently resolved; no species-wide possession, genome assembly, numerical cutoff, universal effector mechanism or automatic sibling reparenting is asserted. The original Millman PDF could not be retrieved and is not newly quoted. A dry-run-first validated writer and controlled-fixture drift/idempotence tests cover this addition.

    • Read this curation session @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 14:33 UTC diff --git a/pages/traits/genomics/lugos_system.html b/pages/traits/genomics/lugos_system.html index 302ba8b0d7d..891e0a497e3 100644 --- a/pages/traits/genomics/lugos_system.html +++ b/pages/traits/genomics/lugos_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Lugos system - traitmech:000283 + traitmech:000283 METPO:2007700

    Lugos-mediated phage restriction realizes the Lugos system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -392,7 +393,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -756,12 +766,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 15:04 UTC diff --git a/pages/traits/genomics/mads_system.html b/pages/traits/genomics/mads_system.html index c13897733ef..365957b3dd8 100644 --- a/pages/traits/genomics/mads_system.html +++ b/pages/traits/genomics/mads_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -287,7 +288,7 @@

    Edge evidence

    confers MADS system - traitmech:000370 + traitmech:000370 METPO:2007700

    MADS-mediated DNA-phage restriction realizes the MADS system trait.

    @@ -412,7 +413,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -615,7 +616,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -979,12 +989,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-25 03:36 UTC diff --git a/pages/traits/genomics/mazef_system.html b/pages/traits/genomics/mazef_system.html index f5060313215..e7374107fa7 100644 --- a/pages/traits/genomics/mazef_system.html +++ b/pages/traits/genomics/mazef_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -166,7 +167,7 @@

    Edge evidence

    confers MazEF system - traitmech:000345 + traitmech:000345 METPO:2007700

    MazEF-associated reduction of RNA phage susceptibility realizes the MazEF system trait.

    @@ -273,7 +274,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -457,7 +458,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -821,12 +831,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 21:05 UTC diff --git a/pages/traits/genomics/mcrbc_system.html b/pages/traits/genomics/mcrbc_system.html index ec790c77538..de011178760 100644 --- a/pages/traits/genomics/mcrbc_system.html +++ b/pages/traits/genomics/mcrbc_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers McrBC system - traitmech:000505 + traitmech:000505 METPO:2007700

    McrBC methylated-DNA restriction realizes the organism-level McrBC system possession trait.

    @@ -263,7 +264,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -501,7 +502,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -865,12 +875,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 03:37 UTC diff --git a/pages/traits/genomics/menshen_system.html b/pages/traits/genomics/menshen_system.html index b9a9b99ed43..d235cb7715c 100644 --- a/pages/traits/genomics/menshen_system.html +++ b/pages/traits/genomics/menshen_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers Menshen system - traitmech:000253 + traitmech:000253 METPO:2007700

    Menshen-mediated phage restriction realizes the Menshen system trait.

    @@ -261,7 +262,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -420,7 +421,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -784,12 +794,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 22:20 UTC diff --git a/pages/traits/genomics/metis_system.html b/pages/traits/genomics/metis_system.html index a7b86a95547..3e8abd0cda6 100644 --- a/pages/traits/genomics/metis_system.html +++ b/pages/traits/genomics/metis_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -192,7 +193,7 @@

    Edge evidence

    confers Metis system - traitmech:000502 + traitmech:000502 METPO:2007700

    Triggered Metis effector toxicity realizes the Metis system trait by aborting phage infection.

    @@ -287,7 +288,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -499,7 +500,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -863,12 +873,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 22:52 UTC diff --git a/pages/traits/genomics/mksbefg_system.html b/pages/traits/genomics/mksbefg_system.html index f324a18dbef..3991e545c0a 100644 --- a/pages/traits/genomics/mksbefg_system.html +++ b/pages/traits/genomics/mksbefg_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -186,7 +187,7 @@

    Edge evidence

    confers MksBEFG system - traitmech:000526 + traitmech:000526 METPO:2007700

    Plasmid DNA degradation realizes the MksBEFG anti-plasmid defense trait.

      @@ -202,11 +203,11 @@

      Edge evidence

    • MksBEFG system - traitmech:000526 + traitmech:000526 is a Wadjet system - traitmech:000218 - rdfs:subClassOf + traitmech:000218 + rdfs:subClassOf

      MksBEFG system possession is a Wadjet system trait.

        @@ -265,7 +266,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -281,7 +282,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -473,7 +474,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add MksBEFG system -

      Minted traitmech:000526 for the MksBEFG anti-plasmid Wadjet child system with DOI:10.1093/nar/gkad130 MksG nuclease and in vivo activation evidence, narrowed the broad Wadjet subfamily discussion, and reserved METPO:1048000 in proposals/metpo_traitmech_v403.

    +

    Minted traitmech:000526 for the MksBEFG anti-plasmid Wadjet child system with DOI:10.1093/nar/gkad130 MksG nuclease and in vivo activation evidence, narrowed the broad Wadjet subfamily discussion, and reserved METPO:1048000 in proposals/metpo_traitmech_v403.

    • Read this curation session @@ -505,7 +506,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -869,12 +879,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 21:15 UTC diff --git a/pages/traits/genomics/mmb_gp29_gp30_system.html b/pages/traits/genomics/mmb_gp29_gp30_system.html index 41afb55f0bf..993da5733cf 100644 --- a/pages/traits/genomics/mmb_gp29_gp30_system.html +++ b/pages/traits/genomics/mmb_gp29_gp30_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -190,7 +191,7 @@

    Edge evidence

    confers MMB gp29-gp30 system - traitmech:000297 + traitmech:000297 METPO:2007700

    MMB-gp29-gp30-mediated restriction of phage propagation realizes the MMB gp29-gp30 system trait.

    @@ -291,7 +292,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -450,7 +451,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -814,12 +824,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 00:13 UTC diff --git a/pages/traits/genomics/mobile_genetic_element.html b/pages/traits/genomics/mobile_genetic_element.html index e76233a6a35..b813eb298f3 100644 --- a/pages/traits/genomics/mobile_genetic_element.html +++ b/pages/traits/genomics/mobile_genetic_element.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • mobile genetic element - traitmech:000089 + traitmech:000089 enables horizontal gene transfer GO:0009292 @@ -267,7 +268,7 @@

    Edge evidence

  • mobile genetic element - traitmech:000089 + traitmech:000089 enables transposition GO:0032196 @@ -402,7 +403,7 @@

    Children (4)

    Synonyms (1)

    • @@ -418,7 +419,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -688,7 +689,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1052,12 +1062,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/genomics/mok_hok_sok_system.html b/pages/traits/genomics/mok_hok_sok_system.html index b50619a7f38..1b49affc909 100644 --- a/pages/traits/genomics/mok_hok_sok_system.html +++ b/pages/traits/genomics/mok_hok_sok_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -166,7 +167,7 @@

    Edge evidence

    confers Mok-Hok-Sok system - traitmech:000372 + traitmech:000372 METPO:2007700

    T4 phage exclusion realizes the Mok-Hok-Sok system trait.

    @@ -279,7 +280,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -438,7 +439,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -802,12 +812,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-25 05:04 UTC diff --git a/pages/traits/genomics/mokosh_system.html b/pages/traits/genomics/mokosh_system.html index 337662d555f..2f562c952ee 100644 --- a/pages/traits/genomics/mokosh_system.html +++ b/pages/traits/genomics/mokosh_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -172,7 +173,7 @@

    Edge evidence

    confers Mokosh system - traitmech:000246 + traitmech:000246 METPO:2007700

    Mokosh-mediated phage restriction realizes the Mokosh system trait.

    @@ -273,7 +274,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -432,7 +433,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -796,12 +806,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 16:53 UTC diff --git a/pages/traits/genomics/mqsrac_system.html b/pages/traits/genomics/mqsrac_system.html index f99f5ddc539..459c7ab89a0 100644 --- a/pages/traits/genomics/mqsrac_system.html +++ b/pages/traits/genomics/mqsrac_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -203,7 +204,7 @@

    Edge evidence

    confers MqsRAC system - traitmech:000368 + traitmech:000368 METPO:2007700

    MqsRAC-dependent survival through persister-cell formation realizes the MqsRAC system trait.

    @@ -329,7 +330,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -530,7 +531,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -894,12 +904,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-22 15:18 UTC diff --git a/pages/traits/genomics/mspji_system.html b/pages/traits/genomics/mspji_system.html index 2f0d5b7d94b..49be1772b3b 100644 --- a/pages/traits/genomics/mspji_system.html +++ b/pages/traits/genomics/mspji_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -167,7 +168,7 @@

    Edge evidence

    confers MspJI system - traitmech:000510 + traitmech:000510 METPO:2007700

    MspJI-family modified-cytosine restriction realizes the organism-level MspJI system possession trait.

    @@ -274,7 +275,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -486,7 +487,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -850,12 +860,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 08:04 UTC diff --git a/pages/traits/genomics/nantosuelta_system.html b/pages/traits/genomics/nantosuelta_system.html index 3fb804ecb72..6c8134967de 100644 --- a/pages/traits/genomics/nantosuelta_system.html +++ b/pages/traits/genomics/nantosuelta_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Nantosuelta system - traitmech:000284 + traitmech:000284 METPO:2007700

    Nantosuelta-mediated phage restriction realizes the Nantosuelta system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -404,7 +405,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -768,12 +778,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 15:47 UTC diff --git a/pages/traits/genomics/nemetona_system.html b/pages/traits/genomics/nemetona_system.html index d271e0b9064..af49bf7d0c1 100644 --- a/pages/traits/genomics/nemetona_system.html +++ b/pages/traits/genomics/nemetona_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Nemetona system - traitmech:000285 + traitmech:000285 METPO:2007700

    Nemetona-mediated phage restriction realizes the Nemetona system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -392,7 +393,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -756,12 +766,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 16:05 UTC diff --git a/pages/traits/genomics/nhi_system.html b/pages/traits/genomics/nhi_system.html index 2c74343a648..0a898112be0 100644 --- a/pages/traits/genomics/nhi_system.html +++ b/pages/traits/genomics/nhi_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -204,7 +205,7 @@

    Edge evidence

    confers Nhi system - traitmech:000332 + traitmech:000332 METPO:2007700

    Preventing phage DNA accumulation realizes the Nhi phage-defense trait.

    @@ -305,7 +306,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -489,7 +490,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -853,12 +863,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 16:05 UTC diff --git a/pages/traits/genomics/nixi_system.html b/pages/traits/genomics/nixi_system.html index c184513e37a..bd987a13663 100644 --- a/pages/traits/genomics/nixi_system.html +++ b/pages/traits/genomics/nixi_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -85,7 +86,7 @@

    Trait evidence (8)

    https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    NixI | 10\.1101/2021\.07\.12\.452122 | A phage parasite deploys a nicking nuclease effector to inhibit replication of its viral host
    -

    The DefenseFinder article registry maps the named NixI model namespace to the LeGault et al. PLE-encoded nicking-nuclease preprint, later published under DOI:10.1093/nar/gkac002.

    +

    The DefenseFinder article registry maps the named NixI model namespace to the LeGault et al. PLE-encoded nicking-nuclease preprint, later published under DOI:10.1093/nar/gkac002.

  • @@ -216,7 +217,7 @@

    Edge evidence

    confers NixI system - traitmech:000333 + traitmech:000333 METPO:2007700

    NixI-dependent ICP1 replication inhibition realizes the NixI system trait.

    @@ -238,11 +239,11 @@

    Edge evidence

  • NixI system - traitmech:000333 + traitmech:000333 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

    NixI system possession is a phage-defense-system trait.

    • @@ -317,7 +318,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -513,7 +514,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -877,12 +887,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 10:31 UTC diff --git a/pages/traits/genomics/nlr_like_bnacht_system.html b/pages/traits/genomics/nlr_like_bnacht_system.html index 8dbf8b9769d..341903f2d58 100644 --- a/pages/traits/genomics/nlr_like_bnacht_system.html +++ b/pages/traits/genomics/nlr_like_bnacht_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -214,7 +215,7 @@

    Edge evidence

    confers NLR-like bNACHT system - traitmech:000408 + traitmech:000408 METPO:2007700

    NACHT-module-dependent phage restriction realizes the NLR-like bNACHT system trait.

    @@ -333,7 +334,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -582,7 +583,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -946,12 +956,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 13:27 UTC diff --git a/pages/traits/genomics/ogmios_system.html b/pages/traits/genomics/ogmios_system.html index e7f37bbfcce..758095facc9 100644 --- a/pages/traits/genomics/ogmios_system.html +++ b/pages/traits/genomics/ogmios_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Ogmios system - traitmech:000286 + traitmech:000286 METPO:2007700

    Ogmios-mediated phage restriction realizes the Ogmios system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -392,7 +393,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -756,12 +766,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 16:34 UTC diff --git a/pages/traits/genomics/old_exonuclease_system.html b/pages/traits/genomics/old_exonuclease_system.html index d35dc10b631..f7ffd02a06d 100644 --- a/pages/traits/genomics/old_exonuclease_system.html +++ b/pages/traits/genomics/old_exonuclease_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -66,13 +67,13 @@

    Trait evidence (11) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md -
    It's been shown to protect against phage lambda :ref{doi=10.1128/jb.177.3.497-501.1995}, and when cloned with the P2 Tin accessory gene, it was shown to protect against other *E. coli* phages :ref{doi=10.1016/j.chom.2022.02.018}.
    +
    It's been shown to protect against phage lambda :ref{doi=10.1128/jb.177.3.497-501.1995}, and when cloned with the P2 Tin accessory gene, it was shown to protect against other *E. coli* phages :ref{doi=10.1016/j.chom.2022.02.018}.

    The pinned DefenseFinder wiki page links Old_exonuclease to lambda protection and to broader P2 Old plus Tin protection.

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md -
    The old_exonuclease is dsDNA exonuclease that digests in the 5' to 3' direction :ref{doi=10.1128/jb.177.3.497-501.1995}. To our knowledge, other aspects of the molecular mechanisms remain unknown.
    +
    The old_exonuclease is dsDNA exonuclease that digests in the 5' to 3' direction :ref{doi=10.1128/jb.177.3.497-501.1995}. To our knowledge, other aspects of the molecular mechanisms remain unknown.

    The pinned DefenseFinder wiki page supports Old dsDNA exonuclease activity while leaving the remaining molecular mechanism unresolved.

    • @@ -90,9 +91,9 @@

    Trait evidence (11) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md -
    Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0 +
    Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0 Origin_0[Enterobacteria phage P2 -<a href='https://ncbi.nlm.nih.gov/protein/NP_046798.1'>NP_046798.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/NP_046798.1'>NP_046798.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> Lambda & T4 & LF82_P8 & Al505_P2

    The DefenseFinder experimental-validation diagram links Rousset et al. to Enterobacteria phage P2 Old expressed in Escherichia coli against lambda, T4, LF82_P8, and Al505_P2.

    @@ -191,7 +192,7 @@

    Edge evidence

    confers Old exonuclease system - traitmech:000399 + traitmech:000399 METPO:2007700

    Old-mediated phage-lambda interference realizes the Old exonuclease system trait.

    @@ -319,7 +320,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -439,7 +440,7 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md -
    The old_exonuclease is dsDNA exonuclease that digests in the 5' to 3' direction :ref{doi=10.1128/jb.177.3.497-501.1995}. To our knowledge, other aspects of the molecular mechanisms remain unknown.
    +
    The old_exonuclease is dsDNA exonuclease that digests in the 5' to 3' direction :ref{doi=10.1128/jb.177.3.497-501.1995}. To our knowledge, other aspects of the molecular mechanisms remain unknown.
    • @@ -524,7 +525,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -888,12 +898,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 01:47 UTC diff --git a/pages/traits/genomics/olokun_system.html b/pages/traits/genomics/olokun_system.html index 0305124b8b3..3cedb805ceb 100644 --- a/pages/traits/genomics/olokun_system.html +++ b/pages/traits/genomics/olokun_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers Olokun system - traitmech:000254 + traitmech:000254 METPO:2007700

    Olokun-mediated phage restriction realizes the Olokun system trait.

    @@ -255,7 +256,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -414,7 +415,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -778,12 +788,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 22:52 UTC diff --git a/pages/traits/genomics/ophion_system.html b/pages/traits/genomics/ophion_system.html index 56198906aa4..d78c3a4ffa2 100644 --- a/pages/traits/genomics/ophion_system.html +++ b/pages/traits/genomics/ophion_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers Ophion system - traitmech:000331 + traitmech:000331 METPO:2007700

    Ophion-mediated phage restriction realizes the Ophion system trait.

      @@ -170,11 +171,11 @@

      Edge evidence

    • Ophion system - traitmech:000331 + traitmech:000331 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Ophion system possession is a phage-defense-system trait.

        @@ -239,7 +240,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -255,7 +256,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -426,7 +427,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -790,12 +800,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 08:48 UTC diff --git a/pages/traits/genomics/oshun_system.html b/pages/traits/genomics/oshun_system.html index b8e461f6cff..21f9e180d8e 100644 --- a/pages/traits/genomics/oshun_system.html +++ b/pages/traits/genomics/oshun_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -142,7 +143,7 @@

    Edge evidence

    confers Oshun system - traitmech:000293 + traitmech:000293 METPO:2007700

    Oshun-mediated phage restriction realizes the Oshun system trait.

    @@ -245,7 +246,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -404,7 +405,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -768,12 +778,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 21:06 UTC diff --git a/pages/traits/genomics/pago_system.html b/pages/traits/genomics/pago_system.html index faff44abb95..19a0e1b0b0b 100644 --- a/pages/traits/genomics/pago_system.html +++ b/pages/traits/genomics/pago_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -132,11 +133,11 @@

    Edge evidence

  • SPARTA system - traitmech:000240 + traitmech:000240 is a prokaryotic Argonaute defense system - traitmech:000419 - rdfs:subClassOf + traitmech:000419 + rdfs:subClassOf

    SPARTA is a short-pAgo TIR-APAZ system within the broader prokaryotic Argonaute defense family.

    • @@ -247,7 +248,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -469,7 +470,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -833,12 +843,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 22:20 UTC diff --git a/pages/traits/genomics/panchino_gp28_system.html b/pages/traits/genomics/panchino_gp28_system.html index 1cad9a7c236..adbf65ad149 100644 --- a/pages/traits/genomics/panchino_gp28_system.html +++ b/pages/traits/genomics/panchino_gp28_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Panchino gp28 system - traitmech:000294 + traitmech:000294 METPO:2007700

    Panchino-gp28-mediated phage restriction realizes the Panchino gp28 system trait.

    @@ -237,7 +238,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -432,7 +433,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -796,12 +806,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 22:13 UTC diff --git a/pages/traits/genomics/pangenome_openness.html b/pages/traits/genomics/pangenome_openness.html index 2a7c8b8a3ab..276a6e0be1d 100644 --- a/pages/traits/genomics/pangenome_openness.html +++ b/pages/traits/genomics/pangenome_openness.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    GO:0009292 causes pangenome openness - traitmech:000102 + traitmech:000102 biolink:causes

    HGT continually adds new accessory genes, keeping the pangenome open.

      @@ -115,7 +116,7 @@

      Edge evidence

    • pangenome openness - traitmech:000102 + traitmech:000102 associated with accessory gene pool @@ -156,7 +157,7 @@

      Edge evidence

      promotes pangenome openness - traitmech:000102 + traitmech:000102 RO:0002213

      Prophage-associated gene flux contributes to recent gain/loss and accessory genome expansion.

        @@ -175,7 +176,7 @@

        Edge evidence

        shapes pangenome openness - traitmech:000102 + traitmech:000102

        Open/closed behavior reflects balance of ongoing gene gain versus loss across sampled lineages.

          @@ -194,7 +195,7 @@

          Edge evidence

          negatively associated with pangenome openness - traitmech:000102 + traitmech:000102

          A larger conserved core leaves less flexible accessory fraction; empirically anticorrelated with openness.

            @@ -213,7 +214,7 @@

            Edge evidence

            positively associated with pangenome openness - traitmech:000102 + traitmech:000102

            A higher proportion of rare genes indicates continued acquisition and non-saturation of the pangenome.

              @@ -311,7 +312,7 @@

              Parent traits (1)

              Synonyms (1)

    @@ -327,7 +328,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -573,7 +574,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -937,12 +947,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/genomics/panoptes_system.html b/pages/traits/genomics/panoptes_system.html index 0b95aa5c44e..cd94f487971 100644 --- a/pages/traits/genomics/panoptes_system.html +++ b/pages/traits/genomics/panoptes_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -324,7 +325,7 @@

    Edge evidence

    confers Panoptes system - traitmech:000407 + traitmech:000407 METPO:2007700

    OptE-mediated inner-membrane disruption is the phage-defense output that realizes the Panoptes system trait.

      @@ -340,11 +341,11 @@

      Edge evidence

    • Panoptes system - traitmech:000407 + traitmech:000407 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Panoptes system possession is a phage-defense-system trait.

        @@ -380,8 +381,8 @@

        Protein and taxon examples

    		 - Vibrio navarrensis -
    NCBITaxon:29495 + Vibrio navarrensis +
    NCBITaxon:29495         		UNREVIEWED
    @@ -416,8 +417,8 @@

    Protein and taxon examples

    		 - Vibrio navarrensis -
    NCBITaxon:29495 + Vibrio navarrensis +
    NCBITaxon:29495         		UNREVIEWED
    @@ -495,11 +496,11 @@

    Parent traits (1)

    Synonyms (3)

    @@ -515,7 +516,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -796,7 +797,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1160,12 +1170,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 12:16 UTC diff --git a/pages/traits/genomics/paris_system.html b/pages/traits/genomics/paris_system.html index 0cfa407aebb..a6b659122c9 100644 --- a/pages/traits/genomics/paris_system.html +++ b/pages/traits/genomics/paris_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -249,7 +250,7 @@

    Edge evidence

    confers PARIS system - traitmech:000237 + traitmech:000237 METPO:2007700

    AriB-dependent translational inhibition realizes the PARIS abortive-infection phenotype.

      @@ -265,11 +266,11 @@

      Edge evidence

    • PARIS system - traitmech:000237 + traitmech:000237 is a abortive infection system - traitmech:000214 - rdfs:subClassOf + traitmech:000214 + rdfs:subClassOf

      PARIS system possession is an abortive-infection system trait.

        @@ -328,9 +329,9 @@

        Parent traits (1)

        Synonyms (2)

          -
        • phage anti-restriction-induced system EXACT_SYNONYM · DOI:10.1016/j.chom.2022.02.018
          • +
        • phage anti-restriction-induced system EXACT_SYNONYM · DOI:10.1016/j.chom.2022.02.018
          • -
        • phage antirestriction induced system EXACT_SYNONYM · DOI:10.1038/s41586-024-07874-3
          • +
        • phage antirestriction induced system EXACT_SYNONYM · DOI:10.1038/s41586-024-07874-3
    @@ -346,7 +347,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -543,7 +544,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -907,12 +917,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 09:16 UTC diff --git a/pages/traits/genomics/pd_lambda_1_system.html b/pages/traits/genomics/pd_lambda_1_system.html index 8653f235dbb..5de2dcda977 100644 --- a/pages/traits/genomics/pd_lambda_1_system.html +++ b/pages/traits/genomics/pd_lambda_1_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -60,7 +61,7 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md -
    The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.
    +
    The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.

    The DefenseFinder wiki describes PD-Lambda-1 as a one-protein system that can confer LambdaVir resistance.

    @@ -84,9 +85,9 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCP76574.1'>RCP76574.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCP76574.1'>RCP76574.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-1 source locus expressed in E. coli against LambdaVir.

    @@ -152,7 +153,7 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md - The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}. + The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}. The DefenseFinder wiki describes PD-Lambda-1 as a one-protein system that can confer LambdaVir resistance.
    • @@ -164,9 +165,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCP76574.1'>RCP76574.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCP76574.1'>RCP76574.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-1 source locus expressed in E. coli against LambdaVir.
    • @@ -198,22 +199,22 @@

    Edge evidence

    confers PD-Lambda-1 system - traitmech:000404 + traitmech:000404 METPO:2007700

    Protection against LambdaVir realizes the PD-Lambda-1 system trait.

    @@ -323,7 +324,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -436,7 +437,7 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md -
    The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.
    +
    The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.
    • @@ -450,9 +451,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCP76574.1'>RCP76574.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCP76574.1'>RCP76574.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir
    • @@ -509,7 +510,7 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md -
    The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.
    +
    The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.
    • @@ -594,7 +595,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -958,12 +968,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 07:20 UTC diff --git a/pages/traits/genomics/pd_lambda_2_system.html b/pages/traits/genomics/pd_lambda_2_system.html index 85b45a62460..e637473bf75 100644 --- a/pages/traits/genomics/pd_lambda_2_system.html +++ b/pages/traits/genomics/pd_lambda_2_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -72,10 +73,10 @@

    Trait evidence (10) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCO93357.1'>RCO93357.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO93356.1'>RCO93356.1</a>, -<a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCO93357.1'>RCO93357.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO93356.1'>RCO93356.1</a>, +<a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-2 source locus and testing in E. coli against LambdaVir, SECphi17, SECphi18, SECphi27, and T3.

    @@ -169,10 +170,10 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCO93357.1'>RCO93357.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO93356.1'>RCO93356.1</a>, -<a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCO93357.1'>RCO93357.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO93356.1'>RCO93356.1</a>, +<a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-2 source locus and testing in E. coli against LambdaVir, SECphi17, SECphi18, SECphi27, and T3.
    • @@ -220,17 +221,17 @@

    Edge evidence

    confers PD-Lambda-2 system - traitmech:000378 + traitmech:000378 METPO:2007700

    Protection against LambdaVir, SECphi17, SECphi18, SECphi27, and T3 realizes the PD-Lambda-2 system trait.

    @@ -348,7 +349,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -468,10 +469,10 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCO93357.1'>RCO93357.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO93356.1'>RCO93356.1</a>, -<a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCO93357.1'>RCO93357.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO93356.1'>RCO93356.1</a>, +<a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3
    • @@ -571,7 +572,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -935,12 +945,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 09:49 UTC diff --git a/pages/traits/genomics/pd_lambda_3_system.html b/pages/traits/genomics/pd_lambda_3_system.html index 9770f9348b8..4ee5477950f 100644 --- a/pages/traits/genomics/pd_lambda_3_system.html +++ b/pages/traits/genomics/pd_lambda_3_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -78,10 +79,10 @@

    Trait evidence (10) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCP74640.1'>RCP74640.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP74641.1'>RCP74641.1</a>, -<a href='https://ncbi.nlm.nih.gov/protein/RCP74642.1'>RCP74642.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCP74640.1'>RCP74640.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP74641.1'>RCP74641.1</a>, +<a href='https://ncbi.nlm.nih.gov/protein/RCP74642.1'>RCP74642.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-3 source locus expressed in E. coli against LambdaVir.

    @@ -165,10 +166,10 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCP74640.1'>RCP74640.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP74641.1'>RCP74641.1</a>, -<a href='https://ncbi.nlm.nih.gov/protein/RCP74642.1'>RCP74642.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCP74640.1'>RCP74640.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP74641.1'>RCP74641.1</a>, +<a href='https://ncbi.nlm.nih.gov/protein/RCP74642.1'>RCP74642.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-3 source locus expressed in E. coli against LambdaVir.
    • @@ -206,17 +207,17 @@

    Edge evidence

    confers PD-Lambda-3 system - traitmech:000382 + traitmech:000382 METPO:2007700

    Protection against LambdaVir realizes the PD-Lambda-3 system trait.

    @@ -328,7 +329,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -455,10 +456,10 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCP74640.1'>RCP74640.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP74641.1'>RCP74641.1</a>, -<a href='https://ncbi.nlm.nih.gov/protein/RCP74642.1'>RCP74642.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCP74640.1'>RCP74640.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP74641.1'>RCP74641.1</a>, +<a href='https://ncbi.nlm.nih.gov/protein/RCP74642.1'>RCP74642.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir
    • @@ -551,7 +552,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -915,12 +925,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 12:33 UTC diff --git a/pages/traits/genomics/pd_lambda_4_system.html b/pages/traits/genomics/pd_lambda_4_system.html index 17fe90f4c3d..e53f440fdba 100644 --- a/pages/traits/genomics/pd_lambda_4_system.html +++ b/pages/traits/genomics/pd_lambda_4_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -72,9 +73,9 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCP47953.1'>RCP47953.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP47952.1'>RCP47952.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCP47953.1'>RCP47953.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP47952.1'>RCP47952.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T4 & LambdaVir & SECphi27 & T7

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-4 source locus expressed in E. coli against T4, LambdaVir, SECphi27, and T7.

    @@ -161,9 +162,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCP47953.1'>RCP47953.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP47952.1'>RCP47952.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCP47953.1'>RCP47953.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP47952.1'>RCP47952.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T4 & LambdaVir & SECphi27 & T7 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-4 source locus expressed in E. coli against T4, LambdaVir, SECphi27, and T7.
    • @@ -204,16 +205,16 @@

    Edge evidence

    confers PD-Lambda-4 system - traitmech:000384 + traitmech:000384 METPO:2007700

    Protection against T4, LambdaVir, SECphi27, and T7 realizes the PD-Lambda-4 system trait.

    @@ -328,7 +329,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -448,9 +449,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCP47953.1'>RCP47953.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP47952.1'>RCP47952.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCP47953.1'>RCP47953.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP47952.1'>RCP47952.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T4 & LambdaVir & SECphi27 & T7
    • @@ -543,7 +544,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -907,12 +917,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 13:36 UTC diff --git a/pages/traits/genomics/pd_lambda_5_system.html b/pages/traits/genomics/pd_lambda_5_system.html index fd70f40e236..88f80a47197 100644 --- a/pages/traits/genomics/pd_lambda_5_system.html +++ b/pages/traits/genomics/pd_lambda_5_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -84,9 +85,9 @@

    Trait evidence (11) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCQ13837.1'>RCQ13837.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCQ13837.1'>RCQ13837.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 & T7

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-5 source locus expressed in E. coli against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7.

    @@ -184,9 +185,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCQ13837.1'>RCQ13837.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCQ13837.1'>RCQ13837.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 & T7 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-5 source locus expressed in E. coli against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7.
    • @@ -232,16 +233,16 @@

    Edge evidence

    confers PD-Lambda-5 system - traitmech:000385 + traitmech:000385 METPO:2007700

    Protection against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 realizes the PD-Lambda-5 system trait.

    @@ -361,7 +362,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -495,9 +496,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCQ13837.1'>RCQ13837.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCQ13837.1'>RCQ13837.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 & T7
    • @@ -590,7 +591,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -954,12 +964,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 14:10 UTC diff --git a/pages/traits/genomics/pd_lambda_6_system.html b/pages/traits/genomics/pd_lambda_6_system.html index f681e241f21..89674368b7f 100644 --- a/pages/traits/genomics/pd_lambda_6_system.html +++ b/pages/traits/genomics/pd_lambda_6_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -72,9 +73,9 @@

    Trait evidence (8)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRK48647.1'>RRK48647.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRK48647.1'>RRK48647.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir & T5

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-6 source locus expressed in E. coli against LambdaVir and T5.

    @@ -153,9 +154,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRK48647.1'>RRK48647.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRK48647.1'>RRK48647.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir & T5 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-6 source locus expressed in E. coli against LambdaVir and T5.
    • @@ -188,16 +189,16 @@

    Edge evidence

    confers PD-Lambda-6 system - traitmech:000383 + traitmech:000383 METPO:2007700

    Protection against LambdaVir and T5 realizes the PD-Lambda-6 system trait.

    @@ -308,7 +309,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -428,9 +429,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRK48647.1'>RRK48647.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRK48647.1'>RRK48647.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir & T5
    • @@ -516,7 +517,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -880,12 +890,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 13:09 UTC diff --git a/pages/traits/genomics/pd_t2_1_system.html b/pages/traits/genomics/pd_t2_1_system.html index 362b489971d..e7d9e76d0fc 100644 --- a/pages/traits/genomics/pd_t2_1_system.html +++ b/pages/traits/genomics/pd_t2_1_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -172,7 +173,7 @@

    Edge evidence

    confers PD-T2-1 system - traitmech:000476 + traitmech:000476 METPO:2007700

    Protection against T2, T6, Bas18, T4, and T5 realizes the PD-T2-1 phage-defense-system trait.

    @@ -277,7 +278,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -482,7 +483,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -846,12 +856,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 22:59 UTC diff --git a/pages/traits/genomics/pd_t4_10_system.html b/pages/traits/genomics/pd_t4_10_system.html index 719cc8458c9..b2ad2b3ba8b 100644 --- a/pages/traits/genomics/pd_t4_10_system.html +++ b/pages/traits/genomics/pd_t4_10_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -60,7 +61,7 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md -
    The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A. These ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes its toxicity, hinting at a toxin-antitoxin (TA) mechanism. It confers resitance to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}.
    +
    The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A. These ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes its toxicity, hinting at a toxin-antitoxin (TA) mechanism. It confers resitance to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}.

    The DefenseFinder wiki describes PD-T4-10 as a two-protein Abi system whose overlapping ORFs include a toxic PD-T4-10_B and neutralizing PD-T4-10_A.

    @@ -78,9 +79,9 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCO36089.1'>RCO36089.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO36088.1'>RCO36088.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCO36089.1'>RCO36089.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO36088.1'>RCO36088.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-10 source locus expressed in E. coli against T2, T4, T6, T5, and SECphi27.

    @@ -157,7 +158,7 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md - The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A. These ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes its toxicity, hinting at a toxin-antitoxin (TA) mechanism. It confers resitance to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}. + The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A. These ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes its toxicity, hinting at a toxin-antitoxin (TA) mechanism. It confers resitance to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}. The DefenseFinder wiki describes PD-T4-10 as a two-protein Abi system whose overlapping ORFs include a toxic PD-T4-10_B and neutralizing PD-T4-10_A.
    • @@ -169,9 +170,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCO36089.1'>RCO36089.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO36088.1'>RCO36088.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCO36089.1'>RCO36089.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO36088.1'>RCO36088.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-10 source locus expressed in E. coli against T2, T4, T6, T5, and SECphi27.
    • @@ -208,16 +209,16 @@

    Edge evidence

    confers PD-T4-10 system - traitmech:000394 + traitmech:000394 METPO:2007700

    Protection against T2, T4, T6, T5, and SECphi27 realizes the PD-T4-10 system trait.

    @@ -339,7 +340,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -452,7 +453,7 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md -
    The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A. These ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes its toxicity, hinting at a toxin-antitoxin (TA) mechanism. It confers resitance to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}.
    +
    The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A. These ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes its toxicity, hinting at a toxin-antitoxin (TA) mechanism. It confers resitance to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}.
    • @@ -466,9 +467,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCO36089.1'>RCO36089.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO36088.1'>RCO36088.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCO36089.1'>RCO36089.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO36088.1'>RCO36088.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27
    • @@ -555,7 +556,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -919,12 +929,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 20:59 UTC diff --git a/pages/traits/genomics/pd_t4_1_system.html b/pages/traits/genomics/pd_t4_1_system.html index 3ab36ed8286..407665a3eb7 100644 --- a/pages/traits/genomics/pd_t4_1_system.html +++ b/pages/traits/genomics/pd_t4_1_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -72,9 +73,9 @@

    Trait evidence (8)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRM93940.1'>RRM93940.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRM93940.1'>RRM93940.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-1 source locus expressed in E. coli against T2, T4, and T6.

    @@ -154,9 +155,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRM93940.1'>RRM93940.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRM93940.1'>RRM93940.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-1 source locus expressed in E. coli against T2, T4, and T6.
    • @@ -190,16 +191,16 @@

    Edge evidence

    confers PD-T4-1 system - traitmech:000386 + traitmech:000386 METPO:2007700

    Protection against T2, T4, and T6 realizes the PD-T4-1 system trait.

    @@ -311,7 +312,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -431,9 +432,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRM93940.1'>RRM93940.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRM93940.1'>RRM93940.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6
    • @@ -519,7 +520,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -883,12 +893,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 15:03 UTC diff --git a/pages/traits/genomics/pd_t4_2_system.html b/pages/traits/genomics/pd_t4_2_system.html index ca94c65c78a..5079ccfa383 100644 --- a/pages/traits/genomics/pd_t4_2_system.html +++ b/pages/traits/genomics/pd_t4_2_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -72,7 +73,7 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-2 source locus expressed in E. coli against T2, T4, T6, T5, and SECphi27.

    @@ -161,7 +162,7 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-2 source locus expressed in E. coli against T2, T4, T6, T5, and SECphi27. @@ -204,14 +205,14 @@

    Edge evidence

    confers PD-T4-2 system - traitmech:000387 + traitmech:000387 METPO:2007700

    Protection against T2, T4, T6, T5, and SECphi27 realizes the PD-T4-2 system trait.

    • @@ -328,7 +329,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -448,7 +449,7 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27
    @@ -542,7 +543,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -906,12 +916,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 15:37 UTC diff --git a/pages/traits/genomics/pd_t4_3_system.html b/pages/traits/genomics/pd_t4_3_system.html index 6381110260d..86a3504a4e2 100644 --- a/pages/traits/genomics/pd_t4_3_system.html +++ b/pages/traits/genomics/pd_t4_3_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -78,9 +79,9 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCO27183.1'>RCO27183.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCO27183.1'>RCO27183.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-3 source locus expressed in E. coli against T2, T4, and T6.

    @@ -166,9 +167,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCO27183.1'>RCO27183.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCO27183.1'>RCO27183.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-3 source locus expressed in E. coli against T2, T4, and T6.
    • @@ -202,16 +203,16 @@

    Edge evidence

    confers PD-T4-3 system - traitmech:000388 + traitmech:000388 METPO:2007700

    Protection against T2, T4, and T6 realizes the PD-T4-3 system trait.

    @@ -323,7 +324,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -450,9 +451,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCO27183.1'>RCO27183.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCO27183.1'>RCO27183.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6
    • @@ -506,7 +507,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add PD-T4-3 system trait -

      Minted traitmech:000388 for a PD-T4-3 DefenseFinder phage-defense system record backed by DOI:10.1038/s41564-022-01219-4, a pinned DefenseFinder wiki page, and pinned DefenseFinder article, rule, and HMM registry rows; left canonical examples empty because current sources support a RefSeq Morganella morganii example and an E. coli expression graph but not endogenous native PD-T4-3 activity.

    +

    Minted traitmech:000388 for a PD-T4-3 DefenseFinder phage-defense system record backed by DOI:10.1038/s41564-022-01219-4, a pinned DefenseFinder wiki page, and pinned DefenseFinder article, rule, and HMM registry rows; left canonical examples empty because current sources support a RefSeq Morganella morganii example and an E. coli expression graph but not endogenous native PD-T4-3 activity.

    • Read this curation session @@ -538,7 +539,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -902,12 +912,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 16:06 UTC diff --git a/pages/traits/genomics/pd_t4_4_system.html b/pages/traits/genomics/pd_t4_4_system.html index f952d64286f..ca273c3219b 100644 --- a/pages/traits/genomics/pd_t4_4_system.html +++ b/pages/traits/genomics/pd_t4_4_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -78,9 +79,9 @@

    Trait evidence (10) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCO57999.1'>RCO57999.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCO57999.1'>RCO57999.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi17

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-4 source locus expressed in E. coli against T2, T4, T6, and SECphi17.

    @@ -173,9 +174,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCO57999.1'>RCO57999.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCO57999.1'>RCO57999.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi17 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-4 source locus expressed in E. coli against T2, T4, T6, and SECphi17.
    • @@ -216,16 +217,16 @@

    Edge evidence

    confers PD-T4-4 system - traitmech:000389 + traitmech:000389 METPO:2007700

    Protection against T2, T4, T6, and SECphi17 realizes the PD-T4-4 system trait.

    @@ -340,7 +341,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -467,9 +468,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCO57999.1'>RCO57999.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCO57999.1'>RCO57999.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi17
    • @@ -536,7 +537,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add PD-T4-4 system phage-defense trait -

      Minted traitmech:000389 for the DOI- and DefenseFinder-backed PD-T4-4 phage-defense system, backed by DOI:10.1038/s41564-022-01219-4, a pinned DefenseFinder wiki page, and pinned DefenseFinder article, rules, and HMM registries. The record models PD-T4-4 as a two-profile system-level GENOMICS trait under phage defense system, leaves canonical_examples empty after reviewing the current evidence, adds a conservative nonmechanistic causal graph and a mechanism-gap discussion, and reserves METPO:1034300 in proposals/metpo_traitmech_v266.

    +

    Minted traitmech:000389 for the DOI- and DefenseFinder-backed PD-T4-4 phage-defense system, backed by DOI:10.1038/s41564-022-01219-4, a pinned DefenseFinder wiki page, and pinned DefenseFinder article, rules, and HMM registries. The record models PD-T4-4 as a two-profile system-level GENOMICS trait under phage defense system, leaves canonical_examples empty after reviewing the current evidence, adds a conservative nonmechanistic causal graph and a mechanism-gap discussion, and reserves METPO:1034300 in proposals/metpo_traitmech_v266.

    • Read this curation session @@ -568,7 +569,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -932,12 +942,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 17:24 UTC diff --git a/pages/traits/genomics/pd_t4_5_system.html b/pages/traits/genomics/pd_t4_5_system.html index f4473324934..818d2dc14e2 100644 --- a/pages/traits/genomics/pd_t4_5_system.html +++ b/pages/traits/genomics/pd_t4_5_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -72,9 +73,9 @@

    Trait evidence (8)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCQ99930.1'>RCQ99930.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCQ99930.1'>RCQ99930.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T4 & T6 & LambdaVir & T5

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-5 source locus expressed in E. coli against T4, T6, LambdaVir, and T5.

    @@ -155,9 +156,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCQ99930.1'>RCQ99930.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCQ99930.1'>RCQ99930.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T4 & T6 & LambdaVir & T5 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-5 source locus expressed in E. coli against T4, T6, LambdaVir, and T5.
    • @@ -192,16 +193,16 @@

    Edge evidence

    confers PD-T4-5 system - traitmech:000390 + traitmech:000390 METPO:2007700

    Protection against T4, T6, LambdaVir, and T5 realizes the PD-T4-5 system trait.

    @@ -314,7 +315,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -434,9 +435,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCQ99930.1'>RCQ99930.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCQ99930.1'>RCQ99930.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T4 & T6 & LambdaVir & T5
    • @@ -490,7 +491,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add PD-T4-5 system phage-defense trait -

      Minted traitmech:000390 for the DOI- and DefenseFinder-backed PD-T4-5 phage-defense system, backed by DOI:10.1038/s41564-022-01219-4, a pinned DefenseFinder wiki page, and pinned DefenseFinder article, rules, and HMM registries. The record models PD-T4-5 as a single-profile system-level GENOMICS trait under phage defense system, leaves canonical_examples empty after reviewing the current evidence, adds a conservative nonmechanistic causal graph and a mechanism-gap discussion, and reserves METPO:1034400 in proposals/metpo_traitmech_v267.

    +

    Minted traitmech:000390 for the DOI- and DefenseFinder-backed PD-T4-5 phage-defense system, backed by DOI:10.1038/s41564-022-01219-4, a pinned DefenseFinder wiki page, and pinned DefenseFinder article, rules, and HMM registries. The record models PD-T4-5 as a single-profile system-level GENOMICS trait under phage defense system, leaves canonical_examples empty after reviewing the current evidence, adds a conservative nonmechanistic causal graph and a mechanism-gap discussion, and reserves METPO:1034400 in proposals/metpo_traitmech_v267.

    • Read this curation session @@ -522,7 +523,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -886,12 +896,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 17:57 UTC diff --git a/pages/traits/genomics/pd_t4_6_system.html b/pages/traits/genomics/pd_t4_6_system.html index c9f544531f4..685622d1322 100644 --- a/pages/traits/genomics/pd_t4_6_system.html +++ b/pages/traits/genomics/pd_t4_6_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -72,9 +73,9 @@

    Trait evidence (8)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRM76169.1'>RRM76169.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRM76169.1'>RRM76169.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-6 source locus expressed in E. coli against T2, T4, and T6.

    @@ -154,9 +155,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRM76169.1'>RRM76169.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRM76169.1'>RRM76169.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-6 source locus expressed in E. coli against T2, T4, and T6.
    • @@ -190,16 +191,16 @@

    Edge evidence

    confers PD-T4-6 system - traitmech:000391 + traitmech:000391 METPO:2007700

    Protection against T2, T4, and T6 realizes the PD-T4-6 system trait.

    @@ -311,7 +312,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -431,9 +432,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRM76169.1'>RRM76169.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRM76169.1'>RRM76169.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6
    • @@ -487,7 +488,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add PD-T4-6 system phage-defense trait -

      Minted traitmech:000391 for the DOI- and DefenseFinder-backed PD-T4-6 phage-defense system, backed by DOI:10.1038/s41564-022-01219-4, a pinned DefenseFinder wiki page, and pinned DefenseFinder article, rules, and HMM registries. The record models PD-T4-6 as a single-profile system-level GENOMICS trait under phage defense system, leaves canonical_examples empty after reviewing the current evidence, adds a conservative nonmechanistic causal graph and a mechanism-gap discussion, and reserves METPO:1034500 in proposals/metpo_traitmech_v268.

    +

    Minted traitmech:000391 for the DOI- and DefenseFinder-backed PD-T4-6 phage-defense system, backed by DOI:10.1038/s41564-022-01219-4, a pinned DefenseFinder wiki page, and pinned DefenseFinder article, rules, and HMM registries. The record models PD-T4-6 as a single-profile system-level GENOMICS trait under phage defense system, leaves canonical_examples empty after reviewing the current evidence, adds a conservative nonmechanistic causal graph and a mechanism-gap discussion, and reserves METPO:1034500 in proposals/metpo_traitmech_v268.

    • Read this curation session @@ -519,7 +520,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -883,12 +893,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 18:35 UTC diff --git a/pages/traits/genomics/pd_t4_7_system.html b/pages/traits/genomics/pd_t4_7_system.html index d63ed92d66d..c7e1d2fe388 100644 --- a/pages/traits/genomics/pd_t4_7_system.html +++ b/pages/traits/genomics/pd_t4_7_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -66,7 +67,7 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md -
    Vassalo et al. :ref{doi=10.1038/s41564-022-01219-4} state that PD-T4-7 functions through an abortive infection mechanism.
    +
    Vassalo et al. :ref{doi=10.1038/s41564-022-01219-4} state that PD-T4-7 functions through an abortive infection mechanism.

    The DefenseFinder wiki reports an abortive-infection mechanism assignment for PD-T4-7 while leaving the direct substrate and effector logic unresolved.

    @@ -78,9 +79,9 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRN43039.1'>RRN43039.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRN43039.1'>RRN43039.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-7 source locus expressed in E. coli against T2, T4, and T6.

    @@ -160,9 +161,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRN43039.1'>RRN43039.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRN43039.1'>RRN43039.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-7 source locus expressed in E. coli against T2, T4, and T6.
    • @@ -196,16 +197,16 @@

    Edge evidence

    confers PD-T4-7 system - traitmech:000392 + traitmech:000392 METPO:2007700

    Protection against T2, T4, and T6 realizes the PD-T4-7 system trait.

    @@ -323,7 +324,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -443,16 +444,16 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md -
    Vassalo et al. :ref{doi=10.1038/s41564-022-01219-4} state that PD-T4-7 functions through an abortive infection mechanism.
    +
    Vassalo et al. :ref{doi=10.1038/s41564-022-01219-4} state that PD-T4-7 functions through an abortive infection mechanism.
  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRN43039.1'>RRN43039.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRN43039.1'>RRN43039.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6
    • @@ -562,7 +563,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -926,12 +936,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 19:55 UTC diff --git a/pages/traits/genomics/pd_t4_8_system.html b/pages/traits/genomics/pd_t4_8_system.html index 738441af5c6..3af9eb5d367 100644 --- a/pages/traits/genomics/pd_t4_8_system.html +++ b/pages/traits/genomics/pd_t4_8_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -60,7 +61,7 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md -
    PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defense system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27.
    +
    PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defense system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27.

    The DefenseFinder wiki reports that PD-T4-8 contains a DUF4263 domain and that the E. coli RCP52534.1 locus confers resistance against T2, T4, T6, SECphi18, and SECphi27.

    @@ -78,9 +79,9 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCP52534.1'>RCP52534.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCP52534.1'>RCP52534.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi18 & SECphi27

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-8 source locus expressed in E. coli against T2, T4, T6, SECphi18, and SECphi27.

    @@ -156,7 +157,7 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md - PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defense system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27. + PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defense system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27. The DefenseFinder wiki reports that PD-T4-8 contains a DUF4263 domain and that the E. coli RCP52534.1 locus confers resistance against T2, T4, T6, SECphi18, and SECphi27.
    • @@ -168,9 +169,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCP52534.1'>RCP52534.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCP52534.1'>RCP52534.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi18 & SECphi27 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-8 source locus expressed in E. coli against T2, T4, T6, SECphi18, and SECphi27.
    • @@ -206,22 +207,22 @@

    Edge evidence

    confers PD-T4-8 system - traitmech:000393 + traitmech:000393 METPO:2007700

    Protection against T2, T4, T6, SECphi18, and SECphi27 realizes the PD-T4-8 system trait.

    @@ -304,7 +305,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -417,7 +418,7 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md -
    PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defense system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27.
    +
    PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defense system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27.
    • @@ -431,9 +432,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCP52534.1'>RCP52534.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCP52534.1'>RCP52534.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi18 & SECphi27
    • @@ -519,7 +520,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -883,12 +893,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 20:08 UTC diff --git a/pages/traits/genomics/pd_t7_1_system.html b/pages/traits/genomics/pd_t7_1_system.html index d3be743d029..85caa1905b8 100644 --- a/pages/traits/genomics/pd_t7_1_system.html +++ b/pages/traits/genomics/pd_t7_1_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -60,7 +61,7 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md -
    PD-T7-1 is a single gene defense system that was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed in *E. coli* and it was shown to be active against T7.
    +
    PD-T7-1 is a single gene defense system that was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed in *E. coli* and it was shown to be active against T7.

    The DefenseFinder wiki describes PD-T7-1 as a single-gene system and names T7 as its experimentally assessed activity.

    @@ -78,9 +79,9 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCQ85672.1'>RCQ85672.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCQ85672.1'>RCQ85672.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-1 source locus expressed in E. coli against T7.

    @@ -152,7 +153,7 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md - PD-T7-1 is a single gene defense system that was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed in *E. coli* and it was shown to be active against T7. + PD-T7-1 is a single gene defense system that was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed in *E. coli* and it was shown to be active against T7. The DefenseFinder wiki describes PD-T7-1 as a single-gene system and names T7 as its experimentally assessed activity.
    • @@ -164,9 +165,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCQ85672.1'>RCQ85672.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCQ85672.1'>RCQ85672.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-1 source locus expressed in E. coli against T7.
    • @@ -198,22 +199,22 @@

    Edge evidence

    confers PD-T7-1 system - traitmech:000395 + traitmech:000395 METPO:2007700

    Protection against T7 realizes the PD-T7-1 system trait.

    @@ -323,7 +324,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -436,7 +437,7 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md -
    PD-T7-1 is a single gene defense system that was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed in *E. coli* and it was shown to be active against T7.
    +
    PD-T7-1 is a single gene defense system that was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed in *E. coli* and it was shown to be active against T7.
    • @@ -450,9 +451,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCQ85672.1'>RCQ85672.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCQ85672.1'>RCQ85672.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7
    • @@ -538,7 +539,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -902,12 +912,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 23:13 UTC diff --git a/pages/traits/genomics/pd_t7_2_system.html b/pages/traits/genomics/pd_t7_2_system.html index 0d135797681..29b3935cc2d 100644 --- a/pages/traits/genomics/pd_t7_2_system.html +++ b/pages/traits/genomics/pd_t7_2_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -72,9 +73,9 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRM73498.1'>RRM73498.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RRM73410.1'>RRM73410.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRM73498.1'>RRM73498.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RRM73410.1'>RRM73410.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & T5 & SECphi18 & SECphi27 & T3 & T7

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-2 source locus expressed in E. coli against T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7.

    @@ -166,9 +167,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRM73498.1'>RRM73498.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RRM73410.1'>RRM73410.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRM73498.1'>RRM73498.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RRM73410.1'>RRM73410.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & T5 & SECphi18 & SECphi27 & T3 & T7 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-2 source locus expressed in E. coli against T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7.
    • @@ -214,16 +215,16 @@

    Edge evidence

    confers PD-T7-2 system - traitmech:000396 + traitmech:000396 METPO:2007700

    Protection against the listed phages realizes the PD-T7-2 system trait.

    @@ -343,7 +344,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -463,9 +464,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRM73498.1'>RRM73498.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RRM73410.1'>RRM73410.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRM73498.1'>RRM73498.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RRM73410.1'>RRM73410.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & T5 & SECphi18 & SECphi27 & T3 & T7
    • @@ -558,7 +559,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -922,12 +932,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 23:49 UTC diff --git a/pages/traits/genomics/pd_t7_3_system.html b/pages/traits/genomics/pd_t7_3_system.html index e0cc99d8d1f..0abeb236151 100644 --- a/pages/traits/genomics/pd_t7_3_system.html +++ b/pages/traits/genomics/pd_t7_3_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -60,7 +61,7 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md -
    PD-T7-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E. coli* strains :ref{doi=10.1038/s41564-022-01219-4}
    +
    PD-T7-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E. coli* strains :ref{doi=10.1038/s41564-022-01219-4}

    The DefenseFinder wiki describes PD-T7-3 as a phage-defense system discovered in an E. coli experimental screen.

    @@ -84,9 +85,9 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCP48690.1'>RCP48690.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCP48690.1'>RCP48690.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi17 & T3 & T7

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-3 source locus expressed in E. coli against T2, T4, T6, T5, SECphi17, T3, and T7.

    @@ -158,7 +159,7 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md - PD-T7-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E. coli* strains :ref{doi=10.1038/s41564-022-01219-4} + PD-T7-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E. coli* strains :ref{doi=10.1038/s41564-022-01219-4} The DefenseFinder wiki describes PD-T7-3 as a phage-defense system discovered in an E. coli experimental screen.
    • @@ -176,9 +177,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCP48690.1'>RCP48690.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCP48690.1'>RCP48690.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi17 & T3 & T7 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-3 source locus expressed in E. coli against T2, T4, T6, T5, SECphi17, T3, and T7.
    • @@ -216,16 +217,16 @@

    Edge evidence

    confers PD-T7-3 system - traitmech:000405 + traitmech:000405 METPO:2007700

    Protection against T2, T4, T6, T5, SECphi17, T3, and T7 realizes the PD-T7-3 system trait.

    @@ -341,7 +342,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -454,7 +455,7 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md -
    PD-T7-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E. coli* strains :ref{doi=10.1038/s41564-022-01219-4}
    +
    PD-T7-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E. coli* strains :ref{doi=10.1038/s41564-022-01219-4}
    • @@ -468,9 +469,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RCP48690.1'>RCP48690.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RCP48690.1'>RCP48690.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi17 & T3 & T7
    • @@ -527,7 +528,7 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md -
    PD-T7-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E. coli* strains :ref{doi=10.1038/s41564-022-01219-4}
    +
    PD-T7-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E. coli* strains :ref{doi=10.1038/s41564-022-01219-4}
    • @@ -612,7 +613,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -976,12 +986,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 08:03 UTC diff --git a/pages/traits/genomics/pd_t7_4_system.html b/pages/traits/genomics/pd_t7_4_system.html index 1e42cf6fb29..70f7ddae25f 100644 --- a/pages/traits/genomics/pd_t7_4_system.html +++ b/pages/traits/genomics/pd_t7_4_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -81,9 +82,9 @@

    Trait evidence (8)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRL46918.1'>RRL46918.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRL46918.1'>RRL46918.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> SECphi18 & SECphi27 & T3 & T7

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-4 source locus expressed in E. coli against SECphi18, SECphi27, T3, and T7.

    @@ -167,9 +168,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRL46918.1'>RRL46918.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRL46918.1'>RRL46918.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> SECphi18 & SECphi27 & T3 & T7 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-4 source locus expressed in E. coli against SECphi18, SECphi27, T3, and T7.
    • @@ -204,16 +205,16 @@

    Edge evidence

    confers PD-T7-4 system - traitmech:000406 + traitmech:000406 METPO:2007700

    Protection against SECphi18, SECphi27, T3, and T7 realizes the PD-T7-4 system trait.

    @@ -326,7 +327,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -449,9 +450,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRL46918.1'>RRL46918.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRL46918.1'>RRL46918.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> SECphi18 & SECphi27 & T3 & T7
    • @@ -593,7 +594,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -957,12 +967,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 08:45 UTC diff --git a/pages/traits/genomics/pd_t7_5_system.html b/pages/traits/genomics/pd_t7_5_system.html index 2e025e205d1..ee3701c7f87 100644 --- a/pages/traits/genomics/pd_t7_5_system.html +++ b/pages/traits/genomics/pd_t7_5_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -60,13 +61,13 @@

    Trait evidence (10) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md -
    PD-T7-5 is a defense system composed of a single protein which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed by heterologous expression in *E. coli* against T7 and to reduce the size of lysis plaques of T3 :ref{doi=10.1038/s41564-022-01219-4}. PD-T7-5 contains a PD(D/E)XK nuclease domain like [PD-T7-1](/defense-systems/pd-t7-1).
    +
    PD-T7-5 is a defense system composed of a single protein which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed by heterologous expression in *E. coli* against T7 and to reduce the size of lysis plaques of T3 :ref{doi=10.1038/s41564-022-01219-4}. PD-T7-5 contains a PD(D/E)XK nuclease domain like [PD-T7-1](/defense-systems/pd-t7-1).

    The DefenseFinder wiki describes PD-T7-5 as a single-protein defense system with heterologous E. coli antiphage activity against T7 and T3 plaque-size reduction.

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md -
    As far as we are aware, the molecular mechanism is unknown. However, the presence of a PD(D/E)XK domain in PD-T7-5 suggests a mechanism of action via DNA degradation :ref{doi=10.1038/s41564-022-01219-4}.
    +
    As far as we are aware, the molecular mechanism is unknown. However, the presence of a PD(D/E)XK domain in PD-T7-5 suggests a mechanism of action via DNA degradation :ref{doi=10.1038/s41564-022-01219-4}.

    The DefenseFinder wiki states that PD-T7-5 molecular mechanism is unresolved and leaves the PD(D/E)XK-mediated DNA degradation interpretation as a hypothesis.

    • @@ -84,9 +85,9 @@

    Trait evidence (10) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRM82777.1'>RRM82777.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRM82777.1'>RRM82777.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> SECphi17 & T3 & T7

    The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-5 source locus expressed in E. coli against SECphi17, T3, and T7.

    @@ -160,13 +161,13 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md - PD-T7-5 is a defense system composed of a single protein which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed by heterologous expression in *E. coli* against T7 and to reduce the size of lysis plaques of T3 :ref{doi=10.1038/s41564-022-01219-4}. PD-T7-5 contains a PD(D/E)XK nuclease domain like [PD-T7-1](/defense-systems/pd-t7-1). + PD-T7-5 is a defense system composed of a single protein which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed by heterologous expression in *E. coli* against T7 and to reduce the size of lysis plaques of T3 :ref{doi=10.1038/s41564-022-01219-4}. PD-T7-5 contains a PD(D/E)XK nuclease domain like [PD-T7-1](/defense-systems/pd-t7-1). The DefenseFinder wiki describes PD-T7-5 as a single-protein defense system with heterologous E. coli antiphage activity against T7 and T3 plaque-size reduction.
  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md - As far as we are aware, the molecular mechanism is unknown. However, the presence of a PD(D/E)XK domain in PD-T7-5 suggests a mechanism of action via DNA degradation :ref{doi=10.1038/s41564-022-01219-4}. + As far as we are aware, the molecular mechanism is unknown. However, the presence of a PD(D/E)XK domain in PD-T7-5 suggests a mechanism of action via DNA degradation :ref{doi=10.1038/s41564-022-01219-4}. The DefenseFinder wiki states that PD-T7-5 molecular mechanism is unresolved and leaves the PD(D/E)XK-mediated DNA degradation interpretation as a hypothesis.
    • @@ -178,9 +179,9 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md - Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 + Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRM82777.1'>RRM82777.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRM82777.1'>RRM82777.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> SECphi17 & T3 & T7 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-5 source locus expressed in E. coli against SECphi17, T3, and T7.
    • @@ -214,16 +215,16 @@

    Edge evidence

    confers PD-T7-5 system - traitmech:000397 + traitmech:000397 METPO:2007700

    Protection against SECphi17, T3, and T7 realizes the PD-T7-5 system trait.

    @@ -335,7 +336,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -448,14 +449,14 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md -
    PD-T7-5 is a defense system composed of a single protein which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed by heterologous expression in *E. coli* against T7 and to reduce the size of lysis plaques of T3 :ref{doi=10.1038/s41564-022-01219-4}. PD-T7-5 contains a PD(D/E)XK nuclease domain like [PD-T7-1](/defense-systems/pd-t7-1).
    +
    PD-T7-5 is a defense system composed of a single protein which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed by heterologous expression in *E. coli* against T7 and to reduce the size of lysis plaques of T3 :ref{doi=10.1038/s41564-022-01219-4}. PD-T7-5 contains a PD(D/E)XK nuclease domain like [PD-T7-1](/defense-systems/pd-t7-1).
  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md -
    As far as we are aware, the molecular mechanism is unknown. However, the presence of a PD(D/E)XK domain in PD-T7-5 suggests a mechanism of action via DNA degradation :ref{doi=10.1038/s41564-022-01219-4}.
    +
    As far as we are aware, the molecular mechanism is unknown. However, the presence of a PD(D/E)XK domain in PD-T7-5 suggests a mechanism of action via DNA degradation :ref{doi=10.1038/s41564-022-01219-4}.
    • @@ -469,9 +470,9 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md -
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 +
    Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli -<a href='https://ncbi.nlm.nih.gov/protein/RRM82777.1'>RRM82777.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/RRM82777.1'>RRM82777.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> SECphi17 & T3 & T7
    • @@ -557,7 +558,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -921,12 +931,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 00:31 UTC diff --git a/pages/traits/genomics/pfiat_system.html b/pages/traits/genomics/pfiat_system.html index d37417bce00..71d61ae1f0d 100644 --- a/pages/traits/genomics/pfiat_system.html +++ b/pages/traits/genomics/pfiat_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -184,7 +185,7 @@

    Edge evidence

    confers PfiAT system - traitmech:000365 + traitmech:000365 METPO:2007700

    PfiT/PfiA-dependent regulation of Pf4 phage production and immunity realizes the PfiAT system trait.

    @@ -289,7 +290,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -466,7 +467,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -830,12 +840,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-22 12:28 UTC diff --git a/pages/traits/genomics/phage_defense_system.html b/pages/traits/genomics/phage_defense_system.html index 840fa993125..0834584a259 100644 --- a/pages/traits/genomics/phage_defense_system.html +++ b/pages/traits/genomics/phage_defense_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -117,7 +118,7 @@

    Edge evidence

    selects for phage defense system - traitmech:000209 + traitmech:000209 METPO:2007401

    Virus-host arms races select for microbial antiviral defense mechanisms.

      @@ -133,11 +134,11 @@

      Edge evidence

    • CRISPR-Cas system - traitmech:000094 + traitmech:000094 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      CRISPR-Cas possession is an adaptive phage-defense system.

        @@ -152,11 +153,11 @@

        Edge evidence

      • restriction-modification system - traitmech:000095 + traitmech:000095 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

        Restriction-modification possession is an innate phage-defense system.

          @@ -746,11 +747,11 @@

          Children (262)

          Synonyms (3)

    @@ -766,7 +767,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -951,7 +952,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1315,12 +1325,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 07:55 UTC diff --git a/pages/traits/genomics/phosphorothioate_defense_system.html b/pages/traits/genomics/phosphorothioate_defense_system.html index 495de09e9a1..5e14da0b2b3 100644 --- a/pages/traits/genomics/phosphorothioate_defense_system.html +++ b/pages/traits/genomics/phosphorothioate_defense_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -217,7 +218,7 @@

    Edge evidence

    confers phosphorothioate defense system - traitmech:000213 + traitmech:000213 METPO:2007700

    Restriction of invading viral DNA realizes phosphorothioate-based antiviral defense.

      @@ -239,11 +240,11 @@

      Edge evidence

    • phosphorothioate defense system - traitmech:000213 + traitmech:000213 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Phosphorothioate restriction-system possession is an antiviral defense-system trait.

        @@ -323,9 +324,9 @@

        Children (4)

        Synonyms (2)

          -
        • PT-associated R-M system EXACT_SYNONYM · DOI:10.1128/mbio.00933-23
          • +
        • PT-associated R-M system EXACT_SYNONYM · DOI:10.1128/mbio.00933-23
          • -
        • PT-related R-M system EXACT_SYNONYM · DOI:10.1128/mbio.00933-23
          • +
        • PT-related R-M system EXACT_SYNONYM · DOI:10.1128/mbio.00933-23
    @@ -341,7 +342,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -568,7 +569,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -932,12 +942,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 17:36 UTC diff --git a/pages/traits/genomics/phrann_gp29_gp30_system.html b/pages/traits/genomics/phrann_gp29_gp30_system.html index 144ac1a04be..98bc98a3fd2 100644 --- a/pages/traits/genomics/phrann_gp29_gp30_system.html +++ b/pages/traits/genomics/phrann_gp29_gp30_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -178,7 +179,7 @@

    Edge evidence

    confers Phrann gp29-gp30 system - traitmech:000296 + traitmech:000296 METPO:2007700

    Phrann-gp29-gp30-mediated defense against Tweety and Gaia realizes the Phrann gp29-gp30 system trait.

    @@ -279,7 +280,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -450,7 +451,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -814,12 +824,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 23:56 UTC diff --git a/pages/traits/genomics/pif_system.html b/pages/traits/genomics/pif_system.html index 755e77080e5..b56b6c6196c 100644 --- a/pages/traits/genomics/pif_system.html +++ b/pages/traits/genomics/pif_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -172,7 +173,7 @@

    Edge evidence

    confers Pif system - traitmech:000323 + traitmech:000323 METPO:2007700

    F-plasmid-pif-specified T7 abortive infection realizes the Pif system trait.

    @@ -254,7 +255,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -419,7 +420,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -783,12 +793,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 01:33 UTC diff --git a/pages/traits/genomics/plasmid_carriage.html b/pages/traits/genomics/plasmid_carriage.html index cae760aa673..d8071a2a7f1 100644 --- a/pages/traits/genomics/plasmid_carriage.html +++ b/pages/traits/genomics/plasmid_carriage.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • plasmid carriage - traitmech:000090 + traitmech:000090 enables conjugation GO:0009291 @@ -115,7 +116,7 @@

    Edge evidence

  • plasmid carriage - traitmech:000090 + traitmech:000090 contributes to accessory function @@ -194,7 +195,7 @@

    Edge evidence

    promotes retention of plasmid carriage - traitmech:000090 + traitmech:000090

    Without selection plasmids tend to be lost; antibiotic pressure promotes retention.

      @@ -210,7 +211,7 @@

      Edge evidence

    • plasmid carriage - traitmech:000090 + traitmech:000090 imposes plasmid fitness cost @@ -292,7 +293,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • plasmid-bearing RELATED_SYNONYM · DOI:10.1128/MMBR.00020-10
        • +
      • plasmid-bearing RELATED_SYNONYM · DOI:10.1128/MMBR.00020-10
    • @@ -308,7 +309,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -587,7 +588,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -951,12 +961,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/genomics/ploidy.html b/pages/traits/genomics/ploidy.html index 855c42ba05f..8f9a898e4c3 100644 --- a/pages/traits/genomics/ploidy.html +++ b/pages/traits/genomics/ploidy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • ploidy - traitmech:000100 + traitmech:000100 enables recombinational repair of damaged DNA GO:0000725 @@ -115,7 +116,7 @@

    Edge evidence

  • ploidy - traitmech:000100 + traitmech:000100 contributes to long-term survival @@ -191,7 +192,7 @@

    Edge evidence

  • ploidy - traitmech:000100 + traitmech:000100 increases segregational drift @@ -273,7 +274,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • polyploidy RELATED_SYNONYM · DOI:10.1159/000368855
      • +
    • polyploidy RELATED_SYNONYM · DOI:10.1159/000368855
    • @@ -296,7 +297,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -548,7 +549,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -912,12 +922,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 06:15 UTC diff --git a/pages/traits/genomics/prithvi_system.html b/pages/traits/genomics/prithvi_system.html index 112fd2ee53c..7a7f264bf47 100644 --- a/pages/traits/genomics/prithvi_system.html +++ b/pages/traits/genomics/prithvi_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -142,7 +143,7 @@

    Edge evidence

    confers Prithvi system - traitmech:000290 + traitmech:000290 METPO:2007700

    Prithvi-mediated phage restriction realizes the Prithvi system trait.

    @@ -245,7 +246,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -404,7 +405,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -768,12 +778,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 19:17 UTC diff --git a/pages/traits/genomics/prometheus_system.html b/pages/traits/genomics/prometheus_system.html index e66e34e11bc..fc772baade6 100644 --- a/pages/traits/genomics/prometheus_system.html +++ b/pages/traits/genomics/prometheus_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -142,7 +143,7 @@

    Edge evidence

    confers Prometheus system - traitmech:000291 + traitmech:000291 METPO:2007700

    Prometheus-mediated phage restriction realizes the Prometheus system trait.

    @@ -243,7 +244,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -402,7 +403,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -766,12 +776,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 20:12 UTC diff --git a/pages/traits/genomics/prophage.html b/pages/traits/genomics/prophage.html index 8ae4ba19270..226dde6b4ab 100644 --- a/pages/traits/genomics/prophage.html +++ b/pages/traits/genomics/prophage.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • prophage - traitmech:000091 + traitmech:000091 enables lysogeny @@ -115,7 +116,7 @@

    Edge evidence

  • prophage - traitmech:000091 + traitmech:000091 contributes to host phenotype @@ -134,7 +135,7 @@

    Edge evidence

  • prophage - traitmech:000091 + traitmech:000091 integrates into bacterial chromosome @@ -311,7 +312,7 @@

    Parent traits (1)

    Synonyms (1)

    • @@ -327,7 +328,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -621,7 +622,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -985,12 +995,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 06:23 UTC diff --git a/pages/traits/genomics/prrc_system.html b/pages/traits/genomics/prrc_system.html index cf185163ff6..0d906d977c9 100644 --- a/pages/traits/genomics/prrc_system.html +++ b/pages/traits/genomics/prrc_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -190,7 +191,7 @@

    Edge evidence

    confers PrrC system - traitmech:000364 + traitmech:000364 METPO:2007700

    T4-induced PrrC RNase defense realizes the PrrC system trait.

    @@ -301,7 +302,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -484,7 +485,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -848,12 +858,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-22 11:43 UTC diff --git a/pages/traits/genomics/psyrta_system.html b/pages/traits/genomics/psyrta_system.html index 3fdc3aca35b..bfffcce1bf3 100644 --- a/pages/traits/genomics/psyrta_system.html +++ b/pages/traits/genomics/psyrta_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers PsyrTA system - traitmech:000257 + traitmech:000257 METPO:2007700

    PsyrTA-mediated phage restriction realizes the PsyrTA system trait.

    @@ -255,7 +256,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -414,7 +415,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -778,12 +788,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 00:48 UTC diff --git a/pages/traits/genomics/pvurts1i_system.html b/pages/traits/genomics/pvurts1i_system.html index 83d8727554e..0583dfc7bd8 100644 --- a/pages/traits/genomics/pvurts1i_system.html +++ b/pages/traits/genomics/pvurts1i_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -167,7 +168,7 @@

    Edge evidence

    confers PvuRts1I system - traitmech:000511 + traitmech:000511 METPO:2007700

    PvuRts1I-family modified-HMC restriction realizes the organism-level PvuRts1I system possession trait.

    @@ -274,7 +275,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -498,7 +499,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -862,12 +872,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 09:28 UTC diff --git a/pages/traits/genomics/pycsar_system.html b/pages/traits/genomics/pycsar_system.html index 128418f6aad..933283527a1 100644 --- a/pages/traits/genomics/pycsar_system.html +++ b/pages/traits/genomics/pycsar_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -243,7 +244,7 @@

    Edge evidence

    confers Pycsar system - traitmech:000236 + traitmech:000236 METPO:2007700

    Cyclic-pyrimidine signaling through a Pycsar receptor realizes the Pycsar antiphage trait.

      @@ -259,11 +260,11 @@

      Edge evidence

    • Pycsar system - traitmech:000236 + traitmech:000236 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Pycsar system possession is a phage-defense-system trait.

        @@ -322,9 +323,9 @@

        Parent traits (1)

        Synonyms (2)

          -
        • Pyrimidine Cyclase System for Antiphage Resistance EXACT_SYNONYM · DOI:10.1016/j.cell.2021.09.031
          • +
        • Pyrimidine Cyclase System for Antiphage Resistance EXACT_SYNONYM · DOI:10.1016/j.cell.2021.09.031
          • -
        • pyrimidine cyclase system for anti-phage resistance EXACT_SYNONYM · DOI:10.1038/s41467-024-49861-2
          • +
        • pyrimidine cyclase system for anti-phage resistance EXACT_SYNONYM · DOI:10.1038/s41467-024-49861-2
    @@ -340,7 +341,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -525,7 +526,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -889,12 +899,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 07:36 UTC diff --git a/pages/traits/genomics/radar_system.html b/pages/traits/genomics/radar_system.html index 7d500c94b1b..68ea00ca770 100644 --- a/pages/traits/genomics/radar_system.html +++ b/pages/traits/genomics/radar_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -180,7 +181,7 @@

    Edge evidence

    confers RADAR system - traitmech:000238 + traitmech:000238 METPO:2007700

    RADAR-mediated adenosine-nucleotide deamination realizes the RADAR antiphage phenotype.

      @@ -196,11 +197,11 @@

      Edge evidence

    • RADAR system - traitmech:000238 + traitmech:000238 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      RADAR system possession is a phage-defense-system trait.

        @@ -259,7 +260,7 @@

        Parent traits (1)

        Synonyms (1)

          -
        • restriction by an adenosine deaminase acting on RNA EXACT_SYNONYM · DOI:10.1016/j.cell.2023.01.012
          • +
        • restriction by an adenosine deaminase acting on RNA EXACT_SYNONYM · DOI:10.1016/j.cell.2023.01.012
    @@ -275,7 +276,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -472,7 +473,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -836,12 +846,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 10:19 UTC diff --git a/pages/traits/genomics/razr_system.html b/pages/traits/genomics/razr_system.html index 2d050b6dd81..88dd262af02 100644 --- a/pages/traits/genomics/razr_system.html +++ b/pages/traits/genomics/razr_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -67,7 +68,7 @@

    Trait evidence (3)

    https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    | RAZR | 10\.1038/s41586-025-10060-8 | Bacterial immune activation via supramolecular assembly with phage triggers |
    -

    The pinned DefenseFinder article registry maps the named RAZR system to the Zhang et al. Nature article; the pinned DefenseFinder HMM inventory (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md) and rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) do not list RAZR, so this row is name-to-paper evidence rather than model-component evidence.

    +

    The pinned DefenseFinder article registry maps the named RAZR system to the Zhang et al. Nature article; the pinned DefenseFinder HMM inventory (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md) and rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) do not list RAZR, so this row is name-to-paper evidence rather than model-component evidence.

    @@ -219,7 +220,7 @@

    Edge evidence

    confers RAZR system - traitmech:000411 + traitmech:000411 METPO:2007700

    RAZR-mediated phage restriction realizes the RAZR system trait.

    @@ -241,11 +242,11 @@

    Edge evidence

  • RAZR system - traitmech:000411 + traitmech:000411 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

    RAZR system possession is a phage-defense-system trait.

    @@ -310,7 +311,7 @@

    Parent traits (1)

    Synonyms (1)

    • @@ -326,7 +327,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -485,7 +486,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -849,12 +859,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 15:45 UTC diff --git a/pages/traits/genomics/resolvase_duf5677_system.html b/pages/traits/genomics/resolvase_duf5677_system.html index 988c240d657..d015344635b 100644 --- a/pages/traits/genomics/resolvase_duf5677_system.html +++ b/pages/traits/genomics/resolvase_duf5677_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -124,7 +125,7 @@

    Edge evidence

    confers Resolvase DUF5677 system - traitmech:000531 + traitmech:000531 METPO:2007700

    Prokaryotic Schlafen antiviral effector activity realizes the organism-level Resolvase DUF5677 system trait.

    @@ -231,7 +232,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -436,7 +437,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -800,12 +810,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 01:50 UTC diff --git a/pages/traits/genomics/resolvase_kap_ntpase_system.html b/pages/traits/genomics/resolvase_kap_ntpase_system.html index b951f747ebf..77cdf4d51ba 100644 --- a/pages/traits/genomics/resolvase_kap_ntpase_system.html +++ b/pages/traits/genomics/resolvase_kap_ntpase_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -124,7 +125,7 @@

    Edge evidence

    confers Resolvase KAP NTPase system - traitmech:000532 + traitmech:000532 METPO:2007700

    Prokaryotic Schlafen antiviral effector activity realizes the organism-level Resolvase KAP NTPase system trait.

    @@ -231,7 +232,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -436,7 +437,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -800,12 +810,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 02:32 UTC diff --git a/pages/traits/genomics/resolvase_schlafen_system.html b/pages/traits/genomics/resolvase_schlafen_system.html index 7b54972eac4..175c4655de6 100644 --- a/pages/traits/genomics/resolvase_schlafen_system.html +++ b/pages/traits/genomics/resolvase_schlafen_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -124,7 +125,7 @@

    Edge evidence

    confers Resolvase Schlafen system - traitmech:000529 + traitmech:000529 METPO:2007700

    Prokaryotic Schlafen antiviral effector activity realizes the organism-level Resolvase Schlafen system trait.

    @@ -231,7 +232,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -436,7 +437,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -800,12 +810,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 23:10 UTC diff --git a/pages/traits/genomics/restriction_modification_system.html b/pages/traits/genomics/restriction_modification_system.html index de5a2c8a31d..4339961953c 100644 --- a/pages/traits/genomics/restriction_modification_system.html +++ b/pages/traits/genomics/restriction_modification_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • restriction-modification system - traitmech:000095 + traitmech:000095 enables DNA restriction-modification system GO:0009307 @@ -269,8 +270,8 @@

    Protein and taxon examples

    		•  - Haemophilus influenzae Rd KW20 -
    NCBITaxon:71421 + Haemophilus influenzae Rd KW20 +
    NCBITaxon:71421         		REVIEWED
    @@ -351,7 +352,7 @@

    Children (4)

    Synonyms (1)

    @@ -367,7 +368,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -667,7 +668,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1031,12 +1041,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/genomics/retron_system.html b/pages/traits/genomics/retron_system.html index d3db3dd6645..f3e81193fd9 100644 --- a/pages/traits/genomics/retron_system.html +++ b/pages/traits/genomics/retron_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -230,7 +231,7 @@

    Edge evidence

    confers Retron system - traitmech:000235 + traitmech:000235 METPO:2007700

    Associated effector activity realizes the Retron system defense phenotype.

      @@ -246,11 +247,11 @@

      Edge evidence

    • Retron system - traitmech:000235 + traitmech:000235 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Retron system possession is a phage-defense-system trait.

        @@ -316,7 +317,7 @@

        kg-microbe context

        via parent_proxy.

          -
        • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
          • +
        • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

        512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

        @@ -501,7 +502,16 @@

        Identifier

        Term kind
        CLASS
        Status
        -
        PROPOSED
        +
        PROPOSED + + +
        + What this status means +

        Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

        +

        Quoted from the schema's status definitions.

        +
        + +
    @@ -865,12 +875,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-16 01:28 UTC diff --git a/pages/traits/genomics/reve_system.html b/pages/traits/genomics/reve_system.html index ac0dc73cb3c..988f66bc8ec 100644 --- a/pages/traits/genomics/reve_system.html +++ b/pages/traits/genomics/reve_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Reve system - traitmech:000499 + traitmech:000499 METPO:2007700

    Reve-mediated phage protection realizes the Reve system trait.

      @@ -152,11 +153,11 @@

      Edge evidence

    • Reve system - traitmech:000499 + traitmech:000499 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Reve system possession is a phage-defense-system trait.

        @@ -215,7 +216,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -231,7 +232,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -429,7 +430,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -793,12 +803,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 19:41 UTC diff --git a/pages/traits/genomics/rexab_system.html b/pages/traits/genomics/rexab_system.html index 1f36a45b6f9..e95ef04c3b8 100644 --- a/pages/traits/genomics/rexab_system.html +++ b/pages/traits/genomics/rexab_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers RexAB system - traitmech:000324 + traitmech:000324 METPO:2007700

    RexA/RexB-dependent abortive exclusion realizes the RexAB system trait.

    @@ -242,7 +243,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -407,7 +408,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -771,12 +781,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 02:18 UTC diff --git a/pages/traits/genomics/rhea_system.html b/pages/traits/genomics/rhea_system.html index 8e515632ecb..0203a73934a 100644 --- a/pages/traits/genomics/rhea_system.html +++ b/pages/traits/genomics/rhea_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Rhea system - traitmech:000311 + traitmech:000311 METPO:2007700

    Rhea-mediated phage restriction realizes the Rhea system trait.

      @@ -152,11 +153,11 @@

      Edge evidence

    • Rhea system - traitmech:000311 + traitmech:000311 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Rhea system possession is a phage-defense-system trait.

        @@ -215,7 +216,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -231,7 +232,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -358,7 +359,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Rhea system trait -

      Added traitmech:000311 Rhea system as a DOI-backed GENOMICS TraitRecord under phage defense system. DOI:10.1093/nar/gkae671 names Rhea among newly described lactococcal antiphage systems, DOI:10.1073/pnas.2426508122 treats Rhea as a plasmid-encoded lactococcal phage-resistance system in an escape-mutant screen, and the pinned DefenseFinder article registry maps Rhea to the Grafakou et al. lactococcal plasmidome discovery paper. Reserved METPO:1026500 in proposals/metpo_traitmech_v188 for the upstream replacement ID.

    +

    Added traitmech:000311 Rhea system as a DOI-backed GENOMICS TraitRecord under phage defense system. DOI:10.1093/nar/gkae671 names Rhea among newly described lactococcal antiphage systems, DOI:10.1073/pnas.2426508122 treats Rhea as a plasmid-encoded lactococcal phage-resistance system in an escape-mutant screen, and the pinned DefenseFinder article registry maps Rhea to the Grafakou et al. lactococcal plasmidome discovery paper. Reserved METPO:1026500 in proposals/metpo_traitmech_v188 for the upstream replacement ID.

    • Read this curation session @@ -390,7 +391,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -754,12 +764,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 14:47 UTC diff --git a/pages/traits/genomics/rloc_system.html b/pages/traits/genomics/rloc_system.html index 3392601e93c..3e353699cfc 100644 --- a/pages/traits/genomics/rloc_system.html +++ b/pages/traits/genomics/rloc_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -184,7 +185,7 @@

    Edge evidence

    confers RloC system - traitmech:000366 + traitmech:000366 METPO:2007700

    DNA-break-responsive RloC anticodon nuclease activation realizes the RloC system trait.

    @@ -293,7 +294,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -470,7 +471,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -834,12 +844,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-22 13:04 UTC diff --git a/pages/traits/genomics/rnlab_system.html b/pages/traits/genomics/rnlab_system.html index a07eb7ca501..c762f9fb30f 100644 --- a/pages/traits/genomics/rnlab_system.html +++ b/pages/traits/genomics/rnlab_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -196,7 +197,7 @@

    Edge evidence

    confers RnlAB system - traitmech:000367 + traitmech:000367 METPO:2007700

    RnlA-dependent RNase LS activity against T4 dmd-mutant mRNAs realizes the RnlAB system trait.

    @@ -307,7 +308,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -503,7 +504,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -867,12 +877,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-22 13:55 UTC diff --git a/pages/traits/genomics/rosmerta_system.html b/pages/traits/genomics/rosmerta_system.html index 17f50610e27..1038586ec2d 100644 --- a/pages/traits/genomics/rosmerta_system.html +++ b/pages/traits/genomics/rosmerta_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers RosmerTA system - traitmech:000256 + traitmech:000256 METPO:2007700

    RosmerTA-mediated phage restriction realizes the RosmerTA system trait.

    @@ -249,7 +250,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -408,7 +409,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -772,12 +782,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 23:50 UTC diff --git a/pages/traits/genomics/rrna_operon_copy_number.html b/pages/traits/genomics/rrna_operon_copy_number.html index 74cdead8a18..b6bae51fb5f 100644 --- a/pages/traits/genomics/rrna_operon_copy_number.html +++ b/pages/traits/genomics/rrna_operon_copy_number.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • rRNA operon copy number - traitmech:000101 + traitmech:000101 enables ribosome biogenesis GO:0042254 @@ -115,7 +116,7 @@

    Edge evidence

  • rRNA operon copy number - traitmech:000101 + traitmech:000101 associated with maximal growth rate @@ -134,7 +135,7 @@

    Edge evidence

  • rRNA operon copy number - traitmech:000101 + traitmech:000101 increases capacity for rRNA transcription GO:0009303 @@ -153,7 +154,7 @@

    Edge evidence

  • rRNA operon copy number - traitmech:000101 + traitmech:000101 decreases growth efficiency @@ -172,7 +173,7 @@

    Edge evidence

  • rRNA operon copy number - traitmech:000101 + traitmech:000101 positively associated with chemotactic motility @@ -191,7 +192,7 @@

    Edge evidence

  • rRNA operon copy number - traitmech:000101 + traitmech:000101 positively correlates with genome size @@ -254,7 +255,7 @@

    Parent traits (1)

    Synonyms (1)

    • @@ -270,7 +271,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -537,7 +538,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -901,12 +911,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/genomics/rst_2tm_1tm_tir_system.html b/pages/traits/genomics/rst_2tm_1tm_tir_system.html index cbecd8b6d14..498e35f2d10 100644 --- a/pages/traits/genomics/rst_2tm_1tm_tir_system.html +++ b/pages/traits/genomics/rst_2tm_1tm_tir_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -60,7 +61,7 @@

    Trait evidence (11) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md -
    The Rst_2TM_1TM_TIR system is carried by the P2-like phage AC1 and protects *Escherichia coli* C against lambda, LF82_P8 and P2 phages. This system is composed of three proteins, Rst_TIR_tm, which contains a TIR (Toll/interleukin-1 receptor) domain, Rst_1TM_TIR, which contains a transmembrane helix (TM) and Rst_2TM_TIR, that contains two TMs :ref{doi=10.1016/j.chom.2022.02.018}.
    +
    The Rst_2TM_1TM_TIR system is carried by the P2-like phage AC1 and protects *Escherichia coli* C against lambda, LF82_P8 and P2 phages. This system is composed of three proteins, Rst_TIR_tm, which contains a TIR (Toll/interleukin-1 receptor) domain, Rst_1TM_TIR, which contains a transmembrane helix (TM) and Rst_2TM_TIR, that contains two TMs :ref{doi=10.1016/j.chom.2022.02.018}.

    The pinned DefenseFinder wiki page names Rst_2TM_1TM_TIR as a three-protein system and links the AC1 locus to lambda, LF82_P8, and P2 protection in Escherichia coli C.

    @@ -90,9 +91,9 @@

    Trait evidence (11) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md -
    Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0 +
    Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli C -<a href='https://ncbi.nlm.nih.gov/protein/WP_001534952.1'>WP_001534952.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001534953.1'>WP_001534953.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001534955.1'>WP_001534955.1</a>] --> Expressed_0[Escherichia coli C] +<a href='https://ncbi.nlm.nih.gov/protein/WP_001534952.1'>WP_001534952.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001534953.1'>WP_001534953.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001534955.1'>WP_001534955.1</a>] --> Expressed_0[Escherichia coli C] Expressed_0[Escherichia coli C] ----> Lambda & LF82_P8 & P2 & SIAC10 & SID07 & DC1 & AC1

    The DefenseFinder experimental-validation diagram links Rousset et al. to an Escherichia coli C source locus expressed in Escherichia coli C against seven phages.

    @@ -172,7 +173,7 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md - The Rst_2TM_1TM_TIR system is carried by the P2-like phage AC1 and protects *Escherichia coli* C against lambda, LF82_P8 and P2 phages. This system is composed of three proteins, Rst_TIR_tm, which contains a TIR (Toll/interleukin-1 receptor) domain, Rst_1TM_TIR, which contains a transmembrane helix (TM) and Rst_2TM_TIR, that contains two TMs :ref{doi=10.1016/j.chom.2022.02.018}. + The Rst_2TM_1TM_TIR system is carried by the P2-like phage AC1 and protects *Escherichia coli* C against lambda, LF82_P8 and P2 phages. This system is composed of three proteins, Rst_TIR_tm, which contains a TIR (Toll/interleukin-1 receptor) domain, Rst_1TM_TIR, which contains a transmembrane helix (TM) and Rst_2TM_TIR, that contains two TMs :ref{doi=10.1016/j.chom.2022.02.018}. The pinned DefenseFinder wiki page names Rst_2TM_1TM_TIR as a three-protein system and links the AC1 locus to lambda, LF82_P8, and P2 protection in Escherichia coli C.
    • @@ -198,16 +199,16 @@

    Edge evidence

    confers Rst_2TM_1TM_TIR system - traitmech:000400 + traitmech:000400 METPO:2007700

    Rst_2TM_1TM_TIR-linked multi-phage resistance realizes the Rst_2TM_1TM_TIR system trait.

    @@ -321,7 +322,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -528,7 +529,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -892,12 +902,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 02:44 UTC diff --git a/pages/traits/genomics/rst_3hp_system.html b/pages/traits/genomics/rst_3hp_system.html index 9d0f4a72e45..a25e4514eba 100644 --- a/pages/traits/genomics/rst_3hp_system.html +++ b/pages/traits/genomics/rst_3hp_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -66,7 +67,7 @@

    Trait evidence (11) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_3hp.md -
    The Rst_3HP system is composed of 3 proteins: Hp1, Hp2 and, Hp3. These proteins do not have clear predicted domains but they confer resistance against the phage P1 in *Escherichia coli* E1114 :ref{doi=10.1016/j.chom.2022.02.018}.
    +
    The Rst_3HP system is composed of 3 proteins: Hp1, Hp2 and, Hp3. These proteins do not have clear predicted domains but they confer resistance against the phage P1 in *Escherichia coli* E1114 :ref{doi=10.1016/j.chom.2022.02.018}.

    The pinned DefenseFinder wiki page names Rst_3HP as a three-protein system and links Hp1, Hp2, and Hp3 to P1 resistance in Escherichia coli E1114.

    @@ -90,10 +91,10 @@

    Trait evidence (11) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_3hp.md -
    Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0 +
    Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli P2 loci -<a href='https://ncbi.nlm.nih.gov/protein/WP_000508501.1'>WP_000508501.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_112026686.1'>WP_112026686.1</a>, -<a href='https://ncbi.nlm.nih.gov/protein/WP_000756244.1'>WP_000756244.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/WP_000508501.1'>WP_000508501.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_112026686.1'>WP_112026686.1</a>, +<a href='https://ncbi.nlm.nih.gov/protein/WP_000756244.1'>WP_000756244.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> P1

    The DefenseFinder experimental-validation diagram links Rousset et al. to an Escherichia coli P2-locus source expressed in Escherichia coli against P1.

    @@ -173,7 +174,7 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_3hp.md - The Rst_3HP system is composed of 3 proteins: Hp1, Hp2 and, Hp3. These proteins do not have clear predicted domains but they confer resistance against the phage P1 in *Escherichia coli* E1114 :ref{doi=10.1016/j.chom.2022.02.018}. + The Rst_3HP system is composed of 3 proteins: Hp1, Hp2 and, Hp3. These proteins do not have clear predicted domains but they confer resistance against the phage P1 in *Escherichia coli* E1114 :ref{doi=10.1016/j.chom.2022.02.018}. The pinned DefenseFinder wiki page names Rst_3HP as a three-protein system and links Hp1, Hp2, and Hp3 to P1 resistance in Escherichia coli E1114.
    • @@ -199,7 +200,7 @@

    Edge evidence

    confers Rst_3HP system - traitmech:000398 + traitmech:000398 METPO:2007700

    Rst_3HP-linked P1 resistance realizes the Rst_3HP system trait.

    @@ -323,7 +324,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -521,7 +522,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -885,12 +895,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 01:04 UTC diff --git a/pages/traits/genomics/rst_duf4238_system.html b/pages/traits/genomics/rst_duf4238_system.html index e9806e68f59..e500b64f27d 100644 --- a/pages/traits/genomics/rst_duf4238_system.html +++ b/pages/traits/genomics/rst_duf4238_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -66,7 +67,7 @@

    Trait evidence (8)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_duf4238.md -
    Rst_DUF4238 is a single gene system found in a screen of phage and phage-satellites antiviral hotspots :ref{doi=10.1016/j.chom.2022.02.018}. It was shown to provide *E.coli* with a strong resistance against phage T7.
    +
    Rst_DUF4238 is a single gene system found in a screen of phage and phage-satellites antiviral hotspots :ref{doi=10.1016/j.chom.2022.02.018}. It was shown to provide *E.coli* with a strong resistance against phage T7.

    The pinned DefenseFinder wiki page names Rst_DUF4238 as a single-gene system and links it to strong T7 resistance.

    @@ -166,7 +167,7 @@

    Edge evidence

    confers Rst_DUF4238 system - traitmech:000374 + traitmech:000374 METPO:2007700

    Strong T7 resistance realizes the Rst_DUF4238 system trait.

    @@ -277,7 +278,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -475,7 +476,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -839,12 +849,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 07:32 UTC diff --git a/pages/traits/genomics/rst_gop_beta_cll_system.html b/pages/traits/genomics/rst_gop_beta_cll_system.html index 856501c9430..b03c81cdbd3 100644 --- a/pages/traits/genomics/rst_gop_beta_cll_system.html +++ b/pages/traits/genomics/rst_gop_beta_cll_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -164,7 +165,7 @@

    Edge evidence

    confers Rst gop-beta-cII system - traitmech:000376 + traitmech:000376 METPO:2007700

    Restriction of lambda and P1 phages realizes the Rst gop-beta-cII system trait.

    @@ -273,7 +274,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -473,7 +474,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -837,12 +847,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 08:53 UTC diff --git a/pages/traits/genomics/rst_helicaseduf2290_system.html b/pages/traits/genomics/rst_helicaseduf2290_system.html index c518d7c164b..295de52746a 100644 --- a/pages/traits/genomics/rst_helicaseduf2290_system.html +++ b/pages/traits/genomics/rst_helicaseduf2290_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -90,9 +91,9 @@

    Trait evidence (11) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_helicaseduf2290.md -
    Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0 +
    Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0 Origin_0[Klebsiella pneumoniae P4 loci -<a href='https://ncbi.nlm.nih.gov/protein/WP_046623503.1'>WP_046623503.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_046623504.1'>WP_046623504.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/WP_046623503.1'>WP_046623503.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_046623504.1'>WP_046623504.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7

    The DefenseFinder experimental-validation diagram links Rousset et al. to a Klebsiella pneumoniae P4-locus source expressed in Escherichia coli against T7.

    @@ -198,7 +199,7 @@

    Edge evidence

    confers Rst_HelicaseDUF2290 system - traitmech:000401 + traitmech:000401 METPO:2007700

    Rst_HelicaseDUF2290-linked T7 resistance realizes the Rst_HelicaseDUF2290 system trait.

    @@ -323,7 +324,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -542,7 +543,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -906,12 +916,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 06:09 UTC diff --git a/pages/traits/genomics/rst_hydrolase_3tm_system.html b/pages/traits/genomics/rst_hydrolase_3tm_system.html index aa56168cc69..5afa63490cc 100644 --- a/pages/traits/genomics/rst_hydrolase_3tm_system.html +++ b/pages/traits/genomics/rst_hydrolase_3tm_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -78,9 +79,9 @@

    Trait evidence (9)

    https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md -
    Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0 +
    Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli P4 loci -<a href='https://ncbi.nlm.nih.gov/protein/WP_000754434.1'>WP_000754434.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001401335.1'>WP_001401335.1</a>] --> Expressed_0[Escherichia coli] +<a href='https://ncbi.nlm.nih.gov/protein/WP_000754434.1'>WP_000754434.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001401335.1'>WP_001401335.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7

    The DefenseFinder experimental-validation diagram links Rousset et al. to an Escherichia coli P4-locus source expressed in Escherichia coli against T7.

    @@ -184,7 +185,7 @@

    Edge evidence

    confers Rst_Hydrolase-3Tm system - traitmech:000402 + traitmech:000402 METPO:2007700

    Rst_Hydrolase-3Tm-linked T7 resistance realizes the Rst_Hydrolase-3Tm system trait.

    @@ -309,7 +310,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -508,7 +509,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -872,12 +882,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 05:07 UTC diff --git a/pages/traits/genomics/rst_rt_nitrilase_tm_system.html b/pages/traits/genomics/rst_rt_nitrilase_tm_system.html index ee6ed1f5df7..5e142de515b 100644 --- a/pages/traits/genomics/rst_rt_nitrilase_tm_system.html +++ b/pages/traits/genomics/rst_rt_nitrilase_tm_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -66,13 +67,13 @@

    Trait evidence (10) https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md -
    RT-nitrilase-Tm (also named UG5-large) is a two-gene defense system. It was discovered from P4-like satellites in *E. coli* genomes :ref{doi=10.1016/j.chom.2022.02.018} :ref{doi=10.1093/nar/gkac467}. Its antiphage activity was shown in *E. coli* against phage AL505_P2 (Myoviridae).
    +
    RT-nitrilase-Tm (also named UG5-large) is a two-gene defense system. It was discovered from P4-like satellites in *E. coli* genomes :ref{doi=10.1016/j.chom.2022.02.018} :ref{doi=10.1093/nar/gkac467}. Its antiphage activity was shown in *E. coli* against phage AL505_P2 (Myoviridae).

    The pinned DefenseFinder wiki page names RT-nitrilase-Tm, also called UG5-large, as a two-gene system and records AL505_P2 antiphage activity in Escherichia coli.

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md -
    The first protein is a reverse transcriptase (RT) fussed with C-N hydrolase domain (nitrilase); the second protein is transmembrane protein :ref{doi=10.1093/nar/gkac467}.
    +
    The first protein is a reverse transcriptase (RT) fussed with C-N hydrolase domain (nitrilase); the second protein is transmembrane protein :ref{doi=10.1093/nar/gkac467}.

    The pinned DefenseFinder wiki page describes the reverse-transcriptase/nitrilase plus transmembrane-protein architecture.

    • @@ -162,7 +163,7 @@

    Edge evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md - The first protein is a reverse transcriptase (RT) fussed with C-N hydrolase domain (nitrilase); the second protein is transmembrane protein :ref{doi=10.1093/nar/gkac467}. + The first protein is a reverse transcriptase (RT) fussed with C-N hydrolase domain (nitrilase); the second protein is transmembrane protein :ref{doi=10.1093/nar/gkac467}. The pinned DefenseFinder wiki page describes the reverse-transcriptase/nitrilase plus transmembrane-protein architecture.
    • @@ -194,7 +195,7 @@

    Edge evidence

    confers Rst_RT-nitrilase-Tm system - traitmech:000403 + traitmech:000403 METPO:2007700

    Rst_RT-nitrilase-Tm-linked AL505_P2 resistance realizes the Rst_RT-nitrilase-Tm system trait.

    @@ -321,7 +322,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -434,7 +435,7 @@

    Evidence

  • https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md -
    RT-nitrilase-Tm (also named UG5-large) is a two-gene defense system. It was discovered from P4-like satellites in *E. coli* genomes :ref{doi=10.1016/j.chom.2022.02.018} :ref{doi=10.1093/nar/gkac467}. Its antiphage activity was shown in *E. coli* against phage AL505_P2 (Myoviridae).
    +
    RT-nitrilase-Tm (also named UG5-large) is a two-gene defense system. It was discovered from P4-like satellites in *E. coli* genomes :ref{doi=10.1016/j.chom.2022.02.018} :ref{doi=10.1093/nar/gkac467}. Its antiphage activity was shown in *E. coli* against phage AL505_P2 (Myoviridae).
    • @@ -521,7 +522,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -885,12 +895,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 06:37 UTC diff --git a/pages/traits/genomics/rst_tir_nlr_system.html b/pages/traits/genomics/rst_tir_nlr_system.html index ea1132ee134..fe80896ff3f 100644 --- a/pages/traits/genomics/rst_tir_nlr_system.html +++ b/pages/traits/genomics/rst_tir_nlr_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -166,7 +167,7 @@

    Edge evidence

    confers Rst TIR-NLR system - traitmech:000377 + traitmech:000377 METPO:2007700

    Restriction of virulent and P2-like phages realizes the Rst TIR-NLR system trait.

    @@ -277,7 +278,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -475,7 +476,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -839,12 +849,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-26 09:17 UTC diff --git a/pages/traits/genomics/rugutis_system.html b/pages/traits/genomics/rugutis_system.html index 636cf495fb3..1e6008d925e 100644 --- a/pages/traits/genomics/rugutis_system.html +++ b/pages/traits/genomics/rugutis_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Rugutis system - traitmech:000315 + traitmech:000315 METPO:2007700

    Rugutis-mediated phage restriction realizes the Rugutis system trait.

      @@ -152,11 +153,11 @@

      Edge evidence

    • Rugutis system - traitmech:000315 + traitmech:000315 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Rugutis system possession is a phage-defense-system trait.

        @@ -215,7 +216,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -231,7 +232,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -358,7 +359,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Rugutis system trait -

      Added traitmech:000315 Rugutis system as a DOI-backed GENOMICS TraitRecord under phage defense system. DOI:10.1093/nar/gkae671 names Rugutis among newly described lactococcal antiphage systems, DOI:10.1073/pnas.2426508122 treats Rugutis as a plasmid-encoded lactococcal phage-resistance system in an escape-mutant screen, and the pinned DefenseFinder article registry maps Rugutis to the Grafakou et al. lactococcal plasmidome discovery paper. Reserved METPO:1026900 in proposals/metpo_traitmech_v192 for the upstream replacement ID.

    +

    Added traitmech:000315 Rugutis system as a DOI-backed GENOMICS TraitRecord under phage defense system. DOI:10.1093/nar/gkae671 names Rugutis among newly described lactococcal antiphage systems, DOI:10.1073/pnas.2426508122 treats Rugutis as a plasmid-encoded lactococcal phage-resistance system in an escape-mutant screen, and the pinned DefenseFinder article registry maps Rugutis to the Grafakou et al. lactococcal plasmidome discovery paper. Reserved METPO:1026900 in proposals/metpo_traitmech_v192 for the upstream replacement ID.

    • Read this curation session @@ -390,7 +391,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -754,12 +764,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 17:44 UTC diff --git a/pages/traits/genomics/sanata_system.html b/pages/traits/genomics/sanata_system.html index a8b50510930..0fb0ba3751d 100644 --- a/pages/traits/genomics/sanata_system.html +++ b/pages/traits/genomics/sanata_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -172,7 +173,7 @@

    Edge evidence

    confers SanaTA system - traitmech:000373 + traitmech:000373 METPO:2007700

    SanaTA-mediated resistance to T7 gene 4.5 mutants realizes the SanaTA system trait.

    @@ -285,7 +286,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -469,7 +470,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -833,12 +843,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-25 06:20 UTC diff --git a/pages/traits/genomics/scomcra_system.html b/pages/traits/genomics/scomcra_system.html index 70d8d93d0fe..a55a5984b3e 100644 --- a/pages/traits/genomics/scomcra_system.html +++ b/pages/traits/genomics/scomcra_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -191,7 +192,7 @@

    Edge evidence

    confers ScoMcrA system - traitmech:000512 + traitmech:000512 METPO:2007700

    ScoMcrA-family phosphorothioated-DNA restriction realizes the organism-level ScoMcrA system possession trait.

    @@ -298,7 +299,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -524,7 +525,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -888,12 +898,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 10:16 UTC diff --git a/pages/traits/genomics/sdic1_system.html b/pages/traits/genomics/sdic1_system.html index 5c9e4ac626a..5a0afab693a 100644 --- a/pages/traits/genomics/sdic1_system.html +++ b/pages/traits/genomics/sdic1_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers SDIC1 system - traitmech:000420 + traitmech:000420 METPO:2007700

    SDIC1-mediated anti-phage immunity realizes the SDIC1 system trait.

    @@ -265,7 +266,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -439,7 +440,7 @@

    Recorded curation sessions

  • · claude-code
    • CREATE — Add SDIC1 system trait -

      Minted traitmech:000420 for the DOI-backed SDIC1 system under phage defense system. DOI:10.1016/j.celrep.2024.115055 supports SDIC1 as a TIR-domain anti-phage system with a ubiquitin-ligase-like component and population-wide immunity; the pinned DefenseFinder article and HMM inventories map SDIC1 to the SDIC1A and SDIC1B custom profiles while the pinned rules table has no SDIC1 row, so the graph stays nonmechanistic at candidate-locus level. Reserved METPO:1037400 in proposals/metpo_traitmech_v297.

    +

    Minted traitmech:000420 for the DOI-backed SDIC1 system under phage defense system. DOI:10.1016/j.celrep.2024.115055 supports SDIC1 as a TIR-domain anti-phage system with a ubiquitin-ligase-like component and population-wide immunity; the pinned DefenseFinder article and HMM inventories map SDIC1 to the SDIC1A and SDIC1B custom profiles while the pinned rules table has no SDIC1 row, so the graph stays nonmechanistic at candidate-locus level. Reserved METPO:1037400 in proposals/metpo_traitmech_v297.

    • Read this curation session @@ -471,7 +472,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -835,12 +845,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 22:50 UTC diff --git a/pages/traits/genomics/sdic3_system.html b/pages/traits/genomics/sdic3_system.html index 6174d10ae26..7461bcd0be3 100644 --- a/pages/traits/genomics/sdic3_system.html +++ b/pages/traits/genomics/sdic3_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -196,7 +197,7 @@

    Edge evidence

    confers SDIC3 system - traitmech:000423 + traitmech:000423 METPO:2007700

    SDIC3-mediated phage restriction realizes the SDIC3 system trait.

    @@ -307,7 +308,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -508,7 +509,7 @@

    Recorded curation sessions

  • · claude-code
    • CREATE — Add SDIC3 system trait -

      Minted traitmech:000423 for the DOI-backed SDIC3 system under phage defense system. DOI:10.1016/j.celrep.2024.115055 supports SDIC3 as a Serratia defense-island candidate anti-phage system that can strongly protect plasmid-expressing E. coli against several bacteriophages; the pinned DefenseFinder article and HMM inventories map SDIC3 to the SDIC3B, SDIC3C, SDIC3D, SDIC3E, and SDIC3F custom profiles while the pinned rules table has no SDIC3 row, so the graph stays nonmechanistic at candidate-locus level and the record keeps SDIC3A scope, ECOR61-system boundaries, native host breadth, phage range, and direct molecular output unresolved. Reserved METPO:1037700 in proposals/metpo_traitmech_v300.

    +

    Minted traitmech:000423 for the DOI-backed SDIC3 system under phage defense system. DOI:10.1016/j.celrep.2024.115055 supports SDIC3 as a Serratia defense-island candidate anti-phage system that can strongly protect plasmid-expressing E. coli against several bacteriophages; the pinned DefenseFinder article and HMM inventories map SDIC3 to the SDIC3B, SDIC3C, SDIC3D, SDIC3E, and SDIC3F custom profiles while the pinned rules table has no SDIC3 row, so the graph stays nonmechanistic at candidate-locus level and the record keeps SDIC3A scope, ECOR61-system boundaries, native host breadth, phage range, and direct molecular output unresolved. Reserved METPO:1037700 in proposals/metpo_traitmech_v300.

    • Read this curation session @@ -540,7 +541,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -904,12 +914,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-28 01:44 UTC diff --git a/pages/traits/genomics/sdic4_system.html b/pages/traits/genomics/sdic4_system.html index 8fc38730133..4616900151a 100644 --- a/pages/traits/genomics/sdic4_system.html +++ b/pages/traits/genomics/sdic4_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers SDIC4 system - traitmech:000421 + traitmech:000421 METPO:2007700

    Reduced phage adsorption realizes the SDIC4 system trait.

    @@ -265,7 +266,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -445,7 +446,7 @@

    Recorded curation sessions

  • · claude-code
    • CREATE — Add SDIC4 system trait -

      Minted traitmech:000421 for the DOI-backed SDIC4 system under phage defense system. DOI:10.1016/j.celrep.2024.115055 supports SDIC4 as a VasI-like anti-phage system that decreases the bacteriophage adsorption rate; the pinned DefenseFinder article and HMM inventories map SDIC4 to the SDIC4A and SDIC4B custom profiles while the pinned rules table has no SDIC4 row, so the graph stays nonmechanistic at candidate-locus level and the record keeps SDIC4 subtype boundaries unresolved. Reserved METPO:1037500 in proposals/metpo_traitmech_v298.

    +

    Minted traitmech:000421 for the DOI-backed SDIC4 system under phage defense system. DOI:10.1016/j.celrep.2024.115055 supports SDIC4 as a VasI-like anti-phage system that decreases the bacteriophage adsorption rate; the pinned DefenseFinder article and HMM inventories map SDIC4 to the SDIC4A and SDIC4B custom profiles while the pinned rules table has no SDIC4 row, so the graph stays nonmechanistic at candidate-locus level and the record keeps SDIC4 subtype boundaries unresolved. Reserved METPO:1037500 in proposals/metpo_traitmech_v298.

    • Read this curation session @@ -477,7 +478,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -841,12 +851,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 23:49 UTC diff --git a/pages/traits/genomics/sefir_system.html b/pages/traits/genomics/sefir_system.html index b99496314b3..6bdc7fabd21 100644 --- a/pages/traits/genomics/sefir_system.html +++ b/pages/traits/genomics/sefir_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers SEFIR system - traitmech:000259 + traitmech:000259 METPO:2007700

    SEFIR-mediated phage restriction realizes the SEFIR system trait.

    @@ -249,7 +250,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -408,7 +409,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -772,12 +782,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 01:52 UTC diff --git a/pages/traits/genomics/septu_system.html b/pages/traits/genomics/septu_system.html index f93f3815e93..dd2a50770f2 100644 --- a/pages/traits/genomics/septu_system.html +++ b/pages/traits/genomics/septu_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -199,7 +200,7 @@

    Edge evidence

    confers Septu system - traitmech:000233 + traitmech:000233 METPO:2007700

    PtuAB-mediated phage genomic DNA cleavage realizes the Septu system trait.

      @@ -215,11 +216,11 @@

      Edge evidence

    • Septu system - traitmech:000233 + traitmech:000233 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Septu system possession is a phage-defense-system trait.

        @@ -278,7 +279,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -294,7 +295,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -479,7 +480,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -843,12 +853,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 23:59 UTC diff --git a/pages/traits/genomics/shango_system.html b/pages/traits/genomics/shango_system.html index 13a6f4a1230..23d51965aa5 100644 --- a/pages/traits/genomics/shango_system.html +++ b/pages/traits/genomics/shango_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers Shango system - traitmech:000255 + traitmech:000255 METPO:2007700

    Shango-mediated phage restriction realizes the Shango system trait.

    @@ -261,7 +262,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -420,7 +421,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -784,12 +794,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-18 23:31 UTC diff --git a/pages/traits/genomics/shedu_system.html b/pages/traits/genomics/shedu_system.html index 0e9a2e18f12..2d8f9340000 100644 --- a/pages/traits/genomics/shedu_system.html +++ b/pages/traits/genomics/shedu_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -217,7 +218,7 @@

    Edge evidence

    confers Shedu system - traitmech:000220 + traitmech:000220 METPO:2007700

    DNA-end nicking is a characterized antiviral output that realizes the Shedu system trait.

      @@ -233,11 +234,11 @@

      Edge evidence

    • Shedu system - traitmech:000220 + traitmech:000220 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Shedu system possession is a phage-defense-system trait.

        @@ -273,8 +274,8 @@

        Protein and taxon examples

    		 - Bacillus cereus (strain B4264) -
    NCBITaxon:405532 + Bacillus cereus (strain B4264) +
    NCBITaxon:405532         		REVIEWED
    @@ -287,13 +288,13 @@

    Protein and taxon examples

  • DOI:10.1016/j.molcel.2024.12.004 we reveal the structural basis for activation of Bacillus cereus Shedu - Gu et al. determined cryo-EM structures of Bacillus cereus Shedu; PDBe maps their entries 8TI8, 8TI9 and 8TIA to UniProtKB:B7HFR2 (Bacillus cereus B4264), so the structurally characterized protein is this accession. Snippet verified verbatim in the Europe PMC abstract of PMID:39742666. + Gu et al. determined cryo-EM structures of Bacillus cereus Shedu; PDBe maps their entries 8TI8, 8TI9 and 8TIA to UniProtKB:B7HFR2 (Bacillus cereus B4264), so the structurally characterized protein is this accession. Snippet verified verbatim in the Europe PMC abstract of PMID:39742666.
  • DOI:10.1016/j.molcel.2024.12.004 Two cryoelectron microscopy structures of Shedu show that it switches between inactive and active states through conformational changes affecting active-site architecture, which are controlled by the protein's N-terminal domain (NTD) - Gu et al. establish the N-terminal domain as the regulator of the nuclease active site in this B. cereus protein. The role statement is scoped to the tested protein; the paper's survey of 79 N-terminal domain types is explicitly about homologs, not about this accession. Snippet verified verbatim in the Europe PMC abstract of PMID:39742666. + Gu et al. establish the N-terminal domain as the regulator of the nuclease active site in this B. cereus protein. The role statement is scoped to the tested protein; the paper's survey of 79 N-terminal domain types is explicitly about homologs, not about this accession. Snippet verified verbatim in the Europe PMC abstract of PMID:39742666.
    • @@ -346,7 +347,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Shedu anti-phage defense system EXACT_SYNONYM · DOI:10.1016/j.cell.2024.11.030
      • +
    • Shedu anti-phage defense system EXACT_SYNONYM · DOI:10.1016/j.cell.2024.11.030
    @@ -362,7 +363,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -511,7 +512,7 @@

    Curation history

  • · ADD_SDUA_PROTEIN_EXAMPLE · claude -

    Added a GENE_OR_PROTEIN node for the single-protein Shedu immune nuclease with UniProtKB:B7HFR2 (Shedu protein SduA, Bacillus cereus B4264, NCBITaxon:405532) as a taxon-paired protein example, plus one contributes-to edge to Shedu nuclease activation. UniProt REST verified the accession anonymously on 2026-10-08 as a current reviewed (Swiss-Prot) primary accession with no secondary accessions, entry version 58 and sequence version 1, organism Bacillus cereus strain B4264 (taxon 405532), cross-referenced to Pfam PF14082 (SduA_C, whose InterPro name history is DUF4263 then SduA_C) and PF21407. Evidence is Gu et al. 2024 Mol Cell (PMID:39742666, DOI:10.1016/j.molcel.2024.12.004), whose cryo-EM entries 8TI8/8TI9/8TIA PDBe maps to this exact accession; both snippets were verified verbatim against the Europe PMC abstract. The node is REVIEWED_LABEL_ONLY because no family-level InterPro, NCBIfam or GO term covers SduA: only the two domain entries IPR025359 and IPR048396 exist, and PF14082 spans 1304 UniProt proteins with 18 domain architectures. Graph scope_status, mapping_status, definition, hierarchy and existing evidence are unchanged.

    +

    Added a GENE_OR_PROTEIN node for the single-protein Shedu immune nuclease with UniProtKB:B7HFR2 (Shedu protein SduA, Bacillus cereus B4264, NCBITaxon:405532) as a taxon-paired protein example, plus one contributes-to edge to Shedu nuclease activation. UniProt REST verified the accession anonymously on 2026-10-08 as a current reviewed (Swiss-Prot) primary accession with no secondary accessions, entry version 58 and sequence version 1, organism Bacillus cereus strain B4264 (taxon 405532), cross-referenced to Pfam PF14082 (SduA_C, whose InterPro name history is DUF4263 then SduA_C) and PF21407. Evidence is Gu et al. 2024 Mol Cell (PMID:39742666, DOI:10.1016/j.molcel.2024.12.004), whose cryo-EM entries 8TI8/8TI9/8TIA PDBe maps to this exact accession; both snippets were verified verbatim against the Europe PMC abstract. The node is REVIEWED_LABEL_ONLY because no family-level InterPro, NCBIfam or GO term covers SduA: only the two domain entries IPR025359 and IPR048396 exist, and PF14082 spans 1304 UniProt proteins with 18 domain architectures. Graph scope_status, mapping_status, definition, hierarchy and existing evidence are unchanged.

    • @@ -527,7 +528,7 @@

    Recorded curation sessions

  • · claude-code
    • EDIT — Add B. cereus B4264 SduA protein example to Shedu system -

      Added a GENE_OR_PROTEIN node (sdua_immune_nuclease) carrying UniProtKB:B7HFR2 as a taxon-paired protein example, plus one contributes-to edge into shedu_nuclease_activation. The node is REVIEWED_LABEL_ONLY because no family-level InterPro, NCBIfam or GO term covers SduA: a bounded search of all InterPro member databases and of GO via OLS4 for 'Shedu' returned only the domain entries IPR025359 (Pfam PF14082, InterPro name history DUF4263 then SduA_C) and IPR048396 (Pfam PF21407), and PF14082 spans 1304 UniProt proteins across 2464 taxa with 18 domain architectures, so a domain term would not denote this protein family. UniProt REST (anonymous, no contact address sent) confirmed B7HFR2 on 2026-10-08 as a current reviewed Swiss-Prot primary accession, no secondary accessions, entry version 58, sequence version 1, organism Bacillus cereus strain B4264 (NCBITaxon:405532, resolved independently at NCBI Datasets). Evidence: Gu et al. 2024 Mol Cell PMID:39742666 / DOI:10.1016/j.molcel.2024.12.004, whose cryo-EM entries 8TI8/8TI9/8TIA PDBe maps to this exact accession; both snippets verified as verbatim substrings of the Europe PMC abstract via just verify-snippets. Candidate UniProtKB:C0VHC9 (Cap4) and UniProtKB:P0DW34 (DruA) were NOT added: Cap4 is a CBASS effector rather than a Gao-Her or Lamassu component, and neither protein has a Europe PMC-verifiable primary snippet for its own role, since both source papers are closed access there. Those two leads and their completed verification are recorded in issue 1807. Written through scripts/add_shedu_sdua_protein_example.py (--apply opt-in, write_validated_trait, record_curation_event). Review fixes from issues 1808-1813 were applied in the same pull request: the uniprot_grounding_audit report was regenerated, the edge description and role wording were scoped to the tested protein and to source wording, the label-only justification was corrected, the curation event carries the real UTC time, and these links were added.

    +

    Added a GENE_OR_PROTEIN node (sdua_immune_nuclease) carrying UniProtKB:B7HFR2 as a taxon-paired protein example, plus one contributes-to edge into shedu_nuclease_activation. The node is REVIEWED_LABEL_ONLY because no family-level InterPro, NCBIfam or GO term covers SduA: a bounded search of all InterPro member databases and of GO via OLS4 for 'Shedu' returned only the domain entries IPR025359 (Pfam PF14082, InterPro name history DUF4263 then SduA_C) and IPR048396 (Pfam PF21407), and PF14082 spans 1304 UniProt proteins across 2464 taxa with 18 domain architectures, so a domain term would not denote this protein family. UniProt REST (anonymous, no contact address sent) confirmed B7HFR2 on 2026-10-08 as a current reviewed Swiss-Prot primary accession, no secondary accessions, entry version 58, sequence version 1, organism Bacillus cereus strain B4264 (NCBITaxon:405532, resolved independently at NCBI Datasets). Evidence: Gu et al. 2024 Mol Cell PMID:39742666 / DOI:10.1016/j.molcel.2024.12.004, whose cryo-EM entries 8TI8/8TI9/8TIA PDBe maps to this exact accession; both snippets verified as verbatim substrings of the Europe PMC abstract via just verify-snippets. Candidate UniProtKB:C0VHC9 (Cap4) and UniProtKB:P0DW34 (DruA) were NOT added: Cap4 is a CBASS effector rather than a Gao-Her or Lamassu component, and neither protein has a Europe PMC-verifiable primary snippet for its own role, since both source papers are closed access there. Those two leads and their completed verification are recorded in issue 1807. Written through scripts/add_shedu_sdua_protein_example.py (--apply opt-in, write_validated_trait, record_curation_event). Review fixes from issues 1808-1813 were applied in the same pull request: the uniprot_grounding_audit report was regenerated, the edge description and role wording were scoped to the tested protein and to source wording, the label-only justification was corrected, the curation event carries the real UTC time, and these links were added.

    • Read this curation session @@ -559,7 +560,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -923,12 +933,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-08 04:22 UTC diff --git a/pages/traits/genomics/short_lamassu_system.html b/pages/traits/genomics/short_lamassu_system.html index 74f7cdf7a0e..1dbe7502492 100644 --- a/pages/traits/genomics/short_lamassu_system.html +++ b/pages/traits/genomics/short_lamassu_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -133,7 +134,7 @@

    Children (1)

    Synonyms (1)

    @@ -149,7 +150,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -310,13 +311,13 @@

    Curation history

  • · CLARIFY_HISTORICAL_SNIPPET_VERIFICATION · codex -

    Correction to the 13:17:37Z event (#1620): withdraw the description of the removed species-name-and-ID quote as contiguous. That check joined text across HTML blocks and did not establish a contiguous source span. The distinct earlier citation-form verification is supported by these exact inline raw HTML bytes from https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=666&mode=Info: Taxonomy ID: 666 <small>(for references in articles please use ncbitaxon:666)</small><br>. The lowercase form is quoted source text, not a curated CURIE. Current evidence and taxon grounding are unchanged; earlier events remain preserved.

    +

    Correction to the 13:17:37Z event (#1620): withdraw the description of the removed species-name-and-ID quote as contiguous. That check joined text across HTML blocks and did not establish a contiguous source span. The distinct earlier citation-form verification is supported by these exact inline raw HTML bytes from https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=666&mode=Info: Taxonomy ID: 666 <small>(for references in articles please use ncbitaxon:666)</small><br>. The lowercase form is quoted source text, not a curated CURIE. Current evidence and taxon grounding are unchanged; earlier events remain preserved.

  • · TRACK_TYPE_I_CLASS · codex -

    Linked traitmech:000573 Lamassu type I system to the existing component-architecture discussion using DOI:10.1073/pnas.2519643122 and DOI:10.1038/s41589-025-02102-z. Preserved all definitions, parents, evidence, examples and prior history. Component absence, LmuB-length family and experimental activity remain separate claims.

    +

    Linked traitmech:000573 Lamassu type I system to the existing component-architecture discussion using DOI:10.1073/pnas.2519643122 and DOI:10.1038/s41589-025-02102-z. Preserved all definitions, parents, evidence, examples and prior history. Component absence, LmuB-length family and experimental activity remain separate claims.

    • @@ -326,7 +327,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add the short Lamassu family -

      Added traitmech:000570 from DOI:10.1073/pnas.2519643122 with six exact snippets across the primary article, RCSB PDB 9NY5 entity 3 JSON, and NCBI taxon 666. Distinguished the short-LmuB phylogenetic and structural family from a numerical length bin, component-number classes, and effector-specific models. Qualified Vibrio cholerae as source organism of Vc-Cap4 and E. coli as heterologous host; no species-wide phenotype or universal mechanism asserted. Ignored-and-hidden novelty searches and fresh METPO seed comparison preceded minting. Reserved METPO:1052400 in v447, including the existing HNH child refinement. Writer dry run, six source exact matches and 24 focused tests passed.

    +

    Added traitmech:000570 from DOI:10.1073/pnas.2519643122 with six exact snippets across the primary article, RCSB PDB 9NY5 entity 3 JSON, and NCBI taxon 666. Distinguished the short-LmuB phylogenetic and structural family from a numerical length bin, component-number classes, and effector-specific models. Qualified Vibrio cholerae as source organism of Vc-Cap4 and E. coli as heterologous host; no species-wide phenotype or universal mechanism asserted. Ignored-and-hidden novelty searches and fresh METPO seed comparison preceded minting. Reserved METPO:1052400 in v447, including the existing HNH child refinement. Writer dry run, six source exact matches and 24 focused tests passed.

    • Read this curation session
  • @@ -344,7 +345,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Clarify the historical cross-block quotation check -

      Addresses #1620 and corrects the verification wording in history/records/short_lamassu_system/2026-10-03T131935Z-codex-e20e84.yaml without editing it. Appended an event withdrawing the contiguous characterization for the removed species-name-and-ID quote: its check joined rendered text across HTML blocks. The distinct earlier citation-form verification remains supported by the exact inline raw HTML included in the new curation event: Taxonomy ID: 666 <small>(for references in articles please use ncbitaxon:666)</small><br>. Source: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=666&mode=Info, HTTP 200 fetch rechecked on 2026-10-03. That lowercase text is a source quotation, not an asserted CURIE. All prior events and substantive trait/proposal fields are unchanged. The writer authorizes only the exact committed preimage for this migration and tests acceptance, drift refusal and full prior-field preservation.

    +

    Addresses #1620 and corrects the verification wording in history/records/short_lamassu_system/2026-10-03T131935Z-codex-e20e84.yaml without editing it. Appended an event withdrawing the contiguous characterization for the removed species-name-and-ID quote: its check joined rendered text across HTML blocks. The distinct earlier citation-form verification remains supported by the exact inline raw HTML included in the new curation event: Taxonomy ID: 666 <small>(for references in articles please use ncbitaxon:666)</small><br>. Source: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=666&mode=Info, HTTP 200 fetch rechecked on 2026-10-03. That lowercase text is a source quotation, not an asserted CURIE. All prior events and substantive trait/proposal fields are unchanged. The writer authorizes only the exact committed preimage for this migration and tests acceptance, drift refusal and full prior-field preservation.

    • Read this curation session
  • @@ -382,7 +383,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -411,12 +421,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 16:01 UTC diff --git a/pages/traits/genomics/shosta_system.html b/pages/traits/genomics/shosta_system.html index 5b169f90d92..b969f829a4c 100644 --- a/pages/traits/genomics/shosta_system.html +++ b/pages/traits/genomics/shosta_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers ShosTA system - traitmech:000258 + traitmech:000258 METPO:2007700

    ShosTA-mediated phage restriction realizes the ShosTA system trait.

    @@ -255,7 +256,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -414,7 +415,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -778,12 +788,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 01:24 UTC diff --git a/pages/traits/genomics/sirona_system.html b/pages/traits/genomics/sirona_system.html index 3c84551b888..1894d66e770 100644 --- a/pages/traits/genomics/sirona_system.html +++ b/pages/traits/genomics/sirona_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Sirona system - traitmech:000264 + traitmech:000264 METPO:2007700

    Sirona-mediated phage restriction realizes the Sirona system trait.

    @@ -239,7 +240,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -410,7 +411,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -774,12 +784,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 04:32 UTC diff --git a/pages/traits/genomics/six_a_mbl_system.html b/pages/traits/genomics/six_a_mbl_system.html index cb9f7249b94..77d6d064a43 100644 --- a/pages/traits/genomics/six_a_mbl_system.html +++ b/pages/traits/genomics/six_a_mbl_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers 6A-MBL system - traitmech:000314 + traitmech:000314 METPO:2007700

    6A-MBL-mediated phage restriction realizes the 6A-MBL system trait.

    @@ -261,7 +262,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -432,7 +433,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -796,12 +806,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 17:16 UTC diff --git a/pages/traits/genomics/snipe_system.html b/pages/traits/genomics/snipe_system.html index 7658ce5112a..b299fd810f6 100644 --- a/pages/traits/genomics/snipe_system.html +++ b/pages/traits/genomics/snipe_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -174,7 +175,7 @@

    Edge evidence

    confers SNIPE system - traitmech:000414 + traitmech:000414 METPO:2007700

    Direct cleavage of injected phage DNA realizes the SNIPE system trait.

      @@ -190,11 +191,11 @@

      Edge evidence

    • SNIPE system - traitmech:000414 + traitmech:000414 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      SNIPE system possession is a phage-defense-system trait.

        @@ -259,7 +260,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -275,7 +276,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -473,7 +474,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -837,12 +847,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 18:24 UTC diff --git a/pages/traits/genomics/sofic_system.html b/pages/traits/genomics/sofic_system.html index d065fc28c92..bb6b9942ed7 100644 --- a/pages/traits/genomics/sofic_system.html +++ b/pages/traits/genomics/sofic_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers SoFIC system - traitmech:000260 + traitmech:000260 METPO:2007700

    SoFIC-mediated phage restriction realizes the SoFIC system trait.

    @@ -249,7 +250,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -408,7 +409,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -772,12 +782,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 02:18 UTC diff --git a/pages/traits/genomics/sparta_system.html b/pages/traits/genomics/sparta_system.html index d1a3f155eb7..0e099fd4429 100644 --- a/pages/traits/genomics/sparta_system.html +++ b/pages/traits/genomics/sparta_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -231,7 +232,7 @@

    Edge evidence

    confers SPARTA system - traitmech:000240 + traitmech:000240 METPO:2007700

    Removal of plasmid-invaded cells is the cellular outcome of the SPARTA possession trait.

      @@ -291,7 +292,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • short prokaryotic Argonaute TIR-APAZ system EXACT_SYNONYM · DOI:10.1016/j.cell.2022.03.012
        • +
      • short prokaryotic Argonaute TIR-APAZ system EXACT_SYNONYM · DOI:10.1016/j.cell.2022.03.012
    @@ -307,7 +308,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -479,7 +480,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -843,12 +853,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 22:12 UTC diff --git a/pages/traits/genomics/spbk_system.html b/pages/traits/genomics/spbk_system.html index 757836b8ee9..013fee087c3 100644 --- a/pages/traits/genomics/spbk_system.html +++ b/pages/traits/genomics/spbk_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers SpbK system - traitmech:000325 + traitmech:000325 METPO:2007700

    SpbK/YonE-dependent abortive infection realizes the SpbK system trait.

    @@ -242,7 +243,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -438,7 +439,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -802,12 +812,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-21 03:45 UTC diff --git a/pages/traits/genomics/sspabcd_sspe_system.html b/pages/traits/genomics/sspabcd_sspe_system.html index 30c64c7961a..c520ced4e0c 100644 --- a/pages/traits/genomics/sspabcd_sspe_system.html +++ b/pages/traits/genomics/sspabcd_sspe_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -237,7 +238,7 @@

    Edge evidence

    confers SspABCD-SspE system - traitmech:000222 + traitmech:000222 METPO:2007700

    SspE DNA nicking realizes the SspABCD-SspE antiphage defense trait.

      @@ -253,11 +254,11 @@

      Edge evidence

    • SspABCD-SspE system - traitmech:000222 + traitmech:000222 is a phosphorothioate defense system - traitmech:000213 - rdfs:subClassOf + traitmech:000213 + rdfs:subClassOf

      SspABCD-SspE possession is a phosphorothioate-defense-system trait.

        @@ -316,7 +317,7 @@

        Parent traits (1)

        Synonyms (1)

          -
        • SspABCD-SspE PT system EXACT_SYNONYM · DOI:10.1038/s41564-020-0700-6
          • +
        • SspABCD-SspE PT system EXACT_SYNONYM · DOI:10.1038/s41564-020-0700-6
    @@ -332,7 +333,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -479,7 +480,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -843,12 +853,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 16:38 UTC diff --git a/pages/traits/genomics/sspabcd_sspfgh_system.html b/pages/traits/genomics/sspabcd_sspfgh_system.html index 99cefe5b64c..eee23a20c0e 100644 --- a/pages/traits/genomics/sspabcd_sspfgh_system.html +++ b/pages/traits/genomics/sspabcd_sspfgh_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -218,7 +219,7 @@

    Edge evidence

    confers SspABCD-SspFGH system - traitmech:000223 + traitmech:000223 METPO:2007700

    SspFGH-dependent non-PT DNA damage realizes the SspABCD-SspFGH antiphage defense trait.

      @@ -234,11 +235,11 @@

      Edge evidence

    • SspABCD-SspFGH system - traitmech:000223 + traitmech:000223 is a phosphorothioate defense system - traitmech:000213 - rdfs:subClassOf + traitmech:000213 + rdfs:subClassOf

      SspABCD-SspFGH possession is a phosphorothioate-defense-system trait.

        @@ -297,7 +298,7 @@

        Parent traits (1)

        Synonyms (1)

          -
        • SspABCD-SspFGH defense system EXACT_SYNONYM · DOI:10.1128/mbio.00613-21
          • +
        • SspABCD-SspFGH defense system EXACT_SYNONYM · DOI:10.1128/mbio.00613-21
    @@ -313,7 +314,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -460,7 +461,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -824,12 +834,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 17:06 UTC diff --git a/pages/traits/genomics/stk2_system.html b/pages/traits/genomics/stk2_system.html index 1c71845a966..4a6fdd831ab 100644 --- a/pages/traits/genomics/stk2_system.html +++ b/pages/traits/genomics/stk2_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -223,7 +224,7 @@

    Edge evidence

    confers Stk2 system - traitmech:000303 + traitmech:000303 METPO:2007700

    Stk2-triggered host-cell death realizes the Stk2 abortive-infection trait.

    @@ -324,7 +325,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -483,7 +484,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -847,12 +857,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-20 07:43 UTC diff --git a/pages/traits/genomics/sucellos_system.html b/pages/traits/genomics/sucellos_system.html index a50d760759b..0189085b8cf 100644 --- a/pages/traits/genomics/sucellos_system.html +++ b/pages/traits/genomics/sucellos_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers Sucellos system - traitmech:000266 + traitmech:000266 METPO:2007700

    Sucellos-mediated phage restriction realizes the Sucellos system trait.

    @@ -247,7 +248,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -406,7 +407,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -770,12 +780,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 05:34 UTC diff --git a/pages/traits/genomics/tab_system.html b/pages/traits/genomics/tab_system.html index 8b15912dcbb..2633d69e85d 100644 --- a/pages/traits/genomics/tab_system.html +++ b/pages/traits/genomics/tab_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -79,7 +80,7 @@

    Trait evidence (5)

    https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    | Tab | 10\.1038/s41467-024-45892-x | Anti-phage defence through inhibition of virion assembly |
    -

    The pinned DefenseFinder article registry maps the named Tab system to the Patel et al. virion-assembly-inhibition paper. The pinned HMM inventory (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md) and pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) do not list Tab, so this row is name-to-paper evidence rather than model-component evidence.

    +

    The pinned DefenseFinder article registry maps the named Tab system to the Patel et al. virion-assembly-inhibition paper. The pinned HMM inventory (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md) and pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) do not list Tab, so this row is name-to-paper evidence rather than model-component evidence.

    @@ -174,7 +175,7 @@

    Edge evidence

    confers Tab system - traitmech:000413 + traitmech:000413 METPO:2007700

    Virion assembly inhibition realizes the Tab system trait.

      @@ -190,11 +191,11 @@

      Edge evidence

    • Tab system - traitmech:000413 + traitmech:000413 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Tab system possession is a phage-defense-system trait.

        @@ -253,7 +254,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -269,7 +270,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -461,7 +462,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -825,12 +835,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 17:41 UTC diff --git a/pages/traits/genomics/tagi_system.html b/pages/traits/genomics/tagi_system.html index f445e8ab88e..c338146ebf2 100644 --- a/pages/traits/genomics/tagi_system.html +++ b/pages/traits/genomics/tagi_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -185,7 +186,7 @@

    Edge evidence

    confers TagI system - traitmech:000513 + traitmech:000513 METPO:2007700

    TagI-family modified-cytosine DNA restriction realizes the organism-level TagI system possession trait.

    @@ -292,7 +293,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -518,7 +519,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -882,12 +892,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 11:10 UTC diff --git a/pages/traits/genomics/taranis_system.html b/pages/traits/genomics/taranis_system.html index 215775bf385..617b7d55e22 100644 --- a/pages/traits/genomics/taranis_system.html +++ b/pages/traits/genomics/taranis_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Taranis system - traitmech:000265 + traitmech:000265 METPO:2007700

    Taranis-mediated phage restriction realizes the Taranis system trait.

    @@ -233,7 +234,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -392,7 +393,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -756,12 +766,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 05:03 UTC diff --git a/pages/traits/genomics/tgvab_system.html b/pages/traits/genomics/tgvab_system.html index 9461b4df5e4..e07a0238c9a 100644 --- a/pages/traits/genomics/tgvab_system.html +++ b/pages/traits/genomics/tgvab_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -79,7 +80,7 @@

    Trait evidence (7)

    https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    | TgvAB | 10\.1128/jb\.00145-24 | Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems |
    -

    The pinned DefenseFinder article registry maps the named TgvAB system to the Vizzarro et al. VPI-2 restriction-systems paper. The pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) does not list TgvAB, so the registry and HMM rows support a named system-possession trait rather than complete DefenseFinder detection criteria.

    +

    The pinned DefenseFinder article registry maps the named TgvAB system to the Vizzarro et al. VPI-2 restriction-systems paper. The pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) does not list TgvAB, so the registry and HMM rows support a named system-possession trait rather than complete DefenseFinder detection criteria.

  • @@ -149,7 +150,7 @@

    Edge evidence

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | TgvAB | 10\.1128/jb\.00145-24 | Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems | - The pinned DefenseFinder article registry maps the named TgvAB system to the Vizzarro et al. VPI-2 restriction-systems paper. The pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) does not list TgvAB, so the registry and HMM rows support a named system-possession trait rather than complete DefenseFinder detection criteria. + The pinned DefenseFinder article registry maps the named TgvAB system to the Vizzarro et al. VPI-2 restriction-systems paper. The pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) does not list TgvAB, so the registry and HMM rows support a named system-possession trait rather than complete DefenseFinder detection criteria.
  • @@ -216,7 +217,7 @@

    Edge evidence

    confers TgvAB system - traitmech:000412 + traitmech:000412 METPO:2007700

    TgvAB-dependent type IV restriction realizes the TgvAB system trait.

    @@ -244,11 +245,11 @@

    Edge evidence

  • TgvAB system - traitmech:000412 + traitmech:000412 is a restriction-modification system - traitmech:000095 - rdfs:subClassOf + traitmech:000095 + rdfs:subClassOf

    TgvAB is a GmrSD-related type IV restriction system in the broader restriction-modification family.

    • @@ -327,7 +328,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -526,7 +527,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -890,12 +900,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-27 16:50 UTC diff --git a/pages/traits/genomics/tha_system.html b/pages/traits/genomics/tha_system.html index ce7a010d5a8..dc6144cfe44 100644 --- a/pages/traits/genomics/tha_system.html +++ b/pages/traits/genomics/tha_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -167,7 +168,7 @@

    Edge evidence

    confers Tha system - traitmech:000497 + traitmech:000497 METPO:2007700

    Tha-mediated nonspecific RNase activity realizes the Tha system trait.

    @@ -266,7 +267,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -489,7 +490,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -853,12 +863,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 17:22 UTC diff --git a/pages/traits/genomics/thoeris_system.html b/pages/traits/genomics/thoeris_system.html index 44027a9af14..d54cb97de38 100644 --- a/pages/traits/genomics/thoeris_system.html +++ b/pages/traits/genomics/thoeris_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -193,7 +194,7 @@

    Edge evidence

    confers Thoeris system - traitmech:000216 + traitmech:000216 METPO:2007700

    ThsA NAD depletion is the antiviral output that realizes the Thoeris system defense phenotype.

      @@ -209,11 +210,11 @@

      Edge evidence

    • Thoeris system - traitmech:000216 + traitmech:000216 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Thoeris system possession is a phage-defense-system trait.

        @@ -272,9 +273,9 @@

        Parent traits (1)

        Synonyms (2)

    @@ -290,7 +291,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -475,7 +476,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -839,12 +849,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 13:12 UTC diff --git a/pages/traits/genomics/tiamat_system.html b/pages/traits/genomics/tiamat_system.html index f740e80dac8..dd8cb4de3ec 100644 --- a/pages/traits/genomics/tiamat_system.html +++ b/pages/traits/genomics/tiamat_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers Tiamat system - traitmech:000261 + traitmech:000261 METPO:2007700

    Tiamat-mediated phage restriction realizes the Tiamat system trait.

    @@ -249,7 +250,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -408,7 +409,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -772,12 +782,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 02:45 UTC diff --git a/pages/traits/genomics/tir_i_system.html b/pages/traits/genomics/tir_i_system.html index 00d97816201..2f4613522d4 100644 --- a/pages/traits/genomics/tir_i_system.html +++ b/pages/traits/genomics/tir_i_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -144,7 +145,7 @@

    Edge evidence

    confers TIR-I system - traitmech:000480 + traitmech:000480 METPO:2007700

    TIR-I-mediated inhibition of bacteriophage plaquing realizes the TIR-I system trait.

    @@ -243,7 +244,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -442,7 +443,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -806,12 +816,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 02:42 UTC diff --git a/pages/traits/genomics/tir_iii_system.html b/pages/traits/genomics/tir_iii_system.html index e8ec335e581..7715b666bd1 100644 --- a/pages/traits/genomics/tir_iii_system.html +++ b/pages/traits/genomics/tir_iii_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -144,7 +145,7 @@

    Edge evidence

    confers TIR-III system - traitmech:000481 + traitmech:000481 METPO:2007700

    TIR-III-mediated inhibition of bacteriophage plaquing realizes the TIR-III system trait.

    @@ -243,7 +244,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -442,7 +443,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -806,12 +816,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 03:32 UTC diff --git a/pages/traits/genomics/tir_iv_system.html b/pages/traits/genomics/tir_iv_system.html index 765d7df56a4..e1cfdd4cfac 100644 --- a/pages/traits/genomics/tir_iv_system.html +++ b/pages/traits/genomics/tir_iv_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -144,7 +145,7 @@

    Edge evidence

    confers TIR-IV system - traitmech:000482 + traitmech:000482 METPO:2007700

    TIR-IV-mediated inhibition of bacteriophage plaquing realizes the TIR-IV system trait.

    @@ -243,7 +244,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -442,7 +443,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -806,12 +816,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 04:30 UTC diff --git a/pages/traits/genomics/tir_vii_system.html b/pages/traits/genomics/tir_vii_system.html index d89a05b22c9..35c73fe634e 100644 --- a/pages/traits/genomics/tir_vii_system.html +++ b/pages/traits/genomics/tir_vii_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -144,7 +145,7 @@

    Edge evidence

    confers TIR-VII system - traitmech:000483 + traitmech:000483 METPO:2007700

    TIR-VII-mediated inhibition of bacteriophage plaquing realizes the TIR-VII system trait.

    @@ -243,7 +244,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -442,7 +443,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -806,12 +816,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 05:13 UTC diff --git a/pages/traits/genomics/tir_viii_system.html b/pages/traits/genomics/tir_viii_system.html index e5257a3ffda..6f84a6d18c9 100644 --- a/pages/traits/genomics/tir_viii_system.html +++ b/pages/traits/genomics/tir_viii_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -144,7 +145,7 @@

    Edge evidence

    confers TIR-VIII system - traitmech:000484 + traitmech:000484 METPO:2007700

    TIR-VIII-mediated inhibition of bacteriophage plaquing realizes the TIR-VIII system trait.

    @@ -243,7 +244,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -442,7 +443,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -806,12 +816,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 06:05 UTC diff --git a/pages/traits/genomics/toga_system.html b/pages/traits/genomics/toga_system.html index 20c1e3a9cbb..62262c1316d 100644 --- a/pages/traits/genomics/toga_system.html +++ b/pages/traits/genomics/toga_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -136,7 +137,7 @@

    Edge evidence

    confers Toga system - traitmech:000498 + traitmech:000498 METPO:2007700

    Toga-mediated phage protection realizes the Toga system trait.

      @@ -152,11 +153,11 @@

      Edge evidence

    • Toga system - traitmech:000498 + traitmech:000498 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Toga system possession is a phage-defense-system trait.

        @@ -215,7 +216,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -231,7 +232,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -429,7 +430,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -793,12 +803,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 18:12 UTC diff --git a/pages/traits/genomics/toutatis_system.html b/pages/traits/genomics/toutatis_system.html index c516cac58f7..2cd923fb63f 100644 --- a/pages/traits/genomics/toutatis_system.html +++ b/pages/traits/genomics/toutatis_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers Toutatis system - traitmech:000267 + traitmech:000267 METPO:2007700

    Toutatis-mediated phage restriction realizes the Toutatis system trait.

    @@ -247,7 +248,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -406,7 +407,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -770,12 +780,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 06:06 UTC diff --git a/pages/traits/genomics/toxin_system.html b/pages/traits/genomics/toxin_system.html index ab9e8d209f1..2514b10ff5b 100644 --- a/pages/traits/genomics/toxin_system.html +++ b/pages/traits/genomics/toxin_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -192,7 +193,7 @@

    Edge evidence

    confers ToxIN system - traitmech:000226 + traitmech:000226 METPO:2007700

    Restriction of phage propagation realizes the ToxIN abortive-infection defense trait.

      @@ -208,11 +209,11 @@

      Edge evidence

    • ToxIN system - traitmech:000226 + traitmech:000226 is a abortive infection system - traitmech:000214 - rdfs:subClassOf + traitmech:000214 + rdfs:subClassOf

      ToxIN system possession is an abortive-infection-system trait.

        @@ -278,7 +279,7 @@

        kg-microbe context

        via parent_proxy.

          -
        • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
          • +
        • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

        512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

        @@ -425,7 +426,16 @@

        Identifier

        Term kind
        CLASS
        Status
        -
        PROPOSED
        +
        PROPOSED + + +
        + What this status means +

        Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

        +

        Quoted from the schema's status definitions.

        +
        + +
    @@ -789,12 +799,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 19:25 UTC diff --git a/pages/traits/genomics/transposable_element.html b/pages/traits/genomics/transposable_element.html index 209de899376..61215d325a4 100644 --- a/pages/traits/genomics/transposable_element.html +++ b/pages/traits/genomics/transposable_element.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • transposable element - traitmech:000092 + traitmech:000092 enables DNA transposition GO:0006313 @@ -134,7 +135,7 @@

    Edge evidence

  • transposable element - traitmech:000092 + traitmech:000092 has participant transposase GO:0004803 @@ -273,9 +274,9 @@

    Parent traits (1)

    Synonyms (2)

    • @@ -291,7 +292,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -564,7 +565,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -928,12 +938,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/genomics/type_i_restriction_modification_system.html b/pages/traits/genomics/type_i_restriction_modification_system.html index 323d60cd6af..92c9c32f482 100644 --- a/pages/traits/genomics/type_i_restriction_modification_system.html +++ b/pages/traits/genomics/type_i_restriction_modification_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -154,7 +155,7 @@

    Edge evidence

    confers type I restriction-modification system - traitmech:000494 + traitmech:000494 METPO:2007700

    Type I restriction-modification activity realizes the organism-level Type I R-M system trait.

    @@ -279,7 +280,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -491,7 +492,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -855,12 +865,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 14:49 UTC diff --git a/pages/traits/genomics/type_ii_restriction_modification_system.html b/pages/traits/genomics/type_ii_restriction_modification_system.html index c97de66b989..84f85c1acca 100644 --- a/pages/traits/genomics/type_ii_restriction_modification_system.html +++ b/pages/traits/genomics/type_ii_restriction_modification_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -160,7 +161,7 @@

    Edge evidence

    confers type II restriction-modification system - traitmech:000493 + traitmech:000493 METPO:2007700

    Type II restriction-modification activity realizes the organism-level Type II R-M system trait.

    @@ -286,7 +287,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -491,7 +492,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -855,12 +865,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 13:45 UTC diff --git a/pages/traits/genomics/type_iig_restriction_modification_system.html b/pages/traits/genomics/type_iig_restriction_modification_system.html index b7649941a3f..9fe49b69742 100644 --- a/pages/traits/genomics/type_iig_restriction_modification_system.html +++ b/pages/traits/genomics/type_iig_restriction_modification_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -173,7 +174,7 @@

    Edge evidence

    confers type IIG restriction-modification system - traitmech:000375 + traitmech:000375 METPO:2007700

    Type IIG restriction-modification activity realizes the organism-level Type IIG R-M system trait.

    @@ -301,7 +302,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -518,7 +519,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -882,12 +892,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 13:45 UTC diff --git a/pages/traits/genomics/type_iii_restriction_modification_system.html b/pages/traits/genomics/type_iii_restriction_modification_system.html index 2663d267821..cf232da371d 100644 --- a/pages/traits/genomics/type_iii_restriction_modification_system.html +++ b/pages/traits/genomics/type_iii_restriction_modification_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -156,7 +157,7 @@

    Edge evidence

    confers type III restriction-modification system - traitmech:000495 + traitmech:000495 METPO:2007700

    Type III restriction-modification activity realizes the organism-level Type III R-M system trait.

    @@ -275,7 +276,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -482,7 +483,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -846,12 +856,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 15:32 UTC diff --git a/pages/traits/genomics/type_iv_modification_dependent_restriction_system.html b/pages/traits/genomics/type_iv_modification_dependent_restriction_system.html index 0d1b102ddd0..8520121ec36 100644 --- a/pages/traits/genomics/type_iv_modification_dependent_restriction_system.html +++ b/pages/traits/genomics/type_iv_modification_dependent_restriction_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -211,7 +212,7 @@

    Edge evidence

    confers type IV modification-dependent restriction system - traitmech:000496 + traitmech:000496 METPO:2007700

    Type IV modification-dependent restriction realizes the organism-level Type IV system-possession trait.

    @@ -364,7 +365,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -673,7 +674,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1037,12 +1047,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 11:48 UTC diff --git a/pages/traits/genomics/ukko_system.html b/pages/traits/genomics/ukko_system.html index c174824a3ec..e81e53d1e74 100644 --- a/pages/traits/genomics/ukko_system.html +++ b/pages/traits/genomics/ukko_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -226,7 +227,7 @@

    Edge evidence

    confers Ukko system - traitmech:000292 + traitmech:000292 METPO:2007700

    Ukko-mediated phage restriction realizes the Ukko system trait.

    @@ -343,7 +344,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -502,7 +503,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -866,12 +876,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 20:28 UTC diff --git a/pages/traits/genomics/uzume_system.html b/pages/traits/genomics/uzume_system.html index b2bd0a596e0..1423dc52347 100644 --- a/pages/traits/genomics/uzume_system.html +++ b/pages/traits/genomics/uzume_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -148,7 +149,7 @@

    Edge evidence

    confers Uzume system - traitmech:000262 + traitmech:000262 METPO:2007700

    Uzume-mediated phage restriction realizes the Uzume system trait.

    @@ -249,7 +250,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -408,7 +409,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -772,12 +782,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 03:15 UTC diff --git a/pages/traits/genomics/vcam4i_system.html b/pages/traits/genomics/vcam4i_system.html index d5e18f00063..211e363a077 100644 --- a/pages/traits/genomics/vcam4i_system.html +++ b/pages/traits/genomics/vcam4i_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -179,7 +180,7 @@

    Edge evidence

    confers VcaM4I system - traitmech:000514 + traitmech:000514 METPO:2007700

    VcaM4I-family EVE-HNH DNA restriction realizes the organism-level VcaM4I system possession trait.

    @@ -280,7 +281,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -499,7 +500,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -863,12 +873,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 11:48 UTC diff --git a/pages/traits/genomics/veles_system.html b/pages/traits/genomics/veles_system.html index f846ff648a5..efa1ce7ba10 100644 --- a/pages/traits/genomics/veles_system.html +++ b/pages/traits/genomics/veles_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -202,7 +203,7 @@

    Edge evidence

    confers Veles system - traitmech:000289 + traitmech:000289 METPO:2007700

    Veles-mediated phage restriction realizes the Veles system trait.

    @@ -315,7 +316,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -474,7 +475,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -838,12 +848,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 18:45 UTC diff --git a/pages/traits/genomics/viperin_system.html b/pages/traits/genomics/viperin_system.html index 9112eafedec..57203594f44 100644 --- a/pages/traits/genomics/viperin_system.html +++ b/pages/traits/genomics/viperin_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -161,7 +162,7 @@

    Edge evidence

    confers Viperin system - traitmech:000263 + traitmech:000263 METPO:2007700

    Inhibition of phage transcription is a source-backed antiviral output that realizes the Viperin system trait.

    @@ -258,7 +259,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -441,7 +442,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -805,12 +815,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-19 04:06 UTC diff --git a/pages/traits/genomics/vp1796_system.html b/pages/traits/genomics/vp1796_system.html index a38de27f1bf..4b4e34ac86b 100644 --- a/pages/traits/genomics/vp1796_system.html +++ b/pages/traits/genomics/vp1796_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -198,7 +199,7 @@

    Edge evidence

    confers VP1796 system - traitmech:000486 + traitmech:000486 METPO:2007700

    VP1796-mediated bacteriophage plaquing reduction realizes the VP1796 system trait.

    @@ -309,7 +310,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -543,7 +544,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -907,12 +917,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 07:49 UTC diff --git a/pages/traits/genomics/vp1817_system.html b/pages/traits/genomics/vp1817_system.html index 5959bf0ee7f..23488ecf6f2 100644 --- a/pages/traits/genomics/vp1817_system.html +++ b/pages/traits/genomics/vp1817_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -198,7 +199,7 @@

    Edge evidence

    confers VP1817 system - traitmech:000487 + traitmech:000487 METPO:2007700

    VP1817-mediated bacteriophage plaquing reduction realizes the VP1817 system trait.

    @@ -307,7 +308,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -548,7 +549,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -912,12 +922,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 08:44 UTC diff --git a/pages/traits/genomics/vp1823_system.html b/pages/traits/genomics/vp1823_system.html index 648590b93bf..1adce6e4cb3 100644 --- a/pages/traits/genomics/vp1823_system.html +++ b/pages/traits/genomics/vp1823_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -198,7 +199,7 @@

    Edge evidence

    confers VP1823 system - traitmech:000485 + traitmech:000485 METPO:2007700

    VP1823-mediated bacteriophage plaquing reduction realizes the VP1823 system trait.

    @@ -307,7 +308,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -541,7 +542,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -905,12 +915,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 06:59 UTC diff --git a/pages/traits/genomics/vp1826_system.html b/pages/traits/genomics/vp1826_system.html index c287422919b..9a3bbbfd105 100644 --- a/pages/traits/genomics/vp1826_system.html +++ b/pages/traits/genomics/vp1826_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -210,7 +211,7 @@

    Edge evidence

    confers VP1826 system - traitmech:000488 + traitmech:000488 METPO:2007700

    VP1826-mediated bacteriophage plaquing reduction realizes the VP1826 system trait.

    @@ -327,7 +328,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -575,7 +576,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -939,12 +949,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 09:52 UTC diff --git a/pages/traits/genomics/vp1839_system.html b/pages/traits/genomics/vp1839_system.html index 97ccf91a001..b213e3a5ce5 100644 --- a/pages/traits/genomics/vp1839_system.html +++ b/pages/traits/genomics/vp1839_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -210,7 +211,7 @@

    Edge evidence

    confers VP1839 system - traitmech:000489 + traitmech:000489 METPO:2007700

    VP1839-mediated bacteriophage plaquing reduction realizes the VP1839 system trait.

    @@ -327,7 +328,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -575,7 +576,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -939,12 +949,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 10:38 UTC diff --git a/pages/traits/genomics/vp1840_system.html b/pages/traits/genomics/vp1840_system.html index b4f98029444..d8a47fd9886 100644 --- a/pages/traits/genomics/vp1840_system.html +++ b/pages/traits/genomics/vp1840_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -198,7 +199,7 @@

    Edge evidence

    confers VP1840 system - traitmech:000450 + traitmech:000450 METPO:2007700

    VP1840-mediated bacteriophage plaquing reduction realizes the VP1840 system trait.

    @@ -309,7 +310,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -567,7 +568,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -931,12 +941,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-29 03:45 UTC diff --git a/pages/traits/genomics/vp1848_system.html b/pages/traits/genomics/vp1848_system.html index d01243d3978..d0cf087b9dc 100644 --- a/pages/traits/genomics/vp1848_system.html +++ b/pages/traits/genomics/vp1848_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -198,7 +199,7 @@

    Edge evidence

    confers VP1848 system - traitmech:000490 + traitmech:000490 METPO:2007700

    VP1848-mediated bacteriophage plaquing reduction realizes the VP1848 system trait.

    @@ -309,7 +310,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -550,7 +551,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -914,12 +924,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 11:32 UTC diff --git a/pages/traits/genomics/vp1851_system.html b/pages/traits/genomics/vp1851_system.html index a51f38bd499..e766cd3fe6f 100644 --- a/pages/traits/genomics/vp1851_system.html +++ b/pages/traits/genomics/vp1851_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -200,7 +201,7 @@

    Edge evidence

    confers VP1851 system - traitmech:000491 + traitmech:000491 METPO:2007700

    VP1851-mediated bacteriophage plaquing reduction realizes the VP1851 system trait.

    @@ -311,7 +312,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -553,7 +554,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -917,12 +927,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 12:17 UTC diff --git a/pages/traits/genomics/vp1853_system.html b/pages/traits/genomics/vp1853_system.html index 74951f2e6c1..e464570e5d9 100644 --- a/pages/traits/genomics/vp1853_system.html +++ b/pages/traits/genomics/vp1853_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -188,7 +189,7 @@

    Edge evidence

    confers VP1853 system - traitmech:000492 + traitmech:000492 METPO:2007700

    VP1853-mediated bacteriophage plaquing reduction realizes the VP1853 system trait.

    @@ -293,7 +294,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -528,7 +529,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -892,12 +902,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-30 12:58 UTC diff --git a/pages/traits/genomics/wadjet_system.html b/pages/traits/genomics/wadjet_system.html index 4b95c888073..2ba5a6f52ba 100644 --- a/pages/traits/genomics/wadjet_system.html +++ b/pages/traits/genomics/wadjet_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -186,7 +187,7 @@

    Edge evidence

    confers Wadjet system - traitmech:000218 + traitmech:000218 METPO:2007700

    Wadjet nuclease-mediated plasmid DNA cleavage is the anti-plasmid output that realizes the Wadjet system trait.

      @@ -255,7 +256,7 @@

      Children (1)

      Synonyms (1)

    @@ -271,7 +272,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -462,7 +463,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -826,12 +836,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 21:15 UTC diff --git a/pages/traits/genomics/zorya_system.html b/pages/traits/genomics/zorya_system.html index cb2991efaff..65cf38c0de2 100644 --- a/pages/traits/genomics/zorya_system.html +++ b/pages/traits/genomics/zorya_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -205,7 +206,7 @@

    Edge evidence

    confers Zorya system - traitmech:000217 + traitmech:000217 METPO:2007700

    Zorya effector activity is the antiviral output that realizes the Zorya system defense phenotype.

      @@ -221,11 +222,11 @@

      Edge evidence

    • Zorya system - traitmech:000217 + traitmech:000217 is a phage defense system - traitmech:000209 - rdfs:subClassOf + traitmech:000209 + rdfs:subClassOf

      Zorya system possession is a phage-defense-system trait.

        @@ -297,9 +298,9 @@

        Children (3)

        Synonyms (2)

          -
        • Zorya anti-phage defence system EXACT_SYNONYM · DOI:10.1038/s41586-024-08493-8
          • +
        • Zorya anti-phage defence system EXACT_SYNONYM · DOI:10.1038/s41586-024-08493-8
          • -
        • Zorya phage defense system EXACT_SYNONYM · DOI:10.1038/s41467-025-57397-2
          • +
        • Zorya phage defense system EXACT_SYNONYM · DOI:10.1038/s41467-025-57397-2
    @@ -315,7 +316,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -476,7 +477,7 @@

    Curation history

  • · TRACK_ZORYA_TYPE_III_CLASS · codex -

    Linked traitmech:000576 using DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57397-2. Kept the family definition, hierarchy, graph, evidence and example unchanged; type-III component functions remain open rather than inheriting type-I/II chemistry.

    +

    Linked traitmech:000576 using DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57397-2. Kept the family definition, hierarchy, graph, evidence and example unchanged; type-III component functions remain open rather than inheriting type-I/II chemistry.

    • @@ -504,7 +505,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Link accepted Zorya type III architecture -

      Appended the accepted traitmech:000576 ZorA/B/F/G class to the existing open subtype discussion using DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57397-2. Recorded the source component discrepancy and incomplete detector-call caveat. Preserved family identity, definition, hierarchy, evidence, canonical example and graph; type-III biochemical questions remain open. The guarded writer uses preimage hashes, validated writes and provenance events; controlled-fixture tests passed.

    +

    Appended the accepted traitmech:000576 ZorA/B/F/G class to the existing open subtype discussion using DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57397-2. Recorded the source component discrepancy and incomplete detector-call caveat. Preserved family identity, definition, hierarchy, evidence, canonical example and graph; type-III biochemical questions remain open. The guarded writer uses preimage hashes, validated writes and provenance events; controlled-fixture tests passed.

    • Read this curation session @@ -536,7 +537,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -900,12 +910,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 19:16 UTC diff --git a/pages/traits/genomics/zorya_type_i_system.html b/pages/traits/genomics/zorya_type_i_system.html index 9f8cdd47b07..c35ce952f18 100644 --- a/pages/traits/genomics/zorya_type_i_system.html +++ b/pages/traits/genomics/zorya_type_i_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -180,7 +181,7 @@

    Edge evidence

    confers Zorya type I system - traitmech:000554 + traitmech:000554 METPO:2007700

    The first-pass Zorya type I system trait is realized by a DefenseFinder Zorya_TypeI subtype locus.

    @@ -301,7 +302,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -512,7 +513,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -876,12 +886,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 20:14 UTC diff --git a/pages/traits/genomics/zorya_type_ii_system.html b/pages/traits/genomics/zorya_type_ii_system.html index d63c843fbfc..754d84cd28c 100644 --- a/pages/traits/genomics/zorya_type_ii_system.html +++ b/pages/traits/genomics/zorya_type_ii_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -156,7 +157,7 @@

    Edge evidence

    confers Zorya type II system - traitmech:000552 + traitmech:000552 METPO:2007700

    The first-pass Zorya type II system trait is realized by a DefenseFinder Zorya_TypeII subtype locus.

    @@ -263,7 +264,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -473,7 +474,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -837,12 +847,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-02 18:08 UTC diff --git a/pages/traits/genomics/zorya_type_iii_system.html b/pages/traits/genomics/zorya_type_iii_system.html index 595c57c3e8f..f436b6bcc39 100644 --- a/pages/traits/genomics/zorya_type_iii_system.html +++ b/pages/traits/genomics/zorya_type_iii_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -122,7 +123,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Zorya type III EXACT_SYNONYM · DOI:10.1093/nar/gkab883
      • +
    • Zorya type III EXACT_SYNONYM · DOI:10.1093/nar/gkab883
    @@ -138,7 +139,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
      • +
    • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -291,7 +292,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add Zorya type III possession class -

      Added traitmech:000576 under traitmech:000217 from DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57397-2, with four directly matched snippets, pinned PADLOC/DefenseFinder executable rules and NCBI-resolved DSM 12575 source evidence at NZ_LDJG01000021.1. Resolved the original Results component discrepancy using its figure and Discussion plus the later paper. Kept three-match detector thresholds, four-component architecture, natural source and BL21-AI assays distinct. Reserved METPO:1053000 in v453; mechanism remains open. Focused writer tests passed.

    +

    Added traitmech:000576 under traitmech:000217 from DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57397-2, with four directly matched snippets, pinned PADLOC/DefenseFinder executable rules and NCBI-resolved DSM 12575 source evidence at NZ_LDJG01000021.1. Resolved the original Results component discrepancy using its figure and Discussion plus the later paper. Kept three-match detector thresholds, four-component architecture, natural source and BL21-AI assays distinct. Reserved METPO:1053000 in v453; mechanism remains open. Focused writer tests passed.

    • Read this curation session @@ -323,7 +324,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -352,12 +362,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 19:16 UTC diff --git a/pages/traits/metabolism/accumulates.html b/pages/traits/metabolism/accumulates.html index c6d305a23ee..9752c29253b 100644 --- a/pages/traits/metabolism/accumulates.html +++ b/pages/traits/metabolism/accumulates.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -243,7 +244,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -272,12 +282,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/acetoclastic_methanogenesis.html b/pages/traits/metabolism/acetoclastic_methanogenesis.html index 176a2bbeacc..c420188d913 100644 --- a/pages/traits/metabolism/acetoclastic_methanogenesis.html +++ b/pages/traits/metabolism/acetoclastic_methanogenesis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • methanogenesis using acetate RELATED_SYNONYM · DOI:10.3389/fmicb.2017.01198
      • +
    • methanogenesis using acetate RELATED_SYNONYM · DOI:10.3389/fmicb.2017.01198
    @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -247,7 +248,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two broad overview snippets (DOI:10.1007/s00253-023-12700-3, DOI:10.3389/fmicb.2017.01198) stating that acetoclastic methanogens split acetate to CH4 and CO2, without enzymatic step quotes or a cited canonical example.

    +

    The current record carries two broad overview snippets (DOI:10.1007/s00253-023-12700-3, DOI:10.3389/fmicb.2017.01198) stating that acetoclastic methanogens split acetate to CH4 and CO2, without enzymatic step quotes or a cited canonical example.

    @@ -297,7 +298,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add acetoclastic methanogenesis trait -

      Minted traitmech:000191 for the acetoclastic methanogenesis metabolism trait with DOI-backed acetate-splitting evidence from 10.1007/s00253-023-12700-3 and 10.3389/fmicb.2017.01198, recorded the open exact-xref boundary, and reserved METPO:1014500 in proposals/metpo_traitmech_v68.

    +

    Minted traitmech:000191 for the acetoclastic methanogenesis metabolism trait with DOI-backed acetate-splitting evidence from 10.1007/s00253-023-12700-3 and 10.3389/fmicb.2017.01198, recorded the open exact-xref boundary, and reserved METPO:1014500 in proposals/metpo_traitmech_v68.

    • Read this curation session @@ -329,7 +330,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -358,12 +368,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/metabolism/acetogenesis.html b/pages/traits/metabolism/acetogenesis.html index 65266071910..a4b277551b5 100644 --- a/pages/traits/metabolism/acetogenesis.html +++ b/pages/traits/metabolism/acetogenesis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -436,8 +437,8 @@

    Protein and taxon examples

    		 - Neomoorella thermoacetica -
    NCBITaxon:1525 + Neomoorella thermoacetica +
    NCBITaxon:1525         		REVIEWED
    @@ -503,7 +504,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Acetate fermentation RELATED_SYNONYM · metpo.owl
      • +
    • Acetate fermentation RELATED_SYNONYM · metpo.owl
    @@ -519,7 +520,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -843,7 +844,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1207,12 +1217,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/acetone_butanol_ethanol_fermentation.html b/pages/traits/metabolism/acetone_butanol_ethanol_fermentation.html index 5103b815a56..bd3d7d4c657 100644 --- a/pages/traits/metabolism/acetone_butanol_ethanol_fermentation.html +++ b/pages/traits/metabolism/acetone_butanol_ethanol_fermentation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,9 +107,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • ABE fermentation EXACT_SYNONYM · DOI:10.1073/pnas.1423143112
      • +
    • ABE fermentation EXACT_SYNONYM · DOI:10.1073/pnas.1423143112
      • -
    • acetone-butanol fermentation RELATED_SYNONYM · DOI:10.1128/mr.50.4.484-524.1986
      • +
    • acetone-butanol fermentation RELATED_SYNONYM · DOI:10.1128/mr.50.4.484-524.1986
    @@ -124,7 +125,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -274,7 +275,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries one overview snippet on Clostridium acetobutylicum acid reassimilation (DOI:10.1073/pnas.1423143112) and one historical industrial fermentation snippet (DOI:10.1002/bit.22003), which cannot ground a multi-edge enzymatic mechanism graph without inventing unsupported edges.

    +

    The current record carries one overview snippet on Clostridium acetobutylicum acid reassimilation (DOI:10.1073/pnas.1423143112) and one historical industrial fermentation snippet (DOI:10.1002/bit.22003), which cannot ground a multi-edge enzymatic mechanism graph without inventing unsupported edges.

    @@ -356,7 +357,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -385,12 +395,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/metabolism/aerobic_respiration.html b/pages/traits/metabolism/aerobic_respiration.html index bdc0009b154..9607bfed2c6 100644 --- a/pages/traits/metabolism/aerobic_respiration.html +++ b/pages/traits/metabolism/aerobic_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -250,8 +251,8 @@

    Protein and taxon examples

    		 - Paracoccus denitrificans -
    NCBITaxon:266 + Paracoccus denitrificans +
    NCBITaxon:266         		REVIEWED
    @@ -317,9 +318,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • Oxic respiration RELATED_SYNONYM · metpo.owl
      • +
    • Oxic respiration RELATED_SYNONYM · metpo.owl
      • -
    • Oxygen respiration RELATED_SYNONYM · metpo.owl
      • +
    • Oxygen respiration RELATED_SYNONYM · metpo.owl
    @@ -342,7 +343,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -684,7 +685,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1048,12 +1058,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/anaerobic_ammonium_oxidation.html b/pages/traits/metabolism/anaerobic_ammonium_oxidation.html index 729b80e95fe..314f3d6cb62 100644 --- a/pages/traits/metabolism/anaerobic_ammonium_oxidation.html +++ b/pages/traits/metabolism/anaerobic_ammonium_oxidation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,9 +113,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • anammox EXACT_SYNONYM · DOI:10.1038/22749
      • +
    • anammox EXACT_SYNONYM · DOI:10.1038/22749
      • -
    • anaerobic ammonia oxidation RELATED_SYNONYM · DOI:10.1038/22749
      • +
    • anaerobic ammonia oxidation RELATED_SYNONYM · DOI:10.1038/22749
    @@ -130,7 +131,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -255,7 +256,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries overall stoichiometry and substrate-affinity snippets (DOI:10.1038/22749, DOI:10.1128/AEM.65.7.3248-3250.1999, DOI:10.1038/nature10453) without intermediate hydrazine-pathway enzyme quotes or a cited canonical example.

    +

    The current record carries overall stoichiometry and substrate-affinity snippets (DOI:10.1038/22749, DOI:10.1128/AEM.65.7.3248-3250.1999, DOI:10.1038/nature10453) without intermediate hydrazine-pathway enzyme quotes or a cited canonical example.

    @@ -305,7 +306,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add anaerobic ammonium oxidation trait -

      Minted traitmech:000188 for the anaerobic ammonium oxidation metabolism trait with DOI-backed ammonia-plus-nitrite-to-dinitrogen evidence from 10.1038/22749, 10.1128/AEM.65.7.3248-3250.1999, and 10.1038/nature10453; recorded the anammox exact synonym and an exact-xref gap; and reserved METPO:1014200 in proposals/metpo_traitmech_v65.

    +

    Minted traitmech:000188 for the anaerobic ammonium oxidation metabolism trait with DOI-backed ammonia-plus-nitrite-to-dinitrogen evidence from 10.1038/22749, 10.1128/AEM.65.7.3248-3250.1999, and 10.1038/nature10453; recorded the anammox exact synonym and an exact-xref gap; and reserved METPO:1014200 in proposals/metpo_traitmech_v65.

    • Read this curation session @@ -337,7 +338,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -366,12 +376,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/metabolism/anaerobic_oxidation_of_methane.html b/pages/traits/metabolism/anaerobic_oxidation_of_methane.html index 1a0c3264320..7bb1df571cb 100644 --- a/pages/traits/metabolism/anaerobic_oxidation_of_methane.html +++ b/pages/traits/metabolism/anaerobic_oxidation_of_methane.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,7 +116,7 @@

    Edge evidence

  • anaerobic oxidation of methane - traitmech:000033 + traitmech:000033 associated with methane CHEBI:16183 @@ -134,7 +135,7 @@

    Edge evidence

  • anaerobic oxidation of methane - traitmech:000033 + traitmech:000033 has core pathway reverse methanogenesis @@ -156,7 +157,7 @@

    Edge evidence

    GO:0044674 catalyzes initial step of anaerobic oxidation of methane - traitmech:000033 + traitmech:000033

    MCR activates methane as the initial step of AOM (reverse methanogenesis).

      @@ -175,7 +176,7 @@

      Edge evidence

      CHEBI:16189 serves as terminal electron acceptor for anaerobic oxidation of methane - traitmech:000033 + traitmech:000033

      Sulfate is the terminal electron acceptor in sulfate-coupled AOM.

        @@ -194,7 +195,7 @@

        Edge evidence

        confers anaerobic oxidation of methane - traitmech:000033 + traitmech:000033 METPO:2007700

        DIET via conserved ANME-to-SRB outer-membrane complexes enables sulfate-coupled AOM syntrophy.

          @@ -213,7 +214,7 @@

          Edge evidence

          CHEBI:17632 serves as terminal electron acceptor for anaerobic oxidation of methane - traitmech:000033 + traitmech:000033

          Nitrate serves as terminal electron acceptor in nitrate-dependent AOM via reverse methanogenesis.

            @@ -232,7 +233,7 @@

            Edge evidence

            CHEBI:16301 serves as terminal electron acceptor for anaerobic oxidation of methane - traitmech:000033 + traitmech:000033

            Nitrite serves as terminal electron acceptor in nitrite-dependent AOM (n-DAMO).

              @@ -269,8 +270,8 @@

              Protein and taxon examples

    		•  - Candidatus Methanoperedens nitratireducens -
    NCBITaxon:1392998 + Candidatus Methanoperedens nitratireducens +
    NCBITaxon:1392998         		UNREVIEWED
    @@ -342,9 +343,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -360,7 +361,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -618,7 +619,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -982,12 +992,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/anaerobic_respiration.html b/pages/traits/metabolism/anaerobic_respiration.html index 47b50721c50..7d2bf692d67 100644 --- a/pages/traits/metabolism/anaerobic_respiration.html +++ b/pages/traits/metabolism/anaerobic_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -284,7 +285,7 @@

    Edge evidence

    example of denitrification reductases - rdfs:subClassOf + rdfs:subClassOf

    Respiratory NarGHI is one of the reductase systems used in denitrifying respiration.

      @@ -303,7 +304,7 @@

      Edge evidence

      example of denitrification reductases - rdfs:subClassOf + rdfs:subClassOf

      NosZ is the terminal member of the denitrification-reductase set.

        @@ -358,8 +359,8 @@

        Protein and taxon examples

    		 - Paracoccus denitrificans -
    NCBITaxon:266 + Paracoccus denitrificans +
    NCBITaxon:266         		REVIEWED
    @@ -460,9 +461,9 @@

    Children (14)

    Synonyms (2)

      -
    • Anoxic respiration RELATED_SYNONYM · metpo.owl
      • +
    • Anoxic respiration RELATED_SYNONYM · metpo.owl
      • -
    • Dissimilatory respiration (non-O₂) RELATED_SYNONYM · metpo.owl
      • +
    • Dissimilatory respiration (non-O₂) RELATED_SYNONYM · metpo.owl
    @@ -485,7 +486,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -824,7 +825,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1188,12 +1198,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 12:15 UTC diff --git a/pages/traits/metabolism/anoxygenic_photosynthesis.html b/pages/traits/metabolism/anoxygenic_photosynthesis.html index 3edb2d23c4b..37bff025899 100644 --- a/pages/traits/metabolism/anoxygenic_photosynthesis.html +++ b/pages/traits/metabolism/anoxygenic_photosynthesis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    GO:0009767 confers anoxygenic photosynthesis - traitmech:000035 + traitmech:000035 METPO:2007700

    Bacteriochlorophyll-based electron flow realizes anoxygenic photosynthesis.

      @@ -175,7 +176,7 @@

      Edge evidence

      InterPro:IPR005781 confers anoxygenic photosynthesis - traitmech:000035 + traitmech:000035 METPO:2007700

      The PufM-containing type II reaction center is required for photosynthetic growth in the purple bacterium Cereibacter sphaeroides.

        @@ -250,8 +251,8 @@

        Protein and taxon examples

    		 - Cereibacter sphaeroides -
    NCBITaxon:1063 + Cereibacter sphaeroides +
    NCBITaxon:1063         		REVIEWED
    @@ -328,7 +329,7 @@

    Children (2)

    Synonyms (1)

      -
    • bacterial photosynthesis RELATED_SYNONYM · DOI:10.1016/j.tim.2006.09.001
      • +
    • bacterial photosynthesis RELATED_SYNONYM · DOI:10.1016/j.tim.2006.09.001
    @@ -344,7 +345,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -602,7 +603,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -966,12 +976,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/aromatic_compound_degradation.html b/pages/traits/metabolism/aromatic_compound_degradation.html index 2b1102f5a28..83f74a271ec 100644 --- a/pages/traits/metabolism/aromatic_compound_degradation.html +++ b/pages/traits/metabolism/aromatic_compound_degradation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -109,7 +110,7 @@

    Children (1)

    Synonyms (1)

      -
    • aromatic_compound_degradation RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • aromatic_compound_degradation RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -221,7 +222,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    The current record carries a single broad FAPROTAX review snippet (DOI:10.3390/ijerph6010278) naming bacterial degradation pathways of aromatic compounds without specific enzyme or intermediate claims; constructing a multi-edge causal graph from that single 60-character phrase would require clause-splitting or unsupported edges.

    +

    The current record carries a single broad FAPROTAX review snippet (DOI:10.3390/ijerph6010278) naming bacterial degradation pathways of aromatic compounds without specific enzyme or intermediate claims; constructing a multi-edge causal graph from that single 60-character phrase would require clause-splitting or unsupported edges.

    @@ -294,7 +295,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -323,12 +333,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 20:01 UTC diff --git a/pages/traits/metabolism/aromatic_hydrocarbon_degradation.html b/pages/traits/metabolism/aromatic_hydrocarbon_degradation.html index 4d5c287d35b..93e803b3ee1 100644 --- a/pages/traits/metabolism/aromatic_hydrocarbon_degradation.html +++ b/pages/traits/metabolism/aromatic_hydrocarbon_degradation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -102,7 +103,7 @@

    Parent traits (2)

    Synonyms (1)

      -
    • aromatic_hydrocarbon_degradation RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • aromatic_hydrocarbon_degradation RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -118,7 +119,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    The current record carries a single substrate-list snippet (DOI:10.1007/BF00058836) enumerating benzene, arenes, biphenyl, and fused aromatic hydrocarbons without catalytic or pathway-step assertions.

    +

    The current record carries a single substrate-list snippet (DOI:10.1007/BF00058836) enumerating benzene, arenes, biphenyl, and fused aromatic hydrocarbons without catalytic or pathway-step assertions.

    @@ -287,7 +288,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -316,12 +326,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 20:01 UTC diff --git a/pages/traits/metabolism/arsenate_respiration.html b/pages/traits/metabolism/arsenate_respiration.html index fe734b0d93f..b2c848377a5 100644 --- a/pages/traits/metabolism/arsenate_respiration.html +++ b/pages/traits/metabolism/arsenate_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -88,7 +89,7 @@

    Trait evidence (4)

    Respiratory arsenate reduction to arsenite and terminal electron acceptor pathway

    Evidence-backed metabolic pathway sketch linking dissimilatory arsenate respiratory reductase (ARR) activity, arsenite production, and arsenate terminal electron acceptance to arsenate respiration.

    -

    MECHANISTIC · Mechanistic graph backed by DOI:10.1073/pnas.1834303100, DOI:10.1128/AEM.69.5.2800-2809.2003, and DOI:10.1128/JB.01110-07; exemplified on arsenate_respiration_arr_complex with Shewanella sp. ANA-3 (NCBITaxon:94122) respiratory arsenate reductase subunits ArrA (UniProtKB:Q7WTU0) and ArrB (UniProtKB:Q7WTT9).

    +

    MECHANISTIC · Mechanistic graph backed by DOI:10.1073/pnas.1834303100, DOI:10.1128/AEM.69.5.2800-2809.2003, and DOI:10.1128/JB.01110-07; exemplified on arsenate_respiration_arr_complex with Shewanella sp. ANA-3 (NCBITaxon:94122) respiratory arsenate reductase subunits ArrA (UniProtKB:Q7WTU0) and ArrB (UniProtKB:Q7WTT9).

    Loading graph…

    @@ -108,7 +109,7 @@

    Edge evidence

  • arsenate respiration - traitmech:000195 + traitmech:000195 has electron acceptor arsenate CHEBI:18231 @@ -149,7 +150,7 @@

    Edge evidence

    GO:0030631 confers arsenate respiration - traitmech:000195 + traitmech:000195 METPO:2007700

    Arsenate respiratory reductase (ARR) is the key enzyme conferring arsenate respiration.

      @@ -205,8 +206,8 @@

      Protein and taxon examples

    		•  - Shewanella sp. ANA-3 -
    NCBITaxon:94122 + Shewanella sp. ANA-3 +
    NCBITaxon:94122         		REVIEWED
    @@ -235,8 +236,8 @@

    Protein and taxon examples

    		 - Shewanella sp. ANA-3 -
    NCBITaxon:94122 + Shewanella sp. ANA-3 +
    NCBITaxon:94122         		REVIEWED
    @@ -302,9 +303,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • As(V) respiration EXACT_SYNONYM · DOI:10.1073/pnas.1834303100
      • +
    • As(V) respiration EXACT_SYNONYM · DOI:10.1073/pnas.1834303100
      • -
    • respiratory As(V) reduction RELATED_SYNONYM · DOI:10.1073/pnas.1834303100
      • +
    • respiratory As(V) reduction RELATED_SYNONYM · DOI:10.1073/pnas.1834303100
    @@ -320,7 +321,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -470,7 +471,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The record's primary literature (DOI:10.1073/pnas.1834303100, DOI:10.1128/AEM.69.5.2800-2809.2003, DOI:10.1128/JB.01110-07) supports respiratory arsenate reduction to arsenite via arsenate respiratory reductase (ARR) in Shewanella sp. ANA-3 (NCBITaxon:94122), but verified UniProtKB accessions and proteome metadata must be added to a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    +

    The record's primary literature (DOI:10.1073/pnas.1834303100, DOI:10.1128/AEM.69.5.2800-2809.2003, DOI:10.1128/JB.01110-07) supports respiratory arsenate reduction to arsenite via arsenate respiratory reductase (ARR) in Shewanella sp. ANA-3 (NCBITaxon:94122), but verified UniProtKB accessions and proteome metadata must be added to a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    @@ -489,7 +490,7 @@

    Evidence

    -

    Resolution: Promoted arsenate_respiration_arr_pathway_sketch to MECHANISTIC by adding InterPro:IPR053686-grounded GENE_OR_PROTEIN node arsenate_respiration_arr_complex with reviewed Shewanella sp. ANA-3 (NCBITaxon:94122) protein_examples UniProtKB:Q7WTU0 (ArrA) and UniProtKB:Q7WTT9 (ArrB) backed by DOI:10.1128/JB.01110-07.

    +

    Resolution: Promoted arsenate_respiration_arr_pathway_sketch to MECHANISTIC by adding InterPro:IPR053686-grounded GENE_OR_PROTEIN node arsenate_respiration_arr_complex with reviewed Shewanella sp. ANA-3 (NCBITaxon:94122) protein_examples UniProtKB:Q7WTU0 (ArrA) and UniProtKB:Q7WTT9 (ArrB) backed by DOI:10.1128/JB.01110-07.

    @@ -524,7 +525,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Promoted arsenate_respiration_arr_pathway_sketch to MECHANISTIC; added InterPro:IPR053686-grounded GENE_OR_PROTEIN node arsenate_respiration_arr_complex with reviewed Shewanella sp. ANA-3 (NCBITaxon:94122) protein_examples UniProtKB:Q7WTU0 (ArrA) and UniProtKB:Q7WTT9 (ArrB) backed by DOI:10.1128/JB.01110-07; resolved arsenate-respiration-protein-example-gap.

    +

    Promoted arsenate_respiration_arr_pathway_sketch to MECHANISTIC; added InterPro:IPR053686-grounded GENE_OR_PROTEIN node arsenate_respiration_arr_complex with reviewed Shewanella sp. ANA-3 (NCBITaxon:94122) protein_examples UniProtKB:Q7WTU0 (ArrA) and UniProtKB:Q7WTT9 (ArrB) backed by DOI:10.1128/JB.01110-07; resolved arsenate-respiration-protein-example-gap.

    • @@ -572,7 +573,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -936,12 +946,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 11:45 UTC diff --git a/pages/traits/metabolism/arsenite_oxidation.html b/pages/traits/metabolism/arsenite_oxidation.html index 2d96c4ec106..b4fb61e88f4 100644 --- a/pages/traits/metabolism/arsenite_oxidation.html +++ b/pages/traits/metabolism/arsenite_oxidation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,9 +113,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • As(III) oxidation EXACT_SYNONYM · DOI:10.3389/fmicb.2020.569282
      • +
    • As(III) oxidation EXACT_SYNONYM · DOI:10.3389/fmicb.2020.569282
      • -
    • microbial arsenite oxidation RELATED_SYNONYM · DOI:10.3389/fmicb.2020.569282
      • +
    • microbial arsenite oxidation RELATED_SYNONYM · DOI:10.3389/fmicb.2020.569282
    @@ -130,7 +131,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -255,7 +256,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries general detoxification/energy and strain-isolation snippets (DOI:10.3389/fmicb.2020.569282, DOI:10.1128/AEM.66.1.92-97.2000, DOI:10.1186/s12866-024-03676-9) without enzyme-level catalytic quotes or a cited canonical example.

    +

    The current record carries general detoxification/energy and strain-isolation snippets (DOI:10.3389/fmicb.2020.569282, DOI:10.1128/AEM.66.1.92-97.2000, DOI:10.1186/s12866-024-03676-9) without enzyme-level catalytic quotes or a cited canonical example.

    @@ -305,7 +306,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add arsenite oxidation trait -

      Minted traitmech:000189 for the arsenite oxidation metabolism trait with DOI-backed As(III)-to-As(V) evidence from 10.3389/fmicb.2020.569282, 10.1128/AEM.66.1.92-97.2000, and 10.1186/s12866-024-03676-9, recorded an exact As(III) oxidation synonym and exact-xref gap, and reserved METPO:1014300 in proposals/metpo_traitmech_v66.

    +

    Minted traitmech:000189 for the arsenite oxidation metabolism trait with DOI-backed As(III)-to-As(V) evidence from 10.3389/fmicb.2020.569282, 10.1128/AEM.66.1.92-97.2000, and 10.1186/s12866-024-03676-9, recorded an exact As(III) oxidation synonym and exact-xref gap, and reserved METPO:1014300 in proposals/metpo_traitmech_v66.

    • Read this curation session @@ -337,7 +338,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -366,12 +376,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/metabolism/assimilates.html b/pages/traits/metabolism/assimilates.html index e4eef35a786..e3b859a47dd 100644 --- a/pages/traits/metabolism/assimilates.html +++ b/pages/traits/metabolism/assimilates.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • assimilation RELATED_SYNONYM · metpo.owl
      • +
    • assimilation RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/biopolymer_degradation.html b/pages/traits/metabolism/biopolymer_degradation.html index 942a3d529a6..e87af164ef7 100644 --- a/pages/traits/metabolism/biopolymer_degradation.html +++ b/pages/traits/metabolism/biopolymer_degradation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    confers biopolymer degradation - traitmech:000110 + traitmech:000110 METPO:2007700

    Secreted enzymes drive extracellular biopolymer breakdown.

      @@ -115,7 +116,7 @@

      Edge evidence

    • biopolymer degradation - traitmech:000110 + traitmech:000110 produces assimilable mono- and oligosaccharides @@ -156,7 +157,7 @@

      Edge evidence

      GO:0008810 contributes to biopolymer degradation - traitmech:000110 + traitmech:000110 RO:0002326

      Endoglucanase contributes the internal-chain-cleavage step of the cellulose-specific branch of biopolymer degradation.

        @@ -194,7 +195,7 @@

        Edge evidence

        GO:0008422 contributes to biopolymer degradation - traitmech:000110 + traitmech:000110 RO:0002326

        Beta-glucosidase contributes terminal saccharification of cellulose-derived oligomers to glucose.

          @@ -232,7 +233,7 @@

          Edge evidence

          contributes to biopolymer degradation - traitmech:000110 + traitmech:000110 RO:0002326

          SusC-like uptake contributes the transport stage of a polysaccharide-utilization branch after extracellular or surface depolymerization.

            @@ -289,7 +290,7 @@

            Edge evidence

            GO:0008843 contributes to biopolymer degradation - traitmech:000110 + traitmech:000110 RO:0002326

            Endo-chitinase contributes the internal-cleavage step of the chitin-specific branch of biopolymer degradation.

              @@ -327,7 +328,7 @@

              Edge evidence

              contributes to biopolymer degradation - traitmech:000110 + traitmech:000110 RO:0002326

              Secreted lignin peroxidases and related oxidoreductases contribute the extracellular oxidative branch of biopolymer degradation.

                @@ -364,8 +365,8 @@

                Protein and taxon examples

    		 - Cellulomonas fimi -
    NCBITaxon:1708 + Cellulomonas fimi +
    NCBITaxon:1708         		REVIEWED
    @@ -452,7 +453,7 @@

    Children (7)

    Synonyms (1)

    @@ -468,7 +469,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -738,7 +739,7 @@

    Curation history

  • · RESTORE_CANONICAL_CITATION · claude -

    Restored the canonical-example citation for NCBITaxon:1708 from DOI:10.1016/0378-1119(86)90196-4 back to PMID:23342046 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.

    +

    Restored the canonical-example citation for NCBITaxon:1708 from DOI:10.1016/0378-1119(86)90196-4 back to PMID:23342046 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.

  • @@ -756,7 +757,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1016/j.cbpa.2015.10.018 (already present on saprotrophy.yaml causal_graphs[0].edges[5].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 5 Stage 5 remediation of F-C5S4-DEF-SRC-004 in group G-C5S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.1016/j.cbpa.2015.10.018 (already present on saprotrophy.yaml causal_graphs[0].edges[5].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 5 Stage 5 remediation of F-C5S4-DEF-SRC-004 in group G-C5S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -798,7 +799,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1162,12 +1172,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 21:40 UTC diff --git a/pages/traits/metabolism/builds_acid_from.html b/pages/traits/metabolism/builds_acid_from.html index 6b589905ffc..15b8aafd18e 100644 --- a/pages/traits/metabolism/builds_acid_from.html +++ b/pages/traits/metabolism/builds_acid_from.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -238,7 +239,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -267,12 +277,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-06-17 04:09 UTC diff --git a/pages/traits/metabolism/builds_base_from.html b/pages/traits/metabolism/builds_base_from.html index 98bf80afa16..e784b01a573 100644 --- a/pages/traits/metabolism/builds_base_from.html +++ b/pages/traits/metabolism/builds_base_from.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -238,7 +239,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -267,12 +277,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-06-17 04:09 UTC diff --git a/pages/traits/metabolism/builds_gas_from.html b/pages/traits/metabolism/builds_gas_from.html index ccb9621a448..4940f46dd8f 100644 --- a/pages/traits/metabolism/builds_gas_from.html +++ b/pages/traits/metabolism/builds_gas_from.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -238,7 +239,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -267,12 +277,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-06-17 04:09 UTC diff --git a/pages/traits/metabolism/butanediol_fermentation.html b/pages/traits/metabolism/butanediol_fermentation.html index 9729b76dba5..a28abdb7ed5 100644 --- a/pages/traits/metabolism/butanediol_fermentation.html +++ b/pages/traits/metabolism/butanediol_fermentation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -88,7 +89,7 @@

    Trait evidence (4)

    Acetoin intermediate formation and reduction to 2,3-butanediol

    Evidence-backed metabolic pathway sketch linking acetoin (3-hydroxybutanone) intermediate reduction and 2,3-butanediol production to the 2,3-butanediol fermentation phenotype.

    -

    MECHANISTIC · Mechanistic graph backed by the ASM Methyl Red / Voges-Proskauer protocol, DOI:10.1007/s00253-014-5526-9, and DOI:10.1038/sj.jim.7000179; exemplified on butanediol_fermentation_budc with Klebsiella pneumoniae (NCBITaxon:573) diacetyl reductase [(S)-acetoin forming] / acetoin reductase BudC (UniProtKB:Q48436).

    +

    MECHANISTIC · Mechanistic graph backed by the ASM Methyl Red / Voges-Proskauer protocol, DOI:10.1007/s00253-014-5526-9, and DOI:10.1038/sj.jim.7000179; exemplified on butanediol_fermentation_budc with Klebsiella pneumoniae (NCBITaxon:573) diacetyl reductase [(S)-acetoin forming] / acetoin reductase BudC (UniProtKB:Q48436).

    Loading graph…

    @@ -130,7 +131,7 @@

    Edge evidence

    CHEBI:16982 confers 2,3-butanediol fermentation - traitmech:000181 + traitmech:000181 METPO:2007700

    Production of meso-2,3-butanediol, (2S,3S)-butanediol, and (2R,3R)-butanediol stereoisomers in culture broth confers the 2,3-butanediol fermentation phenotype.

      @@ -186,8 +187,8 @@

      Protein and taxon examples

    		 - Klebsiella pneumoniae -
    NCBITaxon:573 + Klebsiella pneumoniae +
    NCBITaxon:573         		REVIEWED
    @@ -253,7 +254,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -269,7 +270,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -419,7 +420,7 @@

    Discussions and Knowledge Gaps (3)

    -

    The current record carries metabolite-overview and isomer-detection snippets (DOI:10.1186/s12934-023-02163-6, ASM Voges-Proskauer protocol, DOI:10.1007/s00253-014-5526-9) without enzymatic catalysis quotes for the pyruvate-to-acetoin-to-2,3-butanediol steps.

    +

    The current record carries metabolite-overview and isomer-detection snippets (DOI:10.1186/s12934-023-02163-6, ASM Voges-Proskauer protocol, DOI:10.1007/s00253-014-5526-9) without enzymatic catalysis quotes for the pyruvate-to-acetoin-to-2,3-butanediol steps.

    @@ -462,7 +463,7 @@

    Evidence

    -

    The record's primary literature (DOI:10.1186/s12934-023-02163-6, ASM Methyl Red / Voges-Proskauer protocol, DOI:10.1007/s00253-014-5526-9) establishes acetoin intermediate reduction to 2,3-butanediol and stereoisomer production in Klebsiella pneumoniae (NCBITaxon:573), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    +

    The record's primary literature (DOI:10.1186/s12934-023-02163-6, ASM Methyl Red / Voges-Proskauer protocol, DOI:10.1007/s00253-014-5526-9) establishes acetoin intermediate reduction to 2,3-butanediol and stereoisomer production in Klebsiella pneumoniae (NCBITaxon:573), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    @@ -481,7 +482,7 @@

    Evidence

    -

    Resolution: Promoted butanediol_fermentation_acetoin_sketch to MECHANISTIC by adding InterPro:IPR014007-grounded GENE_OR_PROTEIN node butanediol_fermentation_budc with reviewed Klebsiella pneumoniae (NCBITaxon:573) protein_examples UniProtKB:Q48436 (BudC) backed by DOI:10.1038/sj.jim.7000179.

    +

    Resolution: Promoted butanediol_fermentation_acetoin_sketch to MECHANISTIC by adding InterPro:IPR014007-grounded GENE_OR_PROTEIN node butanediol_fermentation_budc with reviewed Klebsiella pneumoniae (NCBITaxon:573) protein_examples UniProtKB:Q48436 (BudC) backed by DOI:10.1038/sj.jim.7000179.

    @@ -516,7 +517,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Promoted butanediol_fermentation_acetoin_sketch to MECHANISTIC; added InterPro:IPR014007-grounded GENE_OR_PROTEIN node butanediol_fermentation_budc with reviewed Klebsiella pneumoniae (NCBITaxon:573) protein_examples UniProtKB:Q48436 (BudC) backed by DOI:10.1038/sj.jim.7000179; resolved butanediol-fermentation-protein-example-gap.

    +

    Promoted butanediol_fermentation_acetoin_sketch to MECHANISTIC; added InterPro:IPR014007-grounded GENE_OR_PROTEIN node butanediol_fermentation_budc with reviewed Klebsiella pneumoniae (NCBITaxon:573) protein_examples UniProtKB:Q48436 (BudC) backed by DOI:10.1038/sj.jim.7000179; resolved butanediol-fermentation-protein-example-gap.

    • @@ -558,7 +559,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -922,12 +932,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 18:45 UTC diff --git a/pages/traits/metabolism/butyric_acid_fermentation.html b/pages/traits/metabolism/butyric_acid_fermentation.html index 10ce5d1b135..ca2b69e0c77 100644 --- a/pages/traits/metabolism/butyric_acid_fermentation.html +++ b/pages/traits/metabolism/butyric_acid_fermentation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,7 +113,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -128,7 +129,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -278,7 +279,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record summarizes anaerobe energy-conservation history, gene-cluster arrangements, and strain yield (DOI:10.3389/fmicb.2021.703525, DOI:10.1111/j.1574-6968.2009.01514.x, DOI:10.1111/1751-7915.12304) without distinct step-by-step enzymatic reaction quotes.

    +

    The current record summarizes anaerobe energy-conservation history, gene-cluster arrangements, and strain yield (DOI:10.3389/fmicb.2021.703525, DOI:10.1111/j.1574-6968.2009.01514.x, DOI:10.1111/1751-7915.12304) without distinct step-by-step enzymatic reaction quotes.

    @@ -360,7 +361,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -389,12 +399,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/metabolism/cable_bacteria_metabolism.html b/pages/traits/metabolism/cable_bacteria_metabolism.html index 5b1dc69f6b9..923bb510a35 100644 --- a/pages/traits/metabolism/cable_bacteria_metabolism.html +++ b/pages/traits/metabolism/cable_bacteria_metabolism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -402,8 +403,8 @@

    Protein and taxon examples

    		 - Candidatus Electronema aureum -
    NCBITaxon:2005002 + Candidatus Electronema aureum +
    NCBITaxon:2005002         		UNREVIEWED
    @@ -432,8 +433,8 @@

    Protein and taxon examples

    		 - Candidatus Electronema aureum -
    NCBITaxon:2005002 + Candidatus Electronema aureum +
    NCBITaxon:2005002         		UNREVIEWED
    @@ -506,7 +507,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -809,7 +810,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1173,12 +1183,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/calvin_benson_bassham_cycle.html b/pages/traits/metabolism/calvin_benson_bassham_cycle.html index f5c2963b41b..72e2c63b3a5 100644 --- a/pages/traits/metabolism/calvin_benson_bassham_cycle.html +++ b/pages/traits/metabolism/calvin_benson_bassham_cycle.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    GO:0019253 confers Calvin-Benson-Bassham cycle - traitmech:000020 + traitmech:000020 METPO:2007700

    The reductive pentose phosphate cycle realizes the trait.

      @@ -137,7 +138,7 @@

      Edge evidence

      CHEBI:16526 fixed by Calvin-Benson-Bassham cycle - traitmech:000020 + traitmech:000020 METPO:2007404

      CO2 is the substrate fixed by the CBB cycle.

        @@ -364,8 +365,8 @@

        Protein and taxon examples

    		 - Cupriavidus necator H16 -
    NCBITaxon:381666 + Cupriavidus necator H16 +
    NCBITaxon:381666         		REVIEWED
    @@ -431,9 +432,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • Calvin cycle EXACT_SYNONYM · DOI:10.1128/AEM.02473-10
      • +
    • Calvin cycle EXACT_SYNONYM · DOI:10.1128/AEM.02473-10
      • -
    • reductive pentose phosphate cycle RELATED_SYNONYM · DOI:10.1128/AEM.02473-10
      • +
    • reductive pentose phosphate cycle RELATED_SYNONYM · DOI:10.1128/AEM.02473-10
    @@ -449,7 +450,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -713,7 +714,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1128/AEM.02473-10 (already present on parent record carbon_fixation.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-011 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.1128/AEM.02473-10 (already present on parent record carbon_fixation.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-011 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -755,7 +756,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1119,12 +1129,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/metabolism/capable_of.html b/pages/traits/metabolism/capable_of.html index 010189551a3..8513399e695 100644 --- a/pages/traits/metabolism/capable_of.html +++ b/pages/traits/metabolism/capable_of.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -105,7 +106,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:2000103 [-0.096, -0.006, -0.056, -0.047, …]
      • +
    • capable of METPO:2000103 [-0.096, -0.006, -0.056, -0.047, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -236,7 +237,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -265,12 +275,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 17:00 UTC diff --git a/pages/traits/metabolism/carbon_fixation.html b/pages/traits/metabolism/carbon_fixation.html index ee64c7c5bac..6018122a825 100644 --- a/pages/traits/metabolism/carbon_fixation.html +++ b/pages/traits/metabolism/carbon_fixation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    CHEBI:16526 fixed by carbon fixation - traitmech:000019 + traitmech:000019 METPO:2007404

    CO2 is the substrate fixed by autotrophic carbon-fixation pathways.

      @@ -118,7 +119,7 @@

      Edge evidence

      GO:0015977 confers carbon fixation - traitmech:000019 + traitmech:000019 METPO:2007700

      The autotrophic carbon-fixation process realizes the trait.

        @@ -398,8 +399,8 @@

        Protein and taxon examples

    		 - Cupriavidus necator H16 -
    NCBITaxon:381666 + Cupriavidus necator H16 +
    NCBITaxon:381666         		REVIEWED
    @@ -484,15 +485,15 @@

    Children (6)

    Synonyms (5)

    @@ -515,7 +516,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -815,7 +816,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1128/AEM.02473-10 (already present on causal_graphs[0].edges[11]) to record-level evidence[0] to match definition_source (Cycle 2 Stage 5 remediation of F-DEF-SRC-CARBON-FIXATION-010 in group G-C2S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #1995).

    +

    Added verified verbatim snippet from DOI:10.1128/AEM.02473-10 (already present on causal_graphs[0].edges[11]) to record-level evidence[0] to match definition_source (Cycle 2 Stage 5 remediation of F-DEF-SRC-CARBON-FIXATION-010 in group G-C2S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #1995).

    • @@ -857,7 +858,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1221,12 +1231,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 16:05 UTC diff --git a/pages/traits/metabolism/cellulolysis.html b/pages/traits/metabolism/cellulolysis.html index 296943aedd1..961e7ded4cf 100644 --- a/pages/traits/metabolism/cellulolysis.html +++ b/pages/traits/metabolism/cellulolysis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    confers cellulolysis - traitmech:000111 + traitmech:000111 METPO:2007700

    Cellulase systems hydrolyze cellulose extracellularly.

      @@ -115,7 +116,7 @@

      Edge evidence

    • cellulolysis - traitmech:000111 + traitmech:000111 produces glucose CHEBI:17234 @@ -384,7 +385,7 @@

      Edge evidence

      GO:0043263 confers cellulolysis - traitmech:000111 + traitmech:000111 METPO:2007700

      Cellulosomes are one of the alternative cellulase-system architectures that confer cellulolysis; they are taxonomically restricted, not universal.

        @@ -421,8 +422,8 @@

        Protein and taxon examples

    		 - Acetivibrio thermocellus -
    NCBITaxon:1515 + Acetivibrio thermocellus +
    NCBITaxon:1515         		REVIEWED
    @@ -488,9 +489,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -506,7 +507,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -791,7 +792,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1128/MMBR.66.3.506-577.2002 (already present on causal_graphs[0].edges[15]) to record-level evidence[0] to match definition_source (Cycle 2 Stage 5 remediation of F-DEF-SRC-CELLULOLYSIS-014 in group G-C2S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #1995).

    +

    Added verified verbatim snippet from DOI:10.1128/MMBR.66.3.506-577.2002 (already present on causal_graphs[0].edges[15]) to record-level evidence[0] to match definition_source (Cycle 2 Stage 5 remediation of F-DEF-SRC-CELLULOLYSIS-014 in group G-C2S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #1995).

    • @@ -824,7 +825,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1188,12 +1198,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 16:05 UTC diff --git a/pages/traits/metabolism/chitinolysis.html b/pages/traits/metabolism/chitinolysis.html index f85c73abd20..0a86c3d2637 100644 --- a/pages/traits/metabolism/chitinolysis.html +++ b/pages/traits/metabolism/chitinolysis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    GO:0004568 confers chitinolysis - traitmech:000112 + traitmech:000112 METPO:2007700

    Secreted chitinases drive chitin depolymerization.

      @@ -115,7 +116,7 @@

      Edge evidence

    • chitinolysis - traitmech:000112 + traitmech:000112 produces N-acetylglucosamine @@ -281,8 +282,8 @@

      Protein and taxon examples

    		 - Serratia marcescens -
    NCBITaxon:615 + Serratia marcescens +
    NCBITaxon:615         		REVIEWED
    @@ -311,8 +312,8 @@

    Protein and taxon examples

    		 - Serratia marcescens -
    NCBITaxon:615 + Serratia marcescens +
    NCBITaxon:615         		REVIEWED
    @@ -378,9 +379,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -396,7 +397,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -506,19 +507,19 @@

    Deep research

    | subject | predicate | object | taxon/context | confidence | DOI | |---|---|---|---|---|---| -| polymeric chitin | is hydrolyzed by | extracellular chitinases to chitooligosaccharides and chitobiose | general bacterial chitinolysis; three-step hydrolytic model | high (beier2013bacterialchitindegradation—mechanisms pages 2-4, demeester2025unravellingtheregulatory pages 1-5) | 10.3389/fmicb.2013.00149; 10.1111/brv.70020 | -| CBP21 (LPMO) | increases accessibility of | crystalline chitin to hydrolytic chitinases | *Serratia marcescens*; oxidative disruption phase | medium-high, taxon-specific (demeester2025unravellingtheregulatory pages 1-5, demeester2025unravellingtheregulatory pages 5-9) | 10.1111/brv.70020 | -| chitooligosaccharides | are converted by β-N-acetylglucosaminidase/chitobiase | GlcNAc | *Serratia marcescens* and related chitinolytic bacteria | high (demeester2025unravellingtheregulatory pages 1-5, vaaje‐kolstad2019enzymesformodification pages 24-26) | 10.1111/brv.70020; 10.1002/9781119450467.ch8 | -| chitooligosaccharides and chitobiose | pass through outer membrane via | ChiP chitoporin | *Serratia marcescens* | medium-high, taxon-specific (demeester2025unravellingtheregulatory pages 5-9) | 10.1111/brv.70020 | -| chitobiose | is transported across inner membrane by | PTS ChbC | *Serratia marcescens*; chitobiose utilization module | medium-high, taxon-specific (demeester2025unravellingtheregulatory pages 5-9, garciatelles2026chbandnag pages 12-15) | 10.1111/brv.70020; 10.1007/s00253-025-13656-2 | -| GlcNAc | is transported across inner membrane by | PTS NagE | *Serratia marcescens* | medium-high, taxon-specific (demeester2025unravellingtheregulatory pages 5-9) | 10.1111/brv.70020 | -| GlcNAc | is phosphorylated by | NagK to GlcNAc-6-phosphate | picocyanobacteria and general intracellular chitin-derivative catabolism | medium (capovilla2023chitinutilizationby pages 5-6, capovilla2023chitinutilizationby pages 6-8) | 10.1073/pnas.2213271120 | -| GlcNAc-6-phosphate | is deacetylated by | NagA to glucosamine-6-phosphate | general intracellular amino-sugar catabolism | high (vaaje‐kolstad2019enzymesformodification pages 24-26, capovilla2023chitinutilizationby pages 5-6) | 10.1002/9781119450467.ch8; 10.1073/pnas.2213271120 | -| glucosamine-6-phosphate | is deaminated/isomerized by | NagB to fructose-6-phosphate | general intracellular amino-sugar catabolism | high (vaaje‐kolstad2019enzymesformodification pages 24-26, capovilla2023chitinutilizationby pages 5-6) | 10.1002/9781119450467.ch8; 10.1073/pnas.2213271120 | -| glucose scarcity | activates | cAMP-CRP signaling linked to chitinolytic state | *Serratia marcescens* catabolite repression network | medium-high, taxon-specific (demeester2025unravellingtheregulatory pages 22-26, demeester2025unravellingtheregulatory pages 1-5) | 10.1111/brv.70020 | -| GlcNAc or soluble chitin oligomers ((GlcNAc)2-6) | induce | chitinase production/expression | general bacterial chitin degradation regulation | high (beier2013bacterialchitindegradation—mechanisms pages 2-4) | 10.3389/fmicb.2013.00149 | -| ChiWXYZ-dependent secretion system | mediates secretion of | chitinases and CBP21 | *Serratia marcescens*; holin/peptidoglycan hydrolase-associated export | medium, taxon-specific (demeester2025unravellingtheregulatory pages 5-9) | 10.1111/brv.70020 | -| chitin utilization pathway genes | promotes | attachment to chitin particles | marine picocyanobacteria; bead-attachment assays | medium-high, lineage-specific (capovilla2023chitinutilizationby pages 2-3, capovilla2023chitinutilizationby pages 1-2) | 10.1073/pnas.2213271120 | +| polymeric chitin | is hydrolyzed by | extracellular chitinases to chitooligosaccharides and chitobiose | general bacterial chitinolysis; three-step hydrolytic model | high (beier2013bacterialchitindegradation—mechanisms pages 2-4, demeester2025unravellingtheregulatory pages 1-5) | 10.3389/fmicb.2013.00149; 10.1111/brv.70020 | +| CBP21 (LPMO) | increases accessibility of | crystalline chitin to hydrolytic chitinases | *Serratia marcescens*; oxidative disruption phase | medium-high, taxon-specific (demeester2025unravellingtheregulatory pages 1-5, demeester2025unravellingtheregulatory pages 5-9) | 10.1111/brv.70020 | +| chitooligosaccharides | are converted by β-N-acetylglucosaminidase/chitobiase | GlcNAc | *Serratia marcescens* and related chitinolytic bacteria | high (demeester2025unravellingtheregulatory pages 1-5, vaaje‐kolstad2019enzymesformodification pages 24-26) | 10.1111/brv.70020; 10.1002/9781119450467.ch8 | +| chitooligosaccharides and chitobiose | pass through outer membrane via | ChiP chitoporin | *Serratia marcescens* | medium-high, taxon-specific (demeester2025unravellingtheregulatory pages 5-9) | 10.1111/brv.70020 | +| chitobiose | is transported across inner membrane by | PTS ChbC | *Serratia marcescens*; chitobiose utilization module | medium-high, taxon-specific (demeester2025unravellingtheregulatory pages 5-9, garciatelles2026chbandnag pages 12-15) | 10.1111/brv.70020; 10.1007/s00253-025-13656-2 | +| GlcNAc | is transported across inner membrane by | PTS NagE | *Serratia marcescens* | medium-high, taxon-specific (demeester2025unravellingtheregulatory pages 5-9) | 10.1111/brv.70020 | +| GlcNAc | is phosphorylated by | NagK to GlcNAc-6-phosphate | picocyanobacteria and general intracellular chitin-derivative catabolism | medium (capovilla2023chitinutilizationby pages 5-6, capovilla2023chitinutilizationby pages 6-8) | 10.1073/pnas.2213271120 | +| GlcNAc-6-phosphate | is deacetylated by | NagA to glucosamine-6-phosphate | general intracellular amino-sugar catabolism | high (vaaje‐kolstad2019enzymesformodification pages 24-26, capovilla2023chitinutilizationby pages 5-6) | 10.1002/9781119450467.ch8; 10.1073/pnas.2213271120 | +| glucosamine-6-phosphate | is deaminated/isomerized by | NagB to fructose-6-phosphate | general intracellular amino-sugar catabolism | high (vaaje‐kolstad2019enzymesformodification pages 24-26, capovilla2023chitinutilizationby pages 5-6) | 10.1002/9781119450467.ch8; 10.1073/pnas.2213271120 | +| glucose scarcity | activates | cAMP-CRP signaling linked to chitinolytic state | *Serratia marcescens* catabolite repression network | medium-high, taxon-specific (demeester2025unravellingtheregulatory pages 22-26, demeester2025unravellingtheregulatory pages 1-5) | 10.1111/brv.70020 | +| GlcNAc or soluble chitin oligomers ((GlcNAc)2-6) | induce | chitinase production/expression | general bacterial chitin degradation regulation | high (beier2013bacterialchitindegradation—mechanisms pages 2-4) | 10.3389/fmicb.2013.00149 | +| ChiWXYZ-dependent secretion system | mediates secretion of | chitinases and CBP21 | *Serratia marcescens*; holin/peptidoglycan hydrolase-associated export | medium, taxon-specific (demeester2025unravellingtheregulatory pages 5-9) | 10.1111/brv.70020 | +| chitin utilization pathway genes | promotes | attachment to chitin particles | marine picocyanobacteria; bead-attachment assays | medium-high, lineage-specific (capovilla2023chitinutilizationby pages 2-3, capovilla2023chitinutilizationby pages 1-2) | 10.1073/pnas.2213271120 | *Table: This table compiles the strongest curation-ready causal triples for microbial chitinolysis, emphasizing mechanistic steps from extracellular depolymerization through transport, intracellular catabolism, regulation, secretion, and particle attachment. It is useful as a compact starting point for TraitMech graph curation while preserving taxon specificity and confidence.* @@ -639,7 +640,7 @@

    Curation history

  • · RESTORE_CANONICAL_CITATION · claude -

    Restored the canonical-example citation for NCBITaxon:615 from DOI:10.1002/j.1460-2075.1986.tb04235.x back to PMID:23398882 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.

    +

    Restored the canonical-example citation for NCBITaxon:615 from DOI:10.1002/j.1460-2075.1986.tb04235.x back to PMID:23398882 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.

  • @@ -657,7 +658,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.3389/fmicb.2013.00149 (already present on causal_graphs[0].edges[6]) to record-level evidence[0] to match definition_source (Cycle 2 Stage 5 remediation of F-DEF-SRC-CHITINOLYSIS-015 in group G-C2S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #1995).

    +

    Added verified verbatim snippet from DOI:10.3389/fmicb.2013.00149 (already present on causal_graphs[0].edges[6]) to record-level evidence[0] to match definition_source (Cycle 2 Stage 5 remediation of F-DEF-SRC-CHITINOLYSIS-015 in group G-C2S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #1995).

    • @@ -699,7 +700,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1063,12 +1073,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 16:05 UTC diff --git a/pages/traits/metabolism/chlorate_respiration.html b/pages/traits/metabolism/chlorate_respiration.html index 53e64b9c9a4..ca2b86a8915 100644 --- a/pages/traits/metabolism/chlorate_respiration.html +++ b/pages/traits/metabolism/chlorate_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -88,7 +89,7 @@

    Trait evidence (4)

    Two-step dissimilatory chlorate reduction pathway via chlorite

    Evidence-backed metabolic pathway sketch linking chlorate terminal electron acceptance and two-step dissimilatory chlorate reduction via chlorite to chlorate respiration.

    -

    MECHANISTIC · Mechanistic graph backed by DOI:10.1128/AEM.69.9.5585-5592.2003 and DOI:10.1128/AEM.07303-11; exemplified on chlorate_respiration_clr_complex with Ideonella dechloratans (NCBITaxon:36863) chlorate reductase subunits ClrA (UniProtKB:P60068) and ClrB (UniProtKB:P60069).

    +

    MECHANISTIC · Mechanistic graph backed by DOI:10.1128/AEM.69.9.5585-5592.2003 and DOI:10.1128/AEM.07303-11; exemplified on chlorate_respiration_clr_complex with Ideonella dechloratans (NCBITaxon:36863) chlorate reductase subunits ClrA (UniProtKB:P60068) and ClrB (UniProtKB:P60069).

    Loading graph…

    @@ -108,7 +109,7 @@

    Edge evidence

  • chlorate respiration - traitmech:000198 + traitmech:000198 has electron acceptor chlorate CHEBI:17891 @@ -130,7 +131,7 @@

    Edge evidence

    GO:0019645 confers chlorate respiration - traitmech:000198 + traitmech:000198 METPO:2007700

    Chlorate-respiring bacteria use dissimilatory chlorate reduction as an anaerobic respiratory pathway.

      @@ -205,8 +206,8 @@

      Protein and taxon examples

    		•  - Ideonella dechloratans -
    NCBITaxon:36863 + Ideonella dechloratans +
    NCBITaxon:36863         		REVIEWED
    @@ -235,8 +236,8 @@

    Protein and taxon examples

    		 - Ideonella dechloratans -
    NCBITaxon:36863 + Ideonella dechloratans +
    NCBITaxon:36863         		REVIEWED
    @@ -302,7 +303,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • dissimilatory chlorate reduction RELATED_SYNONYM · DOI:10.1128/AEM.07303-11
      • +
    • dissimilatory chlorate reduction RELATED_SYNONYM · DOI:10.1128/AEM.07303-11
    @@ -318,7 +319,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -468,7 +469,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The record's primary literature (DOI:10.1128/AEM.69.9.5585-5592.2003, DOI:10.1128/AEM.07303-11) supports the two-step dissimilatory chlorate reduction pathway (chlorate reduction followed by chlorite decomposition) in Ideonella dechloratans (NCBITaxon:36863), but verified UniProtKB accessions must be added to a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    +

    The record's primary literature (DOI:10.1128/AEM.69.9.5585-5592.2003, DOI:10.1128/AEM.07303-11) supports the two-step dissimilatory chlorate reduction pathway (chlorate reduction followed by chlorite decomposition) in Ideonella dechloratans (NCBITaxon:36863), but verified UniProtKB accessions must be added to a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    @@ -487,7 +488,7 @@

    Evidence

    -

    Resolution: Promoted chlorate_respiration_pathway_sketch to MECHANISTIC by adding InterPro:IPR017840-grounded GENE_OR_PROTEIN node chlorate_respiration_clr_complex with reviewed Ideonella dechloratans (NCBITaxon:36863) protein_examples UniProtKB:P60068 (ClrA) and UniProtKB:P60069 (ClrB) backed by DOI:10.1128/AEM.69.9.5585-5592.2003.

    +

    Resolution: Promoted chlorate_respiration_pathway_sketch to MECHANISTIC by adding InterPro:IPR017840-grounded GENE_OR_PROTEIN node chlorate_respiration_clr_complex with reviewed Ideonella dechloratans (NCBITaxon:36863) protein_examples UniProtKB:P60068 (ClrA) and UniProtKB:P60069 (ClrB) backed by DOI:10.1128/AEM.69.9.5585-5592.2003.

    @@ -516,7 +517,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Promoted chlorate_respiration_pathway_sketch to MECHANISTIC; added InterPro:IPR017840-grounded GENE_OR_PROTEIN node chlorate_respiration_clr_complex with reviewed Ideonella dechloratans (NCBITaxon:36863) protein_examples UniProtKB:P60068 (ClrA) and UniProtKB:P60069 (ClrB) backed by DOI:10.1128/AEM.69.9.5585-5592.2003; resolved chlorate-respiration-protein-example-gap.

    +

    Promoted chlorate_respiration_pathway_sketch to MECHANISTIC; added InterPro:IPR017840-grounded GENE_OR_PROTEIN node chlorate_respiration_clr_complex with reviewed Ideonella dechloratans (NCBITaxon:36863) protein_examples UniProtKB:P60068 (ClrA) and UniProtKB:P60069 (ClrB) backed by DOI:10.1128/AEM.69.9.5585-5592.2003; resolved chlorate-respiration-protein-example-gap.

    • @@ -558,7 +559,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -922,12 +932,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 11:45 UTC diff --git a/pages/traits/metabolism/citrate_fermentation.html b/pages/traits/metabolism/citrate_fermentation.html index 54145199208..cae32bf1d68 100644 --- a/pages/traits/metabolism/citrate_fermentation.html +++ b/pages/traits/metabolism/citrate_fermentation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -263,7 +264,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two growth-and-prevalence snippets in Klebsiella pneumoniae (DOI:10.1128/JB.183.18.5248-5256.2001, DOI:10.1186/1471-2180-9-168) without enzymatic step or intermediate quotes.

    +

    The current record carries two growth-and-prevalence snippets in Klebsiella pneumoniae (DOI:10.1128/JB.183.18.5248-5256.2001, DOI:10.1186/1471-2180-9-168) without enzymatic step or intermediate quotes.

    @@ -351,7 +352,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -380,12 +390,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/metabolism/compartmentalizes.html b/pages/traits/metabolism/compartmentalizes.html index 53d95e318a4..f0819046250 100644 --- a/pages/traits/metabolism/compartmentalizes.html +++ b/pages/traits/metabolism/compartmentalizes.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -232,7 +233,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -261,12 +271,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/complete_ammonia_oxidation.html b/pages/traits/metabolism/complete_ammonia_oxidation.html index 66e6ad2acd9..5850461bf69 100644 --- a/pages/traits/metabolism/complete_ammonia_oxidation.html +++ b/pages/traits/metabolism/complete_ammonia_oxidation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,7 +113,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -128,7 +129,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -278,7 +279,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries three discovery and ecological-dominance snippets on comammox Nitrospira (DOI:10.1038/nature16459, DOI:10.1038/nature16461, DOI:10.1128/aem.01698-23) without distinct intermediate nitrite-step or enzyme quotes.

    +

    The current record carries three discovery and ecological-dominance snippets on comammox Nitrospira (DOI:10.1038/nature16459, DOI:10.1038/nature16461, DOI:10.1128/aem.01698-23) without distinct intermediate nitrite-step or enzyme quotes.

    @@ -328,7 +329,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add complete ammonia oxidation trait -

      Minted traitmech:000187 for the complete ammonia oxidation metabolism trait with DOI-backed one-organism ammonia-to-nitrate oxidation evidence from 10.1038/nature16459, 10.1038/nature16461, and 10.1128/aem.01698-23; added Candidatus Nitrospira inopinata as a canonical comammox Nitrospira example; and reserved METPO:1014100 in proposals/metpo_traitmech_v64.

    +

    Minted traitmech:000187 for the complete ammonia oxidation metabolism trait with DOI-backed one-organism ammonia-to-nitrate oxidation evidence from 10.1038/nature16459, 10.1038/nature16461, and 10.1128/aem.01698-23; added Candidatus Nitrospira inopinata as a canonical comammox Nitrospira example; and reserved METPO:1014100 in proposals/metpo_traitmech_v64.

    • Read this curation session @@ -360,7 +361,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -389,12 +399,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/metabolism/dark_hydrogen_oxidation.html b/pages/traits/metabolism/dark_hydrogen_oxidation.html index 285cc930779..2f14de6aca5 100644 --- a/pages/traits/metabolism/dark_hydrogen_oxidation.html +++ b/pages/traits/metabolism/dark_hydrogen_oxidation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • dark_hydrogen_oxidation RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • dark_hydrogen_oxidation RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -116,7 +117,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -212,7 +213,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    The current record carries a single ecological review snippet (DOI:10.3389/fmicb.2018.02873) describing hydrothermal-vent biomass production by hydrogen-oxidizing organisms without enzyme-level or electron-transport claims.

    +

    The current record carries a single ecological review snippet (DOI:10.3389/fmicb.2018.02873) describing hydrothermal-vent biomass production by hydrogen-oxidizing organisms without enzyme-level or electron-transport claims.

    @@ -285,7 +286,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -314,12 +324,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 20:01 UTC diff --git a/pages/traits/metabolism/dark_oxidation_of_sulfur_compounds.html b/pages/traits/metabolism/dark_oxidation_of_sulfur_compounds.html index 7d324dbd07e..be802b8242e 100644 --- a/pages/traits/metabolism/dark_oxidation_of_sulfur_compounds.html +++ b/pages/traits/metabolism/dark_oxidation_of_sulfur_compounds.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • dark_oxidation_of_sulfur_compounds RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • dark_oxidation_of_sulfur_compounds RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -116,7 +117,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -212,7 +213,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    The current record carries a single physiological rate snippet (DOI:10.1111/1462-2920.14543) coupling dark sulfide oxidation to oxygen consumption without enzyme or intermediate assertions.

    +

    The current record carries a single physiological rate snippet (DOI:10.1111/1462-2920.14543) coupling dark sulfide oxidation to oxygen consumption without enzyme or intermediate assertions.

    @@ -285,7 +286,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -314,12 +324,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 20:01 UTC diff --git a/pages/traits/metabolism/degrades.html b/pages/traits/metabolism/degrades.html index 1a7e74f8a61..f5b831ce30e 100644 --- a/pages/traits/metabolism/degrades.html +++ b/pages/traits/metabolism/degrades.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • degradation RELATED_SYNONYM · metpo.owl
      • +
    • degradation RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:2000007 [-1.236, -0.298, -2.385, -0.099, …]
      • +
    • degrades METPO:2000007 [-1.236, -0.298, -2.385, -0.099, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/denitrification.html b/pages/traits/metabolism/denitrification.html index 9fb3c2f8bae..783ab368f83 100644 --- a/pages/traits/metabolism/denitrification.html +++ b/pages/traits/metabolism/denitrification.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,7 +116,7 @@

    Edge evidence

  • denitrification - traitmech:000104 + traitmech:000104 participates in anaerobic respiration GO:0009061 @@ -213,7 +214,7 @@

    Edge evidence

    GO:0050304 part_of denitrification - traitmech:000104 + traitmech:000104

    NosZ is the final-step component of complete denitrification.

      @@ -232,7 +233,7 @@

      Edge evidence

      negatively regulates denitrification - traitmech:000104 + traitmech:000104 RO:0002212

      Oxygen acts as a superordinate repressor of denitrification.

        @@ -365,7 +366,7 @@

        Edge evidence

        associated with denitrification - traitmech:000104 + traitmech:000104 biolink:associated_with

        Complete and partial denitrification phenotypes reflect the pathway's modular distribution across organisms.

          @@ -402,8 +403,8 @@

          Protein and taxon examples

    		•  - Paracoccus denitrificans -
    NCBITaxon:266 + Paracoccus denitrificans +
    NCBITaxon:266         		REVIEWED
    @@ -469,7 +470,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -485,7 +486,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -734,7 +735,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1128/mmbr.61.4.533-616.1997 (already present on ancestor records nitrogen_respiration.yaml and anaerobic_respiration.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 5 Stage 5 remediation of F-C5S4-DEF-SRC-005 in group G-C5S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.1128/mmbr.61.4.533-616.1997 (already present on ancestor records nitrogen_respiration.yaml and anaerobic_respiration.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 5 Stage 5 remediation of F-C5S4-DEF-SRC-005 in group G-C5S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -776,7 +777,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1140,12 +1150,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 21:40 UTC diff --git a/pages/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.html b/pages/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.html index 620f8b006b5..71712d37987 100644 --- a/pages/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.html +++ b/pages/traits/metabolism/dicarboxylate_four_hydroxybutyrate_cycle.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    CHEBI:16526 fixed by dicarboxylate/4-hydroxybutyrate cycle - traitmech:000025 + traitmech:000025 METPO:2007404

    CO2 is fixed by the anaerobic archaeal DC/4HB cycle.

      @@ -115,7 +116,7 @@

      Edge evidence

    • dicarboxylate/4-hydroxybutyrate cycle - traitmech:000025 + traitmech:000025 contributes to carbon fixation GO:0015977 @@ -137,7 +138,7 @@

      Edge evidence

      CHEBI:15379 negatively regulates dicarboxylate/4-hydroxybutyrate cycle - traitmech:000025 + traitmech:000025 RO:0002212

      O2 constrains the cycle because key enzymes and electron carriers are oxygen-sensitive, restricting it to anoxic conditions.

        @@ -327,7 +328,7 @@

        Edge evidence

        GO:0008964 contributes to dicarboxylate/4-hydroxybutyrate cycle - traitmech:000025 + traitmech:000025 RO:0002326

        PEP carboxylase performs one of the two carboxylating reactions that constitute the DC/4HB carbon-fixation cycle.

          @@ -364,8 +365,8 @@

          Protein and taxon examples

    		 - Ignicoccus hospitalis KIN4/I -
    NCBITaxon:453591 + Ignicoccus hospitalis KIN4/I +
    NCBITaxon:453591         		UNREVIEWED
    @@ -431,7 +432,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -447,7 +448,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -765,7 +766,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1129,12 +1139,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/dimethyl_sulfoxide_respiration.html b/pages/traits/metabolism/dimethyl_sulfoxide_respiration.html index a97ddd6d915..a339c66f104 100644 --- a/pages/traits/metabolism/dimethyl_sulfoxide_respiration.html +++ b/pages/traits/metabolism/dimethyl_sulfoxide_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    Trait evidence (5)

    Membrane and extracellular DMSO reductase respiratory pathway

    Evidence-backed metabolic pathway sketch linking dimethyl sulfoxide terminal electron acceptance and DMSO reductase activity to dimethyl sulfoxide respiration.

    -

    MECHANISTIC · Mechanistic graph backed by DOI:10.1073/pnas.0505959103 and DOI:10.1111/1462-2920.15971; exemplified on dmso_respiration_dms_complex with Shewanella oneidensis MR-1 (NCBITaxon:211586; UP000008186) extracellular DMSO reductase subunits DmsA (UniProtKB:Q8EH03) and DmsB (UniProtKB:Q8EH02).

    +

    MECHANISTIC · Mechanistic graph backed by DOI:10.1073/pnas.0505959103 and DOI:10.1111/1462-2920.15971; exemplified on dmso_respiration_dms_complex with Shewanella oneidensis MR-1 (NCBITaxon:211586; UP000008186) extracellular DMSO reductase subunits DmsA (UniProtKB:Q8EH03) and DmsB (UniProtKB:Q8EH02).

    Loading graph…

    @@ -114,7 +115,7 @@

    Edge evidence

  • dimethyl sulfoxide respiration - traitmech:000201 + traitmech:000201 has electron acceptor dimethyl sulfoxide CHEBI:28262 @@ -136,7 +137,7 @@

    Edge evidence

    GO:0009388 confers dimethyl sulfoxide respiration - traitmech:000201 + traitmech:000201 METPO:2007700

    Membrane-associated DMSO reductase activity confers dimethyl sulfoxide respiration.

      @@ -155,7 +156,7 @@

      Edge evidence

      GO:0019645 contributes to dimethyl sulfoxide respiration - traitmech:000201 + traitmech:000201 RO:0002326

      The SO1427-SO1432 gene cluster mediates extracellular anaerobic respiration of DMSO.

        @@ -211,8 +212,8 @@

        Protein and taxon examples

    		•  - Shewanella oneidensis MR-1 -
    NCBITaxon:211586 + Shewanella oneidensis MR-1 +
    NCBITaxon:211586         		UNREVIEWED
    @@ -241,8 +242,8 @@

    Protein and taxon examples

    		 - Shewanella oneidensis MR-1 -
    NCBITaxon:211586 + Shewanella oneidensis MR-1 +
    NCBITaxon:211586         		UNREVIEWED
    @@ -324,7 +325,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -474,7 +475,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The record's primary literature (DOI:10.1073/pnas.0505959103, DOI:10.1111/1462-2920.15971) establishes the SO1427-SO1432 gene cluster required for extracellular DMSO respiration in Shewanella oneidensis MR-1 (NCBITaxon:211586), but verified UniProtKB accessions must be curated on a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    +

    The record's primary literature (DOI:10.1073/pnas.0505959103, DOI:10.1111/1462-2920.15971) establishes the SO1427-SO1432 gene cluster required for extracellular DMSO respiration in Shewanella oneidensis MR-1 (NCBITaxon:211586), but verified UniProtKB accessions must be curated on a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    @@ -493,7 +494,7 @@

    Evidence

    -

    Resolution: Promoted dmso_respiration_reductase_sketch to MECHANISTIC by adding InterPro:IPR011888-grounded GENE_OR_PROTEIN node dmso_respiration_dms_complex with Shewanella oneidensis MR-1 (NCBITaxon:211586; UP000008186) protein_examples UniProtKB:Q8EH03 (DmsA) and UniProtKB:Q8EH02 (DmsB) backed by DOI:10.1073/pnas.0505959103.

    +

    Resolution: Promoted dmso_respiration_reductase_sketch to MECHANISTIC by adding InterPro:IPR011888-grounded GENE_OR_PROTEIN node dmso_respiration_dms_complex with Shewanella oneidensis MR-1 (NCBITaxon:211586; UP000008186) protein_examples UniProtKB:Q8EH03 (DmsA) and UniProtKB:Q8EH02 (DmsB) backed by DOI:10.1073/pnas.0505959103.

    @@ -522,7 +523,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Promoted dmso_respiration_reductase_sketch to MECHANISTIC; added InterPro:IPR011888-grounded GENE_OR_PROTEIN node dmso_respiration_dms_complex with Shewanella oneidensis MR-1 (NCBITaxon:211586; UP000008186) protein_examples UniProtKB:Q8EH03 (DmsA) and UniProtKB:Q8EH02 (DmsB) backed by DOI:10.1073/pnas.0505959103; resolved dimethyl-sulfoxide-respiration-protein-example-gap.

    +

    Promoted dmso_respiration_reductase_sketch to MECHANISTIC; added InterPro:IPR011888-grounded GENE_OR_PROTEIN node dmso_respiration_dms_complex with Shewanella oneidensis MR-1 (NCBITaxon:211586; UP000008186) protein_examples UniProtKB:Q8EH03 (DmsA) and UniProtKB:Q8EH02 (DmsB) backed by DOI:10.1073/pnas.0505959103; resolved dimethyl-sulfoxide-respiration-protein-example-gap.

    • @@ -564,7 +565,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -928,12 +938,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 11:45 UTC diff --git a/pages/traits/metabolism/disproportionates.html b/pages/traits/metabolism/disproportionates.html index d3530cef4ce..0b753a32fc0 100644 --- a/pages/traits/metabolism/disproportionates.html +++ b/pages/traits/metabolism/disproportionates.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • dismutates RELATED_SYNONYM · metpo.owl
      • +
    • dismutates RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/disproportionation.html b/pages/traits/metabolism/disproportionation.html index 42d31317a25..1406c377ff1 100644 --- a/pages/traits/metabolism/disproportionation.html +++ b/pages/traits/metabolism/disproportionation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -138,7 +139,7 @@

    Edge evidence

    example of inorganic sulfur intermediate - rdfs:subClassOf + rdfs:subClassOf

    Elemental sulfur is a disproportionation substrate.

      @@ -157,7 +158,7 @@

      Edge evidence

      example of inorganic sulfur intermediate - rdfs:subClassOf + rdfs:subClassOf

      Thiosulfate is a disproportionation substrate.

        @@ -402,8 +403,8 @@

        Protein and taxon examples

    		 - Acidianus ambivalens -
    NCBITaxon:2283 + Acidianus ambivalens +
    NCBITaxon:2283         		REVIEWED
    @@ -476,7 +477,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -815,7 +816,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1179,12 +1189,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/dissimilatory_iron_reduction.html b/pages/traits/metabolism/dissimilatory_iron_reduction.html index 9b43d7b1138..bbc2fb03ca7 100644 --- a/pages/traits/metabolism/dissimilatory_iron_reduction.html +++ b/pages/traits/metabolism/dissimilatory_iron_reduction.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,7 +116,7 @@

    Edge evidence

  • dissimilatory iron reduction - traitmech:000031 + traitmech:000031 has electron acceptor iron(3+) CHEBI:29034 @@ -134,11 +135,11 @@

    Edge evidence

  • dissimilatory iron reduction - traitmech:000031 + traitmech:000031 is a energy-conserving anaerobic respiration - rdfs:subClassOf + rdfs:subClassOf

    DIR is a form of energy-conserving anaerobic respiration.

      @@ -210,7 +211,7 @@

      Edge evidence

    • dissimilatory iron reduction - traitmech:000031 + traitmech:000031 has electron acceptor solid Fe(III) mineral @@ -229,7 +230,7 @@

      Edge evidence

    • dissimilatory iron reduction - traitmech:000031 + traitmech:000031 has electron acceptor dissolved Fe(III)-organic-matter complex @@ -288,8 +289,8 @@

      Protein and taxon examples

    		•  - Shewanella oneidensis MR-1 -
    NCBITaxon:211586 + Shewanella oneidensis MR-1 +
    NCBITaxon:211586         		UNREVIEWED
    @@ -355,9 +356,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • ferric iron respiration RELATED_SYNONYM · DOI:10.1128/mr.55.2.259-287.1991
      • +
    • ferric iron respiration RELATED_SYNONYM · DOI:10.1128/mr.55.2.259-287.1991
      • -
    • dissimilatory Fe(III) reduction EXACT_SYNONYM · DOI:10.1128/mr.55.2.259-287.1991
      • +
    • dissimilatory Fe(III) reduction EXACT_SYNONYM · DOI:10.1128/mr.55.2.259-287.1991
    @@ -373,7 +374,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -595,7 +596,7 @@

    Curation history

  • · ENRICH_CAUSAL_GRAPH · claude -

    Added 2 evidence-backed edges connecting the stranded Fe(III)-pool component to the trait (issue 183): dir_trait uses electron acceptor solid_fe3_mineral, and dir_trait uses electron acceptor dissolved_fe3_om_complex, both grounded METPO:2000008 to match the established uses-electron-donor convention. Both carry verbatim snippets from PMID:15518832, checked character-for-character against the PubMed abstract rather than lifted from the deep-research report, whose evidence text is paraphrase (issue 247). Resolves this graph's FRAGMENTED_GRAPH and its 2 UNREACHABLE_FROM_TRAIT findings.

    +

    Added 2 evidence-backed edges connecting the stranded Fe(III)-pool component to the trait (issue 183): dir_trait uses electron acceptor solid_fe3_mineral, and dir_trait uses electron acceptor dissolved_fe3_om_complex, both grounded METPO:2000008 to match the established uses-electron-donor convention. Both carry verbatim snippets from PMID:15518832, checked character-for-character against the PubMed abstract rather than lifted from the deep-research report, whose evidence text is paraphrase (issue 247). Resolves this graph's FRAGMENTED_GRAPH and its 2 UNREACHABLE_FROM_TRAIT findings.

  • @@ -629,7 +630,7 @@

    Recorded curation sessions

  • · claude-code
    • EDIT — Connect the stranded Fe(III)-pool component to the trait -

      The pair dissolved_fe3_om_complex -> solid_fe3_mineral had no undirected path to dir_trait, so the graph carried a free-standing geochemical rate comparison beside a respiration mechanism. Both nodes are pools of the acceptor the organism reduces, so dir_trait now uses each as an electron acceptor (METPO:2000008), matching the TRAIT -> CHEMICAL shape of the 13 existing uses-electron-donor edges (METPO:2000009). Both snippets are verbatim from PMID:15518832, pulled via PubMed efetch and compared character-for-character in the same run rather than lifted from the deep-research report, whose evidence text is paraphrase (issue 247). Resolves this graph's FRAGMENTED_GRAPH and 2 UNREACHABLE_FROM_TRAIT findings. Scope caveat recorded in issue 297: the dissolved-pool quote concerns chelators the organism secretes, while the node is ambient Fe(III)-organic-matter complex.

    +

    The pair dissolved_fe3_om_complex -> solid_fe3_mineral had no undirected path to dir_trait, so the graph carried a free-standing geochemical rate comparison beside a respiration mechanism. Both nodes are pools of the acceptor the organism reduces, so dir_trait now uses each as an electron acceptor (METPO:2000008), matching the TRAIT -> CHEMICAL shape of the 13 existing uses-electron-donor edges (METPO:2000009). Both snippets are verbatim from PMID:15518832, pulled via PubMed efetch and compared character-for-character in the same run rather than lifted from the deep-research report, whose evidence text is paraphrase (issue 247). Resolves this graph's FRAGMENTED_GRAPH and 2 UNREACHABLE_FROM_TRAIT findings. Scope caveat recorded in issue 297: the dissolved-pool quote concerns chelators the organism secretes, while the node is ambient Fe(III)-organic-matter complex.

    • Read this curation session @@ -661,7 +662,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1025,12 +1035,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/dissimilatory_manganese_reduction.html b/pages/traits/metabolism/dissimilatory_manganese_reduction.html index 503cb36b4a8..54ce37a39be 100644 --- a/pages/traits/metabolism/dissimilatory_manganese_reduction.html +++ b/pages/traits/metabolism/dissimilatory_manganese_reduction.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,7 +116,7 @@

    Edge evidence

  • dissimilatory manganese reduction - traitmech:000108 + traitmech:000108 has electron acceptor Mn(IV) oxide @@ -137,7 +138,7 @@

    Edge evidence

    is oxidized coupled to dissimilatory manganese reduction - traitmech:000108 + traitmech:000108

    Oxidation of organic matter is coupled to Mn(IV) reduction.

      @@ -156,7 +157,7 @@

      Edge evidence

      CHEBI:18276 donates electrons to dissimilatory manganese reduction - traitmech:000108 + traitmech:000108 METPO:2007403

      H2 serves as electron donor for dissimilatory manganese reduction.

        @@ -175,7 +176,7 @@

        Edge evidence

        confers dissimilatory manganese reduction - traitmech:000108 + traitmech:000108 METPO:2007700

        Anoxic conditions enable anaerobic Mn(IV) respiration.

          @@ -194,7 +195,7 @@

          Edge evidence

          is coupled to dissimilatory manganese reduction - traitmech:000108 + traitmech:000108

          Anaerobic methane oxidation can be coupled to Mn reduction (Fe-Mn-AOM).

            @@ -250,8 +251,8 @@

            Protein and taxon examples

    		•  - Shewanella oneidensis MR-1 -
    NCBITaxon:211586 + Shewanella oneidensis MR-1 +
    NCBITaxon:211586         		UNREVIEWED
    @@ -317,7 +318,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -333,7 +334,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -585,7 +586,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1128/mr.55.2.259-287.1991 (already present on parent record dissimilatory_metal_reduction.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-012 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.1128/mr.55.2.259-287.1991 (already present on parent record dissimilatory_metal_reduction.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-012 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -618,7 +619,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -982,12 +992,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/metabolism/dissimilatory_metal_reduction.html b/pages/traits/metabolism/dissimilatory_metal_reduction.html index 7fcb80c249e..5ea43219e6a 100644 --- a/pages/traits/metabolism/dissimilatory_metal_reduction.html +++ b/pages/traits/metabolism/dissimilatory_metal_reduction.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • dissimilatory metal reduction - traitmech:000039 + traitmech:000039 has electron acceptor terminal electron acceptor METPO:1007504 @@ -115,7 +116,7 @@

    Edge evidence

  • dissimilatory metal reduction - traitmech:000039 + traitmech:000039 participates in anaerobic respiration GO:0009061 @@ -194,7 +195,7 @@

    Edge evidence

    serves as respiratory substrate for dissimilatory metal reduction - traitmech:000039 + traitmech:000039

    Oxidized insoluble metals serve as an abundant respiratory substrate for metal reduction.

      @@ -232,7 +233,7 @@

      Edge evidence

      contributes to dissimilatory metal reduction - traitmech:000039 + traitmech:000039 RO:0002326

      Ferric-iron reduction is a defining process within dissimilatory metal reduction.

        @@ -252,7 +253,7 @@

        Edge evidence

        example of extracellular electron acceptor - rdfs:subClassOf + rdfs:subClassOf

        Oxidized insoluble metals are extracellular respiratory electron acceptors.

          @@ -288,8 +289,8 @@

          Protein and taxon examples

    		•  - Shewanella oneidensis MR-1 -
    NCBITaxon:211586 + Shewanella oneidensis MR-1 +
    NCBITaxon:211586         		UNREVIEWED
    @@ -366,7 +367,7 @@

    Children (2)

    Synonyms (1)

      -
    • dissimilatory metal-ion reduction RELATED_SYNONYM · DOI:10.1128/mr.55.2.259-287.1991
      • +
    • dissimilatory metal-ion reduction RELATED_SYNONYM · DOI:10.1128/mr.55.2.259-287.1991
    @@ -382,7 +383,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -664,7 +665,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1028,12 +1038,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/dissimilatory_nitrate_reduction_to_ammonium.html b/pages/traits/metabolism/dissimilatory_nitrate_reduction_to_ammonium.html index 4f8a8331c55..3fef0f2155b 100644 --- a/pages/traits/metabolism/dissimilatory_nitrate_reduction_to_ammonium.html +++ b/pages/traits/metabolism/dissimilatory_nitrate_reduction_to_ammonium.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    selects for dissimilatory nitrate reduction to ammonium - traitmech:000030 + traitmech:000030 METPO:2007401

    High donor-to-acceptor ratio favors DNRA over denitrification.

      @@ -251,7 +252,7 @@

      Edge evidence

      permits dissimilatory nitrate reduction to ammonium - traitmech:000030 + traitmech:000030

      Anaerobic conditions, sensed via FNR, permit DNRA respiration.

        @@ -270,7 +271,7 @@

        Edge evidence

        GO:0042279 contributes to dissimilatory nitrate reduction to ammonium - traitmech:000030 + traitmech:000030 RO:0002326

        NrfA executes the canonical nitrite-to-ammonium step of DNRA.

          @@ -289,7 +290,7 @@

          Edge evidence

          contributes to dissimilatory nitrate reduction to ammonium - traitmech:000030 + traitmech:000030 RO:0002326

          Regulated expression of the nrf operon supplies the Nrf machinery for DNRA.

            @@ -326,8 +327,8 @@

            Protein and taxon examples

    		 - Wolinella succinogenes ATCC 29543 -
    NCBITaxon:273121 + Wolinella succinogenes ATCC 29543 +
    NCBITaxon:273121         		REVIEWED
    @@ -393,9 +394,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -411,7 +412,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -534,20 +535,20 @@

    Deep research

    | subject | predicate | object | evidence strength/qualifier | DOI | |---|---|---|---|---| -| DNRA | retains | fixed nitrogen as ammonium rather than gaseous N loss | strong; scope-defining contrast with denitrification; ecological framing, not a molecular edge (egas2024anovelmechanism pages 1-2) | 10.1128/msystems.00967-23 | -| NapAB / NarGHI | catalyzes | nitrate → nitrite | strong; canonical DNRA first step; review/background in mechanistic study (egas2024anovelmechanism pages 1-2) | 10.1128/msystems.00967-23 | -| NrfAH | catalyzes | nitrite → ammonium | strong for canonical DNRA pathway as established background; not newly demonstrated in these papers (egas2024anovelmechanism pages 1-2) | 10.1128/msystems.00967-23 | -| octaheme nitrite reductase (ONR) | catalyzes | nitrite → ammonium | strong but taxon-specific; biochemically active in Trichlorobacter ammonificans and expressed during ammonifying growth (sorokin2023trichlorobacterammonificansa pages 2-3, sorokin2023trichlorobacterammonificansa pages 6-7) | 10.1038/s41396-023-01473-2 | -| nitrate-limited conditions | selects for / enriches | Trichlorobacter ammonificans DNRA over denitrifiers | strong but cultivation-specific; enrichment achieved by increasing acetate:nitrate ratio to nitrate-limited conditions (sorokin2023trichlorobacterammonificansa pages 2-3) | 10.1038/s41396-023-01473-2 | -| low redox potential | enables | complete nitrite reduction to ammonia in Trichlorobacter ammonificans | strong but taxon-specific; resting-cell and cultivation evidence (sorokin2023trichlorobacterammonificansa pages 2-3, sorokin2023trichlorobacterammonificansa pages 6-7) | 10.1038/s41396-023-01473-2 | -| high redox potential | increases | N2O formation during nitrite reduction in Trichlorobacter ammonificans | strong but taxon-specific; argues against complete DNRA endpoint under oxidized conditions (sorokin2023trichlorobacterammonificansa pages 2-3) | 10.1038/s41396-023-01473-2 | -| NarK | transports | nitrate into Acididesulfobacillus acetoxydans DNRA pathway | moderate; proposed in pathway model/figure, not directly assayed (egas2024anovelmechanism pages 10-13, egas2024anovelmechanism media 55eb6de8) | 10.1128/msystems.00967-23 | -| NarG | catalyzes | nitrate → nitrite in Acididesulfobacillus acetoxydans | strong; organism encodes Nar-type reductase and pathway model supports first step (egas2024anovelmechanism pages 1-2, egas2024anovelmechanism pages 10-13) | 10.1128/msystems.00967-23 | -| AsrABC | may reduce | nitrite → ammonia in Acididesulfobacillus acetoxydans | uncertain, taxon-specific; authors propose previously undescribed nitrite reductase activity (egas2024anovelmechanism pages 1-2, egas2024anovelmechanism pages 10-13) | 10.1128/msystems.00967-23 | -| DEACI_1836 (putative NirA homolog) | may reduce | nitrite → ammonia in Acididesulfobacillus acetoxydans | uncertain, taxon-specific; inferred candidate enzyme (egas2024anovelmechanism pages 1-2, egas2024anovelmechanism pages 10-13) | 10.1128/msystems.00967-23 | -| nitrite accumulation | upregulates / promotes | DNRA in “Ca. Alkanivorans nitratireducens” | moderate to strong but taxon-specific consortium evidence (wu2024anaerobicoxidationof pages 1-2) | 10.1093/ismejo/wrae063 | -| increased short-chain gaseous alkane supply | promotes | DNRA in “Ca. Alkanivorans nitratireducens” | moderate to strong but taxon-specific; electron-donor increase favored DNRA (wu2024anaerobicoxidationof pages 1-2) | 10.1093/ismejo/wrae063 | -| 40 mT static magnetic field | increases | DNRA potential rate and nrfA enrichment | strong for engineered application; reactor-specific, not general ecology (xie2024usingstaticmagnetic pages 1-2) | 10.1038/s41545-024-00352-3 | +| DNRA | retains | fixed nitrogen as ammonium rather than gaseous N loss | strong; scope-defining contrast with denitrification; ecological framing, not a molecular edge (egas2024anovelmechanism pages 1-2) | 10.1128/msystems.00967-23 | +| NapAB / NarGHI | catalyzes | nitrate → nitrite | strong; canonical DNRA first step; review/background in mechanistic study (egas2024anovelmechanism pages 1-2) | 10.1128/msystems.00967-23 | +| NrfAH | catalyzes | nitrite → ammonium | strong for canonical DNRA pathway as established background; not newly demonstrated in these papers (egas2024anovelmechanism pages 1-2) | 10.1128/msystems.00967-23 | +| octaheme nitrite reductase (ONR) | catalyzes | nitrite → ammonium | strong but taxon-specific; biochemically active in Trichlorobacter ammonificans and expressed during ammonifying growth (sorokin2023trichlorobacterammonificansa pages 2-3, sorokin2023trichlorobacterammonificansa pages 6-7) | 10.1038/s41396-023-01473-2 | +| nitrate-limited conditions | selects for / enriches | Trichlorobacter ammonificans DNRA over denitrifiers | strong but cultivation-specific; enrichment achieved by increasing acetate:nitrate ratio to nitrate-limited conditions (sorokin2023trichlorobacterammonificansa pages 2-3) | 10.1038/s41396-023-01473-2 | +| low redox potential | enables | complete nitrite reduction to ammonia in Trichlorobacter ammonificans | strong but taxon-specific; resting-cell and cultivation evidence (sorokin2023trichlorobacterammonificansa pages 2-3, sorokin2023trichlorobacterammonificansa pages 6-7) | 10.1038/s41396-023-01473-2 | +| high redox potential | increases | N2O formation during nitrite reduction in Trichlorobacter ammonificans | strong but taxon-specific; argues against complete DNRA endpoint under oxidized conditions (sorokin2023trichlorobacterammonificansa pages 2-3) | 10.1038/s41396-023-01473-2 | +| NarK | transports | nitrate into Acididesulfobacillus acetoxydans DNRA pathway | moderate; proposed in pathway model/figure, not directly assayed (egas2024anovelmechanism pages 10-13, egas2024anovelmechanism media 55eb6de8) | 10.1128/msystems.00967-23 | +| NarG | catalyzes | nitrate → nitrite in Acididesulfobacillus acetoxydans | strong; organism encodes Nar-type reductase and pathway model supports first step (egas2024anovelmechanism pages 1-2, egas2024anovelmechanism pages 10-13) | 10.1128/msystems.00967-23 | +| AsrABC | may reduce | nitrite → ammonia in Acididesulfobacillus acetoxydans | uncertain, taxon-specific; authors propose previously undescribed nitrite reductase activity (egas2024anovelmechanism pages 1-2, egas2024anovelmechanism pages 10-13) | 10.1128/msystems.00967-23 | +| DEACI_1836 (putative NirA homolog) | may reduce | nitrite → ammonia in Acididesulfobacillus acetoxydans | uncertain, taxon-specific; inferred candidate enzyme (egas2024anovelmechanism pages 1-2, egas2024anovelmechanism pages 10-13) | 10.1128/msystems.00967-23 | +| nitrite accumulation | upregulates / promotes | DNRA in “Ca. Alkanivorans nitratireducens” | moderate to strong but taxon-specific consortium evidence (wu2024anaerobicoxidationof pages 1-2) | 10.1093/ismejo/wrae063 | +| increased short-chain gaseous alkane supply | promotes | DNRA in “Ca. Alkanivorans nitratireducens” | moderate to strong but taxon-specific; electron-donor increase favored DNRA (wu2024anaerobicoxidationof pages 1-2) | 10.1093/ismejo/wrae063 | +| 40 mT static magnetic field | increases | DNRA potential rate and nrfA enrichment | strong for engineered application; reactor-specific, not general ecology (xie2024usingstaticmagnetic pages 1-2) | 10.1038/s41545-024-00352-3 |

    Showing the first 60 of 276 lines of findings; the linked file also carries the @@ -657,7 +658,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1126/science.1254070 (already present on parent record nitrate_respiration.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-013 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.1126/science.1254070 (already present on parent record nitrate_respiration.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-013 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -699,7 +700,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1063,12 +1073,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/metabolism/dissimilatory_sulfate_reduction.html b/pages/traits/metabolism/dissimilatory_sulfate_reduction.html index 50e958736e4..7316fd78d8a 100644 --- a/pages/traits/metabolism/dissimilatory_sulfate_reduction.html +++ b/pages/traits/metabolism/dissimilatory_sulfate_reduction.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,7 +116,7 @@

    Edge evidence

  • dissimilatory sulfate reduction - traitmech:000105 + traitmech:000105 participates in anaerobic respiration GO:0009061 @@ -289,7 +290,7 @@

    Edge evidence

    CHEBI:16189 participates in dissimilatory sulfate reduction - traitmech:000105 + traitmech:000105 biolink:participates_in

    Sulfate participates in dissimilatory sulfate reduction as the alternative terminal electron acceptor.

      @@ -326,8 +327,8 @@

      Protein and taxon examples

    		•  - Nitratidesulfovibrio vulgaris str. Hildenborough -
    NCBITaxon:882 + Nitratidesulfovibrio vulgaris str. Hildenborough +
    NCBITaxon:882         		REVIEWED
    @@ -356,8 +357,8 @@

    Protein and taxon examples

    		 - Nitratidesulfovibrio vulgaris str. Hildenborough -
    NCBITaxon:882 + Nitratidesulfovibrio vulgaris str. Hildenborough +
    NCBITaxon:882         		REVIEWED
    @@ -423,9 +424,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -448,7 +449,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -727,7 +728,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1091,12 +1101,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/does_not_accumulate.html b/pages/traits/metabolism/does_not_accumulate.html index a56d6412052..d3a922e8b99 100644 --- a/pages/traits/metabolism/does_not_accumulate.html +++ b/pages/traits/metabolism/does_not_accumulate.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -243,7 +244,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -272,12 +282,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_assimilate.html b/pages/traits/metabolism/does_not_assimilate.html index 81507995c16..20160e9b5c7 100644 --- a/pages/traits/metabolism/does_not_assimilate.html +++ b/pages/traits/metabolism/does_not_assimilate.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • assimilation RELATED_SYNONYM · metpo.owl
      • +
    • assimilation RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_build_acid_from.html b/pages/traits/metabolism/does_not_build_acid_from.html index 5555c60723a..e9e5fb6a898 100644 --- a/pages/traits/metabolism/does_not_build_acid_from.html +++ b/pages/traits/metabolism/does_not_build_acid_from.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • builds acid from RELATED_SYNONYM · metpo.owl
      • +
    • builds acid from RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_build_base_from.html b/pages/traits/metabolism/does_not_build_base_from.html index 553a1292647..a034bb6ff9f 100644 --- a/pages/traits/metabolism/does_not_build_base_from.html +++ b/pages/traits/metabolism/does_not_build_base_from.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • builds base from RELATED_SYNONYM · metpo.owl
      • +
    • builds base from RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_build_gas_from.html b/pages/traits/metabolism/does_not_build_gas_from.html index 5e37aa0592e..dcbeb9b3992 100644 --- a/pages/traits/metabolism/does_not_build_gas_from.html +++ b/pages/traits/metabolism/does_not_build_gas_from.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • builds gas from RELATED_SYNONYM · metpo.owl
      • +
    • builds gas from RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_compartmentalize.html b/pages/traits/metabolism/does_not_compartmentalize.html index 467fa1455cb..25daaff3651 100644 --- a/pages/traits/metabolism/does_not_compartmentalize.html +++ b/pages/traits/metabolism/does_not_compartmentalize.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -232,7 +233,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -261,12 +271,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_degrade.html b/pages/traits/metabolism/does_not_degrade.html index 7c7b9c8d57b..89afb9d930a 100644 --- a/pages/traits/metabolism/does_not_degrade.html +++ b/pages/traits/metabolism/does_not_degrade.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • degradation RELATED_SYNONYM · metpo.owl
      • +
    • degradation RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_disproportionate.html b/pages/traits/metabolism/does_not_disproportionate.html index 6c321554e51..85b6941a133 100644 --- a/pages/traits/metabolism/does_not_disproportionate.html +++ b/pages/traits/metabolism/does_not_disproportionate.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • dismutates RELATED_SYNONYM · metpo.owl
      • +
    • dismutates RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_export.html b/pages/traits/metabolism/does_not_export.html index 20636f2c56c..6d806d313d4 100644 --- a/pages/traits/metabolism/does_not_export.html +++ b/pages/traits/metabolism/does_not_export.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -232,7 +233,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -261,12 +271,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_ferment.html b/pages/traits/metabolism/does_not_ferment.html index bcd347afd22..3cdcadbe93d 100644 --- a/pages/traits/metabolism/does_not_ferment.html +++ b/pages/traits/metabolism/does_not_ferment.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • fermentation RELATED_SYNONYM · metpo.owl
      • +
    • fermentation RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_hydrolyze.html b/pages/traits/metabolism/does_not_hydrolyze.html index 27d2f3338e3..e93cf480336 100644 --- a/pages/traits/metabolism/does_not_hydrolyze.html +++ b/pages/traits/metabolism/does_not_hydrolyze.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • hydrolysis RELATED_SYNONYM · metpo.owl
      • +
    • hydrolysis RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_import.html b/pages/traits/metabolism/does_not_import.html index 812a1d2afc5..c3a7db2bc52 100644 --- a/pages/traits/metabolism/does_not_import.html +++ b/pages/traits/metabolism/does_not_import.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -232,7 +233,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -261,12 +271,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_oxidize.html b/pages/traits/metabolism/does_not_oxidize.html index edadfd4893a..58ae1c8ef36 100644 --- a/pages/traits/metabolism/does_not_oxidize.html +++ b/pages/traits/metabolism/does_not_oxidize.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • oxidation RELATED_SYNONYM · metpo.owl
      • +
    • oxidation RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_produce.html b/pages/traits/metabolism/does_not_produce.html index 138b15687f1..0718d906829 100644 --- a/pages/traits/metabolism/does_not_produce.html +++ b/pages/traits/metabolism/does_not_produce.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • produces RELATED_SYNONYM · metpo.owl
      • +
    • produces RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_reduce.html b/pages/traits/metabolism/does_not_reduce.html index ba7e9972f92..8e45a30d4f0 100644 --- a/pages/traits/metabolism/does_not_reduce.html +++ b/pages/traits/metabolism/does_not_reduce.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • reduction RELATED_SYNONYM · metpo.owl
      • +
    • reduction RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_sequester.html b/pages/traits/metabolism/does_not_sequester.html index 3dd39fa864e..858330ad56c 100644 --- a/pages/traits/metabolism/does_not_sequester.html +++ b/pages/traits/metabolism/does_not_sequester.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -232,7 +233,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -261,12 +271,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_show_activity_of.html b/pages/traits/metabolism/does_not_show_activity_of.html index a313b31b156..2a73b7d48ef 100644 --- a/pages/traits/metabolism/does_not_show_activity_of.html +++ b/pages/traits/metabolism/does_not_show_activity_of.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Physiology and metabolism.enzymes.[].activity RELATED_SYNONYM · metpo.owl
      • +
    • Physiology and metabolism.enzymes.[].activity RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_transport.html b/pages/traits/metabolism/does_not_transport.html index 021f6b9c847..dbe6af80b4d 100644 --- a/pages/traits/metabolism/does_not_transport.html +++ b/pages/traits/metabolism/does_not_transport.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -243,7 +244,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -272,12 +282,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_use_as_carbon_source.html b/pages/traits/metabolism/does_not_use_as_carbon_source.html index 711c5b9d4bd..c5bdaeead87 100644 --- a/pages/traits/metabolism/does_not_use_as_carbon_source.html +++ b/pages/traits/metabolism/does_not_use_as_carbon_source.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • carbon source RELATED_SYNONYM · metpo.owl
      • +
    • carbon source RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_use_as_electron_acceptor.html b/pages/traits/metabolism/does_not_use_as_electron_acceptor.html index b6d449e12d0..6ed8f39e900 100644 --- a/pages/traits/metabolism/does_not_use_as_electron_acceptor.html +++ b/pages/traits/metabolism/does_not_use_as_electron_acceptor.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • electron acceptor RELATED_SYNONYM · metpo.owl
      • +
    • electron acceptor RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_use_as_electron_donor.html b/pages/traits/metabolism/does_not_use_as_electron_donor.html index 702a4a80881..08752bdf9a6 100644 --- a/pages/traits/metabolism/does_not_use_as_electron_donor.html +++ b/pages/traits/metabolism/does_not_use_as_electron_donor.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • electron donor RELATED_SYNONYM · metpo.owl
      • +
    • electron donor RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_use_as_energy_source.html b/pages/traits/metabolism/does_not_use_as_energy_source.html index 12e1be8dd3e..1d1610cfe77 100644 --- a/pages/traits/metabolism/does_not_use_as_energy_source.html +++ b/pages/traits/metabolism/does_not_use_as_energy_source.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • energy source RELATED_SYNONYM · metpo.owl
      • +
    • energy source RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_use_as_nitrogen_source.html b/pages/traits/metabolism/does_not_use_as_nitrogen_source.html index 5cd507e5c6a..850f525b624 100644 --- a/pages/traits/metabolism/does_not_use_as_nitrogen_source.html +++ b/pages/traits/metabolism/does_not_use_as_nitrogen_source.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • nitrogen source RELATED_SYNONYM · metpo.owl
      • +
    • nitrogen source RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Curation history

  • · TIGHTENED_RANGE_TO_CHEBI_SUBCLASS · claude -

    Narrowed range_ from http://purl.obolibrary.org/obo/CHEBI_24431 to http://purl.obolibrary.org/obo/CHEBI_51143 ('nitrogen molecular entity'). The earlier CHEBI:24431 root was used as a safe default during bulk un-deprecation (PR #54); the more specific CHEBI subclass better reflects the predicate's intended substrates.

    +

    Narrowed range_ from http://purl.obolibrary.org/obo/CHEBI_24431 to http://purl.obolibrary.org/obo/CHEBI_51143 ('nitrogen molecular entity'). The earlier CHEBI:24431 root was used as a safe default during bulk un-deprecation (PR #54); the more specific CHEBI subclass better reflects the predicate's intended substrates.

    • @@ -247,7 +248,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -276,12 +286,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 16:35 UTC diff --git a/pages/traits/metabolism/does_not_use_as_sulfur_source.html b/pages/traits/metabolism/does_not_use_as_sulfur_source.html index 857008e6ac1..7798d3cb51b 100644 --- a/pages/traits/metabolism/does_not_use_as_sulfur_source.html +++ b/pages/traits/metabolism/does_not_use_as_sulfur_source.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • sulfur source RELATED_SYNONYM · metpo.owl
      • +
    • sulfur source RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Curation history

  • · TIGHTENED_RANGE_TO_CHEBI_SUBCLASS · claude -

    Narrowed range_ from http://purl.obolibrary.org/obo/CHEBI_24431 to http://purl.obolibrary.org/obo/CHEBI_26835 ('sulfur molecular entity'). The earlier CHEBI:24431 root was used as a safe default during bulk un-deprecation (PR #54); the more specific CHEBI subclass better reflects the predicate's intended substrates.

    +

    Narrowed range_ from http://purl.obolibrary.org/obo/CHEBI_24431 to http://purl.obolibrary.org/obo/CHEBI_26835 ('sulfur molecular entity'). The earlier CHEBI:24431 root was used as a safe default during bulk un-deprecation (PR #54); the more specific CHEBI subclass better reflects the predicate's intended substrates.

    • @@ -247,7 +248,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -276,12 +286,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 16:35 UTC diff --git a/pages/traits/metabolism/does_not_use_for_aerobic_catabolization.html b/pages/traits/metabolism/does_not_use_for_aerobic_catabolization.html index 82282bf5f41..b89c2ee31ed 100644 --- a/pages/traits/metabolism/does_not_use_for_aerobic_catabolization.html +++ b/pages/traits/metabolism/does_not_use_for_aerobic_catabolization.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • aerobic catabolization RELATED_SYNONYM · metpo.owl
      • +
    • aerobic catabolization RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_use_for_aerobic_growth.html b/pages/traits/metabolism/does_not_use_for_aerobic_growth.html index b9cc40a989a..3cc716c4b25 100644 --- a/pages/traits/metabolism/does_not_use_for_aerobic_growth.html +++ b/pages/traits/metabolism/does_not_use_for_aerobic_growth.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • aerobic growth RELATED_SYNONYM · metpo.owl
      • +
    • aerobic growth RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_use_for_anaerobic_catabolization.html b/pages/traits/metabolism/does_not_use_for_anaerobic_catabolization.html index e490da3f6b0..b936b1c4b1f 100644 --- a/pages/traits/metabolism/does_not_use_for_anaerobic_catabolization.html +++ b/pages/traits/metabolism/does_not_use_for_anaerobic_catabolization.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • anaerobic catabolization RELATED_SYNONYM · metpo.owl
      • +
    • anaerobic catabolization RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_use_for_anaerobic_growth.html b/pages/traits/metabolism/does_not_use_for_anaerobic_growth.html index 85d59dc1a1a..ab3a62d1293 100644 --- a/pages/traits/metabolism/does_not_use_for_anaerobic_growth.html +++ b/pages/traits/metabolism/does_not_use_for_anaerobic_growth.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • anaerobic growth RELATED_SYNONYM · metpo.owl
      • +
    • anaerobic growth RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_use_for_anaerobic_growth_in_the_dark.html b/pages/traits/metabolism/does_not_use_for_anaerobic_growth_in_the_dark.html index 53059f94bb5..69db3efc92c 100644 --- a/pages/traits/metabolism/does_not_use_for_anaerobic_growth_in_the_dark.html +++ b/pages/traits/metabolism/does_not_use_for_anaerobic_growth_in_the_dark.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • anaerobic growth in the dark RELATED_SYNONYM · metpo.owl
      • +
    • anaerobic growth in the dark RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_use_for_anaerobic_growth_with_light.html b/pages/traits/metabolism/does_not_use_for_anaerobic_growth_with_light.html index 5fe6819ed42..8b1a9aa7e73 100644 --- a/pages/traits/metabolism/does_not_use_for_anaerobic_growth_with_light.html +++ b/pages/traits/metabolism/does_not_use_for_anaerobic_growth_with_light.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • anaerobic growth with light RELATED_SYNONYM · metpo.owl
      • +
    • anaerobic growth with light RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_use_for_growth.html b/pages/traits/metabolism/does_not_use_for_growth.html index 3774c5b0636..bcb25eb6644 100644 --- a/pages/traits/metabolism/does_not_use_for_growth.html +++ b/pages/traits/metabolism/does_not_use_for_growth.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • growth RELATED_SYNONYM · metpo.owl
      • +
    • growth RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_use_for_respiration.html b/pages/traits/metabolism/does_not_use_for_respiration.html index fabc02da04a..9de850f1594 100644 --- a/pages/traits/metabolism/does_not_use_for_respiration.html +++ b/pages/traits/metabolism/does_not_use_for_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • respiration RELATED_SYNONYM · metpo.owl
      • +
    • respiration RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/does_not_use_in_other_way.html b/pages/traits/metabolism/does_not_use_in_other_way.html index 12ad08cf766..3aad7c69c79 100644 --- a/pages/traits/metabolism/does_not_use_in_other_way.html +++ b/pages/traits/metabolism/does_not_use_in_other_way.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • other RELATED_SYNONYM · metpo.owl
      • +
    • other RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/electron_transfer.html b/pages/traits/metabolism/electron_transfer.html index 19b806b1a96..184dfc64213 100644 --- a/pages/traits/metabolism/electron_transfer.html +++ b/pages/traits/metabolism/electron_transfer.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -157,7 +158,7 @@

    Edge evidence

    example of redox protein - rdfs:subClassOf + rdfs:subClassOf

    c-type cytochromes are electron-transfer proteins.

      @@ -385,7 +386,7 @@

      Edge evidence

      example of c-type cytochrome - rdfs:subClassOf + rdfs:subClassOf

      Cytochrome c is a mobile member of the cytochrome electron-carrier class.

        @@ -421,8 +422,8 @@

        Protein and taxon examples

    		 - Shewanella oneidensis MR-1 -
    NCBITaxon:211586 + Shewanella oneidensis MR-1 +
    NCBITaxon:211586         		UNREVIEWED
    @@ -495,7 +496,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -864,7 +865,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1228,12 +1238,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/enzyme_activity_analyzed.html b/pages/traits/metabolism/enzyme_activity_analyzed.html index 50f7911eaab..aef9959faed 100644 --- a/pages/traits/metabolism/enzyme_activity_analyzed.html +++ b/pages/traits/metabolism/enzyme_activity_analyzed.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -102,7 +103,7 @@

    Children (2)

    Synonyms (1)

      -
    • Physiology and metabolism.enzymes.[].activity RELATED_SYNONYM · metpo.owl
      • +
    • Physiology and metabolism.enzymes.[].activity RELATED_SYNONYM · metpo.owl
    @@ -118,7 +119,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -243,7 +244,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -272,12 +282,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/ethanol_fermentation.html b/pages/traits/metabolism/ethanol_fermentation.html index ae0fc379ad8..8359f4936ee 100644 --- a/pages/traits/metabolism/ethanol_fermentation.html +++ b/pages/traits/metabolism/ethanol_fermentation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • ethanol fermentation - traitmech:000028 + traitmech:000028 participates in fermentation GO:0006113 @@ -115,7 +116,7 @@

    Edge evidence

  • ethanol fermentation - traitmech:000028 + traitmech:000028 produces ethanol CHEBI:16236 @@ -288,8 +289,8 @@

    Protein and taxon examples

    		•  - Zymomonas mobilis subsp. mobilis ZM4 -
    NCBITaxon:264203 + Zymomonas mobilis subsp. mobilis ZM4 +
    NCBITaxon:264203         		REVIEWED
    @@ -355,9 +356,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -380,7 +381,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -668,7 +669,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.3389/fmicb.2021.703525 (already present on causal_graphs[0].edges[0].evidence[0]) to record-level evidence[1] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-007 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.3389/fmicb.2021.703525 (already present on causal_graphs[0].edges[0].evidence[0]) to record-level evidence[1] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-007 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -701,7 +702,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1065,12 +1075,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/metabolism/exports.html b/pages/traits/metabolism/exports.html index cd74880dcbe..090f6d4dfc3 100644 --- a/pages/traits/metabolism/exports.html +++ b/pages/traits/metabolism/exports.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:2000209 [-1.508, -0.086, -2.445, -0.073, …]
      • +
    • exports METPO:2000209 [-1.508, -0.086, -2.445, -0.073, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -232,7 +233,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -261,12 +271,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/fermentation.html b/pages/traits/metabolism/fermentation.html index 55802e4eaa5..41a3d65f98e 100644 --- a/pages/traits/metabolism/fermentation.html +++ b/pages/traits/metabolism/fermentation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -156,7 +157,7 @@

    Edge evidence

    METPO:1002005 conserves energy by substrate-level phosphorylation - METPO:1000804 + METPO:1000804

    Substrate-level phosphorylation is a major fermentative energy-conservation route.

    		 - Clostridium acetobutylicum ATCC 824 -
    NCBITaxon:272562 + Clostridium acetobutylicum ATCC 824 +
    NCBITaxon:272562         		UNREVIEWED
    @@ -508,7 +509,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -874,7 +875,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1238,12 +1248,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/fermentative_hydrogen_production.html b/pages/traits/metabolism/fermentative_hydrogen_production.html index 1eb6b4188db..56598ffe986 100644 --- a/pages/traits/metabolism/fermentative_hydrogen_production.html +++ b/pages/traits/metabolism/fermentative_hydrogen_production.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • fermentative hydrogen production - traitmech:000109 + traitmech:000109 participates in fermentation GO:0006113 @@ -115,7 +116,7 @@

    Edge evidence

  • fermentative hydrogen production - traitmech:000109 + traitmech:000109 produces molecular hydrogen CHEBI:18276 @@ -156,7 +157,7 @@

    Edge evidence

    stimulates fermentative hydrogen production - traitmech:000109 + traitmech:000109

    Low ambient H2 partial pressure stimulates H2 formation.

      @@ -175,7 +176,7 @@

      Edge evidence

      inhibits fermentative hydrogen production - traitmech:000109 + traitmech:000109 RO:0002212

      High ambient H2 partial pressure inhibits H2 formation (product feedback).

        @@ -194,7 +195,7 @@

        Edge evidence

        PATO:0001842 affects fermentative hydrogen production - traitmech:000109 + traitmech:000109

        pH affects the activity of hydrogenase enzymes and thus dark fermentative H2 yield.

          @@ -231,8 +232,8 @@

          Protein and taxon examples

    		•  - Thermotoga maritima MSB8 -
    NCBITaxon:243274 + Thermotoga maritima MSB8 +
    NCBITaxon:243274         		REVIEWED
    @@ -298,7 +299,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -314,7 +315,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -554,7 +555,7 @@

    Curation history

  • · REVIEW_EVIDENCE_REFERENCE_CHURN · codex -

    Offline review for issue 520 retained 1 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.3390/en16083321 -> DOI:10.1128/JB.01582-08 (1 edge).

    +

    Offline review for issue 520 retained 1 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.3390/en16083321 -> DOI:10.1128/JB.01582-08 (1 edge).

  • @@ -566,7 +567,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.3389/fmicb.2021.703525 (already present on sibling ethanol_fermentation.yaml and lactic_acid_fermentation.yaml causal_graphs[0].edges[0].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-010 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.3389/fmicb.2021.703525 (already present on sibling ethanol_fermentation.yaml and lactic_acid_fermentation.yaml causal_graphs[0].edges[0].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-010 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -599,7 +600,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -963,12 +973,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/metabolism/ferments.html b/pages/traits/metabolism/ferments.html index 50494edd6ca..8ff5171f0ac 100644 --- a/pages/traits/metabolism/ferments.html +++ b/pages/traits/metabolism/ferments.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • fermentation RELATED_SYNONYM · metpo.owl
      • +
    • fermentation RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:2000011 [-1.137, -0.154, -2.250, -0.147, …]
      • +
    • ferments METPO:2000011 [-1.137, -0.154, -2.250, -0.147, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/fumarate_respiration.html b/pages/traits/metabolism/fumarate_respiration.html index 7a2fc52d645..7e8a74e2b08 100644 --- a/pages/traits/metabolism/fumarate_respiration.html +++ b/pages/traits/metabolism/fumarate_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -82,7 +83,7 @@

    Trait evidence (3)

    NADH dehydrogenase to fumarate reductase anaerobic respiratory chain

    Evidence-backed metabolic pathway sketch linking NADH dehydrogenase activity, fumarate reductase (FRD) catalysis, and succinate production to fumarate respiration.

    -

    NONMECHANISTIC · Pathway-and-activity sketch backed by DOI:10.1128/mBio.03238-19 and DOI:10.1128/JB.00389-22; strain-matched UniProtKB protein examples for Bacteroides fragilis fumarate reductase subunits (FrdCAB) remain to be curated.

    +

    NONMECHANISTIC · Pathway-and-activity sketch backed by DOI:10.1128/mBio.03238-19 and DOI:10.1128/JB.00389-22; strain-matched UniProtKB protein examples for Bacteroides fragilis fumarate reductase subunits (FrdCAB) remain to be curated.

    Loading graph…

    @@ -143,7 +144,7 @@

    Edge evidence

    GO:0000104 confers fumarate respiration - traitmech:000196 + traitmech:000196 METPO:2007700

    Synthesis and catalytic activity of fumarate reductase under anaerobic and nanaerobic conditions confers fumarate respiration.

      @@ -203,7 +204,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • anaerobic respiration on fumarate RELATED_SYNONYM · DOI:10.1128/JB.00389-22
        • +
      • anaerobic respiration on fumarate RELATED_SYNONYM · DOI:10.1128/JB.00389-22
    @@ -219,7 +220,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -369,7 +370,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The record's primary literature (DOI:10.1128/mBio.03238-19, DOI:10.1128/JB.00389-22) establishes fumarate reductase (FRD) catalysis and NADH-to-fumarate respiratory electron transfer in Bacteroides fragilis (NCBITaxon:817), but verified UniProtKB accessions must be curated on a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    +

    The record's primary literature (DOI:10.1128/mBio.03238-19, DOI:10.1128/JB.00389-22) establishes fumarate reductase (FRD) catalysis and NADH-to-fumarate respiratory electron transfer in Bacteroides fragilis (NCBITaxon:817), but verified UniProtKB accessions must be curated on a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    @@ -462,7 +463,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -826,12 +836,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 11:45 UTC diff --git a/pages/traits/metabolism/has_growth_nacl_observation.html b/pages/traits/metabolism/has_growth_nacl_observation.html index 45578deb341..8f8d5803013 100644 --- a/pages/traits/metabolism/has_growth_nacl_observation.html +++ b/pages/traits/metabolism/has_growth_nacl_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_growth_oxygen_observation.html b/pages/traits/metabolism/has_growth_oxygen_observation.html index a33213db324..3dbbe00cad4 100644 --- a/pages/traits/metabolism/has_growth_oxygen_observation.html +++ b/pages/traits/metabolism/has_growth_oxygen_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_growth_ph_observation.html b/pages/traits/metabolism/has_growth_ph_observation.html index d986b87e88e..1ecd03d00bf 100644 --- a/pages/traits/metabolism/has_growth_ph_observation.html +++ b/pages/traits/metabolism/has_growth_ph_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_growth_temperature_observation.html b/pages/traits/metabolism/has_growth_temperature_observation.html index 0b749286eec..c3f5bfd8c8b 100644 --- a/pages/traits/metabolism/has_growth_temperature_observation.html +++ b/pages/traits/metabolism/has_growth_temperature_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_nacl_delta_observation.html b/pages/traits/metabolism/has_nacl_delta_observation.html index 45098f72b6a..996f4296cf4 100644 --- a/pages/traits/metabolism/has_nacl_delta_observation.html +++ b/pages/traits/metabolism/has_nacl_delta_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_nacl_observation.html b/pages/traits/metabolism/has_nacl_observation.html index 25328d5f92d..dfe442c6af0 100644 --- a/pages/traits/metabolism/has_nacl_observation.html +++ b/pages/traits/metabolism/has_nacl_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -109,7 +110,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_observation.html b/pages/traits/metabolism/has_observation.html index 72c364fd849..b2e3ebb32c6 100644 --- a/pages/traits/metabolism/has_observation.html +++ b/pages/traits/metabolism/has_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -98,7 +99,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -230,7 +231,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -259,12 +269,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_optimum_nacl_observation.html b/pages/traits/metabolism/has_optimum_nacl_observation.html index 129c1820780..a5dc31279bc 100644 --- a/pages/traits/metabolism/has_optimum_nacl_observation.html +++ b/pages/traits/metabolism/has_optimum_nacl_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_optimum_oxygen_observation.html b/pages/traits/metabolism/has_optimum_oxygen_observation.html index cb14b360f8a..9c02ab1fd79 100644 --- a/pages/traits/metabolism/has_optimum_oxygen_observation.html +++ b/pages/traits/metabolism/has_optimum_oxygen_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_optimum_ph_observation.html b/pages/traits/metabolism/has_optimum_ph_observation.html index 9bc4da12e7f..f14c8c45305 100644 --- a/pages/traits/metabolism/has_optimum_ph_observation.html +++ b/pages/traits/metabolism/has_optimum_ph_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_optimum_temperature_observation.html b/pages/traits/metabolism/has_optimum_temperature_observation.html index f46b2c92804..3f2ef20f026 100644 --- a/pages/traits/metabolism/has_optimum_temperature_observation.html +++ b/pages/traits/metabolism/has_optimum_temperature_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_oxygen_delta_observation.html b/pages/traits/metabolism/has_oxygen_delta_observation.html index dabe492b9f7..4441fe9e243 100644 --- a/pages/traits/metabolism/has_oxygen_delta_observation.html +++ b/pages/traits/metabolism/has_oxygen_delta_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_oxygen_observation.html b/pages/traits/metabolism/has_oxygen_observation.html index f85efc4a35c..54723e41fbe 100644 --- a/pages/traits/metabolism/has_oxygen_observation.html +++ b/pages/traits/metabolism/has_oxygen_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -109,7 +110,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_ph_delta_observation.html b/pages/traits/metabolism/has_ph_delta_observation.html index 49b56710ee2..3e5e8a0901c 100644 --- a/pages/traits/metabolism/has_ph_delta_observation.html +++ b/pages/traits/metabolism/has_ph_delta_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_ph_observation.html b/pages/traits/metabolism/has_ph_observation.html index 417f01616cb..5212b6df891 100644 --- a/pages/traits/metabolism/has_ph_observation.html +++ b/pages/traits/metabolism/has_ph_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -109,7 +110,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_phenotype.html b/pages/traits/metabolism/has_phenotype.html index c566b930f56..8d1335bab06 100644 --- a/pages/traits/metabolism/has_phenotype.html +++ b/pages/traits/metabolism/has_phenotype.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -237,7 +238,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -266,12 +276,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 01:14 UTC diff --git a/pages/traits/metabolism/has_quality.html b/pages/traits/metabolism/has_quality.html index 607da48da8c..fdc0bfddf24 100644 --- a/pages/traits/metabolism/has_quality.html +++ b/pages/traits/metabolism/has_quality.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -237,7 +238,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -266,12 +276,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 01:14 UTC diff --git a/pages/traits/metabolism/has_range_nacl_observation.html b/pages/traits/metabolism/has_range_nacl_observation.html index 1020ce7dcea..850f0ea5e93 100644 --- a/pages/traits/metabolism/has_range_nacl_observation.html +++ b/pages/traits/metabolism/has_range_nacl_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_range_oxygen_observation.html b/pages/traits/metabolism/has_range_oxygen_observation.html index 2061a6b9382..7e11441c48f 100644 --- a/pages/traits/metabolism/has_range_oxygen_observation.html +++ b/pages/traits/metabolism/has_range_oxygen_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_range_ph_observation.html b/pages/traits/metabolism/has_range_ph_observation.html index 11b0824cb37..47c800e1503 100644 --- a/pages/traits/metabolism/has_range_ph_observation.html +++ b/pages/traits/metabolism/has_range_ph_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_range_temperature_observation.html b/pages/traits/metabolism/has_range_temperature_observation.html index 11ebc7090b5..8efcab97bdc 100644 --- a/pages/traits/metabolism/has_range_temperature_observation.html +++ b/pages/traits/metabolism/has_range_temperature_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_temperature_delta_observation.html b/pages/traits/metabolism/has_temperature_delta_observation.html index 62cd8b03746..c8afe8b675d 100644 --- a/pages/traits/metabolism/has_temperature_delta_observation.html +++ b/pages/traits/metabolism/has_temperature_delta_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/has_temperature_observation.html b/pages/traits/metabolism/has_temperature_observation.html index 0c8705181e9..7dd3215a259 100644 --- a/pages/traits/metabolism/has_temperature_observation.html +++ b/pages/traits/metabolism/has_temperature_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -109,7 +110,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/metabolism/homoacetogenesis.html b/pages/traits/metabolism/homoacetogenesis.html index 4bc1f2e101c..eea16d7f812 100644 --- a/pages/traits/metabolism/homoacetogenesis.html +++ b/pages/traits/metabolism/homoacetogenesis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -537,8 +538,8 @@

    Protein and taxon examples

    		 - Neomoorella thermoacetica -
    NCBITaxon:1525 + Neomoorella thermoacetica +
    NCBITaxon:1525         		REVIEWED
    @@ -604,9 +605,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • Reductive acetyl-CoA pathway RELATED_SYNONYM · metpo.owl
      • +
    • Reductive acetyl-CoA pathway RELATED_SYNONYM · metpo.owl
      • -
    • Wood-Ljungdahl pathway RELATED_SYNONYM · metpo.owl
      • +
    • Wood-Ljungdahl pathway RELATED_SYNONYM · metpo.owl
    @@ -622,7 +623,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -928,7 +929,7 @@

    Curation history

  • · RESTORE_CANONICAL_CITATION · claude -

    Restored the canonical-example citation for NCBITaxon:33952 from DOI:10.1128/JB.00357-18 back to PMID:22479398 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.

    +

    Restored the canonical-example citation for NCBITaxon:33952 from DOI:10.1128/JB.00357-18 back to PMID:22479398 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.

  • @@ -988,7 +989,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1352,12 +1362,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/hydrocarbon_degradation.html b/pages/traits/metabolism/hydrocarbon_degradation.html index 20a08694712..490454a1e92 100644 --- a/pages/traits/metabolism/hydrocarbon_degradation.html +++ b/pages/traits/metabolism/hydrocarbon_degradation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -109,7 +110,7 @@

    Children (1)

    Synonyms (1)

      -
    • hydrocarbon_degradation RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • hydrocarbon_degradation RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -132,7 +133,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -228,7 +229,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    The current record carries a single high-level review snippet (DOI:10.1128/MR.54.3.305-315.1990) stating that hydrocarbons are degraded primarily by bacteria and fungi, which is insufficient to ground a multi-edge mechanism graph without inventing unsupported edges.

    +

    The current record carries a single high-level review snippet (DOI:10.1128/MR.54.3.305-315.1990) stating that hydrocarbons are degraded primarily by bacteria and fungi, which is insufficient to ground a multi-edge mechanism graph without inventing unsupported edges.

    @@ -301,7 +302,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -330,12 +340,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 20:01 UTC diff --git a/pages/traits/metabolism/hydrogenotrophic_methanogenesis.html b/pages/traits/metabolism/hydrogenotrophic_methanogenesis.html index adb0bdd489d..c9cfe891407 100644 --- a/pages/traits/metabolism/hydrogenotrophic_methanogenesis.html +++ b/pages/traits/metabolism/hydrogenotrophic_methanogenesis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,9 +101,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • hydrogenotrophic_methanogenesis RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • hydrogenotrophic_methanogenesis RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • -
    • methanogenesis_by_CO2_reduction_with_H2 RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • methanogenesis_by_CO2_reduction_with_H2 RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -118,7 +119,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    The current record carries a single 26-character phrase ('from CO2 and H2 to methane' in DOI:10.1146/annurev-micro-011720-122807); building a multi-edge graph from one short phrase would violate the snippet-diversity and anti-clause-splitting rules.

    +

    The current record carries a single 26-character phrase ('from CO2 and H2 to methane' in DOI:10.1146/annurev-micro-011720-122807); building a multi-edge graph from one short phrase would violate the snippet-diversity and anti-clause-splitting rules.

    @@ -287,7 +288,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -316,12 +326,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 20:01 UTC diff --git a/pages/traits/metabolism/hydrolyzes.html b/pages/traits/metabolism/hydrolyzes.html index 58727737c9a..d3a73ba754d 100644 --- a/pages/traits/metabolism/hydrolyzes.html +++ b/pages/traits/metabolism/hydrolyzes.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • hydrolysis RELATED_SYNONYM · metpo.owl
      • +
    • hydrolysis RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:2000013 [-1.446, -0.206, -2.474, +0.001, …]
      • +
    • hydrolyzes METPO:2000013 [-1.446, -0.206, -2.474, +0.001, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/imports.html b/pages/traits/metabolism/imports.html index 70b8b5969d0..92451a45f5e 100644 --- a/pages/traits/metabolism/imports.html +++ b/pages/traits/metabolism/imports.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:2000208 [-1.353, -0.126, -2.494, -0.028, …]
      • +
    • imports METPO:2000208 [-1.353, -0.126, -2.494, -0.028, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -232,7 +233,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -261,12 +271,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/iodate_respiration.html b/pages/traits/metabolism/iodate_respiration.html index 636ad02db3d..1f030d89aee 100644 --- a/pages/traits/metabolism/iodate_respiration.html +++ b/pages/traits/metabolism/iodate_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -134,7 +135,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -284,7 +285,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries growth and whole-cell IO3- to I- reduction snippets across three taxa (DOI:10.1128/AEM.00241-07, DOI:10.1038/s41396-021-01034-5, DOI:10.3389/fmicb.2021.804181) without enzyme-complex or electron-transfer quotes.

    +

    The current record carries growth and whole-cell IO3- to I- reduction snippets across three taxa (DOI:10.1128/AEM.00241-07, DOI:10.1038/s41396-021-01034-5, DOI:10.3389/fmicb.2021.804181) without enzyme-complex or electron-transfer quotes.

    @@ -366,7 +367,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -395,12 +405,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/metabolism/iron_oxidation.html b/pages/traits/metabolism/iron_oxidation.html index 6b7d8023e6e..ce52a712365 100644 --- a/pages/traits/metabolism/iron_oxidation.html +++ b/pages/traits/metabolism/iron_oxidation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • iron oxidation - traitmech:000107 + traitmech:000107 oxidizes ferrous iron CHEBI:29033 @@ -115,7 +116,7 @@

    Edge evidence

  • iron oxidation - traitmech:000107 + traitmech:000107 produces ferric iron CHEBI:29034 @@ -232,7 +233,7 @@

    Edge evidence

    contributes to iron oxidation - traitmech:000107 + traitmech:000107 RO:0002326

    High-affinity terminal oxidation supports iron-oxidizer respiration in microaerobic niches.

      @@ -252,7 +253,7 @@

      Edge evidence

      example of microaerobic conditions - rdfs:subClassOf + rdfs:subClassOf

      A low-oxygen, organic-rich setting is a specific microaerobic condition.

        @@ -270,7 +271,7 @@

        Edge evidence

        contributes to iron oxidation - traitmech:000107 + traitmech:000107 RO:0002326

        Enzymatic Fe(II) oxidation realizes the biological iron-oxidation capacity.

          @@ -289,7 +290,7 @@

          Edge evidence

          contributes to iron oxidation - traitmech:000107 + traitmech:000107 RO:0002326

          Extracellular electron uptake extends iron oxidation across mineral substrates.

            @@ -326,8 +327,8 @@

            Protein and taxon examples

    		•  - Acidithiobacillus ferrooxidans ATCC 23270 -
    NCBITaxon:243159 + Acidithiobacillus ferrooxidans ATCC 23270 +
    NCBITaxon:243159         		UNREVIEWED
    @@ -402,7 +403,7 @@

    Children (1)

    Synonyms (1)

    @@ -418,7 +419,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -700,7 +701,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1064,12 +1074,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 12:15 UTC diff --git a/pages/traits/metabolism/is_not_required_for_growth.html b/pages/traits/metabolism/is_not_required_for_growth.html index dd82602b4d6..58252180e81 100644 --- a/pages/traits/metabolism/is_not_required_for_growth.html +++ b/pages/traits/metabolism/is_not_required_for_growth.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • required for growth RELATED_SYNONYM · metpo.owl
      • +
    • required for growth RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/lactic_acid_fermentation.html b/pages/traits/metabolism/lactic_acid_fermentation.html index be2eb8b9e1c..32ad1b54905 100644 --- a/pages/traits/metabolism/lactic_acid_fermentation.html +++ b/pages/traits/metabolism/lactic_acid_fermentation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • lactic acid fermentation - traitmech:000026 + traitmech:000026 participates in fermentation GO:0006113 @@ -115,7 +116,7 @@

    Edge evidence

  • lactic acid fermentation - traitmech:000026 + traitmech:000026 produces lactate CHEBI:24996 @@ -326,8 +327,8 @@

    Protein and taxon examples

    		•  - Lactococcus lactis subsp. lactis IL1403 -
    NCBITaxon:272623 + Lactococcus lactis subsp. lactis IL1403 +
    NCBITaxon:272623         		REVIEWED
    @@ -393,7 +394,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • lactate fermentation RELATED_SYNONYM · DOI:10.3389/fmicb.2021.703525
      • +
    • lactate fermentation RELATED_SYNONYM · DOI:10.3389/fmicb.2021.703525
    @@ -409,7 +410,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -685,13 +686,13 @@

    Curation history

  • · REVIEW_EVIDENCE_REFERENCE_CHURN · codex -

    Offline review for issue 520 retained 6 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.3390/fermentation10030168 -> DOI:10.3390/molecules31020333 (6 edges).

    +

    Offline review for issue 520 retained 6 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.3390/fermentation10030168 -> DOI:10.3390/molecules31020333 (6 edges).

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.3389/fmicb.2021.703525 (already present on causal_graphs[0].edges[0].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-008 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.3389/fmicb.2021.703525 (already present on causal_graphs[0].edges[0].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-008 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -724,7 +725,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1088,12 +1098,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/metabolism/lignin_degradation.html b/pages/traits/metabolism/lignin_degradation.html index e536a7db7ac..15f1f3b8aa2 100644 --- a/pages/traits/metabolism/lignin_degradation.html +++ b/pages/traits/metabolism/lignin_degradation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    confers lignin degradation - traitmech:000114 + traitmech:000114 METPO:2007700

    Peroxidases and laccases drive oxidative lignin breakdown.

      @@ -115,7 +116,7 @@

      Edge evidence

    • lignin degradation - traitmech:000114 + traitmech:000114 produces aromatic monomers / oligomers @@ -290,7 +291,7 @@

      Edge evidence

      example of peroxidases and laccases - rdfs:subClassOf + rdfs:subClassOf

      Manganese peroxidase is a lignin-modifying oxidative enzyme.

        @@ -309,7 +310,7 @@

        Edge evidence

        example of peroxidases and laccases - rdfs:subClassOf + rdfs:subClassOf

        Lignin peroxidase is a lignin-modifying oxidative enzyme.

          @@ -345,8 +346,8 @@

          Protein and taxon examples

    		 - Streptomyces coelicolor A3(2) -
    NCBITaxon:100226 + Streptomyces coelicolor A3(2) +
    NCBITaxon:100226         		UNREVIEWED
    @@ -412,11 +413,11 @@

    Parent traits (1)

    Synonyms (3)

    @@ -439,7 +440,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -772,7 +773,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1136,12 +1146,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/lipolysis.html b/pages/traits/metabolism/lipolysis.html index e04fec19312..52d6f9745f9 100644 --- a/pages/traits/metabolism/lipolysis.html +++ b/pages/traits/metabolism/lipolysis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -238,7 +239,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two general definition snippets for microbial lipases EC 3.1.1.3 (DOI:10.1186/s12934-020-01428-8, DOI:10.1007/s00253-004-1568-8) without a cited canonical example or multi-step catabolic mechanism quotes.

    +

    The current record carries two general definition snippets for microbial lipases EC 3.1.1.3 (DOI:10.1186/s12934-020-01428-8, DOI:10.1007/s00253-004-1568-8) without a cited canonical example or multi-step catabolic mechanism quotes.

    @@ -288,7 +289,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add lipolysis trait -

      Minted traitmech:000190 for the lipolysis metabolism trait with DOI-backed microbial lipase evidence from 10.1186/s12934-020-01428-8 and 10.1007/s00253-004-1568-8, recorded organismal lipolysis exact-xref boundaries, and reserved METPO:1014400 in proposals/metpo_traitmech_v67.

    +

    Minted traitmech:000190 for the lipolysis metabolism trait with DOI-backed microbial lipase evidence from 10.1186/s12934-020-01428-8 and 10.1007/s00253-004-1568-8, recorded organismal lipolysis exact-xref boundaries, and reserved METPO:1014400 in proposals/metpo_traitmech_v67.

    • Read this curation session @@ -320,7 +321,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -349,12 +359,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/metabolism/manganese_oxidation.html b/pages/traits/metabolism/manganese_oxidation.html index 12dc7ede719..a6b74821a43 100644 --- a/pages/traits/metabolism/manganese_oxidation.html +++ b/pages/traits/metabolism/manganese_oxidation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -143,7 +144,7 @@

    Edge evidence

    GO:0016689 confers manganese oxidation - traitmech:000032 + traitmech:000032 METPO:2007700

    MnP-1 confers the Mn(II)-oxidizing capacity represented by the fungal branch of this trait.

      @@ -162,7 +163,7 @@

      Edge evidence

      InterPro:IPR045087 confers manganese oxidation - traitmech:000032 + traitmech:000032 METPO:2007700

      Multicopper oxidases catalyze the Mn(II) → Mn(III/IV) oxidation step.

        @@ -178,7 +179,7 @@

        Edge evidence

      • manganese oxidation - traitmech:000032 + traitmech:000032 produces Mn(III/IV) oxides @@ -197,7 +198,7 @@

        Edge evidence

      • manganese oxidation - traitmech:000032 + traitmech:000032 has electron acceptor molecular oxygen (O2) @@ -216,7 +217,7 @@

        Edge evidence

      • manganese oxidation - traitmech:000032 + traitmech:000032 produces Mn(III)(OH)Mn(III) intermediate @@ -277,7 +278,7 @@

        Edge evidence

        is a Mn(III/IV) oxides - rdfs:subClassOf + rdfs:subClassOf

        MnO2 nanoparticles are a form of the insoluble biogenic Mn(III/IV) oxide product.

          @@ -313,8 +314,8 @@

          Protein and taxon examples

    		 - Phanerodontia chrysosporium -
    NCBITaxon:2822231 + Phanerodontia chrysosporium +
    NCBITaxon:2822231         		REVIEWED
    @@ -380,7 +381,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -396,7 +397,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -491,12 +492,12 @@

    Deep research

    | Candidate causal module / edge set | Strongest model taxon | Evidence type | Curation confidence | Principal DOI | |---|---|---|---|---| -| **MnxE3F3G direct oxidation complex**: MnxG multicopper oxidase + MnxE/MnxF accessory ring; complex directly oxidizes Mn and supports biomineralization; **structure-based tunnel/intermediate details are inferential** | *Bacillus* sp. PL-12 / SG-1 lineage | Direct biochemistry + 2024 cryo-EM structure; structural mechanism partly inferred (butterfield2013mn(iiiii)oxidationand pages 1-1, novikova2024cryoemstructureof pages 1-2) | **High** for `Mnx complex enables Mn oxidation`; **Medium** for `tunnel guides binuclear intermediates` | 10.1021/jacs.3c06537 | -| **Stepwise Mn(II)→Mn(III)→Mn(IV)**: multicopper oxidase participates in both oxidation steps during MnO2 formation | *Bacillus* sp. SG-1 / PL-12 | Direct spectroscopy/biochemical evidence with trapped Mn(III) intermediate (soldatova2012multicopperoxidaseinvolvement pages 1-2, soldatova2012multicopperoxidaseinvolvement pages 12-16, butterfield2013mn(iiiii)oxidationand pages 1-1) | **High** | 10.1007/s00775-012-0928-6 | -| **c-di-GMP / PilZ / mop regulatory branch**: elevated c-di-GMP promotes mop expression and patterned biofilm Mn oxidation; PilZ-linked cascade supported, but some steps remain pathway-level | *Pseudomonas resinovorans* MOB-513 | Direct genetics, reporters, proteomics, phenotype correlation; **taxon-specific regulatory branch** (piazza2022cyclicdigmpsignaling pages 1-2, piazza2022cyclicdigmpsignaling pages 14-15) | **Medium-High** for `c-di-GMP positively regulates Mn oxidation via mop`; **Medium** for exact cascade topology | 10.1128/mbio.02734-22 | -| **RpoN / cold-tolerant Pseudomonas branch**: rpoN required for Mn oxidation in psychrotolerant isolates; oxidation retained at 4°C; broader regulatory mechanism still unresolved | *Pseudomonas* spp. DSV-1 / MS-1 | Direct transposon mutagenesis + complementation + growth/oxidation phenotypes; **taxon-specific** (jones2024isolationcharacterizationand pages 7-11, jones2024isolationcharacterizationand pages 13-15, jones2024isolationcharacterizationand pages 11-13, jones2024isolationcharacterizationand pages 2-5) | **Medium** | 10.1128/aem.00510-24 | -| **ROS indirect branch**: superoxide/peroxide chemistry can mediate Mn oxidation outside the canonical MCO route; mechanism supported mainly by review synthesis here | Diverse MnOB; no single strongest model in retrieved direct evidence | **Review-only / indirect evidence in current set**; should be curated cautiously until primary paper is added (wu2022manganesepollutionand pages 8-10) | **Low-Medium** | 10.3390/microorganisms10122411 | -| **Biogenic oxide downstream remediation effects**: Mn biooxides sorb metals and act as strong oxidants, enabling contaminant removal; this is mainly a downstream consequence of the trait, not the core oxidation mechanism | Environmental mixed systems; exemplar MnOB include *Bacillus*, *Leptothrix*, *Pseudomonas* | Authoritative review-level environmental evidence; some application framing, but mostly **downstream phenotype/effect** rather than direct causal core (tebo2004biogenicmanganeseoxides pages 19-23, tebo2004biogenicmanganeseoxides pages 8-10, tebo2004biogenicmanganeseoxides pages 1-3, tebo2004biogenicmanganeseoxides pages 31-33, wu2022manganesepollutionand pages 7-8) | **Medium** for downstream effect node; **do not overstate as universal engineered outcome** | 10.1146/annurev.earth.32.101802.120213 | +| **MnxE3F3G direct oxidation complex**: MnxG multicopper oxidase + MnxE/MnxF accessory ring; complex directly oxidizes Mn and supports biomineralization; **structure-based tunnel/intermediate details are inferential** | *Bacillus* sp. PL-12 / SG-1 lineage | Direct biochemistry + 2024 cryo-EM structure; structural mechanism partly inferred (butterfield2013mn(iiiii)oxidationand pages 1-1, novikova2024cryoemstructureof pages 1-2) | **High** for `Mnx complex enables Mn oxidation`; **Medium** for `tunnel guides binuclear intermediates` | 10.1021/jacs.3c06537 | +| **Stepwise Mn(II)→Mn(III)→Mn(IV)**: multicopper oxidase participates in both oxidation steps during MnO2 formation | *Bacillus* sp. SG-1 / PL-12 | Direct spectroscopy/biochemical evidence with trapped Mn(III) intermediate (soldatova2012multicopperoxidaseinvolvement pages 1-2, soldatova2012multicopperoxidaseinvolvement pages 12-16, butterfield2013mn(iiiii)oxidationand pages 1-1) | **High** | 10.1007/s00775-012-0928-6 | +| **c-di-GMP / PilZ / mop regulatory branch**: elevated c-di-GMP promotes mop expression and patterned biofilm Mn oxidation; PilZ-linked cascade supported, but some steps remain pathway-level | *Pseudomonas resinovorans* MOB-513 | Direct genetics, reporters, proteomics, phenotype correlation; **taxon-specific regulatory branch** (piazza2022cyclicdigmpsignaling pages 1-2, piazza2022cyclicdigmpsignaling pages 14-15) | **Medium-High** for `c-di-GMP positively regulates Mn oxidation via mop`; **Medium** for exact cascade topology | 10.1128/mbio.02734-22 | +| **RpoN / cold-tolerant Pseudomonas branch**: rpoN required for Mn oxidation in psychrotolerant isolates; oxidation retained at 4°C; broader regulatory mechanism still unresolved | *Pseudomonas* spp. DSV-1 / MS-1 | Direct transposon mutagenesis + complementation + growth/oxidation phenotypes; **taxon-specific** (jones2024isolationcharacterizationand pages 7-11, jones2024isolationcharacterizationand pages 13-15, jones2024isolationcharacterizationand pages 11-13, jones2024isolationcharacterizationand pages 2-5) | **Medium** | 10.1128/aem.00510-24 | +| **ROS indirect branch**: superoxide/peroxide chemistry can mediate Mn oxidation outside the canonical MCO route; mechanism supported mainly by review synthesis here | Diverse MnOB; no single strongest model in retrieved direct evidence | **Review-only / indirect evidence in current set**; should be curated cautiously until primary paper is added (wu2022manganesepollutionand pages 8-10) | **Low-Medium** | 10.3390/microorganisms10122411 | +| **Biogenic oxide downstream remediation effects**: Mn biooxides sorb metals and act as strong oxidants, enabling contaminant removal; this is mainly a downstream consequence of the trait, not the core oxidation mechanism | Environmental mixed systems; exemplar MnOB include *Bacillus*, *Leptothrix*, *Pseudomonas* | Authoritative review-level environmental evidence; some application framing, but mostly **downstream phenotype/effect** rather than direct causal core (tebo2004biogenicmanganeseoxides pages 19-23, tebo2004biogenicmanganeseoxides pages 8-10, tebo2004biogenicmanganeseoxides pages 1-3, tebo2004biogenicmanganeseoxides pages 31-33, wu2022manganesepollutionand pages 7-8) | **Medium** for downstream effect node; **do not overstate as universal engineered outcome** | 10.1146/annurev.earth.32.101802.120213 | *Table: This table prioritizes major candidate causal modules for curating microbial manganese oxidation, distinguishing direct mechanistic evidence from structural inference, taxon-specific regulation, and review-only claims. It helps decide which edges are ready for TraitMech curation versus which need stronger primary support.* @@ -654,7 +655,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1016/j.tim.2005.07.009 (already present on causal_graphs[0].edges[3]) to record-level evidence[0] to match definition_source (Cycle 2 Stage 5 remediation of F-DEF-SRC-MANGANESE-OX-013 in group G-C2S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #1995).

    +

    Added verified verbatim snippet from DOI:10.1016/j.tim.2005.07.009 (already present on causal_graphs[0].edges[3]) to record-level evidence[0] to match definition_source (Cycle 2 Stage 5 remediation of F-DEF-SRC-MANGANESE-OX-013 in group G-C2S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #1995).

    • @@ -687,7 +688,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1051,12 +1061,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 16:05 UTC diff --git a/pages/traits/metabolism/metabolism.html b/pages/traits/metabolism/metabolism.html index c966e905a92..8a456f273ff 100644 --- a/pages/traits/metabolism/metabolism.html +++ b/pages/traits/metabolism/metabolism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -364,8 +365,8 @@

    Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -500,7 +501,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -845,7 +846,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1209,12 +1219,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/methanogenesis.html b/pages/traits/metabolism/methanogenesis.html index 80f6e3a5adc..7e0eab9f2fb 100644 --- a/pages/traits/metabolism/methanogenesis.html +++ b/pages/traits/metabolism/methanogenesis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -194,7 +195,7 @@

    Edge evidence

    CHEBI:30089 serves as substrate for acetoclastic methanogenesis - traitmech:000191 + traitmech:000191

    Acetate is the substrate split to methane and CO2 in acetoclastic methanogenesis.

      @@ -213,7 +214,7 @@

      Edge evidence

      serves as substrate for methyl-based methanogenesis - traitmech:000192 + traitmech:000192

      Methylated compounds are the substrates for methyl-based methanogenesis.

        @@ -305,7 +306,7 @@

        Edge evidence

      • acetoclastic methanogenesis - traitmech:000191 + traitmech:000191 part of Methanogenesis METPO:1000844 @@ -324,7 +325,7 @@

        Edge evidence

      • methyl-based methanogenesis - traitmech:000192 + traitmech:000192 part of Methanogenesis METPO:1000844 @@ -364,8 +365,8 @@

        Protein and taxon examples

    		 - Methanocaldococcus jannaschii DSM 2661 -
    NCBITaxon:243232 + Methanocaldococcus jannaschii DSM 2661 +
    NCBITaxon:243232         		REVIEWED
    @@ -450,15 +451,15 @@

    Children (3)

    Synonyms (5)

      -
    • Biological methanation RELATED_SYNONYM · metpo.owl
      • +
    • Biological methanation RELATED_SYNONYM · metpo.owl
      • -
    • Biomethanation RELATED_SYNONYM · metpo.owl
      • +
    • Biomethanation RELATED_SYNONYM · metpo.owl
      • -
    • Carbonate respiration RELATED_SYNONYM · metpo.owl
      • +
    • Carbonate respiration RELATED_SYNONYM · metpo.owl
      • -
    • methane biosynthesis EXACT_SYNONYM · http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo
      • +
    • methane biosynthesis EXACT_SYNONYM · http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo
      • -
    • methane biosynthetic process EXACT_SYNONYM · http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo
      • +
    • methane biosynthetic process EXACT_SYNONYM · http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo
    @@ -481,7 +482,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -787,7 +788,7 @@

    Curation history

  • · REVIEW_EVIDENCE_REFERENCE_CHURN · codex -

    Offline review for issue 520 retained 3 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1007/s00253-023-12700-3 -> DOI:10.3389/fmicb.2017.01198 (2 edges); DOI:10.1128/mmbr.00024-22 -> DOI:10.1021/ja906367h (1 edge).

    +

    Offline review for issue 520 retained 3 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1007/s00253-023-12700-3 -> DOI:10.3389/fmicb.2017.01198 (2 edges); DOI:10.1128/mmbr.00024-22 -> DOI:10.1021/ja906367h (1 edge).

  • @@ -865,7 +866,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1229,12 +1239,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/methanol_oxidation.html b/pages/traits/metabolism/methanol_oxidation.html index 1ce991cefef..83519e328de 100644 --- a/pages/traits/metabolism/methanol_oxidation.html +++ b/pages/traits/metabolism/methanol_oxidation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • methanol_oxidation RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • methanol_oxidation RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -123,7 +124,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -219,7 +220,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    The current record carries a single 37-character phrase ('methanol utilization in methylotrophy' in DOI:10.3389/fbioe.2021.787791) without verbatim catalytic or electron-transfer quotes in the evidence block.

    +

    The current record carries a single 37-character phrase ('methanol utilization in methylotrophy' in DOI:10.3389/fbioe.2021.787791) without verbatim catalytic or electron-transfer quotes in the evidence block.

    @@ -292,7 +293,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -321,12 +331,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 20:01 UTC diff --git a/pages/traits/metabolism/methyl_based_methanogenesis.html b/pages/traits/metabolism/methyl_based_methanogenesis.html index f98b6d2b706..141320bae07 100644 --- a/pages/traits/metabolism/methyl_based_methanogenesis.html +++ b/pages/traits/metabolism/methyl_based_methanogenesis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,9 +107,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • methylotrophic methanogenesis RELATED_SYNONYM · DOI:10.3389/fmicb.2017.01198
      • +
    • methylotrophic methanogenesis RELATED_SYNONYM · DOI:10.3389/fmicb.2017.01198
      • -
    • methanogenesis using methylated compounds RELATED_SYNONYM · DOI:10.3389/fmicb.2017.01198
      • +
    • methanogenesis using methylated compounds RELATED_SYNONYM · DOI:10.3389/fmicb.2017.01198
    @@ -124,7 +125,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -249,7 +250,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two pathway-classification snippets (DOI:10.1128/mmbr.00024-22, DOI:10.3389/fmicb.2017.01198) without enzymatic step quotes or a cited canonical example.

    +

    The current record carries two pathway-classification snippets (DOI:10.1128/mmbr.00024-22, DOI:10.3389/fmicb.2017.01198) without enzymatic step quotes or a cited canonical example.

    @@ -299,7 +300,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add methyl-based methanogenesis trait -

      Minted traitmech:000192 for the methyl-based methanogenesis metabolism trait with DOI-backed methyl-substrate evidence from 10.1128/mmbr.00024-22 and 10.3389/fmicb.2017.01198, recorded the open exact-xref boundary, and reserved METPO:1014600 in proposals/metpo_traitmech_v69.

    +

    Minted traitmech:000192 for the methyl-based methanogenesis metabolism trait with DOI-backed methyl-substrate evidence from 10.1128/mmbr.00024-22 and 10.3389/fmicb.2017.01198, recorded the open exact-xref boundary, and reserved METPO:1014600 in proposals/metpo_traitmech_v69.

    • Read this curation session
    • @@ -331,7 +332,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -360,12 +370,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/metabolism/mixed_acid_fermentation.html b/pages/traits/metabolism/mixed_acid_fermentation.html index 52fcddbe312..ea515472b46 100644 --- a/pages/traits/metabolism/mixed_acid_fermentation.html +++ b/pages/traits/metabolism/mixed_acid_fermentation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • mixed-acid fermentation - traitmech:000027 + traitmech:000027 participates in fermentation GO:0006113 @@ -115,7 +116,7 @@

    Edge evidence

  • mixed-acid fermentation - traitmech:000027 + traitmech:000027 produces mixed acid + ethanol + CO2/H2 products @@ -134,7 +135,7 @@

    Edge evidence

  • mixed-acid fermentation - traitmech:000027 + traitmech:000027 has output pyruvate CHEBI:15361 @@ -305,7 +306,7 @@

    Edge evidence

  • mixed-acid fermentation - traitmech:000027 + traitmech:000027 lowers cytoplasmic pH @@ -383,8 +384,8 @@

    Protein and taxon examples

    		•  - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -457,7 +458,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -733,7 +734,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.3389/fmicb.2021.703525 (already present on sibling ethanol_fermentation.yaml and lactic_acid_fermentation.yaml causal_graphs[0].edges[0].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-009 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.3389/fmicb.2021.703525 (already present on sibling ethanol_fermentation.yaml and lactic_acid_fermentation.yaml causal_graphs[0].edges[0].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-009 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -775,7 +776,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1139,12 +1149,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/metabolism/nitrate_reduction.html b/pages/traits/metabolism/nitrate_reduction.html index f2f943ac756..521c4aca5b5 100644 --- a/pages/traits/metabolism/nitrate_reduction.html +++ b/pages/traits/metabolism/nitrate_reduction.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -109,7 +110,7 @@

    Children (1)

    Synonyms (1)

      -
    • nitrate_reduction RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • nitrate_reduction RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -221,7 +222,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    The current record carries a single overview snippet (DOI:10.1128/JB.181.21.6573-6584.1999) noting that nitrate reduction serves three purposes, without verbatim quotes for the individual reductase branches.

    +

    The current record carries a single overview snippet (DOI:10.1128/JB.181.21.6573-6584.1999) noting that nitrate reduction serves three purposes, without verbatim quotes for the individual reductase branches.

    @@ -294,7 +295,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -323,12 +333,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 20:01 UTC diff --git a/pages/traits/metabolism/nitrate_respiration.html b/pages/traits/metabolism/nitrate_respiration.html index 5bd015dbf28..c28e4d149c3 100644 --- a/pages/traits/metabolism/nitrate_respiration.html +++ b/pages/traits/metabolism/nitrate_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    Children (2)

    Synonyms (1)

      -
    • nitrate_respiration RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • nitrate_respiration RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -129,7 +130,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -225,7 +226,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    The current record carries a single snippet (DOI:10.1126/science.1254070) contrasting denitrification and ammonification endpoints without enzyme-level nitrate-to-nitrite respiratory mechanism quotes.

    +

    The current record carries a single snippet (DOI:10.1126/science.1254070) contrasting denitrification and ammonification endpoints without enzyme-level nitrate-to-nitrite respiratory mechanism quotes.

    @@ -298,7 +299,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -327,12 +337,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 20:01 UTC diff --git a/pages/traits/metabolism/nitrification.html b/pages/traits/metabolism/nitrification.html index c9e37600c1d..087077de1a4 100644 --- a/pages/traits/metabolism/nitrification.html +++ b/pages/traits/metabolism/nitrification.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries a single overview snippet (DOI:10.3389/fmicb.2020.01900) describing two-step oxidation of ammonia to nitrite and nitrate; a connected multi-edge graph requires at least two independent verbatim snippets without clause-splitting.

    +

    The current record carries a single overview snippet (DOI:10.3389/fmicb.2020.01900) describing two-step oxidation of ammonia to nitrite and nitrate; a connected multi-edge graph requires at least two independent verbatim snippets without clause-splitting.

    @@ -329,7 +330,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -358,12 +368,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/metabolism/nitrite_respiration.html b/pages/traits/metabolism/nitrite_respiration.html index 23812674210..086759eef7d 100644 --- a/pages/traits/metabolism/nitrite_respiration.html +++ b/pages/traits/metabolism/nitrite_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • nitrite_respiration RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • nitrite_respiration RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -116,7 +117,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -212,7 +213,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    The current record carries a single evidence item (DOI:10.1074/jbc.M709090200) on Escherichia coli NrfA reduction of nitrite to ammonium; a connected multi-edge graph requires at least two independent verbatim snippets so no single quote is reused or clause-split across edges.

    +

    The current record carries a single evidence item (DOI:10.1074/jbc.M709090200) on Escherichia coli NrfA reduction of nitrite to ammonium; a connected multi-edge graph requires at least two independent verbatim snippets so no single quote is reused or clause-split across edges.

    @@ -285,7 +286,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -314,12 +324,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 20:01 UTC diff --git a/pages/traits/metabolism/nitrogen_fixation.html b/pages/traits/metabolism/nitrogen_fixation.html index dff98fecb51..7907edf1eac 100644 --- a/pages/traits/metabolism/nitrogen_fixation.html +++ b/pages/traits/metabolism/nitrogen_fixation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -153,7 +154,7 @@

    Edge evidence

  • nitrogen fixation - traitmech:000103 + traitmech:000103 depends on nitrogenase GO:0016610 @@ -307,8 +308,8 @@

    Protein and taxon examples

    		•  - Azotobacter vinelandii -
    NCBITaxon:354 + Azotobacter vinelandii +
    NCBITaxon:354         		REVIEWED
    @@ -374,7 +375,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • diazotrophy RELATED_SYNONYM · DOI:10.1038/nrmicro954
      • +
    • diazotrophy RELATED_SYNONYM · DOI:10.1038/nrmicro954
    @@ -397,7 +398,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -652,7 +653,7 @@

    Curation history

  • · REVIEW_EVIDENCE_REFERENCE_CHURN · codex -

    Offline review for issue 520 retained 5 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1038/nrmicro.2018.9 -> DOI:10.34133/bdr.0005 (1 edge); DOI:10.1038/nrmicro954 -> DOI:10.34133/bdr.0005 (3 edges); DOI:10.1128/aem.00378-23 -> DOI:10.34133/bdr.0005 (1 edge).

    +

    Offline review for issue 520 retained 5 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1038/nrmicro.2018.9 -> DOI:10.34133/bdr.0005 (1 edge); DOI:10.1038/nrmicro954 -> DOI:10.34133/bdr.0005 (3 edges); DOI:10.1128/aem.00378-23 -> DOI:10.34133/bdr.0005 (1 edge).

  • @@ -691,7 +692,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1055,12 +1065,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/nitrogen_respiration.html b/pages/traits/metabolism/nitrogen_respiration.html index ccfdf9fd99f..2e745f4ddc6 100644 --- a/pages/traits/metabolism/nitrogen_respiration.html +++ b/pages/traits/metabolism/nitrogen_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    Children (3)

    Synonyms (1)

      -
    • nitrogen_respiration RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • nitrogen_respiration RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -129,7 +130,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -225,7 +226,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    The current record carries a single 38-character snippet ('N oxides as terminal electron acceptors' in DOI:10.1128/mmbr.61.4.533-616.1997), which supports the upper-level class definition but not a multi-edge mechanism graph.

    +

    The current record carries a single 38-character snippet ('N oxides as terminal electron acceptors' in DOI:10.1128/mmbr.61.4.533-616.1997), which supports the upper-level class definition but not a multi-edge mechanism graph.

    @@ -298,7 +299,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -327,12 +337,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 20:01 UTC diff --git a/pages/traits/metabolism/organism_interacts_with_chemical.html b/pages/traits/metabolism/organism_interacts_with_chemical.html index c4ded2b905d..c625a8d001b 100644 --- a/pages/traits/metabolism/organism_interacts_with_chemical.html +++ b/pages/traits/metabolism/organism_interacts_with_chemical.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -221,7 +222,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -358,7 +359,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -387,12 +397,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:00 UTC diff --git a/pages/traits/metabolism/organohalide_respiration.html b/pages/traits/metabolism/organohalide_respiration.html index 992adf0ff74..c372ec362e5 100644 --- a/pages/traits/metabolism/organohalide_respiration.html +++ b/pages/traits/metabolism/organohalide_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -269,7 +270,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries definition, phylogenetic-distribution, and mixed-culture cofactor snippets (DOI:10.1098/rstb.2012.0322, DOI:10.1126/science.276.5318.1568) without reductive dehalogenase enzyme or dechlorination-product quotes.

    +

    The current record carries definition, phylogenetic-distribution, and mixed-culture cofactor snippets (DOI:10.1098/rstb.2012.0322, DOI:10.1126/science.276.5318.1568) without reductive dehalogenase enzyme or dechlorination-product quotes.

    @@ -351,7 +352,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -380,12 +390,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/metabolism/oxidative_phosphorylation.html b/pages/traits/metabolism/oxidative_phosphorylation.html index b8c0c3a16a1..abeac724068 100644 --- a/pages/traits/metabolism/oxidative_phosphorylation.html +++ b/pages/traits/metabolism/oxidative_phosphorylation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -383,8 +384,8 @@

    Protein and taxon examples

    		•  - Paracoccus denitrificans -
    NCBITaxon:266 + Paracoccus denitrificans +
    NCBITaxon:266         		REVIEWED
    @@ -450,7 +451,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -473,7 +474,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -758,7 +759,7 @@

    Curation history

  • · RESTORE_CANONICAL_CITATION · claude -

    Restored the canonical-example citation for NCBITaxon:266 from DOI:10.1016/S0005-2728(98)00092-9 back to PMID:30428155 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.

    +

    Restored the canonical-example citation for NCBITaxon:266 from DOI:10.1016/S0005-2728(98)00092-9 back to PMID:30428155 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.

  • @@ -803,7 +804,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1167,12 +1177,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/oxidizes.html b/pages/traits/metabolism/oxidizes.html index 336fd398657..34ad6327632 100644 --- a/pages/traits/metabolism/oxidizes.html +++ b/pages/traits/metabolism/oxidizes.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • oxidation RELATED_SYNONYM · metpo.owl
      • +
    • oxidation RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:2000016 [-1.419, -0.244, -2.446, -0.185, …]
      • +
    • oxidizes METPO:2000016 [-1.419, -0.244, -2.446, -0.185, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/oxygenic_photosynthesis.html b/pages/traits/metabolism/oxygenic_photosynthesis.html index 2f1a00dd3fb..d5db73bda55 100644 --- a/pages/traits/metabolism/oxygenic_photosynthesis.html +++ b/pages/traits/metabolism/oxygenic_photosynthesis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    GO:0009767 confers oxygenic photosynthesis - traitmech:000034 + traitmech:000034 METPO:2007700

    Two linked photosystems power electron flow from water to NADP+.

      @@ -289,7 +290,7 @@

      Edge evidence

      GO:0009523 contributes to oxygenic photosynthesis - traitmech:000034 + traitmech:000034 RO:0002326

      PSII supplies the water-oxidation entry point.

        @@ -345,8 +346,8 @@

        Protein and taxon examples

    		•  - Synechocystis sp. PCC 6803 -
    NCBITaxon:1111708 + Synechocystis sp. PCC 6803 +
    NCBITaxon:1111708         		REVIEWED
    @@ -412,7 +413,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • oxygenic_photoautotrophy RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • oxygenic_photoautotrophy RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -428,7 +429,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -764,7 +765,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1128,12 +1138,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/pectin_degradation.html b/pages/traits/metabolism/pectin_degradation.html index 9a72389b29c..ede6a60c18b 100644 --- a/pages/traits/metabolism/pectin_degradation.html +++ b/pages/traits/metabolism/pectin_degradation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    GO:0045490 confers pectin degradation - traitmech:000135 + traitmech:000135 METPO:2007700

    Compartmentalized catabolism of pectin and its breakdown products confers the pectin degradation trait.

      @@ -155,8 +156,8 @@

      Protein and taxon examples

    		 - Dickeya dadantii (strain 3937) -
    NCBITaxon:198628 + Dickeya dadantii (strain 3937) +
    NCBITaxon:198628         		REVIEWED
    @@ -222,13 +223,13 @@

    Parent traits (1)

    Synonyms (4)

    @@ -251,7 +252,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -362,7 +363,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · claude -

    Added source-backed canonical example Dickeya dadantii 3937 (NCBITaxon:198628; DOI:10.1146/annurev.micro.50.1.213) from existing record evidence on Erwinia chrysanthemi strain 3937.

    +

    Added source-backed canonical example Dickeya dadantii 3937 (NCBITaxon:198628; DOI:10.1146/annurev.micro.50.1.213) from existing record evidence on Erwinia chrysanthemi strain 3937.

  • @@ -410,7 +411,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -774,12 +784,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 21:12 UTC diff --git a/pages/traits/metabolism/perchlorate_respiration.html b/pages/traits/metabolism/perchlorate_respiration.html index bcadb70a71a..f015792ffa3 100644 --- a/pages/traits/metabolism/perchlorate_respiration.html +++ b/pages/traits/metabolism/perchlorate_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -82,7 +83,7 @@

    Trait evidence (3)

    Anaerobic respiratory perchlorate reduction to chloride

    Evidence-backed metabolic pathway sketch linking anaerobic respiratory perchlorate reduction and chloride formation to perchlorate respiration.

    -

    MECHANISTIC · Mechanistic graph backed by DOI:10.1186/s12864-015-2011-5, DOI:10.1128/AEM.05758-11, and DOI:10.1128/jb.187.15.5090-5096.2005; exemplified on perchlorate_respiration_pcr_reductase with Dechloromonas aromatica RCB (NCBITaxon:159087) perchlorate reductase subunit alpha PcrA (UniProtKB:Q47CW6).

    +

    MECHANISTIC · Mechanistic graph backed by DOI:10.1186/s12864-015-2011-5, DOI:10.1128/AEM.05758-11, and DOI:10.1128/jb.187.15.5090-5096.2005; exemplified on perchlorate_respiration_pcr_reductase with Dechloromonas aromatica RCB (NCBITaxon:159087) perchlorate reductase subunit alpha PcrA (UniProtKB:Q47CW6).

    Loading graph…

    @@ -105,7 +106,7 @@

    Edge evidence

    GO:0019645 confers perchlorate respiration - traitmech:000197 + traitmech:000197 METPO:2007700

    Perchlorate reductase and chlorite dismutase encoded by pcrABCD and cld confer perchlorate respiration.

      @@ -180,8 +181,8 @@

      Protein and taxon examples

    		•  - Dechloromonas aromatica RCB -
    NCBITaxon:159087 + Dechloromonas aromatica RCB +
    NCBITaxon:159087         		REVIEWED
    @@ -247,7 +248,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • dissimilatory perchlorate reduction RELATED_SYNONYM · DOI:10.1186/s12864-015-2011-5
      • +
    • dissimilatory perchlorate reduction RELATED_SYNONYM · DOI:10.1186/s12864-015-2011-5
    @@ -263,7 +264,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -413,7 +414,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The record's primary literature by Melnyk et al. (DOI:10.1186/s12864-015-2011-5, DOI:10.1128/AEM.05758-11) supports periplasmic reduction of perchlorate to chlorite by perchlorate reductase (PcrABCD) and chlorite dismutation to chloride and O2 by chlorite dismutase (Cld), but canonical_examples and verified strain-matched UniProtKB accessions must be curated before marking the graph MECHANISTIC.

    +

    The record's primary literature by Melnyk et al. (DOI:10.1186/s12864-015-2011-5, DOI:10.1128/AEM.05758-11) supports periplasmic reduction of perchlorate to chlorite by perchlorate reductase (PcrABCD) and chlorite dismutation to chloride and O2 by chlorite dismutase (Cld), but canonical_examples and verified strain-matched UniProtKB accessions must be curated before marking the graph MECHANISTIC.

    @@ -432,7 +433,7 @@

    Evidence

    -

    Resolution: Added canonical_examples entry Dechloromonas aromatica RCB (NCBITaxon:159087) and promoted perchlorate_respiration_reduction_sketch to MECHANISTIC by adding InterPro:IPR017840-grounded GENE_OR_PROTEIN node perchlorate_respiration_pcr_reductase with reviewed UniProtKB:Q47CW6 (PcrA) backed by DOI:10.1128/jb.187.15.5090-5096.2005.

    +

    Resolution: Added canonical_examples entry Dechloromonas aromatica RCB (NCBITaxon:159087) and promoted perchlorate_respiration_reduction_sketch to MECHANISTIC by adding InterPro:IPR017840-grounded GENE_OR_PROTEIN node perchlorate_respiration_pcr_reductase with reviewed UniProtKB:Q47CW6 (PcrA) backed by DOI:10.1128/jb.187.15.5090-5096.2005.

    @@ -461,7 +462,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Added Dechloromonas aromatica RCB (NCBITaxon:159087; DOI:10.1128/jb.187.15.5090-5096.2005) canonical example; promoted perchlorate_respiration_reduction_sketch to MECHANISTIC with InterPro:IPR017840-grounded GENE_OR_PROTEIN node perchlorate_respiration_pcr_reductase and reviewed UniProtKB:Q47CW6 (PcrA); resolved perchlorate-respiration-protein-example-gap.

    +

    Added Dechloromonas aromatica RCB (NCBITaxon:159087; DOI:10.1128/jb.187.15.5090-5096.2005) canonical example; promoted perchlorate_respiration_reduction_sketch to MECHANISTIC with InterPro:IPR017840-grounded GENE_OR_PROTEIN node perchlorate_respiration_pcr_reductase and reviewed UniProtKB:Q47CW6 (PcrA); resolved perchlorate-respiration-protein-example-gap.

    • @@ -503,7 +504,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -867,12 +877,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 11:45 UTC diff --git a/pages/traits/metabolism/photoferrotrophy.html b/pages/traits/metabolism/photoferrotrophy.html index 89c266e3572..5952fb892ff 100644 --- a/pages/traits/metabolism/photoferrotrophy.html +++ b/pages/traits/metabolism/photoferrotrophy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -102,7 +103,7 @@

    Edge evidence

  • photoferrotrophy - traitmech:000193 + traitmech:000193 has energy source light PATO:0001717 @@ -121,7 +122,7 @@

    Edge evidence

  • photoferrotrophy - traitmech:000193 + traitmech:000193 has electron donor ferrous iron CHEBI:29033 @@ -300,9 +301,9 @@

    Parent traits (2)

    Synonyms (2)

      -
    • phototrophic Fe(II) oxidation EXACT_SYNONYM · DOI:10.3389/fmicb.2014.00713
      • +
    • phototrophic Fe(II) oxidation EXACT_SYNONYM · DOI:10.3389/fmicb.2014.00713
      • -
    • anoxygenic phototrophic Fe(II) oxidation EXACT_SYNONYM · DOI:10.3389/fmicb.2017.00323
      • +
    • anoxygenic phototrophic Fe(II) oxidation EXACT_SYNONYM · DOI:10.3389/fmicb.2017.00323
    • @@ -318,7 +319,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -525,7 +526,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -889,12 +899,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-14 22:08 UTC diff --git a/pages/traits/metabolism/photosynthesis.html b/pages/traits/metabolism/photosynthesis.html index f29edd34c0a..aad8f35a081 100644 --- a/pages/traits/metabolism/photosynthesis.html +++ b/pages/traits/metabolism/photosynthesis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    GO:0015979 confers photosynthesis - traitmech:000038 + traitmech:000038 METPO:2007700

    Reaction-center photochemistry underlies the photosynthetic trait.

      @@ -115,7 +116,7 @@

      Edge evidence

    • photosynthesis - traitmech:000038 + traitmech:000038 contributes to carbon fixation GO:0015977 @@ -326,8 +327,8 @@

      Protein and taxon examples

    		 - Synechocystis sp. PCC 6803 -
    NCBITaxon:1111708 + Synechocystis sp. PCC 6803 +
    NCBITaxon:1111708         		REVIEWED
    @@ -418,7 +419,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -739,7 +740,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1103,12 +1113,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/phototrophy.html b/pages/traits/metabolism/phototrophy.html index 3f956e7803f..2d826d0ed9b 100644 --- a/pages/traits/metabolism/phototrophy.html +++ b/pages/traits/metabolism/phototrophy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    PATO:0001717 causes phototrophy - traitmech:000037 + traitmech:000037 biolink:causes

    Light availability is the input the phototrophic trait realizes.

      @@ -115,7 +116,7 @@

      Edge evidence

    • phototrophy - traitmech:000037 + traitmech:000037 contributes to proton motive force METPO:1007500 @@ -270,7 +271,7 @@

      Edge evidence

      GO:0009523 contributes to phototrophy - traitmech:000037 + traitmech:000037 RO:0002326

      Photosystem II contributes the light-sensing and reaction-center machinery of the graph's oxygenic phototrophy branch.

        @@ -307,8 +308,8 @@

        Protein and taxon examples

    		 - Synechocystis sp. PCC 6803 -
    NCBITaxon:1111708 + Synechocystis sp. PCC 6803 +
    NCBITaxon:1111708         		REVIEWED
    @@ -385,7 +386,7 @@

    Children (2)

    Synonyms (1)

      -
    • phototrophic metabolism RELATED_SYNONYM · DOI:10.1016/j.tim.2006.09.001
      • +
    • phototrophic metabolism RELATED_SYNONYM · DOI:10.1016/j.tim.2006.09.001
    @@ -401,7 +402,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -728,7 +729,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1092,12 +1102,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/produces.html b/pages/traits/metabolism/produces.html index 0076a14cde1..72d6eaa01b4 100644 --- a/pages/traits/metabolism/produces.html +++ b/pages/traits/metabolism/produces.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -114,7 +115,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:2000202 [-1.210, -0.273, -2.355, -0.086, …]
      • +
    • produces METPO:2000202 [-1.210, -0.273, -2.355, -0.086, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -251,7 +252,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -280,12 +290,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-06-17 04:09 UTC diff --git a/pages/traits/metabolism/propionic_acid_fermentation.html b/pages/traits/metabolism/propionic_acid_fermentation.html index 2b05c0b6663..e1c936d9dc7 100644 --- a/pages/traits/metabolism/propionic_acid_fermentation.html +++ b/pages/traits/metabolism/propionic_acid_fermentation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • propionic acid fermentation - traitmech:000029 + traitmech:000029 participates in fermentation GO:0006113 @@ -115,7 +116,7 @@

    Edge evidence

  • propionic acid fermentation - traitmech:000029 + traitmech:000029 produces propionate CHEBI:17272 @@ -134,7 +135,7 @@

    Edge evidence

  • propionic acid fermentation - traitmech:000029 + traitmech:000029 has major pathway Wood-Werkman cycle @@ -286,7 +287,7 @@

    Edge evidence

  • propionic acid fermentation - traitmech:000029 + traitmech:000029 has byproduct acetate @@ -383,8 +384,8 @@

    Protein and taxon examples

    		•  - Propionibacterium freudenreichii subsp. shermanii -
    NCBITaxon:1752 + Propionibacterium freudenreichii subsp. shermanii +
    NCBITaxon:1752         		REVIEWED
    @@ -450,7 +451,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • propionate fermentation RELATED_SYNONYM · DOI:10.3390/molecules31020333
      • +
    • propionate fermentation RELATED_SYNONYM · DOI:10.3390/molecules31020333
    @@ -466,7 +467,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -742,7 +743,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.3390/molecules31020333 (already present on causal_graphs[0].edges[1]) to record-level evidence[0] to match definition_source (Cycle 2 Stage 5 remediation of F-DEF-SRC-PROPIONIC-FERM-012 in group G-C2S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #1995).

    +

    Added verified verbatim snippet from DOI:10.3390/molecules31020333 (already present on causal_graphs[0].edges[1]) to record-level evidence[0] to match definition_source (Cycle 2 Stage 5 remediation of F-DEF-SRC-PROPIONIC-FERM-012 in group G-C2S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #1995).

    • @@ -784,7 +785,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1148,12 +1158,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 16:05 UTC diff --git a/pages/traits/metabolism/proteolysis.html b/pages/traits/metabolism/proteolysis.html index 73f812061ea..8682f5bb85e 100644 --- a/pages/traits/metabolism/proteolysis.html +++ b/pages/traits/metabolism/proteolysis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    confers proteolysis - traitmech:000116 + traitmech:000116 METPO:2007700

    Secreted proteases drive extracellular protein hydrolysis.

      @@ -115,7 +116,7 @@

      Edge evidence

    • proteolysis - traitmech:000116 + traitmech:000116 produces amino acids / short peptides @@ -134,7 +135,7 @@

      Edge evidence

    • proteolysis - traitmech:000116 + traitmech:000116 produces peptides / oligopeptides @@ -213,7 +214,7 @@

      Edge evidence

      necessitates proteolysis - traitmech:000116 + traitmech:000116

      Proteins too large for direct uptake necessitate extracellular hydrolysis.

        @@ -269,8 +270,8 @@

        Protein and taxon examples

    		 - Bacillus subtilis 168 -
    NCBITaxon:224308 + Bacillus subtilis 168 +
    NCBITaxon:224308         		REVIEWED
    @@ -336,9 +337,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -354,7 +355,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -633,7 +634,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -997,12 +1007,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/proteorhodopsin_phototrophy.html b/pages/traits/metabolism/proteorhodopsin_phototrophy.html index e048e954d47..75267d78ad9 100644 --- a/pages/traits/metabolism/proteorhodopsin_phototrophy.html +++ b/pages/traits/metabolism/proteorhodopsin_phototrophy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    InterPro:IPR017402 confers proteorhodopsin phototrophy - traitmech:000036 + traitmech:000036 METPO:2007700

    The retinal-binding pump realizes proteorhodopsin phototrophy.

      @@ -115,7 +116,7 @@

      Edge evidence

    • proteorhodopsin phototrophy - traitmech:000036 + traitmech:000036 contributes to proton motive force METPO:1007500 @@ -172,7 +173,7 @@

      Edge evidence

    • proteorhodopsin phototrophy - traitmech:000036 + traitmech:000036 does not produce NAD(P)H CHEBI:13392 @@ -250,8 +251,8 @@

      Protein and taxon examples

    		 - gamma proteobacterium EBAC31A08 -
    NCBITaxon:133804 + gamma proteobacterium EBAC31A08 +
    NCBITaxon:133804         		REVIEWED
    @@ -317,7 +318,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • rhodopsin-based phototrophy RELATED_SYNONYM · DOI:10.1038/35081051
      • +
    • rhodopsin-based phototrophy RELATED_SYNONYM · DOI:10.1038/35081051
    @@ -333,7 +334,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -440,12 +441,12 @@

    Deep research

    | Subject | Predicate | Object | Confidence | Key evidence | |---|---|---|---|---| -| light | activates | retinal-bound proteorhodopsin | High | PR is a "light-driven proton pump" whose mechanism depends on retinal/photoisomerization; foundational identification in marine bacteria and later mechanistic summaries support light activation (DOI:10.1126/science.289.5486.1902; DOI:10.1038/35081051; DOI:10.25959/23241740) (feng2023isproteorhodopsina pages 17-23, feng2023isproteorhodopsina pages 28-34) | -| retinal-bound proteorhodopsin | exports | protons (H+) across the membrane | High | Direct functional evidence from illuminated cells and heterologous expression shows outward proton pumping / external pH change; recent work summarizes PR as bacterial proton pumps (DOI:10.1128/AEM.02425-09; DOI:10.25959/23241740; DOI:10.1126/sciadv.adu5303) (johnson2010enhancementofsurvival pages 1-2, feng2023isproteorhodopsina pages 89-95, bukhdruker2025proteorhodopsininsightsinto pages 18-19) | -| proton export by proteorhodopsin | generates | proton motive force | High | Multiple sources explicitly state PR translocates protons to create membrane potential/PMF; direct in engineered Shewanella, established across PR literature (DOI:10.1128/AEM.02425-09; DOI:10.25959/23241740) (johnson2010enhancementofsurvival pages 1-2, feng2023isproteorhodopsina pages 28-34, feng2023isproteorhodopsina pages 17-23) | -| proton motive force | drives | F-type ATP synthase | Medium-High | Established bioenergetic coupling rather than directly reconstituted in every PR study: sources state PR-generated PMF drives ATP synthesis via F0F1-ATPase / proton-translocating ATPase (DOI:10.25959/23241740; DOI:10.1128/AEM.02425-09) (feng2023isproteorhodopsina pages 28-34, feng2023isproteorhodopsina pages 17-23, feng2023isproteorhodopsina pages 34-38, johnson2010enhancementofsurvival pages 1-2) | -| F-type ATP synthase | produces | ATP | High | Established ATP synthase function; PR studies cite ATP increases or ATP synthesis supported by PR-generated PMF in heterologous/native systems (DOI:10.1128/AEM.02425-09; DOI:10.25959/23241740) (johnson2010enhancementofsurvival pages 1-2, feng2023isproteorhodopsina pages 28-34) | -| beta-carotene cleavage / retinal supply | enables | functional proteorhodopsin | High | Genome and biochemical evidence link PR function to retinal availability: PR-containing marine genomes carry retinal biosynthesis genes including blh and carotenoid genes; PR requires retinal/retinol for functionality (DOI:10.1073/pnas.0712027105; DOI:10.1038/ismej.2011.189) (dupont2012genomicinsightsto pages 8-9) | +| light | activates | retinal-bound proteorhodopsin | High | PR is a "light-driven proton pump" whose mechanism depends on retinal/photoisomerization; foundational identification in marine bacteria and later mechanistic summaries support light activation (DOI:10.1126/science.289.5486.1902; DOI:10.1038/35081051; DOI:10.25959/23241740) (feng2023isproteorhodopsina pages 17-23, feng2023isproteorhodopsina pages 28-34) | +| retinal-bound proteorhodopsin | exports | protons (H+) across the membrane | High | Direct functional evidence from illuminated cells and heterologous expression shows outward proton pumping / external pH change; recent work summarizes PR as bacterial proton pumps (DOI:10.1128/AEM.02425-09; DOI:10.25959/23241740; DOI:10.1126/sciadv.adu5303) (johnson2010enhancementofsurvival pages 1-2, feng2023isproteorhodopsina pages 89-95, bukhdruker2025proteorhodopsininsightsinto pages 18-19) | +| proton export by proteorhodopsin | generates | proton motive force | High | Multiple sources explicitly state PR translocates protons to create membrane potential/PMF; direct in engineered Shewanella, established across PR literature (DOI:10.1128/AEM.02425-09; DOI:10.25959/23241740) (johnson2010enhancementofsurvival pages 1-2, feng2023isproteorhodopsina pages 28-34, feng2023isproteorhodopsina pages 17-23) | +| proton motive force | drives | F-type ATP synthase | Medium-High | Established bioenergetic coupling rather than directly reconstituted in every PR study: sources state PR-generated PMF drives ATP synthesis via F0F1-ATPase / proton-translocating ATPase (DOI:10.25959/23241740; DOI:10.1128/AEM.02425-09) (feng2023isproteorhodopsina pages 28-34, feng2023isproteorhodopsina pages 17-23, feng2023isproteorhodopsina pages 34-38, johnson2010enhancementofsurvival pages 1-2) | +| F-type ATP synthase | produces | ATP | High | Established ATP synthase function; PR studies cite ATP increases or ATP synthesis supported by PR-generated PMF in heterologous/native systems (DOI:10.1128/AEM.02425-09; DOI:10.25959/23241740) (johnson2010enhancementofsurvival pages 1-2, feng2023isproteorhodopsina pages 28-34) | +| beta-carotene cleavage / retinal supply | enables | functional proteorhodopsin | High | Genome and biochemical evidence link PR function to retinal availability: PR-containing marine genomes carry retinal biosynthesis genes including blh and carotenoid genes; PR requires retinal/retinol for functionality (DOI:10.1073/pnas.0712027105; DOI:10.1038/ismej.2011.189) (dupont2012genomicinsightsto pages 8-9) | *Table: Compact curation table of the strongest mechanistic edges for proteorhodopsin phototrophy, from light activation and proton export to PMF-coupled ATP production, plus retinal supply. It distinguishes directly shown PR steps from the broader established ATP synthase coupling used in TraitMech curation.* @@ -603,7 +604,7 @@

    Curation history

  • · REVIEW_EVIDENCE_REFERENCE_CHURN · codex -

    Offline review for issue 520 retained 4 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1007/s12275-024-00125-0 -> DOI:10.1073/pnas.0611035104 (1 edge); DOI:10.1038/35081051 -> DOI:10.1073/pnas.0611035104 (1 edge); DOI:10.34133/2022/9782712 -> DOI:10.1128/MMBR.69.1.51-78.2005 (1 edge); DOI:10.4014/jmb.2410.10034 -> DOI:10.1073/pnas.0611035104 (1 edge).

    +

    Offline review for issue 520 retained 4 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1007/s12275-024-00125-0 -> DOI:10.1073/pnas.0611035104 (1 edge); DOI:10.1038/35081051 -> DOI:10.1073/pnas.0611035104 (1 edge); DOI:10.34133/2022/9782712 -> DOI:10.1128/MMBR.69.1.51-78.2005 (1 edge); DOI:10.4014/jmb.2410.10034 -> DOI:10.1073/pnas.0611035104 (1 edge).

  • @@ -615,7 +616,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1126/science.289.5486.1902 (already present on causal_graphs[0].edges[0].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-004 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.1126/science.289.5486.1902 (already present on causal_graphs[0].edges[0].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-004 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -648,7 +649,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1012,12 +1022,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/metabolism/reduces.html b/pages/traits/metabolism/reduces.html index 64957f7e66b..05afaf55455 100644 --- a/pages/traits/metabolism/reduces.html +++ b/pages/traits/metabolism/reduces.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • reduction RELATED_SYNONYM · metpo.owl
      • +
    • reduction RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:2000017 [-1.152, -0.339, -2.249, -0.170, …]
      • +
    • reduces METPO:2000017 [-1.152, -0.339, -2.249, -0.170, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/reductive_tca_cycle.html b/pages/traits/metabolism/reductive_tca_cycle.html index 843d6878277..4f1a21a60ec 100644 --- a/pages/traits/metabolism/reductive_tca_cycle.html +++ b/pages/traits/metabolism/reductive_tca_cycle.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    CHEBI:16526 fixed by reductive tricarboxylic acid cycle - traitmech:000021 + traitmech:000021 METPO:2007404

    CO2 is fixed by the reverse TCA cycle in anaerobic autotrophs.

      @@ -115,7 +116,7 @@

      Edge evidence

    • reductive tricarboxylic acid cycle - traitmech:000021 + traitmech:000021 produces citrate CHEBI:16947 @@ -137,7 +138,7 @@

      Edge evidence

      confers reductive tricarboxylic acid cycle - traitmech:000021 + traitmech:000021 METPO:2007700

      ATP citrate lyase cleaves citrate into oxaloacetate and acetyl-CoA, enabling the rTCA cycle.

        @@ -175,7 +176,7 @@

        Edge evidence

        GO:0019164 part of reductive tricarboxylic acid cycle - traitmech:000021 + traitmech:000021 biolink:part_of

        Pyruvate:ferredoxin oxidoreductase is a canonical key enzyme of the rTCA cycle.

          @@ -194,7 +195,7 @@

          Edge evidence

          part of reductive tricarboxylic acid cycle - traitmech:000021 + traitmech:000021 biolink:part_of

          2-oxoglutarate:ferredoxin oxidoreductase is a canonical key enzyme of the rTCA cycle.

            @@ -269,8 +270,8 @@

            Protein and taxon examples

    		 - Chlorobaculum tepidum TLS -
    NCBITaxon:194439 + Chlorobaculum tepidum TLS +
    NCBITaxon:194439         		UNREVIEWED
    @@ -299,8 +300,8 @@

    Protein and taxon examples

    		 - Chlorobaculum tepidum TLS -
    NCBITaxon:194439 + Chlorobaculum tepidum TLS +
    NCBITaxon:194439         		UNREVIEWED
    @@ -366,21 +367,21 @@

    Parent traits (1)

    Synonyms (8)

    @@ -403,7 +404,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -661,7 +662,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1128/AEM.02473-10 (already present on parent record carbon_fixation.yaml causal_graphs[0].edges[12].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-003 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.1128/AEM.02473-10 (already present on parent record carbon_fixation.yaml causal_graphs[0].edges[12].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-003 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -694,7 +695,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1058,12 +1068,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/metabolism/requires_for_growth.html b/pages/traits/metabolism/requires_for_growth.html index 4363934e049..0f34a449a26 100644 --- a/pages/traits/metabolism/requires_for_growth.html +++ b/pages/traits/metabolism/requires_for_growth.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • required for growth RELATED_SYNONYM · metpo.owl
      • +
    • required for growth RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/respiration.html b/pages/traits/metabolism/respiration.html index c2b4809d79e..d2c5b988c2c 100644 --- a/pages/traits/metabolism/respiration.html +++ b/pages/traits/metabolism/respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -138,7 +139,7 @@

    Edge evidence

    example of terminal electron acceptor METPO:1007504 - rdfs:subClassOf + rdfs:subClassOf

    Oxygen is the terminal electron acceptor in aerobic respiration.

      @@ -157,7 +158,7 @@

      Edge evidence

      example of terminal electron acceptor METPO:1007504 - rdfs:subClassOf + rdfs:subClassOf

      Nitrate is a representative anaerobic terminal electron acceptor.

        @@ -345,8 +346,8 @@

        Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -425,7 +426,7 @@

    Children (3)

    Synonyms (1)

      -
    • pathways RELATED_SYNONYM · metpo.owl
      • +
    • pathways RELATED_SYNONYM · metpo.owl
    @@ -441,7 +442,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -822,7 +823,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1186,12 +1196,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/respiration_of_sulfur_compounds.html b/pages/traits/metabolism/respiration_of_sulfur_compounds.html index 2132603d138..5e6a40a6b5a 100644 --- a/pages/traits/metabolism/respiration_of_sulfur_compounds.html +++ b/pages/traits/metabolism/respiration_of_sulfur_compounds.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    Children (3)

    Synonyms (1)

      -
    • respiration_of_sulfur_compounds RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • respiration_of_sulfur_compounds RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -129,7 +130,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -225,7 +226,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    The current record carries a single 42-character snippet ('sulfate, sulfur, or thiosulfate respiration' in DOI:10.3389/fmicb.2023.1108245) enumerating the respiratory subclasses without enzymatic mechanism quotes.

    +

    The current record carries a single 42-character snippet ('sulfate, sulfur, or thiosulfate respiration' in DOI:10.3389/fmicb.2023.1108245) enumerating the respiratory subclasses without enzymatic mechanism quotes.

    @@ -298,7 +299,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -327,12 +337,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 20:01 UTC diff --git a/pages/traits/metabolism/selenate_respiration.html b/pages/traits/metabolism/selenate_respiration.html index 1e0e5f9a408..4670f508e82 100644 --- a/pages/traits/metabolism/selenate_respiration.html +++ b/pages/traits/metabolism/selenate_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -134,7 +135,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -284,7 +285,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries strain-isolation and terminal-electron-acceptor snippets (DOI:10.1128/aem.60.8.3011-3019.1994, DOI:10.1128/AEM.02737-06, DOI:10.1016/j.syapm.2005.12.011) without enzymatic reductase or selenite-product quotes.

    +

    The current record carries strain-isolation and terminal-electron-acceptor snippets (DOI:10.1128/aem.60.8.3011-3019.1994, DOI:10.1128/AEM.02737-06, DOI:10.1016/j.syapm.2005.12.011) without enzymatic reductase or selenite-product quotes.

    @@ -366,7 +367,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -395,12 +405,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/metabolism/sequesters.html b/pages/traits/metabolism/sequesters.html index eaa8fb1231e..0882609ac38 100644 --- a/pages/traits/metabolism/sequesters.html +++ b/pages/traits/metabolism/sequesters.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:2000211 [-1.868, -0.826, -3.392, -0.381, …]
      • +
    • sequesters METPO:2000211 [-1.868, -0.826, -3.392, -0.381, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -232,7 +233,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -261,12 +271,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/shows_activity_of.html b/pages/traits/metabolism/shows_activity_of.html index ad27b35fd44..3231845dc05 100644 --- a/pages/traits/metabolism/shows_activity_of.html +++ b/pages/traits/metabolism/shows_activity_of.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Physiology and metabolism.enzymes.[].activity RELATED_SYNONYM · metpo.owl
      • +
    • Physiology and metabolism.enzymes.[].activity RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/starch_degradation.html b/pages/traits/metabolism/starch_degradation.html index ba4a4a2d086..b12cc031e02 100644 --- a/pages/traits/metabolism/starch_degradation.html +++ b/pages/traits/metabolism/starch_degradation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    GO:0004556 confers starch degradation - traitmech:000115 + traitmech:000115 METPO:2007700

    Alpha-amylase endo-hydrolyzes starch alpha-1,4 linkages and initiates production of shorter glucans.

      @@ -115,7 +116,7 @@

      Edge evidence

    • starch degradation - traitmech:000115 + traitmech:000115 produces glucose CHEBI:17234 @@ -231,8 +232,8 @@

      Protein and taxon examples

    		 - Bacillus licheniformis -
    NCBITaxon:1402 + Bacillus licheniformis +
    NCBITaxon:1402         		REVIEWED
    @@ -298,11 +299,11 @@

    Parent traits (1)

    Synonyms (3)

    @@ -325,7 +326,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -586,7 +587,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1016/S0168-1656(01)00407-2 (already present on causal_graphs[0].edges[0].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-005 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.1016/S0168-1656(01)00407-2 (already present on causal_graphs[0].edges[0].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-005 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -619,7 +620,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -983,12 +993,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/metabolism/substrate_level_phosphorylation.html b/pages/traits/metabolism/substrate_level_phosphorylation.html index 5164b922367..41033e66879 100644 --- a/pages/traits/metabolism/substrate_level_phosphorylation.html +++ b/pages/traits/metabolism/substrate_level_phosphorylation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -367,8 +368,8 @@

    Protein and taxon examples

    		 - Streptococcus pyogenes serotype M1 -
    NCBITaxon:301447 + Streptococcus pyogenes serotype M1 +
    NCBITaxon:301447         		UNREVIEWED
    @@ -441,7 +442,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -804,7 +805,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1168,12 +1178,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/sulfur_oxidation.html b/pages/traits/metabolism/sulfur_oxidation.html index d819dfd2bca..44d78c32383 100644 --- a/pages/traits/metabolism/sulfur_oxidation.html +++ b/pages/traits/metabolism/sulfur_oxidation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    confers sulfur oxidation - traitmech:000106 + traitmech:000106 METPO:2007700

    The Sox system enables lithotrophic sulfur oxidation.

      @@ -115,7 +116,7 @@

      Edge evidence

    • sulfur oxidation - traitmech:000106 + traitmech:000106 oxidizes hydrogen sulfide CHEBI:16136 @@ -134,7 +135,7 @@

      Edge evidence

    • sulfur oxidation - traitmech:000106 + traitmech:000106 produces sulfate CHEBI:16189 @@ -345,8 +346,8 @@

      Protein and taxon examples

    		 - Thiobacillus denitrificans ATCC 25259 -
    NCBITaxon:292415 + Thiobacillus denitrificans ATCC 25259 +
    NCBITaxon:292415         		UNREVIEWED
    @@ -421,7 +422,7 @@

    Children (1)

    Synonyms (1)

    @@ -437,7 +438,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -689,7 +690,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1111/j.1574-6976.2009.00187.x (already present on lithotrophic.yaml causal_graphs[0].edges[2].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 5 Stage 5 remediation of F-C5S4-DEF-SRC-006 in group G-C5S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.1111/j.1574-6976.2009.00187.x (already present on lithotrophic.yaml causal_graphs[0].edges[2].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 5 Stage 5 remediation of F-C5S4-DEF-SRC-006 in group G-C5S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -722,7 +723,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1086,12 +1096,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 21:40 UTC diff --git a/pages/traits/metabolism/sulfur_respiration.html b/pages/traits/metabolism/sulfur_respiration.html index 14a580b52ce..5b928a89ee0 100644 --- a/pages/traits/metabolism/sulfur_respiration.html +++ b/pages/traits/metabolism/sulfur_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • sulfur_respiration RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • sulfur_respiration RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -116,7 +117,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -212,7 +213,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    The current record carries a single 48-character snippet ('using sulfur as an alternative electron acceptor' in DOI:10.3389/fmicb.2023.1108245) without a second independent mechanistic quote to support a connected multi-edge graph.

    +

    The current record carries a single 48-character snippet ('using sulfur as an alternative electron acceptor' in DOI:10.3389/fmicb.2023.1108245) without a second independent mechanistic quote to support a connected multi-edge graph.

    @@ -285,7 +286,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -314,12 +324,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 20:01 UTC diff --git a/pages/traits/metabolism/syntrophy.html b/pages/traits/metabolism/syntrophy.html index a48f241d1a4..1cc84a2b9ff 100644 --- a/pages/traits/metabolism/syntrophy.html +++ b/pages/traits/metabolism/syntrophy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    		 - Syntrophomonas wolfei subsp. wolfei (strain DSM 2245B / Goettingen) -
    NCBITaxon:335541 + Syntrophomonas wolfei subsp. wolfei (strain DSM 2245B / Goettingen) +
    NCBITaxon:335541         		REVIEWED
    @@ -489,7 +490,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1002006 [-0.312, -0.639, -1.585, +0.222, …]
      • +
    • Syntrophy METPO:1002006 [-0.312, -0.639, -1.585, +0.222, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -575,7 +576,7 @@

    Deep research

    **Category:** METABOLISM; **term kind:** CLASS; **mapping:** REVIEWED **Parent:** METPO:1000060 -For TraitMech purposes, syntrophy should be modeled as a **community-dependent metabolic capacity**, not simply metabolite exchange. Its defining feature is that one organism’s reaction is thermodynamically feasible only because another organism removes products or accepts electrons. In classical methanogenic syntrophy, bacteria oxidize fatty acids or alcohols to acetate, H₂, and/or formate, while methanogens maintain sufficiently low H₂/formate activities and convert the products to CH₄ and CO₂. This is consistent with the supplied definition and the foundational interspecies-electron-transfer interpretation of DOI [10.1038/nrmicro2166](https://doi.org/10.1038/nrmicro2166). Recent literature recognizes both mediated interspecies electron transfer through H₂/formate and direct interspecies electron transfer (DIET). (muller2010syntrophicbutyrateand pages 1-2, nozhevnikova2020syntrophyandinterspecies pages 1-2, jin2023syntrophicpropionateoxidation pages 1-2) +For TraitMech purposes, syntrophy should be modeled as a **community-dependent metabolic capacity**, not simply metabolite exchange. Its defining feature is that one organism’s reaction is thermodynamically feasible only because another organism removes products or accepts electrons. In classical methanogenic syntrophy, bacteria oxidize fatty acids or alcohols to acetate, H₂, and/or formate, while methanogens maintain sufficiently low H₂/formate activities and convert the products to CH₄ and CO₂. This is consistent with the supplied definition and the foundational interspecies-electron-transfer interpretation of DOI [10.1038/nrmicro2166](https://doi.org/10.1038/nrmicro2166). Recent literature recognizes both mediated interspecies electron transfer through H₂/formate and direct interspecies electron transfer (DIET). (muller2010syntrophicbutyrateand pages 1-2, nozhevnikova2020syntrophyandinterspecies pages 1-2, jin2023syntrophicpropionateoxidation pages 1-2) The most defensible core graph is therefore: @@ -801,7 +802,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1165,12 +1175,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/tetrathionate_respiration.html b/pages/traits/metabolism/tetrathionate_respiration.html index d7c53cbb175..6eedbb8b47e 100644 --- a/pages/traits/metabolism/tetrathionate_respiration.html +++ b/pages/traits/metabolism/tetrathionate_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    Trait evidence (5)

    Tetrathionate reductase catalysis and anaerobic reduction to thiosulfate

    Evidence-backed metabolic pathway sketch linking tetrathionate terminal electron acceptance, TtrABC tetrathionate reductase activity, and thiosulfate production to tetrathionate respiration.

    -

    MECHANISTIC · Mechanistic graph backed by DOI:10.1046/j.1365-2958.1999.01345.x and DOI:10.1128/JB.183.8.2463-2475.2001; exemplified on tetrathionate_respiration_ttr_complex with Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (NCBITaxon:99287; UP000001014) tetrathionate reductase subunits TtrA (UniProtKB:Q9Z4S6) and TtrB (UniProtKB:Q7CQM9).

    +

    MECHANISTIC · Mechanistic graph backed by DOI:10.1046/j.1365-2958.1999.01345.x and DOI:10.1128/JB.183.8.2463-2475.2001; exemplified on tetrathionate_respiration_ttr_complex with Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (NCBITaxon:99287; UP000001014) tetrathionate reductase subunits TtrA (UniProtKB:Q9Z4S6) and TtrB (UniProtKB:Q7CQM9).

    Loading graph…

    @@ -114,7 +115,7 @@

    Edge evidence

  • tetrathionate respiration - traitmech:000200 + traitmech:000200 has electron acceptor tetrathionate CHEBI:29892 @@ -136,7 +137,7 @@

    Edge evidence

    GO:0018523 confers tetrathionate respiration - traitmech:000200 + traitmech:000200 METPO:2007700

    Tetrathionate reductase encoded by ttrA, ttrB, and ttrC confers tetrathionate respiration.

      @@ -211,8 +212,8 @@

      Protein and taxon examples

    		•  - Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 -
    NCBITaxon:99287 + Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 +
    NCBITaxon:99287         		REVIEWED
    @@ -241,8 +242,8 @@

    Protein and taxon examples

    		 - Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 -
    NCBITaxon:99287 + Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 +
    NCBITaxon:99287         		REVIEWED
    @@ -315,7 +316,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -465,7 +466,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The record's primary literature (DOI:10.1046/j.1365-2958.1999.01345.x, DOI:10.1128/JB.183.8.2463-2475.2001) identifies the ttrABC structural genes and tetrathionate-to-thiosulfate reduction in Salmonella enterica serovar Typhimurium LT2 (NCBITaxon:99287), but verified UniProtKB accessions must be curated on a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    +

    The record's primary literature (DOI:10.1046/j.1365-2958.1999.01345.x, DOI:10.1128/JB.183.8.2463-2475.2001) identifies the ttrABC structural genes and tetrathionate-to-thiosulfate reduction in Salmonella enterica serovar Typhimurium LT2 (NCBITaxon:99287), but verified UniProtKB accessions must be curated on a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    @@ -484,7 +485,7 @@

    Evidence

    -

    Resolution: Promoted tetrathionate_respiration_ttr_pathway_sketch to MECHANISTIC by adding InterPro:IPR037946-grounded GENE_OR_PROTEIN node tetrathionate_respiration_ttr_complex with reviewed Salmonella enterica serovar Typhimurium LT2 (NCBITaxon:99287; UP000001014) protein_examples UniProtKB:Q9Z4S6 (TtrA) and UniProtKB:Q7CQM9 (TtrB) backed by DOI:10.1046/j.1365-2958.1999.01345.x.

    +

    Resolution: Promoted tetrathionate_respiration_ttr_pathway_sketch to MECHANISTIC by adding InterPro:IPR037946-grounded GENE_OR_PROTEIN node tetrathionate_respiration_ttr_complex with reviewed Salmonella enterica serovar Typhimurium LT2 (NCBITaxon:99287; UP000001014) protein_examples UniProtKB:Q9Z4S6 (TtrA) and UniProtKB:Q7CQM9 (TtrB) backed by DOI:10.1046/j.1365-2958.1999.01345.x.

    @@ -513,7 +514,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Promoted tetrathionate_respiration_ttr_pathway_sketch to MECHANISTIC; added InterPro:IPR037946-grounded GENE_OR_PROTEIN node tetrathionate_respiration_ttr_complex with reviewed Salmonella enterica serovar Typhimurium LT2 (NCBITaxon:99287; UP000001014) protein_examples UniProtKB:Q9Z4S6 (TtrA) and UniProtKB:Q7CQM9 (TtrB) backed by DOI:10.1046/j.1365-2958.1999.01345.x; resolved tetrathionate-respiration-protein-example-gap.

    +

    Promoted tetrathionate_respiration_ttr_pathway_sketch to MECHANISTIC; added InterPro:IPR037946-grounded GENE_OR_PROTEIN node tetrathionate_respiration_ttr_complex with reviewed Salmonella enterica serovar Typhimurium LT2 (NCBITaxon:99287; UP000001014) protein_examples UniProtKB:Q9Z4S6 (TtrA) and UniProtKB:Q7CQM9 (TtrB) backed by DOI:10.1046/j.1365-2958.1999.01345.x; resolved tetrathionate-respiration-protein-example-gap.

    • @@ -555,7 +556,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -919,12 +929,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 11:45 UTC diff --git a/pages/traits/metabolism/thiosulfate_respiration.html b/pages/traits/metabolism/thiosulfate_respiration.html index def4c6edfa4..2824099be60 100644 --- a/pages/traits/metabolism/thiosulfate_respiration.html +++ b/pages/traits/metabolism/thiosulfate_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • thiosulfate_respiration RELATED_SYNONYM · DOI:10.1126/science.aaf4507
      • +
    • thiosulfate_respiration RELATED_SYNONYM · DOI:10.1126/science.aaf4507
    @@ -116,7 +117,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -212,7 +213,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    The current record carries a single 45-character snippet ('sulfur- and thiosulfate reducing type strain' in DOI:10.3389/fmicb.2023.1108245) without enzymatic or product-level quotes needed for a multi-edge causal graph.

    +

    The current record carries a single 45-character snippet ('sulfur- and thiosulfate reducing type strain' in DOI:10.3389/fmicb.2023.1108245) without enzymatic or product-level quotes needed for a multi-edge causal graph.

    @@ -285,7 +286,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -314,12 +324,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 20:01 UTC diff --git a/pages/traits/metabolism/three_hydroxypropionate_bicycle.html b/pages/traits/metabolism/three_hydroxypropionate_bicycle.html index 07f85eb6c8f..2d1b8776819 100644 --- a/pages/traits/metabolism/three_hydroxypropionate_bicycle.html +++ b/pages/traits/metabolism/three_hydroxypropionate_bicycle.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    CHEBI:17544 fixed by 3-hydroxypropionate bicycle - traitmech:000023 + traitmech:000023 METPO:2007404

    Two molecules of bicarbonate are fixed per cycle turn.

      @@ -115,7 +116,7 @@

      Edge evidence

    • 3-hydroxypropionate bicycle - traitmech:000023 + traitmech:000023 contributes to carbon fixation GO:0015977 @@ -248,7 +249,7 @@

      Edge evidence

    • 3-hydroxypropionate bicycle - traitmech:000023 + traitmech:000023 has output pyruvate CHEBI:15361 @@ -270,7 +271,7 @@

      Edge evidence

      GO:0003989 contributes to 3-hydroxypropionate bicycle - traitmech:000023 + traitmech:000023 RO:0002326

      Acetyl-CoA carboxylase is an enzyme of the 3HP bicycle.

        @@ -289,7 +290,7 @@

        Edge evidence

        contributes to 3-hydroxypropionate bicycle - traitmech:000023 + traitmech:000023 RO:0002326

        Malonyl-CoA reductase is an enzyme of the 3HP bicycle.

          @@ -308,7 +309,7 @@

          Edge evidence

          contributes to 3-hydroxypropionate bicycle - traitmech:000023 + traitmech:000023 RO:0002326

          Propionyl-CoA synthase is an enzyme of the 3HP bicycle.

            @@ -327,7 +328,7 @@

            Edge evidence

            GO:0004658 contributes to 3-hydroxypropionate bicycle - traitmech:000023 + traitmech:000023 RO:0002326

            Propionyl-CoA carboxylase is an enzyme of the 3HP bicycle.

              @@ -364,8 +365,8 @@

              Protein and taxon examples

    		 - Chloroflexus aurantiacus -
    NCBITaxon:1108 + Chloroflexus aurantiacus +
    NCBITaxon:1108         		REVIEWED
    @@ -431,7 +432,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • 3-hydroxypropionate cycle RELATED_SYNONYM · DOI:10.1128/AEM.02473-10
      • +
    • 3-hydroxypropionate cycle RELATED_SYNONYM · DOI:10.1128/AEM.02473-10
    @@ -447,7 +448,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -690,7 +691,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1128/AEM.02473-10 (already present on causal_graphs[0].edges[9].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-006 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.1128/AEM.02473-10 (already present on causal_graphs[0].edges[9].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-006 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -732,7 +733,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1096,12 +1106,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/metabolism/three_hydroxypropionate_four_hydroxybutyrate_cycle.html b/pages/traits/metabolism/three_hydroxypropionate_four_hydroxybutyrate_cycle.html index bc43c506701..38c68c90ed8 100644 --- a/pages/traits/metabolism/three_hydroxypropionate_four_hydroxybutyrate_cycle.html +++ b/pages/traits/metabolism/three_hydroxypropionate_four_hydroxybutyrate_cycle.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    CHEBI:17544 fixed by 3-hydroxypropionate/4-hydroxybutyrate cycle - traitmech:000024 + traitmech:000024 METPO:2007404

    Two molecules of bicarbonate are fixed per cycle turn.

      @@ -115,7 +116,7 @@

      Edge evidence

    • 3-hydroxypropionate/4-hydroxybutyrate cycle - traitmech:000024 + traitmech:000024 contributes to carbon fixation GO:0015977 @@ -134,7 +135,7 @@

      Edge evidence

    • 3-hydroxypropionate/4-hydroxybutyrate cycle - traitmech:000024 + traitmech:000024 produces acetyl-CoA @@ -153,7 +154,7 @@

      Edge evidence

    • 3-hydroxypropionate/4-hydroxybutyrate cycle - traitmech:000024 + traitmech:000024 forms intermediate succinyl-CoA @@ -251,7 +252,7 @@

      Edge evidence

      CHEBI:16474 is required by 3-hydroxypropionate/4-hydroxybutyrate cycle - traitmech:000024 + traitmech:000024

      Reductive steps of the cycle consume NADPH (about four NADPH per turn).

        @@ -270,7 +271,7 @@

        Edge evidence

        mediates carboxylation in 3-hydroxypropionate/4-hydroxybutyrate cycle - traitmech:000024 + traitmech:000024

        Acetyl-CoA/propionyl-CoA carboxylase is the primary carboxylase fixing inorganic carbon.

          @@ -307,8 +308,8 @@

          Protein and taxon examples

    		 - Metallosphaera sedula DSM 5348 -
    NCBITaxon:399549 + Metallosphaera sedula DSM 5348 +
    NCBITaxon:399549         		UNREVIEWED
    @@ -337,8 +338,8 @@

    Protein and taxon examples

    		 - Metallosphaera sedula DSM 5348 -
    NCBITaxon:399549 + Metallosphaera sedula DSM 5348 +
    NCBITaxon:399549         		UNREVIEWED
    @@ -367,8 +368,8 @@

    Protein and taxon examples

    		 - Metallosphaera sedula DSM 5348 -
    NCBITaxon:399549 + Metallosphaera sedula DSM 5348 +
    NCBITaxon:399549         		UNREVIEWED
    @@ -397,8 +398,8 @@

    Protein and taxon examples

    		 - Metallosphaera sedula DSM 5348 -
    NCBITaxon:399549 + Metallosphaera sedula DSM 5348 +
    NCBITaxon:399549         		UNREVIEWED
    @@ -464,7 +465,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -480,7 +481,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -777,7 +778,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1141,12 +1151,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/metabolism/transports.html b/pages/traits/metabolism/transports.html index 56d726057df..0a4ee8be42c 100644 --- a/pages/traits/metabolism/transports.html +++ b/pages/traits/metabolism/transports.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:2000207 [-1.261, -0.133, -2.951, -0.069, …]
      • +
    • transports METPO:2000207 [-1.261, -0.133, -2.951, -0.069, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -243,7 +244,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -272,12 +282,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/trimethylamine_n_oxide_respiration.html b/pages/traits/metabolism/trimethylamine_n_oxide_respiration.html index ba7fa7e9e66..94106bb234f 100644 --- a/pages/traits/metabolism/trimethylamine_n_oxide_respiration.html +++ b/pages/traits/metabolism/trimethylamine_n_oxide_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -88,7 +89,7 @@

    Trait evidence (4)

    torCAD-encoded TMAO reductase anaerobic respiratory pathway

    Evidence-backed metabolic pathway sketch linking TMAO terminal electron acceptance, torCAD-encoded TMAO reductase catalysis, and trimethylamine formation to TMAO respiration.

    -

    MECHANISTIC · Mechanistic graph backed by DOI:10.1111/1462-2920.12726 and DOI:10.3389/fmicb.2024.1467153; exemplified on tmao_respiration_tor_system with Escherichia coli K-12 (NCBITaxon:83333; UP000000625) TMAO reductase subunits TorA (UniProtKB:P33225) and TorC (UniProtKB:P33226).

    +

    MECHANISTIC · Mechanistic graph backed by DOI:10.1111/1462-2920.12726 and DOI:10.3389/fmicb.2024.1467153; exemplified on tmao_respiration_tor_system with Escherichia coli K-12 (NCBITaxon:83333; UP000000625) TMAO reductase subunits TorA (UniProtKB:P33225) and TorC (UniProtKB:P33226).

    Loading graph…

    @@ -108,7 +109,7 @@

    Edge evidence

  • trimethylamine N-oxide respiration - traitmech:000199 + traitmech:000199 has electron acceptor trimethylamine N-oxide CHEBI:15724 @@ -149,7 +150,7 @@

    Edge evidence

    GO:0008810 confers trimethylamine N-oxide respiration - traitmech:000199 + traitmech:000199 METPO:2007700

    Respiratory TMAO reduction confers the trimethylamine N-oxide respiration energy-metabolism mode.

      @@ -205,8 +206,8 @@

      Protein and taxon examples

    		•  - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -235,8 +236,8 @@

    Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -302,7 +303,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -318,7 +319,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -468,7 +469,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The record's primary literature (DOI:10.1111/1462-2920.12726, DOI:10.3389/fmicb.2024.1467153) establishes anaerobic respiratory growth on TMAO and reduction of TMAO to trimethylamine by torCAD-encoded TMAO reductase in Escherichia coli K-12 (NCBITaxon:83333), but verified UniProtKB accessions must be curated on a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    +

    The record's primary literature (DOI:10.1111/1462-2920.12726, DOI:10.3389/fmicb.2024.1467153) establishes anaerobic respiratory growth on TMAO and reduction of TMAO to trimethylamine by torCAD-encoded TMAO reductase in Escherichia coli K-12 (NCBITaxon:83333), but verified UniProtKB accessions must be curated on a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    @@ -487,7 +488,7 @@

    Evidence

    -

    Resolution: Promoted tmao_respiration_tor_pathway_sketch to MECHANISTIC by adding InterPro:IPR041954-grounded GENE_OR_PROTEIN node tmao_respiration_tor_system with reviewed Escherichia coli K-12 (NCBITaxon:83333; UP000000625) protein_examples UniProtKB:P33225 (TorA) and UniProtKB:P33226 (TorC) backed by DOI:10.1111/1462-2920.12726.

    +

    Resolution: Promoted tmao_respiration_tor_pathway_sketch to MECHANISTIC by adding InterPro:IPR041954-grounded GENE_OR_PROTEIN node tmao_respiration_tor_system with reviewed Escherichia coli K-12 (NCBITaxon:83333; UP000000625) protein_examples UniProtKB:P33225 (TorA) and UniProtKB:P33226 (TorC) backed by DOI:10.1111/1462-2920.12726.

    @@ -516,7 +517,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Promoted tmao_respiration_tor_pathway_sketch to MECHANISTIC; added InterPro:IPR041954-grounded GENE_OR_PROTEIN node tmao_respiration_tor_system with reviewed Escherichia coli K-12 (NCBITaxon:83333; UP000000625) protein_examples UniProtKB:P33225 (TorA) and UniProtKB:P33226 (TorC) backed by DOI:10.1111/1462-2920.12726; resolved trimethylamine-n-oxide-respiration-protein-example-gap.

    +

    Promoted tmao_respiration_tor_pathway_sketch to MECHANISTIC; added InterPro:IPR041954-grounded GENE_OR_PROTEIN node tmao_respiration_tor_system with reviewed Escherichia coli K-12 (NCBITaxon:83333; UP000000625) protein_examples UniProtKB:P33225 (TorA) and UniProtKB:P33226 (TorC) backed by DOI:10.1111/1462-2920.12726; resolved trimethylamine-n-oxide-respiration-protein-example-gap.

    • @@ -558,7 +559,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -922,12 +932,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 11:45 UTC diff --git a/pages/traits/metabolism/uses_as_carbon_source.html b/pages/traits/metabolism/uses_as_carbon_source.html index 416676a6098..96f36afa41b 100644 --- a/pages/traits/metabolism/uses_as_carbon_source.html +++ b/pages/traits/metabolism/uses_as_carbon_source.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • carbon source RELATED_SYNONYM · metpo.owl
      • +
    • carbon source RELATED_SYNONYM · metpo.owl
    @@ -110,7 +111,7 @@

    Synonyms (1)

    Cross-references

    @@ -123,7 +124,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -254,7 +255,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -283,12 +293,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 17:00 UTC diff --git a/pages/traits/metabolism/uses_as_electron_acceptor.html b/pages/traits/metabolism/uses_as_electron_acceptor.html index 156038f5f8e..b664b34026f 100644 --- a/pages/traits/metabolism/uses_as_electron_acceptor.html +++ b/pages/traits/metabolism/uses_as_electron_acceptor.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • electron acceptor RELATED_SYNONYM · metpo.owl
      • +
    • electron acceptor RELATED_SYNONYM · metpo.owl
    @@ -110,7 +111,7 @@

    Synonyms (1)

    Cross-references

    @@ -123,7 +124,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -254,7 +255,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -283,12 +293,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 17:00 UTC diff --git a/pages/traits/metabolism/uses_as_electron_donor.html b/pages/traits/metabolism/uses_as_electron_donor.html index 8897d41fc51..fd3fbe79ba2 100644 --- a/pages/traits/metabolism/uses_as_electron_donor.html +++ b/pages/traits/metabolism/uses_as_electron_donor.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • electron donor RELATED_SYNONYM · metpo.owl
      • +
    • electron donor RELATED_SYNONYM · metpo.owl
    @@ -110,7 +111,7 @@

    Synonyms (1)

    Cross-references

    @@ -123,7 +124,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -254,7 +255,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -283,12 +293,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 17:00 UTC diff --git a/pages/traits/metabolism/uses_as_energy_source.html b/pages/traits/metabolism/uses_as_energy_source.html index b7ca7f30753..cbba0ea7d85 100644 --- a/pages/traits/metabolism/uses_as_energy_source.html +++ b/pages/traits/metabolism/uses_as_energy_source.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • energy source RELATED_SYNONYM · metpo.owl
      • +
    • energy source RELATED_SYNONYM · metpo.owl
    @@ -110,7 +111,7 @@

    Synonyms (1)

    Cross-references

    @@ -123,7 +124,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -254,7 +255,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -283,12 +293,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 17:00 UTC diff --git a/pages/traits/metabolism/uses_as_nitrogen_source.html b/pages/traits/metabolism/uses_as_nitrogen_source.html index d084a70107e..814f2cb458d 100644 --- a/pages/traits/metabolism/uses_as_nitrogen_source.html +++ b/pages/traits/metabolism/uses_as_nitrogen_source.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • nitrogen source RELATED_SYNONYM · metpo.owl
      • +
    • nitrogen source RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Curation history

  • · TIGHTENED_RANGE_TO_CHEBI_SUBCLASS · claude -

    Narrowed range_ from http://purl.obolibrary.org/obo/CHEBI_24431 to http://purl.obolibrary.org/obo/CHEBI_51143 ('nitrogen molecular entity'). The earlier CHEBI:24431 root was used as a safe default during bulk un-deprecation (PR #54); the more specific CHEBI subclass better reflects the predicate's intended substrates.

    +

    Narrowed range_ from http://purl.obolibrary.org/obo/CHEBI_24431 to http://purl.obolibrary.org/obo/CHEBI_51143 ('nitrogen molecular entity'). The earlier CHEBI:24431 root was used as a safe default during bulk un-deprecation (PR #54); the more specific CHEBI subclass better reflects the predicate's intended substrates.

    • @@ -247,7 +248,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -276,12 +286,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 16:35 UTC diff --git a/pages/traits/metabolism/uses_as_sulfur_source.html b/pages/traits/metabolism/uses_as_sulfur_source.html index 26d4b507a92..34fcc97718d 100644 --- a/pages/traits/metabolism/uses_as_sulfur_source.html +++ b/pages/traits/metabolism/uses_as_sulfur_source.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • sulfur source RELATED_SYNONYM · metpo.owl
      • +
    • sulfur source RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Curation history

  • · TIGHTENED_RANGE_TO_CHEBI_SUBCLASS · claude -

    Narrowed range_ from http://purl.obolibrary.org/obo/CHEBI_24431 to http://purl.obolibrary.org/obo/CHEBI_26835 ('sulfur molecular entity'). The earlier CHEBI:24431 root was used as a safe default during bulk un-deprecation (PR #54); the more specific CHEBI subclass better reflects the predicate's intended substrates.

    +

    Narrowed range_ from http://purl.obolibrary.org/obo/CHEBI_24431 to http://purl.obolibrary.org/obo/CHEBI_26835 ('sulfur molecular entity'). The earlier CHEBI:24431 root was used as a safe default during bulk un-deprecation (PR #54); the more specific CHEBI subclass better reflects the predicate's intended substrates.

    • @@ -247,7 +248,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -276,12 +286,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 16:35 UTC diff --git a/pages/traits/metabolism/uses_for_aerobic_catabolization.html b/pages/traits/metabolism/uses_for_aerobic_catabolization.html index 10554a75207..b387f931277 100644 --- a/pages/traits/metabolism/uses_for_aerobic_catabolization.html +++ b/pages/traits/metabolism/uses_for_aerobic_catabolization.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • aerobic catabolization RELATED_SYNONYM · metpo.owl
      • +
    • aerobic catabolization RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/uses_for_aerobic_growth.html b/pages/traits/metabolism/uses_for_aerobic_growth.html index 28e7448cc86..e048330478f 100644 --- a/pages/traits/metabolism/uses_for_aerobic_growth.html +++ b/pages/traits/metabolism/uses_for_aerobic_growth.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • aerobic growth RELATED_SYNONYM · metpo.owl
      • +
    • aerobic growth RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/uses_for_anaerobic_catabolization.html b/pages/traits/metabolism/uses_for_anaerobic_catabolization.html index 517785ad89b..007c91aa16d 100644 --- a/pages/traits/metabolism/uses_for_anaerobic_catabolization.html +++ b/pages/traits/metabolism/uses_for_anaerobic_catabolization.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • anaerobic catabolization RELATED_SYNONYM · metpo.owl
      • +
    • anaerobic catabolization RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/uses_for_anaerobic_growth.html b/pages/traits/metabolism/uses_for_anaerobic_growth.html index 2cb997be91f..dbc11b1ed4b 100644 --- a/pages/traits/metabolism/uses_for_anaerobic_growth.html +++ b/pages/traits/metabolism/uses_for_anaerobic_growth.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • anaerobic growth RELATED_SYNONYM · metpo.owl
      • +
    • anaerobic growth RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/uses_for_anaerobic_growth_in_the_dark.html b/pages/traits/metabolism/uses_for_anaerobic_growth_in_the_dark.html index c6f3c20e257..13fca7da986 100644 --- a/pages/traits/metabolism/uses_for_anaerobic_growth_in_the_dark.html +++ b/pages/traits/metabolism/uses_for_anaerobic_growth_in_the_dark.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • anaerobic growth in the dark RELATED_SYNONYM · metpo.owl
      • +
    • anaerobic growth in the dark RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/uses_for_anaerobic_growth_with_light.html b/pages/traits/metabolism/uses_for_anaerobic_growth_with_light.html index b46d183877d..4ed7c1bc783 100644 --- a/pages/traits/metabolism/uses_for_anaerobic_growth_with_light.html +++ b/pages/traits/metabolism/uses_for_anaerobic_growth_with_light.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • anaerobic growth with light RELATED_SYNONYM · metpo.owl
      • +
    • anaerobic growth with light RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/uses_for_growth.html b/pages/traits/metabolism/uses_for_growth.html index a02bc257ca3..07085228049 100644 --- a/pages/traits/metabolism/uses_for_growth.html +++ b/pages/traits/metabolism/uses_for_growth.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • growth RELATED_SYNONYM · metpo.owl
      • +
    • growth RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/uses_for_respiration.html b/pages/traits/metabolism/uses_for_respiration.html index 66933668c74..e7e7b0f7af3 100644 --- a/pages/traits/metabolism/uses_for_respiration.html +++ b/pages/traits/metabolism/uses_for_respiration.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • respiration RELATED_SYNONYM · metpo.owl
      • +
    • respiration RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/uses_in_other_way.html b/pages/traits/metabolism/uses_in_other_way.html index 8e55445eaad..d7fe0384359 100644 --- a/pages/traits/metabolism/uses_in_other_way.html +++ b/pages/traits/metabolism/uses_in_other_way.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • other RELATED_SYNONYM · metpo.owl
      • +
    • other RELATED_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,16 @@

    Identifier

    Term kind
    OBJECT_PROPERTY
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -270,12 +280,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 15:50 UTC diff --git a/pages/traits/metabolism/wood_ljungdahl_pathway.html b/pages/traits/metabolism/wood_ljungdahl_pathway.html index 1f4579d1b92..ce436e7fdb4 100644 --- a/pages/traits/metabolism/wood_ljungdahl_pathway.html +++ b/pages/traits/metabolism/wood_ljungdahl_pathway.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    GO:0030634 confers Wood-Ljungdahl pathway - traitmech:000022 + traitmech:000022 METPO:2007700

    The reductive acetyl-CoA pathway underlies the trait.

      @@ -118,7 +119,7 @@

      Edge evidence

      CHEBI:16526 fixed by Wood-Ljungdahl pathway - traitmech:000022 + traitmech:000022 METPO:2007404

      Two molecules of CO2 are fixed and combined into acetyl-CoA.

        @@ -398,8 +399,8 @@

        Protein and taxon examples

    		 - Neomoorella thermoacetica -
    NCBITaxon:1525 + Neomoorella thermoacetica +
    NCBITaxon:1525         		REVIEWED
    @@ -465,7 +466,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • reductive acetyl-CoA pathway EXACT_SYNONYM · DOI:10.1016/j.bbapap.2008.08.012
      • +
    • reductive acetyl-CoA pathway EXACT_SYNONYM · DOI:10.1016/j.bbapap.2008.08.012
    @@ -481,7 +482,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -730,7 +731,7 @@

    Curation history

  • · REVIEW_EVIDENCE_REFERENCE_CHURN · codex -

    Offline review for issue 520 retained 2 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1039/d4cb00099d -> DOI:10.3389/fbioe.2024.1395540 (1 edge); DOI:10.1128/AEM.02473-10 -> DOI:10.3389/fbioe.2024.1395540 (1 edge).

    +

    Offline review for issue 520 retained 2 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1039/d4cb00099d -> DOI:10.3389/fbioe.2024.1395540 (1 edge); DOI:10.1128/AEM.02473-10 -> DOI:10.3389/fbioe.2024.1395540 (1 edge).

  • @@ -754,7 +755,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1016/j.bbapap.2008.08.012 (already present on causal_graphs[0].edges[0]) to record-level evidence[0] to match definition_source (Cycle 2 Stage 5 remediation of F-DEF-SRC-WOOD-LJUNGDAHL-011 in group G-C2S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #1995).

    +

    Added verified verbatim snippet from DOI:10.1016/j.bbapap.2008.08.012 (already present on causal_graphs[0].edges[0]) to record-level evidence[0] to match definition_source (Cycle 2 Stage 5 remediation of F-DEF-SRC-WOOD-LJUNGDAHL-011 in group G-C2S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #1995).

    • @@ -796,7 +797,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1160,12 +1170,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 16:05 UTC diff --git a/pages/traits/metabolism/xylan_degradation.html b/pages/traits/metabolism/xylan_degradation.html index 85a276a57e4..6315e5564ce 100644 --- a/pages/traits/metabolism/xylan_degradation.html +++ b/pages/traits/metabolism/xylan_degradation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    confers xylan degradation - traitmech:000113 + traitmech:000113 METPO:2007700

    Xylanase systems drive xylan depolymerization extracellularly.

      @@ -115,7 +116,7 @@

      Edge evidence

    • xylan degradation - traitmech:000113 + traitmech:000113 produces xylose CHEBI:18222 @@ -250,8 +251,8 @@

      Protein and taxon examples

    		 - Caldicellulosiruptor saccharolyticus -
    NCBITaxon:44001 + Caldicellulosiruptor saccharolyticus +
    NCBITaxon:44001         		REVIEWED
    @@ -317,15 +318,15 @@

    Parent traits (1)

    Synonyms (5)

    @@ -348,7 +349,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]
      • +
    • metabolism METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -600,7 +601,7 @@

    Curation history

  • · RESTORE_CANONICAL_CITATION · claude -

    Restored the canonical-example citation for NCBITaxon:44001 from DOI:10.1128/aem.56.4.1017-1024.1990 back to PMID:18776029 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.

    +

    Restored the canonical-example citation for NCBITaxon:44001 from DOI:10.1128/aem.56.4.1017-1024.1990 back to PMID:18776029 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.

  • @@ -666,7 +667,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1030,12 +1040,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/akinete.html b/pages/traits/morphology/akinete.html index e8cea160dc7..58a9bfec88a 100644 --- a/pages/traits/morphology/akinete.html +++ b/pages/traits/morphology/akinete.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -269,7 +270,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries morphological and ecological-survival snippets in Nostocales (DOI:10.1159/000517443, DOI:10.3389/fmicb.2025.1677844) without developmental gene or biosynthetic pathway quotes.

    +

    The current record carries morphological and ecological-survival snippets in Nostocales (DOI:10.1159/000517443, DOI:10.3389/fmicb.2025.1677844) without developmental gene or biosynthetic pathway quotes.

    @@ -319,7 +320,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add akinete trait -

      Minted traitmech:000185 for the cyanobacterial akinete morphology trait with DOI-backed Nostocales evidence from 10.1159/000517443 and 10.3389/fmicb.2025.1677844, a Trichormus variabilis ATCC 29413 canonical example, and a v62 METPO proposal for the upstream placeholder.

    +

    Minted traitmech:000185 for the cyanobacterial akinete morphology trait with DOI-backed Nostocales evidence from 10.1159/000517443 and 10.3389/fmicb.2025.1677844, a Trichormus variabilis ATCC 29413 canonical example, and a v62 METPO proposal for the upstream placeholder.

    • Read this curation session
    • @@ -351,7 +352,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -380,12 +390,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/morphology/amphitrichous.html b/pages/traits/morphology/amphitrichous.html index 3a77241d561..cd9d1ac61cb 100644 --- a/pages/traits/morphology/amphitrichous.html +++ b/pages/traits/morphology/amphitrichous.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    GO:0009288 defines amphitrichous - traitmech:000059 + traitmech:000059 METPO:2007500

    Flagella at both cell poles define the amphitrichous arrangement.

      @@ -115,7 +116,7 @@

      Edge evidence

    • amphitrichous - traitmech:000059 + traitmech:000059 associated with bipolar placement @@ -318,7 +319,7 @@

      kg-microbe context

      via parent_proxy.

      512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

      @@ -555,7 +556,7 @@

      Curation history

    • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

      Added verified verbatim snippet from DOI:10.1093/femsre/fuv034 (already present on sibling record polar_flagellation.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-015 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

      +

      Added verified verbatim snippet from DOI:10.1093/femsre/fuv034 (already present on sibling record polar_flagellation.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-015 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

      • @@ -588,7 +589,16 @@

      Identifier

      Term kind
      CLASS
      Status
      -
      REVIEWED
      +
      REVIEWED + + +
      + What this status means +

      Curator has signed off on label / definition / parents.

      +

      Quoted from the schema's status definitions.

      +
      + +
    @@ -952,12 +962,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/morphology/axially_filamented.html b/pages/traits/morphology/axially_filamented.html index caf16516486..1b6001c004a 100644 --- a/pages/traits/morphology/axially_filamented.html +++ b/pages/traits/morphology/axially_filamented.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -324,7 +325,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • axial filament RELATED_SYNONYM · metpo.owl
      • +
    • axial filament RELATED_SYNONYM · metpo.owl
    @@ -340,7 +341,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -427,7 +428,7 @@

    Deep research

    **Parent:** METPO:1000702 **Synonym:** axial filament -The trait should denote a bacterium possessing one or more **flagellar filaments confined to the periplasm**, rather than flagella projecting beyond the outer membrane. In spirochetes these structures are usually called **periplasmic flagella (PFs), endoflagella, or axial filaments**. They arise from motors at one or both poles and run along the protoplasmic cylinder beneath the outer membrane. Their rotation deforms or rotates the cell body, producing rolling or undulatory propulsion; in several taxa they also mechanically determine cell shape. The defining feature is therefore **filament topology/localization**, not motility alone and not merely a spiral cell shape. Nakamura states that spirochetal flagella are “hidden within the periplasmic space,” whereas external flagella directly interact with the surrounding fluid (published 4 April 2020; DOI [10.3390/biom10040550](https://doi.org/10.3390/biom10040550)). (nakamura2020spirocheteflagellaand pages 1-3) +The trait should denote a bacterium possessing one or more **flagellar filaments confined to the periplasm**, rather than flagella projecting beyond the outer membrane. In spirochetes these structures are usually called **periplasmic flagella (PFs), endoflagella, or axial filaments**. They arise from motors at one or both poles and run along the protoplasmic cylinder beneath the outer membrane. Their rotation deforms or rotates the cell body, producing rolling or undulatory propulsion; in several taxa they also mechanically determine cell shape. The defining feature is therefore **filament topology/localization**, not motility alone and not merely a spiral cell shape. Nakamura states that spirochetal flagella are “hidden within the periplasmic space,” whereas external flagella directly interact with the surrounding fluid (published 4 April 2020; DOI [10.3390/biom10040550](https://doi.org/10.3390/biom10040550)). (nakamura2020spirocheteflagellaand pages 1-3) The most defensible TraitMech causal chain is: @@ -604,7 +605,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -968,12 +978,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/bacillus_shaped.html b/pages/traits/morphology/bacillus_shaped.html index 1d61a6e663b..4a7c373f042 100644 --- a/pages/traits/morphology/bacillus_shaped.html +++ b/pages/traits/morphology/bacillus_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -324,7 +325,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • bacillus RELATED_SYNONYM · metpo.owl
      • +
    • bacillus RELATED_SYNONYM · metpo.owl
    @@ -340,7 +341,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -670,7 +671,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1034,12 +1044,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/baeocyte_formation.html b/pages/traits/morphology/baeocyte_formation.html index 29a098c86cd..24806d13a6b 100644 --- a/pages/traits/morphology/baeocyte_formation.html +++ b/pages/traits/morphology/baeocyte_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -61,7 +62,7 @@

    Trait evidence (2)

    PMID:18365724
    Electron microscopy of cyanobacteria Pleurocapsa sp. CALU 1126 revealed that multiple fission proceeds by successive binary fissions.
    -

    Pinevich et al. (2008), English scientific abstract directly retrieved at https://pubmed.ncbi.nlm.nih.gov/18365724/. Its following sentence identifies baeocytes as multiple-fission products and macrocytes as binary-fission products. This supports the reported division sequence in CALU 1126, not a universal simultaneous-cleavage requirement. Juvenile-cell differences and metabolic uncoupling are source-specific observations and interpretation, not the class definition. The Russian full paper, figures and strain provenance were not inspected; no CALU 1126 canonical example is assigned.

    +

    Pinevich et al. (2008), English scientific abstract directly retrieved at https://pubmed.ncbi.nlm.nih.gov/18365724/. Its following sentence identifies baeocytes as multiple-fission products and macrocytes as binary-fission products. This supports the reported division sequence in CALU 1126, not a universal simultaneous-cleavage requirement. Juvenile-cell differences and metabolic uncoupling are source-specific observations and interpretation, not the class definition. The Russian full paper, figures and strain provenance were not inspected; no CALU 1126 canonical example is assigned.

    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Canonical examples DOI:10.1007/s10482-021-01672-x - KI4, a non-axenic culture from seaweed apical material collected at Falckensteiner Strand near Kiel, Germany. Collection Methods report 15-degree near-dark artificial-seawater incubation and host-free subculture; the species description reports low-light liquid BG11 at 20 PSU. These are distinct culture descriptions, not an asserted Figure 4 acquisition protocol. C-A-99685 is a lyophilized filter herbarium specimen, not a living-culture accession. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2874699 confirms the strain-level current name with rank no rank, not a species-level ID or an independent phenotype assay. + KI4, a non-axenic culture from seaweed apical material collected at Falckensteiner Strand near Kiel, Germany. Collection Methods report 15-degree near-dark artificial-seawater incubation and host-free subculture; the species description reports low-light liquid BG11 at 20 PSU. These are distinct culture descriptions, not an asserted Figure 4 acquisition protocol. C-A-99685 is a lyophilized filter herbarium specimen, not a living-culture accession. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2874699 confirms the strain-level current name with rank no rank, not a species-level ID or an independent phenotype assay. @@ -296,7 +297,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add source-qualified baeocyte formation -

      Added traitmech:000672 with DOI:10.1007/s10482-021-01672-x and PMID:18365724, two verbatim source snippets, a non-axenic Waterburya agarophytonicola KI4 example independently identified as NCBITaxon:2874699, and open hierarchy/mechanism discussions. Directly inspected publisher taxonomy descriptions, Collection Methods and actual Figure 4; used the directly retrieved English scientific abstract for the Russian second paper. Reserved v548 / METPO:1062500-1062599 after ignored-and-hidden whole-repository/worktree and complete open-PR reservation checks. No protein graph, exact synonyms or xrefs asserted; existing traits unchanged. Writer is dry-run by default and prevalidates before mutation; broader validations remain pending at scaffolding.

    +

    Added traitmech:000672 with DOI:10.1007/s10482-021-01672-x and PMID:18365724, two verbatim source snippets, a non-axenic Waterburya agarophytonicola KI4 example independently identified as NCBITaxon:2874699, and open hierarchy/mechanism discussions. Directly inspected publisher taxonomy descriptions, Collection Methods and actual Figure 4; used the directly retrieved English scientific abstract for the Russian second paper. Reserved v548 / METPO:1062500-1062599 after ignored-and-hidden whole-repository/worktree and complete open-PR reservation checks. No protein graph, exact synonyms or xrefs asserted; existing traits unchanged. Writer is dry-run by default and prevalidates before mutation; broader validations remain pending at scaffolding.

    • Read this curation session @@ -328,7 +329,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -357,12 +367,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-08 03:23 UTC diff --git a/pages/traits/morphology/black_pigmented.html b/pages/traits/morphology/black_pigmented.html index dc3c5325bb9..314a2701199 100644 --- a/pages/traits/morphology/black_pigmented.html +++ b/pages/traits/morphology/black_pigmented.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -362,7 +363,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Pigment_black RELATED_SYNONYM · metpo.owl
      • +
    • Pigment_black RELATED_SYNONYM · metpo.owl
    @@ -378,7 +379,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -687,7 +688,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1051,12 +1061,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/branched_shaped.html b/pages/traits/morphology/branched_shaped.html index e3be8ba5b1d..f9098d55e06 100644 --- a/pages/traits/morphology/branched_shaped.html +++ b/pages/traits/morphology/branched_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -343,9 +344,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • branced RELATED_SYNONYM · metpo.owl
      • +
    • branced RELATED_SYNONYM · metpo.owl
      • -
    • branched RELATED_SYNONYM · corrected-from-metpo.owl
      • +
    • branched RELATED_SYNONYM · corrected-from-metpo.owl
    @@ -361,7 +362,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -625,7 +626,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -989,12 +999,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/brown_pigmented.html b/pages/traits/morphology/brown_pigmented.html index 53566dd76d5..80356e53f51 100644 --- a/pages/traits/morphology/brown_pigmented.html +++ b/pages/traits/morphology/brown_pigmented.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -320,8 +321,8 @@

    Protein and taxon examples

    		 - Aeromonas media -
    NCBITaxon:651 + Aeromonas media +
    NCBITaxon:651         		UNREVIEWED
    @@ -387,7 +388,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Pigment_brown RELATED_SYNONYM · metpo.owl
      • +
    • Pigment_brown RELATED_SYNONYM · metpo.owl
    @@ -403,7 +404,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -730,7 +731,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1094,12 +1104,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/capsule.html b/pages/traits/morphology/capsule.html index 3f801325e16..6cc241a77b3 100644 --- a/pages/traits/morphology/capsule.html +++ b/pages/traits/morphology/capsule.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    confers capsule - traitmech:000063 + traitmech:000063 METPO:2007700

    Surface assembly of capsule polymers realizes the capsulated phenotype.

      @@ -134,7 +135,7 @@

      Edge evidence

    • capsule - traitmech:000063 + traitmech:000063 contributes to host immune evasion @@ -292,9 +293,9 @@

      Parent traits (1)

      Synonyms (2)

    @@ -317,7 +318,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -605,7 +606,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -969,12 +979,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 06:15 UTC diff --git a/pages/traits/morphology/carboxysome.html b/pages/traits/morphology/carboxysome.html index f6d8186411a..b92acfcc31d 100644 --- a/pages/traits/morphology/carboxysome.html +++ b/pages/traits/morphology/carboxysome.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,11 +97,11 @@

    Edge evidence

  • carboxysome - traitmech:000072 + traitmech:000072 example of bacterial microcompartment GO:0031469 - rdfs:subClassOf + rdfs:subClassOf

    The carboxysome is the archetypal bacterial microcompartment.

      @@ -115,7 +116,7 @@

      Edge evidence

    • carboxysome - traitmech:000072 + traitmech:000072 contributes to carbon fixation GO:0015977 @@ -137,7 +138,7 @@

      Edge evidence

      CHEBI:16526 located in carboxysome - traitmech:000072 + traitmech:000072 biolink:located_in

      CO2 is concentrated within the carboxysome shell for fixation.

        @@ -307,8 +308,8 @@

        Protein and taxon examples

    		•  - Synechococcus elongatus PCC 7942 -
    NCBITaxon:1140 + Synechococcus elongatus PCC 7942 +
    NCBITaxon:1140         		REVIEWED
    @@ -374,7 +375,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • bacterial microcompartment RELATED_SYNONYM · DOI:10.1038/nrmicro.2018.10
      • +
    • bacterial microcompartment RELATED_SYNONYM · DOI:10.1038/nrmicro.2018.10
    @@ -397,7 +398,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -688,7 +689,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1052,12 +1062,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/carotenoid_pigmentation.html b/pages/traits/morphology/carotenoid_pigmentation.html index b9d333d9079..b77aedb320b 100644 --- a/pages/traits/morphology/carotenoid_pigmentation.html +++ b/pages/traits/morphology/carotenoid_pigmentation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -284,7 +285,7 @@

    Edge evidence

    is a conjugated carotenoids - rdfs:subClassOf + rdfs:subClassOf

    Cyclic carotenes are conjugated carotenoid pigments contributing to coloration.

      @@ -343,7 +344,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • Pigment_carotenoid RELATED_SYNONYM · metpo.owl
        • +
      • Pigment_carotenoid RELATED_SYNONYM · metpo.owl
    @@ -359,7 +360,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -665,7 +666,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1029,12 +1039,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/cell_length.html b/pages/traits/morphology/cell_length.html index db6dca5abe3..d65053a8fe8 100644 --- a/pages/traits/morphology/cell_length.html +++ b/pages/traits/morphology/cell_length.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -390,7 +391,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -627,7 +628,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; DOI:10.1016/j.cell.2014.11.022). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; DOI:10.1016/j.cell.2014.11.022). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -660,7 +661,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1024,12 +1034,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/morphology/cell_length_large.html b/pages/traits/morphology/cell_length_large.html index 09e4c179a8a..99b8365cccf 100644 --- a/pages/traits/morphology/cell_length_large.html +++ b/pages/traits/morphology/cell_length_large.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -137,8 +138,8 @@

    Edge evidence

    METPO:1000886 is a cell length - METPO:1000881 - rdfs:subClassOf + METPO:1000881 + rdfs:subClassOf

    Large cell length is a quantitative bin of the cell-length phenotype.

      @@ -311,7 +312,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • L_>3 RELATED_SYNONYM · metpo.owl
        • +
      • L_>3 RELATED_SYNONYM · metpo.owl
    @@ -327,7 +328,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -564,7 +565,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Spirochaeta dissipatitropha (NCBITaxon:324679; DOI:10.1099/ijs.0.65862-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Spirochaeta dissipatitropha (NCBITaxon:324679; DOI:10.1099/ijs.0.65862-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -598,7 +599,7 @@

    Recorded curation sessions

  • · claude-code
    • EDIT — Connect cell_length_large FtsZ graph -

      Repaired data/traits/morphology/cell_length_large.yaml after ranking it as the highest-score DEEPEN_CAUSAL_GRAPH target in scripts/trait_priority.py. The edit re-cited the SOS/SulA branch to DOI:10.1002/advs.202203260, replaced the residual ungrounded FtsZ/SulA predicates with RO:0002212/RO:0002213 groundings, and added three DOI-backed connector edges so the nonmechanistic FtsZ/SOS division-delay graph moves from four disconnected components to one. Existing paid Falcon research at research/traits/morphology/cell_length_large-deep-research-falcon.md was used as a lead. No paid research service was called. Validation used write_validated_trait, linkml-validate for the edited YAML, validate_strict.py, audit_causal_graphs.py, audit_predicate_domains.py, audit_evidence_snippets.py, audit_graph_protein_taxa.py, the record-repair regression tests, and the trait-priority regression tests.

    +

    Repaired data/traits/morphology/cell_length_large.yaml after ranking it as the highest-score DEEPEN_CAUSAL_GRAPH target in scripts/trait_priority.py. The edit re-cited the SOS/SulA branch to DOI:10.1002/advs.202203260, replaced the residual ungrounded FtsZ/SulA predicates with RO:0002212/RO:0002213 groundings, and added three DOI-backed connector edges so the nonmechanistic FtsZ/SOS division-delay graph moves from four disconnected components to one. Existing paid Falcon research at research/traits/morphology/cell_length_large-deep-research-falcon.md was used as a lead. No paid research service was called. Validation used write_validated_trait, linkml-validate for the edited YAML, validate_strict.py, audit_causal_graphs.py, audit_predicate_domains.py, audit_evidence_snippets.py, audit_graph_protein_taxa.py, the record-repair regression tests, and the trait-priority regression tests.

    • Read this curation session @@ -630,7 +631,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -994,12 +1004,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-07 20:05 UTC diff --git a/pages/traits/morphology/cell_length_medium.html b/pages/traits/morphology/cell_length_medium.html index f5a0eb40e97..d3692a946c2 100644 --- a/pages/traits/morphology/cell_length_medium.html +++ b/pages/traits/morphology/cell_length_medium.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000885 is a cell length - METPO:1000881 - rdfs:subClassOf + METPO:1000881 + rdfs:subClassOf

    Medium cell length is a quantitative bin of the cell-length phenotype.

      @@ -286,7 +287,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • L_2_3 RELATED_SYNONYM · metpo.owl
        • +
      • L_2_3 RELATED_SYNONYM · metpo.owl
    @@ -302,7 +303,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -527,7 +528,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Marinobacterium lacunae (NCBITaxon:1232683; DOI:10.1007/s00203-023-03627-4). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Marinobacterium lacunae (NCBITaxon:1232683; DOI:10.1007/s00203-023-03627-4). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -560,7 +561,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -924,12 +934,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/morphology/cell_length_small.html b/pages/traits/morphology/cell_length_small.html index 8e721a10557..44caeeab4e2 100644 --- a/pages/traits/morphology/cell_length_small.html +++ b/pages/traits/morphology/cell_length_small.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000884 is a cell length - METPO:1000881 - rdfs:subClassOf + METPO:1000881 + rdfs:subClassOf

    Small cell length is a quantitative bin of the cell-length phenotype.

      @@ -169,7 +170,7 @@

      Edge evidence

      modulates cell length - METPO:1000881 + METPO:1000881 RO:0002211

      Delayed FtsZ ring formation delays division until the cell reaches a larger size, increasing cell length.

        @@ -305,7 +306,7 @@

        Parent traits (1)

        Synonyms (1)

          -
        • L_1.3_2 RELATED_SYNONYM · metpo.owl
          • +
        • L_1.3_2 RELATED_SYNONYM · metpo.owl
    @@ -321,7 +322,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -570,7 +571,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -618,7 +619,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -982,12 +992,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-04 05:40 UTC diff --git a/pages/traits/morphology/cell_length_very_small.html b/pages/traits/morphology/cell_length_very_small.html index 876c7d9fea3..1fc37556e7f 100644 --- a/pages/traits/morphology/cell_length_very_small.html +++ b/pages/traits/morphology/cell_length_very_small.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000883 is a cell length - METPO:1000881 - rdfs:subClassOf + METPO:1000881 + rdfs:subClassOf

    Very small cell length is a quantitative bin of the cell-length phenotype.

      @@ -286,7 +287,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • L_<=1.3 RELATED_SYNONYM · metpo.owl
        • +
      • L_<=1.3 RELATED_SYNONYM · metpo.owl
    @@ -302,7 +303,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -539,7 +540,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Flavicella sediminum (NCBITaxon:2585141; DOI:10.1099/ijsem.0.003839). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Flavicella sediminum (NCBITaxon:2585141; DOI:10.1099/ijsem.0.003839). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -572,7 +573,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -936,12 +946,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/morphology/cell_shape.html b/pages/traits/morphology/cell_shape.html index e3cb020a541..826bcb4fbda 100644 --- a/pages/traits/morphology/cell_shape.html +++ b/pages/traits/morphology/cell_shape.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -437,9 +438,9 @@

    Children (34)

    Synonyms (2)

      -
    • Morphology.cell morphology.cell shape RELATED_SYNONYM · metpo.owl
      • +
    • Morphology.cell morphology.cell shape RELATED_SYNONYM · metpo.owl
      • -
    • cell_shape RELATED_SYNONYM · metpo.owl
      • +
    • cell_shape RELATED_SYNONYM · metpo.owl
    @@ -455,7 +456,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]
      • +
    • cell shape METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -728,13 +729,13 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; DOI:10.1038/nrmicro1205). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; DOI:10.1038/nrmicro1205). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Replaced elliptical record-level evidence[0].snippet on DOI:10.1038/nrmicro1205 with contiguous verbatim snippet already present on causal_graphs[0].edges[0].evidence[0] (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-004 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Replaced elliptical record-level evidence[0].snippet on DOI:10.1038/nrmicro1205 with contiguous verbatim snippet already present on causal_graphs[0].edges[0].evidence[0] (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-004 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -767,7 +768,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1131,12 +1141,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/morphology/cell_width.html b/pages/traits/morphology/cell_width.html index efba61658cf..9ffa5f2880c 100644 --- a/pages/traits/morphology/cell_width.html +++ b/pages/traits/morphology/cell_width.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -314,7 +315,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000882 [-1.477, -0.754, -1.899, +0.480, …]
      • +
    • cell width METPO:1000882 [-1.477, -0.754, -1.899, +0.480, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -402,7 +403,7 @@

    Deep research

    Cell width is the lateral or radial dimension of rod-shaped bacterial cells, perpendicular to the long axis. It is mechanistically distinct from cell length (axial elongation), although both dimensions contribute to overall rod shape and aspect ratio. Width is primarily controlled by the orientation and activity of circumferential peptidoglycan (PG) synthesis machinery, specifically the MreB-directed Rod complex (elongasome). Width excludes processes governing septation, cell division septum thickness, or specialized stalk width in organisms like *Caulobacter crescentus*. -The most direct mechanistic insight is provided by Hussain et al. (2018, DOI:10.1101/197475), who demonstrate that MreB filaments orient along the greatest principal membrane curvature—the circumference of rod-shaped cells—and propose a model where "bacterial width may be specified by opposing actions... a decreasing, 'thinning' activity from the action of MreB and its associated SEDS family PG synthases, and an increasing 'fattening' activity from the non-MreB associated Class A PG synthases" (hussain2017mrebfilamentscreate pages 35-39). This establishes width as a dynamic equilibrium phenotype determined by spatially distinct PG synthesis systems. +The most direct mechanistic insight is provided by Hussain et al. (2018, DOI:10.1101/197475), who demonstrate that MreB filaments orient along the greatest principal membrane curvature—the circumference of rod-shaped cells—and propose a model where "bacterial width may be specified by opposing actions... a decreasing, 'thinning' activity from the action of MreB and its associated SEDS family PG synthases, and an increasing 'fattening' activity from the non-MreB associated Class A PG synthases" (hussain2017mrebfilamentscreate pages 35-39). This establishes width as a dynamic equilibrium phenotype determined by spatially distinct PG synthesis systems. --- @@ -608,7 +609,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -972,12 +982,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/cell_width_large.html b/pages/traits/morphology/cell_width_large.html index 6f1bcdaf4e1..5fdfae99419 100644 --- a/pages/traits/morphology/cell_width_large.html +++ b/pages/traits/morphology/cell_width_large.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -137,8 +138,8 @@

    Edge evidence

    METPO:1000890 is a cell width - METPO:1000882 - rdfs:subClassOf + METPO:1000882 + rdfs:subClassOf

    Large cell width is a quantitative bin of the cell-width phenotype.

      @@ -330,7 +331,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • W_>0.9 RELATED_SYNONYM · metpo.owl
        • +
      • W_>0.9 RELATED_SYNONYM · metpo.owl
    @@ -346,7 +347,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -589,7 +590,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Marinobacterium lacunae (NCBITaxon:1232683; DOI:10.1007/s00203-023-03627-4). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Marinobacterium lacunae (NCBITaxon:1232683; DOI:10.1007/s00203-023-03627-4). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -622,7 +623,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -986,12 +996,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/morphology/cell_width_medium.html b/pages/traits/morphology/cell_width_medium.html index cd2214f671b..c548e8928f1 100644 --- a/pages/traits/morphology/cell_width_medium.html +++ b/pages/traits/morphology/cell_width_medium.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000889 is a cell width - METPO:1000882 - rdfs:subClassOf + METPO:1000882 + rdfs:subClassOf

    Medium cell width is a quantitative bin of the cell-width phenotype.

      @@ -245,7 +246,7 @@

      Edge evidence

      regulates cell width - METPO:1000882 + METPO:1000882 RO:0002211

      Class A PBPs regulate cell diameter; loss of aPBPs yields shorter, wider cells.

        @@ -305,7 +306,7 @@

        Parent traits (1)

        Synonyms (1)

          -
        • W_0.65_0.9 RELATED_SYNONYM · metpo.owl
          • +
        • W_0.65_0.9 RELATED_SYNONYM · metpo.owl
    @@ -321,7 +322,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -576,7 +577,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Ruixingdingia sedimenti (NCBITaxon:3073604; DOI:10.1099/ijsem.0.006350). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Ruixingdingia sedimenti (NCBITaxon:3073604; DOI:10.1099/ijsem.0.006350). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -609,7 +610,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -973,12 +983,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/morphology/cell_width_small.html b/pages/traits/morphology/cell_width_small.html index 33ab9efb6b7..c970bc7aad5 100644 --- a/pages/traits/morphology/cell_width_small.html +++ b/pages/traits/morphology/cell_width_small.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000888 is a cell width - METPO:1000882 - rdfs:subClassOf + METPO:1000882 + rdfs:subClassOf

    Small cell width is a quantitative bin of the cell-width phenotype.

      @@ -305,7 +306,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • W_0.5_0.65 RELATED_SYNONYM · metpo.owl
        • +
      • W_0.5_0.65 RELATED_SYNONYM · metpo.owl
    @@ -321,7 +322,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -576,7 +577,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -609,7 +610,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -973,12 +983,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/morphology/cell_width_very_small.html b/pages/traits/morphology/cell_width_very_small.html index d497137d5a0..b29b0f99cc8 100644 --- a/pages/traits/morphology/cell_width_very_small.html +++ b/pages/traits/morphology/cell_width_very_small.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -131,8 +132,8 @@

    Edge evidence

    METPO:1000887 is a cell width - METPO:1000882 - rdfs:subClassOf + METPO:1000882 + rdfs:subClassOf

    Very small cell width is a quantitative bin of the cell-width phenotype.

      @@ -207,7 +208,7 @@

      Edge evidence

      decreases cell width - METPO:1000882 + METPO:1000882 RO:0002212

      Rod-complex-mediated organized circumferential PG insertion reduces cell width (rod-shaped bacteria).

        @@ -226,7 +227,7 @@

        Edge evidence

        increases cell width - METPO:1000882 + METPO:1000882 RO:0002213

        aPBP-mediated isotropic PG insertion enlarges the cell cylinder, increasing width.

          @@ -286,7 +287,7 @@

          Parent traits (1)

          Synonyms (1)

            -
          • W_<=0.5 RELATED_SYNONYM · metpo.owl
            • +
          • W_<=0.5 RELATED_SYNONYM · metpo.owl
    @@ -302,7 +303,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -539,7 +540,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Spirochaeta dissipatitropha (NCBITaxon:324679; DOI:10.1099/ijs.0.65862-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Spirochaeta dissipatitropha (NCBITaxon:324679; DOI:10.1099/ijs.0.65862-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -572,7 +573,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -936,12 +946,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/morphology/coccobacillus_shaped.html b/pages/traits/morphology/coccobacillus_shaped.html index 88c3f059c9d..23a8b9e1f82 100644 --- a/pages/traits/morphology/coccobacillus_shaped.html +++ b/pages/traits/morphology/coccobacillus_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -324,7 +325,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • coccobacillus RELATED_SYNONYM · metpo.owl
      • +
    • coccobacillus RELATED_SYNONYM · metpo.owl
    @@ -340,7 +341,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -634,7 +635,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -998,12 +1008,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/coccus_shaped.html b/pages/traits/morphology/coccus_shaped.html index b9408004b5f..4cf0cba2f8f 100644 --- a/pages/traits/morphology/coccus_shaped.html +++ b/pages/traits/morphology/coccus_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -311,9 +312,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • coccus RELATED_SYNONYM · metpo.owl
      • +
    • coccus RELATED_SYNONYM · metpo.owl
      • -
    • coccus-shaped RELATED_SYNONYM · metpo.owl
      • +
    • coccus-shaped RELATED_SYNONYM · metpo.owl
    @@ -329,7 +330,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000668 [+298.218, -515.508, -75.836, -35.326, …]
      • +
    • coccus shaped METPO:1000668 [+298.218, -515.508, -75.836, -35.326, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -605,7 +606,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -969,12 +979,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/coenobium_formation.html b/pages/traits/morphology/coenobium_formation.html index 1d8d9a71238..f4c524437a3 100644 --- a/pages/traits/morphology/coenobium_formation.html +++ b/pages/traits/morphology/coenobium_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1098/rspb.2023.1882
    characteristically form clonal colonies of fixed cell number known as coenobia.
    -

    Harvey (2023), PMID:37876191, PMC10598416, Comparisons with extant taxa. Direct full-text terminology passage covers Volvocales, Scenedesmaceae and Hydrodictyaceae. Growth after colony formation is by cell expansion; a later reproductive cycle makes daughter colonies. This comparison supports terminology, not a new experiment on living algae; the paper's fossil developmental reconstruction remains an inference.

    +

    Harvey (2023), PMID:37876191, PMC10598416, Comparisons with extant taxa. Direct full-text terminology passage covers Volvocales, Scenedesmaceae and Hydrodictyaceae. Growth after colony formation is by cell expansion; a later reproductive cycle makes daughter colonies. This comparison supports terminology, not a new experiment on living algae; the paper's fossil developmental reconstruction remains an inference.

  • DOI:10.1242/jcs.212233
    progeny were unicellular in three species and multicellular (joined in a sheet-like coenobium) in two.
    -

    Cardon et al. (2018), PMID:29487180, scientific abstract. Primary Results, Methods and actual Figure 1 were inspected. The coenobial species are Enallax costatus and Tetradesmus obliquus; multiple fission occurs in all five tested species and alone does not establish coenobial progeny. Figure 1 supports joined-cell morphology. Release is author-reported in the Results, not visible in Figure 3; supplementary Figure S1 and movies were not directly inspected.

    +

    Cardon et al. (2018), PMID:29487180, scientific abstract. Primary Results, Methods and actual Figure 1 were inspected. The coenobial species are Enallax costatus and Tetradesmus obliquus; multiple fission occurs in all five tested species and alone does not establish coenobial progeny. Figure 1 supports joined-cell morphology. Release is author-reported in the Results, not visible in Figure 3; supplementary Figure S1 and movies were not directly inspected.

  • DOI:10.1038/s41598-018-28627-z
    monocultures of D. opoliensis in the control groups (without IAA treatment) were dominated by two-celled and four-celled coenobia
    -

    Chung et al. (2018), PMID:29980731, PMC6035231, Results. Direct full text reports this morphology after one week; Methods describes native isolates cultured in CA medium. Higher indole-3-acetic acid concentrations favor unicells in the tested monocultures, so IAA is not a universal coenobium inducer. No percentage, causal protein claim or direct figure inspection is asserted here.

    +

    Chung et al. (2018), PMID:29980731, PMC6035231, Results. Direct full text reports this morphology after one week; Methods describes native isolates cultured in CA medium. Higher indole-3-acetic acid concentrations favor unicells in the tested monocultures, so IAA is not a universal coenobium inducer. No percentage, causal protein claim or direct figure inspection is asserted here.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1242/jcs.212233 - CCAP 276/31 (paper: CCAP 276-31), grown at 25 C on a 12:12 light/dark cycle in a 1:1 mixture of Bold's basal medium with micronutrients and Woods Hole medium. Figure 1 and Results document coenobial morphology, not an invariant state for every life stage. Collection provenance at https://www.ccap.ac.uk/catalogue/strain-276-31 identifies Hegewald's 1980 Finnish lake isolate and lists GMO: No. The paper describes unialgal cultures, not axenic cultures. + CCAP 276/31 (paper: CCAP 276-31), grown at 25 C on a 12:12 light/dark cycle in a 1:1 mixture of Bold's basal medium with micronutrients and Woods Hole medium. Figure 1 and Results document coenobial morphology, not an invariant state for every life stage. Collection provenance at https://www.ccap.ac.uk/catalogue/strain-276-31 identifies Hegewald's 1980 Finnish lake isolate and lists GMO: No. The paper describes unialgal cultures, not axenic cultures. @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 01:59 UTC diff --git a/pages/traits/morphology/cream_pigmented.html b/pages/traits/morphology/cream_pigmented.html index 8cbf9f4c60f..0d9dad9b2d4 100644 --- a/pages/traits/morphology/cream_pigmented.html +++ b/pages/traits/morphology/cream_pigmented.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -248,7 +249,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Pigment_cream RELATED_SYNONYM · metpo.owl
      • +
    • Pigment_cream RELATED_SYNONYM · metpo.owl
    @@ -264,7 +265,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -501,7 +502,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Seongchinamella unica (NCBITaxon:2547392; DOI:10.1099/ijsem.0.003914). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Seongchinamella unica (NCBITaxon:2547392; DOI:10.1099/ijsem.0.003914). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -534,7 +535,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -898,12 +908,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/morphology/crescent_shaped.html b/pages/traits/morphology/crescent_shaped.html index 28ecf941c27..f66bbe7ea11 100644 --- a/pages/traits/morphology/crescent_shaped.html +++ b/pages/traits/morphology/crescent_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -263,8 +264,8 @@

    Protein and taxon examples

    		 - Caulobacter vibrioides NA1000 -
    NCBITaxon:565050 + Caulobacter vibrioides NA1000 +
    NCBITaxon:565050         		UNREVIEWED
    @@ -330,7 +331,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • crescent-shaped RELATED_SYNONYM · metpo.owl
      • +
    • crescent-shaped RELATED_SYNONYM · metpo.owl
    @@ -346,7 +347,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -643,7 +644,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1007,12 +1017,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/curved_shaped.html b/pages/traits/morphology/curved_shaped.html index 28c71b837cb..5ea6977e16c 100644 --- a/pages/traits/morphology/curved_shaped.html +++ b/pages/traits/morphology/curved_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -286,9 +287,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • S_curved_spiral RELATED_SYNONYM · metpo.owl
      • +
    • S_curved_spiral RELATED_SYNONYM · metpo.owl
      • -
    • curved-shaped RELATED_SYNONYM · metpo.owl
      • +
    • curved-shaped RELATED_SYNONYM · metpo.owl
    @@ -304,7 +305,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -577,7 +578,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -941,12 +951,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/cyanobacterial_multiseriate_trichome_formation.html b/pages/traits/morphology/cyanobacterial_multiseriate_trichome_formation.html index c72740d5136..8af6c438246 100644 --- a/pages/traits/morphology/cyanobacterial_multiseriate_trichome_formation.html +++ b/pages/traits/morphology/cyanobacterial_multiseriate_trichome_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1002/2211-5463.13016
    cells divide at a right angle to the longitudinal filament axis and in planes parallel or oblique to the primary trichomes.
    -

    Springstein et al. (2020), Introduction; primary full-text XML https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7714070/fullTextXML and actual Figure 2E inspected. The text links multiplanar division to multiseriate Chlorogloeopsis fritschii PCC 6912 trichomes, contrasting them with lateral Fischerella branches. Figure 2E shows a mature multiseriate stage, distinct from the linear hormogonium in 2D. Methods describe stock cultures at 37 degrees C in BG11 or BG11(0), with an 18:6 light-dark cycle; Van-FL microscopy follows a one-hour stain. This morphology evidence is not the separate FtsZ-overexpression phenotype.

    +

    Springstein et al. (2020), Introduction; primary full-text XML https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7714070/fullTextXML and actual Figure 2E inspected. The text links multiplanar division to multiseriate Chlorogloeopsis fritschii PCC 6912 trichomes, contrasting them with lateral Fischerella branches. Figure 2E shows a mature multiseriate stage, distinct from the linear hormogonium in 2D. Methods describe stock cultures at 37 degrees C in BG11 or BG11(0), with an 18:6 light-dark cycle; Van-FL microscopy follows a one-hour stain. This morphology evidence is not the separate FtsZ-overexpression phenotype.

  • DOI:10.1186/s12862-017-1053-5
    When grown in BG11, C. fritschii developed multi-seriate filaments.
    -

    Koch et al. (2017), Additional file 1, Figure S6A caption, PDF page 8; actual S6 and S1 images and supplementary text pages 1-2 inspected at https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs12862-017-1053-5/MediaObjects/12862_2017_1053_MOESM1_ESM.pdf. S6B instead shows aseriate clusters with 100 mM NaCl; loose clusters are not automatically multiseriate trichomes. Main Results and S1 report salt-associated multiseriate main filaments in Fischerella, showing that branching and multiseriality can coexist and that salt responses are taxon-specific. Transcript correlations do not establish a universal mechanism.

    +

    Koch et al. (2017), Additional file 1, Figure S6A caption, PDF page 8; actual S6 and S1 images and supplementary text pages 1-2 inspected at https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs12862-017-1053-5/MediaObjects/12862_2017_1053_MOESM1_ESM.pdf. S6B instead shows aseriate clusters with 100 mM NaCl; loose clusters are not automatically multiseriate trichomes. Main Results and S1 report salt-associated multiseriate main filaments in Fischerella, showing that branching and multiseriality can coexist and that salt responses are taxon-specific. Transcript correlations do not establish a universal mechanism.

  • DOI:10.3126/on.v14i1.16445
    The present algal taxon exhibited vertical and horizontal divisions of cells and has a tendency to form filamentous structure.
    -

    Halder (2016), Results and discussion, article page 95, https://www.nepjol.info/index.php/ON/article/view/16445/13360. Methods, description and actual Figure 1A-D on page 96 inspected. The description records cell rows and Conclusions describe progression from uniseriate to multiseriate filaments. This is light-microscopy-based identification of field material, not sequence-confirmed identity, a controlled time-lapse lineage experiment, or proof of the paper's suggested fertilizer benefit.

    +

    Halder (2016), Results and discussion, article page 95, https://www.nepjol.info/index.php/ON/article/view/16445/13360. Methods, description and actual Figure 1A-D on page 96 inspected. The description records cell rows and Conclusions describe progression from uniseriate to multiseriate filaments. This is light-microscopy-based identification of field material, not sequence-confirmed identity, a controlled time-lapse lineage experiment, or proof of the paper's suggested fertilizer benefit.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.3126/on.v14i1.16445 - Restricted to the multiseriate stage described for field collection NH-1260, sampled on 18 March 2013 in a rice field at Balagarh, Hooghly, West Bengal, India. Provenance and herbarium deposition are reported in Methods/Results at https://www.nepjol.info/index.php/ON/article/view/16445/13360. The source identifies the material morphologically; it is not assigned a PCC strain identity. Live NCBI efetch https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=1124 confirms the current species name and rank species, not an NH-1260 accession or independent phenotype evidence. Not every cell, stage or condition is multiseriate. + Restricted to the multiseriate stage described for field collection NH-1260, sampled on 18 March 2013 in a rice field at Balagarh, Hooghly, West Bengal, India. Provenance and herbarium deposition are reported in Methods/Results at https://www.nepjol.info/index.php/ON/article/view/16445/13360. The source identifies the material morphologically; it is not assigned a PCC strain identity. Live NCBI efetch https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=1124 confirms the current species name and rank species, not an NH-1260 accession or independent phenotype evidence. Not every cell, stage or condition is multiseriate. @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-08 07:49 UTC diff --git a/pages/traits/morphology/cyanophycin_granule.html b/pages/traits/morphology/cyanophycin_granule.html index 11b35f5c0b1..785e6695da2 100644 --- a/pages/traits/morphology/cyanophycin_granule.html +++ b/pages/traits/morphology/cyanophycin_granule.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (2)

    DOI:10.1007/s002030100281
    Cyanophycin granules reached a maximum after the peak of nitrogenase activity and eventually were utilized completely.
    -

    Li et al. (2001), publisher scientific abstract directly read at https://link.springer.com/article/10.1007/s002030100281. Electron microscopy and biochemistry identified granules in Cyanothece ATCC 51142 during nitrogen-fixing growth on a 12-hour light/12-hour dark cycle. Full text and figures were not accessible; timing is condition-specific, not a universal granule property. The separate PCC 6803 mutant observations do not establish a universal cyanophycinase requirement.

    +

    Li et al. (2001), publisher scientific abstract directly read at https://link.springer.com/article/10.1007/s002030100281. Electron microscopy and biochemistry identified granules in Cyanothece ATCC 51142 during nitrogen-fixing growth on a 12-hour light/12-hour dark cycle. Full text and figures were not accessible; timing is condition-specific, not a universal granule property. The separate PCC 6803 mutant observations do not establish a universal cyanophycinase requirement.

  • @@ -137,7 +138,7 @@

    Edge evidence

    CHEBI:65318 located in cyanophycin granule - traitmech:000673 + traitmech:000673 biolink:located_in

    Accumulated cyanophycin forms the material of the inclusion.

      @@ -153,7 +154,7 @@

      Edge evidence

    • cyanophycin granule - traitmech:000673 + traitmech:000673 contributes to temporary nitrogen storage @@ -193,8 +194,8 @@

      Protein and taxon examples

    		•  - Geminocystis herdmanii PCC 6308 -
    NCBITaxon:113355 + Geminocystis herdmanii PCC 6308 +
    NCBITaxon:113355         		REVIEWED
    @@ -207,7 +208,7 @@

    Protein and taxon examples

  • DOI:10.1007/s002030000206 The functionality of cphA was proven by heterologous expression of active enzyme and synthesis of cyanophycin in Escherichia coli - Aboulmagd et al. (2000), scientific abstract directly read in DOI-matched Europe PMC core metadata (PMID:11131019); full paper not inspected. UniProt REST P56947 links this paper and AF220099/AAF43647.2 to PCC 6308; its entry version 91, sequence version 2 and NCBITaxon:113355 were checked live. The paper's Synechocystis name is historical. The accession is not PCC 6803 or the heterologous expression host. + Aboulmagd et al. (2000), scientific abstract directly read in DOI-matched Europe PMC core metadata (PMID:11131019); full paper not inspected. UniProt REST P56947 links this paper and AF220099/AAF43647.2 to PCC 6308; its entry version 91, sequence version 2 and NCBITaxon:113355 were checked live. The paper's Synechocystis name is historical. The accession is not PCC 6803 or the heterologous expression host.
    • @@ -267,7 +268,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -356,7 +357,7 @@

    Canonical examples DOI:10.1007/s002030100281 - Historical Cyanothece ATCC 51142: granules observed during nitrogen-fixing light/dark culture, not constitutively in every cell. NCBI directly confirms the current strain name, rank no rank, and BH68/BH68K synonym: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=43989. The directly read scientific abstract of the original isolation paper, https://doi.org/10.1128/jb.175.5.1284-1292.1993, places BH68 in intertidal sands of the Texas Gulf coast. This is provenance support, not an independent cyanophycin assay. + Historical Cyanothece ATCC 51142: granules observed during nitrogen-fixing light/dark culture, not constitutively in every cell. NCBI directly confirms the current strain name, rank no rank, and BH68/BH68K synonym: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=43989. The directly read scientific abstract of the original isolation paper, https://doi.org/10.1128/jb.175.5.1284-1292.1993, places BH68 in intertidal sands of the Texas Gulf coast. This is provenance support, not an independent cyanophycin assay. @@ -452,7 +453,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added DOI:10.1128/AEM.01298-18 with verified verbatim snippet to record-level evidence to match definition_source (Stage 5 remediation of F-DEF-SRC-CYANOPHYCIN-001 in group G-STAGE4-RECORD-LEVEL-DEFINITION-SOURCE, issue #1981).

    +

    Added DOI:10.1128/AEM.01298-18 with verified verbatim snippet to record-level evidence to match definition_source (Stage 5 remediation of F-DEF-SRC-CYANOPHYCIN-001 in group G-STAGE4-RECORD-LEVEL-DEFINITION-SOURCE, issue #1981).

    • @@ -500,7 +501,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -864,12 +874,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 05:20 UTC diff --git a/pages/traits/morphology/diplococcus_shaped.html b/pages/traits/morphology/diplococcus_shaped.html index 484483a4540..7ad75e6a301 100644 --- a/pages/traits/morphology/diplococcus_shaped.html +++ b/pages/traits/morphology/diplococcus_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -324,7 +325,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • diplococcus-shaped RELATED_SYNONYM · metpo.owl
      • +
    • diplococcus-shaped RELATED_SYNONYM · metpo.owl
    @@ -340,7 +341,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -604,7 +605,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -968,12 +978,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/disc_shaped.html b/pages/traits/morphology/disc_shaped.html index 6eeac9b83a1..2e2b90c18b1 100644 --- a/pages/traits/morphology/disc_shaped.html +++ b/pages/traits/morphology/disc_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -235,7 +236,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • disc RELATED_SYNONYM · metpo.owl
      • +
    • disc RELATED_SYNONYM · metpo.owl
    @@ -251,7 +252,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -521,7 +522,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -885,12 +895,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 09:40 UTC diff --git a/pages/traits/morphology/dumbbell_shaped.html b/pages/traits/morphology/dumbbell_shaped.html index da62671b1ea..6cfa62e1071 100644 --- a/pages/traits/morphology/dumbbell_shaped.html +++ b/pages/traits/morphology/dumbbell_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -305,9 +306,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • S_star_dumbbell_pleomorphic RELATED_SYNONYM · metpo.owl
      • +
    • S_star_dumbbell_pleomorphic RELATED_SYNONYM · metpo.owl
      • -
    • dumbbell-shaped RELATED_SYNONYM · metpo.owl
      • +
    • dumbbell-shaped RELATED_SYNONYM · metpo.owl
    @@ -323,7 +324,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -566,7 +567,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Corynebacterium diphtheriae (NCBITaxon:1717; DOI:10.1111/j.1574-6976.2011.00298.x). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Corynebacterium diphtheriae (NCBITaxon:1717; DOI:10.1111/j.1574-6976.2011.00298.x). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -608,7 +609,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -972,12 +982,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/morphology/ellipsoidal.html b/pages/traits/morphology/ellipsoidal.html index 550d76a669d..30220c02696 100644 --- a/pages/traits/morphology/ellipsoidal.html +++ b/pages/traits/morphology/ellipsoidal.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -339,8 +340,8 @@

    Protein and taxon examples

    		 - Streptococcus pneumoniae R6 -
    NCBITaxon:171101 + Streptococcus pneumoniae R6 +
    NCBITaxon:171101         		REVIEWED
    @@ -413,7 +414,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -734,7 +735,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1098,12 +1108,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/expansion_driven_sliding_motility.html b/pages/traits/morphology/expansion_driven_sliding_motility.html index 4ba9a3d543a..df7716685d8 100644 --- a/pages/traits/morphology/expansion_driven_sliding_motility.html +++ b/pages/traits/morphology/expansion_driven_sliding_motility.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1111/1758-2229.70214
    Passive sliding motility allows Mycobacterium smegmatis to spread over soft agar surfaces.
    -

    Pollitt et al. 2025, PMID:41152213, PMC12568390; scientific abstract, not graphical abstract. Full text, Figure 1 and the actual DOCX supplement were inspected. Results 2.8-2.9 interpret digitate-colony expansion as hydraulic displacement, not a direct force measurement; unobserved division does not establish absent growth. Supplementary Methods identify mc2 155. The Figure 1 comparison varies both gel material and concentration, not material alone. The qualified definition includes this interpretation without making cell-division pressure universal. Raw movies were not reanalyzed. Qualified MED, Crossref and the retrieved publisher page exposed no linked correction or retraction at the 2026-10-11 check.

    +

    Pollitt et al. 2025, PMID:41152213, PMC12568390; scientific abstract, not graphical abstract. Full text, Figure 1 and the actual DOCX supplement were inspected. Results 2.8-2.9 interpret digitate-colony expansion as hydraulic displacement, not a direct force measurement; unobserved division does not establish absent growth. Supplementary Methods identify mc2 155. The Figure 1 comparison varies both gel material and concentration, not material alone. The qualified definition includes this interpretation without making cell-division pressure universal. Raw movies were not reanalyzed. Qualified MED, Crossref and the retrieved publisher page exposed no linked correction or retraction at the 2026-10-11 check.

  • DOI:10.1186/1471-2180-6-31
    sliding motility is a passive mode of translocation for spreading over surfaces.
    -

    Fall et al. 2006, PMID:16545127, PMC1501027; Background's source-attributed terminology, not an abstract quote. Results and Methods directly describe surface expansion of constructed B. subtilis DS64 hag-replacement material. Growth-associated, surfactin-dependent spreading supports the conventional case, not a universal transporter or surfactant requirement. Actual Figure 1 says 24 hours, whereas its caption and Results say 18 hours; retain this unresolved discrepancy. Proposed plant-root benefit is not observed natural colonization. Qualified MED, Crossref and the retrieved publisher page exposed no linked correction or retraction at the 2026-10-11 check.

    +

    Fall et al. 2006, PMID:16545127, PMC1501027; Background's source-attributed terminology, not an abstract quote. Results and Methods directly describe surface expansion of constructed B. subtilis DS64 hag-replacement material. Growth-associated, surfactin-dependent spreading supports the conventional case, not a universal transporter or surfactant requirement. Actual Figure 1 says 24 hours, whereas its caption and Results say 18 hours; retain this unresolved discrepancy. Proposed plant-root benefit is not observed natural colonization. Qualified MED, Crossref and the retrieved publisher page exposed no linked correction or retraction at the 2026-10-11 check.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -258,7 +259,7 @@

    Evidence

    mechanism it concerns.

    -

    Pinned and current METPO contain deprecated METPO:0000096, METPO:000097 and METPO:1000388, without replacement annotations. Their reason codes were assigned by ID era in generator commit 38fbfb82c6cc962009582eb7f8652e48ede0f9c2, not by a sliding-specific biological assessment. https://github.com/berkeleybop/metpo/issues/521 still disputes this metadata; issue 271 requests motility coverage. Neither authorizes reactivation or resolves equivalence to this qualified class. Independent primary evidence supports the present scope, and no active exact replacement was found in the inspected ontology and pending proposals. Keep historical IDs out of xrefs and replaces; the new v579 proposal is not an upstream acceptance.

    +

    Pinned and current METPO contain deprecated METPO:0000096, METPO:000097 and METPO:1000388, without replacement annotations. Their reason codes were assigned by ID era in generator commit 38fbfb82c6cc962009582eb7f8652e48ede0f9c2, not by a sliding-specific biological assessment. https://github.com/berkeleybop/metpo/issues/521 still disputes this metadata; issue 271 requests motility coverage. Neither authorizes reactivation or resolves equivalence to this qualified class. Independent primary evidence supports the present scope, and no active exact replacement was found in the inspected ontology and pending proposals. Keep historical IDs out of xrefs and replaces; the new v579 proposal is not an upstream acceptance.

    @@ -288,7 +289,7 @@

    Evidence

    mechanism it concerns.

    -

    DS64 is engineered hag-replacement material. For mc2 155, the first-person provenance account DOI:10.1128/microbiolspec.MGM2-0037-2013 describes a laboratory-selected, plasmid-cured mutant derivative. Neither is presented as an unqualified natural canonical example. These qualifications do not invalidate the observed phenotype. No exact taxon-paired protein branch is established here, and the hydraulic molecular mechanism remains unresolved. Defer the graph rather than impose one lineage's mechanism or use NONMECHANISTIC to bypass grounding. Gene presence, appendage absence and predicted motility annotations cannot establish observed passive surface expansion. External equivalences remain unasserted.

    +

    DS64 is engineered hag-replacement material. For mc2 155, the first-person provenance account DOI:10.1128/microbiolspec.MGM2-0037-2013 describes a laboratory-selected, plasmid-cured mutant derivative. Neither is presented as an unqualified natural canonical example. These qualifications do not invalidate the observed phenotype. No exact taxon-paired protein branch is established here, and the hydraulic molecular mechanism remains unresolved. Defer the graph rather than impose one lineage's mechanism or use NONMECHANISTIC to bypass grounding. Gene presence, appendage absence and predicted motility annotations cannot establish observed passive surface expansion. External equivalences remain unasserted.

    @@ -352,7 +353,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -381,12 +391,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-11 21:28 UTC diff --git a/pages/traits/morphology/false_branching.html b/pages/traits/morphology/false_branching.html index 97682658163..c80b908edc3 100644 --- a/pages/traits/morphology/false_branching.html +++ b/pages/traits/morphology/false_branching.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1127/algol_stud/83/1996/303
    Two basic types of false branching (by bundle partitioning and by lateral trichome protrusion)
    -

    Golubic et al. (1996), scientific abstract directly read on the publisher page https://www.schweizerbart.de/papers/algol_stud/detail/83/91090/Developmental_aspects_of_branching_in_filamentous_. Crossref confirms DOI, title and authors. The developmental analysis distinguishes false from true branching by branch-point cells contacting at least three neighbors. This terminology authority supports both listed modes, not only sheath rupture following necridium formation. Full article and figures were not inspected; no new experimental replication or universal molecular mechanism is inferred from the abstract.

    +

    Golubic et al. (1996), scientific abstract directly read on the publisher page https://www.schweizerbart.de/papers/algol_stud/detail/83/91090/Developmental_aspects_of_branching_in_filamentous_. Crossref confirms DOI, title and authors. The developmental analysis distinguishes false from true branching by branch-point cells contacting at least three neighbors. This terminology authority supports both listed modes, not only sheath rupture following necridium formation. Full article and figures were not inspected; no new experimental replication or universal molecular mechanism is inferred from the abstract.

  • DOI:10.5507/fot.2021.017
    initiation of branching after disintegrating of sheath at the site of a necridia cell
    -

    Tawong et al. (2022), Figure 1k caption, article page 82 in https://fottea.czechphycology.cz/pdfs/fot/2022/01/05.pdf (PDF page 5); actual Figure 1 panels and Methods/Results read. Source grammar is retained. Results page 81 points to Figs 2e-k for false branching, but the microscopy is Figure 1e-k; Figure 2 is phylogeny. NUACC05/06 show single and binary false branches associated with separation, heterocytes and loop rupture. The captioned necridium route is not required for every branch or for bundle partitioning.

    +

    Tawong et al. (2022), Figure 1k caption, article page 82 in https://fottea.czechphycology.cz/pdfs/fot/2022/01/05.pdf (PDF page 5); actual Figure 1 panels and Methods/Results read. Source grammar is retained. Results page 81 points to Figs 2e-k for false branching, but the microscopy is Figure 1e-k; Figure 2 is phylogeny. NUACC05/06 show single and binary false branches associated with separation, heterocytes and loop rupture. The captioned necridium route is not required for every branch or for bundle partitioning.

  • DOI:10.1111/jpy.13256
    False branches developed adjacent to necridic cells or heterocytes, or by separation of vegetative cells at compression folds in the trichome.
    -

    Masumoto and Sanders (2022), scientific abstract directly read at https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13256. Microscopy of lichen cyanobionts reports multiple branching modes within a strain, so false and true branching are not disjoint organism-level traits. Secondary attachment of freed apical segments is separately described as pseudo-branching; that term is not imported as an exact synonym. Full text, figures and supplements were not inspected.

    +

    Masumoto and Sanders (2022), scientific abstract directly read at https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13256. Microscopy of lichen cyanobionts reports multiple branching modes within a strain, so false and true branching are not disjoint organism-level traits. Secondary attachment of freed apical segments is separately described as pseudo-branching; that term is not imported as an exact synonym. Full text, figures and supplements were not inspected.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.5507/fot.2021.017 - Example restricted to false-branched filaments of natural isolate NUACC06, not every cell or stage. Methods describe single-filament isolation from wet Khek River bank soil, Thailand, April 2019, followed by CT/2 liquid culture at 25 degrees C with a 12:12 light-dark cycle. Live NCBI Taxonomy efetch https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=2929979 confirms this current species name, rank species and NUACC06 type material; it is not a strain-rank accession. Taxonomy supports identity, not independent phenotype evidence. + Example restricted to false-branched filaments of natural isolate NUACC06, not every cell or stage. Methods describe single-filament isolation from wet Khek River bank soil, Thailand, April 2019, followed by CT/2 liquid culture at 25 degrees C with a 12:12 light-dark cycle. Live NCBI Taxonomy efetch https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=2929979 confirms this current species name, rank species and NUACC06 type material; it is not a strain-rank accession. Taxonomy supports identity, not independent phenotype evidence. @@ -240,7 +241,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Use phenotype METPO:1000059 below quality METPO:1000188. Branched shaped METPO:1000687 concerns lateral branches in cell shape, not necessarily this arrangement of trichomes; no subclass or equivalence is asserted. The Golubic 1996 definition authority includes bundle partitioning as well as lateral protrusion. The Scytonema example demonstrates the latter and must not narrow the whole class. Necridium formation traitmech:000674 describes a separation cell, not all false branches. Hormogonium formation traitmech:000651 describes dispersal filaments, not the branching topology. Obsolete cell-arrangement METPO terms redirect to flagellar arrangement, which is not a suitable parent here. No exact synonyms, xrefs, SSSOM mappings or organism-level disjointness are asserted; historical pseudo-branch usages need review. The label is qualified as cyanobacterial false branching because the directly read English scientific abstract of Nesterenko et al. (1980), PMID:6782438 (https://pubmed.ncbi.nlm.nih.gov/6782438/), uses false branching for growth of separated cell ends in the organism historically named Brevibacterium helvolum ATCC 19239. That distinct usage is not evidence for cyanobacterial trichome development. Its full text and modern taxonomic identity were not inspected. No unqualified exact synonym or cross-taxon mechanism is asserted. See review issue #1821.

    +

    Use phenotype METPO:1000059 below quality METPO:1000188. Branched shaped METPO:1000687 concerns lateral branches in cell shape, not necessarily this arrangement of trichomes; no subclass or equivalence is asserted. The Golubic 1996 definition authority includes bundle partitioning as well as lateral protrusion. The Scytonema example demonstrates the latter and must not narrow the whole class. Necridium formation traitmech:000674 describes a separation cell, not all false branches. Hormogonium formation traitmech:000651 describes dispersal filaments, not the branching topology. Obsolete cell-arrangement METPO terms redirect to flagellar arrangement, which is not a suitable parent here. No exact synonyms, xrefs, SSSOM mappings or organism-level disjointness are asserted; historical pseudo-branch usages need review. The label is qualified as cyanobacterial false branching because the directly read English scientific abstract of Nesterenko et al. (1980), PMID:6782438 (https://pubmed.ncbi.nlm.nih.gov/6782438/), uses false branching for growth of separated cell ends in the organism historically named Brevibacterium helvolum ATCC 19239. That distinct usage is not evidence for cyanobacterial trichome development. Its full text and modern taxonomic identity were not inspected. No unqualified exact synonym or cross-taxon mechanism is asserted. See review issue #1821.

    @@ -298,7 +299,7 @@

    Curation history

  • · QUALIFY_TRAIT_LABEL · codex -

    Addressed #1821: qualified the label to its cyanobacterial scope after directly checking the non-cyanobacterial usage in PMID:6782438. Preserved definition, evidence, example, identifier, proposal block and original curation event. Added source-qualified terminology discussion without an unqualified exact synonym.

    +

    Addressed #1821: qualified the label to its cyanobacterial scope after directly checking the non-cyanobacterial usage in PMID:6782438. Preserved definition, evidence, example, identifier, proposal block and original curation event. Added source-qualified terminology discussion without an unqualified exact synonym.

    • @@ -314,7 +315,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Qualify cyanobacterial false branching after adversarial review -

      Address #1821 after directly reading PMID:6782438: qualify the label, document the non-cyanobacterial terminology boundary, and keep the original definition, evidence, example and ID reservation. Preserve 2026-10-08T063135Z-codex-0b8330.yaml and the original per-record event unchanged; append a correction event and regenerate artifacts.

    +

    Address #1821 after directly reading PMID:6782438: qualify the label, document the non-cyanobacterial terminology boundary, and keep the original definition, evidence, example and ID reservation. Preserve 2026-10-08T063135Z-codex-0b8330.yaml and the original per-record event unchanged; append a correction event and regenerate artifacts.

    • Read this curation session @@ -346,7 +347,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -375,12 +385,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-08 06:52 UTC diff --git a/pages/traits/morphology/ferrosome.html b/pages/traits/morphology/ferrosome.html index e3b89147595..d316dd8d262 100644 --- a/pages/traits/morphology/ferrosome.html +++ b/pages/traits/morphology/ferrosome.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -117,7 +118,7 @@

    Edge evidence

    has output ferrosome - traitmech:000527 + traitmech:000527 RO:0002234

    Fez-dependent ferrosome formation produces the ferrosome intracellular organelle.

      @@ -154,7 +155,7 @@

      Edge evidence

      located in ferrosome - traitmech:000527 + traitmech:000527 biolink:located_in

      Non-crystalline iron phosphate biominerals are stored within ferrosome organelles.

        @@ -170,7 +171,7 @@

        Edge evidence

      • ferrosome - traitmech:000527 + traitmech:000527 enables iron storage @@ -246,7 +247,7 @@

        kg-microbe context

        via parent_proxy.

          -
        • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
          • +
        • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

        512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

        @@ -431,7 +432,16 @@

        Identifier

        Term kind
        CLASS
        Status
        -
        PROPOSED
        +
        PROPOSED + + +
        + What this status means +

        Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

        +

        Quoted from the schema's status definitions.

        +
        + +
    @@ -795,12 +805,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 22:05 UTC diff --git a/pages/traits/morphology/filament_shaped.html b/pages/traits/morphology/filament_shaped.html index 43bf575f462..02a24f00743 100644 --- a/pages/traits/morphology/filament_shaped.html +++ b/pages/traits/morphology/filament_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -362,11 +363,11 @@

    Parent traits (1)

    Synonyms (3)

      -
    • S_filament RELATED_SYNONYM · metpo.owl
      • +
    • S_filament RELATED_SYNONYM · metpo.owl
      • -
    • filament RELATED_SYNONYM · metpo.owl
      • +
    • filament RELATED_SYNONYM · metpo.owl
      • -
    • filament-shaped RELATED_SYNONYM · metpo.owl
      • +
    • filament-shaped RELATED_SYNONYM · metpo.owl
    @@ -382,7 +383,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -703,7 +704,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1067,12 +1077,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 06:23 UTC diff --git a/pages/traits/morphology/flagellar_arrangement.html b/pages/traits/morphology/flagellar_arrangement.html index 43c0cf5c5f9..b76a6852b48 100644 --- a/pages/traits/morphology/flagellar_arrangement.html +++ b/pages/traits/morphology/flagellar_arrangement.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    GO:0009288 defines flagellar arrangement - traitmech:000056 + traitmech:000056 METPO:2007500

    The cellular distribution of flagella defines the arrangement.

      @@ -118,7 +119,7 @@

      Edge evidence

      regulates flagellar arrangement - traitmech:000056 + traitmech:000056 RO:0002211

      FlhF/FlhG set the species-specific flagellation pattern.

        @@ -315,7 +316,7 @@

        Children (8)

        Synonyms (1)

          -
        • flagellation pattern RELATED_SYNONYM · DOI:10.1093/femsre/fuv034
          • +
        • flagellation pattern RELATED_SYNONYM · DOI:10.1093/femsre/fuv034
    @@ -331,7 +332,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -422,16 +423,16 @@

    Deep research

    | Proposed causal edge | Evidence class | Primary taxon | Confidence / curation status | DOI | |---|---|---|---|---| -| HubP/FimV directly interacts with FlhF | Direct protein-protein interaction; structural/biochemical plus localization genetics | *Shewanella putrefaciens* CN-32 | High; curate as taxon-supported polar landmark interaction, not universal across all polar flagellates (dornes2024polarconfinementof pages 1-2, dornes2024polarconfinementof pages 2-4, dornes2024polarconfinementof pages 4-6) | 10.1038/s41467-024-50274-4 | -| FipA directly interacts with FlhF | Direct interaction by co-IP/MS and BACTH; conserved mutational support | *Vibrio parahaemolyticus*; also supported in *Pseudomonas putida* and *Shewanella putrefaciens* | High; curate as strong 2024 node-edge for FlhF-dependent polar synthesis pathway (arroyoperez2024aconservedcellpole pages 2-3, arroyoperez2024aconservedcellpole pages 14-15, arroyoperez2024aconservedcellpole pages 12-14, arroyoperez2024aconservedcellpole pages 8-11) | 10.7554/eLife.93004.3 | -| FlhF directly binds FliG | Direct interaction; structural and biochemical mapping of FlhF FID/B-domain to FliG | *Shewanella putrefaciens* CN-32 | High; curate as core mechanistic recruitment edge for polar assembly (dornes2024polarconfinementof pages 1-2, dornes2024polarconfinementof pages 2-4, dornes2024polarconfinementof pages 6-7) | 10.1038/s41467-024-50274-4 | -| FliG promotes/captures FliF MS-ring assembly | Biochemical assembly and localization evidence | *Vibrio* spp.; *Shewanella putrefaciens* | High but taxon-scoped; curate as assembly-promoting edge upstream of arrangement phenotype (dornes2024polarconfinementof pages 2-4, dornes2024polarconfinementof pages 6-7) | 10.1038/s41467-024-50274-4; 10.1128/JB.00236-20 | -| FlhF-bound FliG is prevented from interacting with FliM/FliN | Direct interaction antagonism/gating from biochemical interaction assays | *Shewanella putrefaciens* CN-32 | High; curate as mechanistic checkpoint edge with explicit taxon note (dornes2024polarconfinementof pages 1-2, dornes2024polarconfinementof pages 2-4, dornes2024polarconfinementof pages 6-7) | 10.1038/s41467-024-50274-4 | -| FlhG stimulates FlhF GTP hydrolysis | Biochemical/regulatory interaction supported by review synthesis and current model | Multiple polar-flagellated bacteria | Moderate-high; curate as conserved regulatory edge, but usually supported across taxa rather than a single universal assay system here (schuhmacher2015howbacteriamaintain pages 8-9, dornes2024polarconfinementof pages 7-8, dornes2024polarconfinementof pages 6-7) | 10.1093/femsre/fuv034; 10.1038/s41467-024-50274-4 | -| FlhF promotes polar flagellar placement | Mutant phenotypes, localization microscopy, rescue/inference from assembly mutants | *Helicobacter pylori*; also Vibrio/*Pseudomonas*/*Shewanella* | High; curate as trait-proximal positive edge to polar placement with species-specific quantitative manifestations (gibson2023controlofthe pages 11-13, gibson2023controlofthe pages 1-2, arroyoperez2024aconservedcellpole pages 14-15) | 10.1128/JB.00110-23; 10.7554/eLife.93004.3 | -| FlhG restricts flagellar number | Mutant phenotype genetics and review synthesis | *Helicobacter pylori*; Vibrio/*Pseudomonas*/*Shewanella* | High; curate as trait-proximal negative edge to flagellar number, with taxon-specific output distributions (gibson2023controlofthe pages 1-2, arroyoperez2024aconservedcellpole pages 1-2, gibson2023controlofthe pages 11-13) | 10.1128/JB.00110-23; 10.7554/eLife.93004.3 | -| FipA promotes FlhF polar localization and thereby polar flagellar synthesis | Localization genetics plus loss-of-function phenotype | *Vibrio parahaemolyticus*; *Pseudomonas putida*; *Shewanella putrefaciens* | High; curate as strong 2024 licensing/localization edge, noting some species retain polar positioning despite reduced number (arroyoperez2024aconservedcellpole pages 11-12, arroyoperez2024aconservedcellpole pages 14-15, arroyoperez2024aconservedcellpole pages 12-14, arroyoperez2024aconservedcellpole pages 8-11) | 10.7554/eLife.93004.3 | -| HubP/FimV contributes to proper polar flagellar placement/number via FlhF/FlhG pathway | Localization genetics and comparative phenotypes | *Vibrio parahaemolyticus*; *Shewanella putrefaciens* | Moderate; curate only with explicit species-variation warning because phenotypic strength differs across taxa (dornes2024polarconfinementof pages 7-8, arroyoperez2024aconservedcellpole pages 14-15) | 10.1038/s41467-024-50274-4; 10.7554/eLife.93004.3 | +| HubP/FimV directly interacts with FlhF | Direct protein-protein interaction; structural/biochemical plus localization genetics | *Shewanella putrefaciens* CN-32 | High; curate as taxon-supported polar landmark interaction, not universal across all polar flagellates (dornes2024polarconfinementof pages 1-2, dornes2024polarconfinementof pages 2-4, dornes2024polarconfinementof pages 4-6) | 10.1038/s41467-024-50274-4 | +| FipA directly interacts with FlhF | Direct interaction by co-IP/MS and BACTH; conserved mutational support | *Vibrio parahaemolyticus*; also supported in *Pseudomonas putida* and *Shewanella putrefaciens* | High; curate as strong 2024 node-edge for FlhF-dependent polar synthesis pathway (arroyoperez2024aconservedcellpole pages 2-3, arroyoperez2024aconservedcellpole pages 14-15, arroyoperez2024aconservedcellpole pages 12-14, arroyoperez2024aconservedcellpole pages 8-11) | 10.7554/eLife.93004.3 | +| FlhF directly binds FliG | Direct interaction; structural and biochemical mapping of FlhF FID/B-domain to FliG | *Shewanella putrefaciens* CN-32 | High; curate as core mechanistic recruitment edge for polar assembly (dornes2024polarconfinementof pages 1-2, dornes2024polarconfinementof pages 2-4, dornes2024polarconfinementof pages 6-7) | 10.1038/s41467-024-50274-4 | +| FliG promotes/captures FliF MS-ring assembly | Biochemical assembly and localization evidence | *Vibrio* spp.; *Shewanella putrefaciens* | High but taxon-scoped; curate as assembly-promoting edge upstream of arrangement phenotype (dornes2024polarconfinementof pages 2-4, dornes2024polarconfinementof pages 6-7) | 10.1038/s41467-024-50274-4; 10.1128/JB.00236-20 | +| FlhF-bound FliG is prevented from interacting with FliM/FliN | Direct interaction antagonism/gating from biochemical interaction assays | *Shewanella putrefaciens* CN-32 | High; curate as mechanistic checkpoint edge with explicit taxon note (dornes2024polarconfinementof pages 1-2, dornes2024polarconfinementof pages 2-4, dornes2024polarconfinementof pages 6-7) | 10.1038/s41467-024-50274-4 | +| FlhG stimulates FlhF GTP hydrolysis | Biochemical/regulatory interaction supported by review synthesis and current model | Multiple polar-flagellated bacteria | Moderate-high; curate as conserved regulatory edge, but usually supported across taxa rather than a single universal assay system here (schuhmacher2015howbacteriamaintain pages 8-9, dornes2024polarconfinementof pages 7-8, dornes2024polarconfinementof pages 6-7) | 10.1093/femsre/fuv034; 10.1038/s41467-024-50274-4 | +| FlhF promotes polar flagellar placement | Mutant phenotypes, localization microscopy, rescue/inference from assembly mutants | *Helicobacter pylori*; also Vibrio/*Pseudomonas*/*Shewanella* | High; curate as trait-proximal positive edge to polar placement with species-specific quantitative manifestations (gibson2023controlofthe pages 11-13, gibson2023controlofthe pages 1-2, arroyoperez2024aconservedcellpole pages 14-15) | 10.1128/JB.00110-23; 10.7554/eLife.93004.3 | +| FlhG restricts flagellar number | Mutant phenotype genetics and review synthesis | *Helicobacter pylori*; Vibrio/*Pseudomonas*/*Shewanella* | High; curate as trait-proximal negative edge to flagellar number, with taxon-specific output distributions (gibson2023controlofthe pages 1-2, arroyoperez2024aconservedcellpole pages 1-2, gibson2023controlofthe pages 11-13) | 10.1128/JB.00110-23; 10.7554/eLife.93004.3 | +| FipA promotes FlhF polar localization and thereby polar flagellar synthesis | Localization genetics plus loss-of-function phenotype | *Vibrio parahaemolyticus*; *Pseudomonas putida*; *Shewanella putrefaciens* | High; curate as strong 2024 licensing/localization edge, noting some species retain polar positioning despite reduced number (arroyoperez2024aconservedcellpole pages 11-12, arroyoperez2024aconservedcellpole pages 14-15, arroyoperez2024aconservedcellpole pages 12-14, arroyoperez2024aconservedcellpole pages 8-11) | 10.7554/eLife.93004.3 | +| HubP/FimV contributes to proper polar flagellar placement/number via FlhF/FlhG pathway | Localization genetics and comparative phenotypes | *Vibrio parahaemolyticus*; *Shewanella putrefaciens* | Moderate; curate only with explicit species-variation warning because phenotypic strength differs across taxa (dornes2024polarconfinementof pages 7-8, arroyoperez2024aconservedcellpole pages 14-15) | 10.1038/s41467-024-50274-4; 10.7554/eLife.93004.3 | *Table: This table prioritizes the strongest causal edges currently supported for curating traitmech:000056. It highlights which interactions are direct and high-confidence versus those that are taxon-dependent and should be curated with explicit scope notes.* @@ -583,7 +584,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1093/femsre/fuv034 (already present on child records polar_flagellation.yaml, amphitrichous.yaml, lophotrichous.yaml, and monotrichous.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-005 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.1093/femsre/fuv034 (already present on child records polar_flagellation.yaml, amphitrichous.yaml, lophotrichous.yaml, and monotrichous.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-005 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -616,7 +617,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -980,12 +990,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/morphology/flagellated.html b/pages/traits/morphology/flagellated.html index 954f8de8394..8c4149696d9 100644 --- a/pages/traits/morphology/flagellated.html +++ b/pages/traits/morphology/flagellated.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -339,8 +340,8 @@

    Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -415,7 +416,7 @@

    Children (1)

    Synonyms (1)

      -
    • flagella RELATED_SYNONYM · metpo.owl
      • +
    • flagella RELATED_SYNONYM · metpo.owl
    @@ -431,7 +432,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -776,7 +777,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1140,12 +1150,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 06:16 UTC diff --git a/pages/traits/morphology/flask_shaped.html b/pages/traits/morphology/flask_shaped.html index 8bc3dd5de14..4af581ed589 100644 --- a/pages/traits/morphology/flask_shaped.html +++ b/pages/traits/morphology/flask_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -267,9 +268,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • flask RELATED_SYNONYM · metpo.owl
      • +
    • flask RELATED_SYNONYM · metpo.owl
      • -
    • flask-shaped RELATED_SYNONYM · metpo.owl
      • +
    • flask-shaped RELATED_SYNONYM · metpo.owl
    @@ -285,7 +286,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -370,7 +371,7 @@

    Deep research

    The strongest mechanistic model is not yet a direct knockout-to-flask-shape pathway in a canonical flask-shaped planctomycete. Rather, it is a taxon-specific model from the stalked budding alphaproteobacterium *Hyphomonas neptunium*: cell-cycle-regulated switching among dispersed and zonal peptidoglycan (PG) insertion sites generates an asymmetric cell with a rounded old pole and tapered new/stalked pole. By contrast, deletion of `mreB`, `ftsI`, or `ftsW` in pear-shaped *Planctopirus limnophila* caused no observable phenotype under the tested conditions, arguing against importing the *H. neptunium* pathway wholesale into Planctomycetota (cserti2017dynamicsofthe pages 7-9, cserti2017dynamicsofthe pages 4-7, wiegand2020cultivationandfunctional pages 5-6). -The user-supplied DOI `10.1146/annurev-cellbio-101011-155745` is **not a bacterial cell-shape review**; it resolves to Lamkanfi and Dixit’s 2012 review, *Inflammasomes and Their Roles in Health and Disease*. It should therefore be removed from the existing causal graph unless a different DOI was intended. +The user-supplied DOI `10.1146/annurev-cellbio-101011-155745` is **not a bacterial cell-shape review**; it resolves to Lamkanfi and Dixit’s 2012 review, *Inflammasomes and Their Roles in Health and Disease*. It should therefore be removed from the existing causal graph unless a different DOI was intended. ## 1. Trait scope and boundaries @@ -555,7 +556,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -919,12 +929,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 09:40 UTC diff --git a/pages/traits/morphology/fungal_adhesive_column_trap_formation.html b/pages/traits/morphology/fungal_adhesive_column_trap_formation.html index 61ba3977582..47f34fb0704 100644 --- a/pages/traits/morphology/fungal_adhesive_column_trap_formation.html +++ b/pages/traits/morphology/fungal_adhesive_column_trap_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1016/j.isci.2020.101057
    Fungi with the AC device form a string of cells with adhesive surfaces
    -

    Ji et al. (2020), Introduction, third paragraph; AC means adhesive column. Primary full-text XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7186526/fullTextXML and actual Figure 1 inspected. Figure 1C shows a column attributed to source-named Dactylellina cionopagum; Figure 1G shows nematode capture by multiple columns. This morphology differs from the network, knob and constricting-ring comparators. Gene-family expansion and expression correlations do not establish a causal protein requirement for column formation. The cited adhesion-gene disruption experiment concerns Arthrobotrys oligospora, not this column-forming organism. Supplemental Methods were not retrieved completely; no strain identity or universal culture condition is inferred from this paper.

    +

    Ji et al. (2020), Introduction, third paragraph; AC means adhesive column. Primary full-text XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7186526/fullTextXML and actual Figure 1 inspected. Figure 1C shows a column attributed to source-named Dactylellina cionopagum; Figure 1G shows nematode capture by multiple columns. This morphology differs from the network, knob and constricting-ring comparators. Gene-family expansion and expression correlations do not establish a causal protein requirement for column formation. The cited adhesion-gene disruption experiment concerns Arthrobotrys oligospora, not this column-forming organism. Supplemental Methods were not retrieved completely; no strain identity or universal culture condition is inferred from this paper.

  • DOI:10.1111/lam.12557
    Dactylellina cionopaga YMF1·01472, producing adhesive columns
    -

    Su et al. (2016), scientific Abstract, final sentence, directly retrieved from NCBI XML for PMID:26928264 at https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=26928264&retmode=xml. Abstract-only access: full Methods and figures were not retrieved. The abstract reports ammonia-associated trap induction in several fungi and names this culture as column-producing. The initial 11-bacterium assay and its detailed volatile-compound analysis concern A. oligospora, not eleven independent column-forming isolates. No universal ammonia requirement, dosage, effect size or molecular induction pathway is asserted. Strain provenance remains unresolved; this is qualified phenotype evidence, not a natural canonical exemplar.

    +

    Su et al. (2016), scientific Abstract, final sentence, directly retrieved from NCBI XML for PMID:26928264 at https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=26928264&retmode=xml. Abstract-only access: full Methods and figures were not retrieved. The abstract reports ammonia-associated trap induction in several fungi and names this culture as column-producing. The initial 11-bacterium assay and its detailed volatile-compound analysis concern A. oligospora, not eleven independent column-forming isolates. No universal ammonia requirement, dosage, effect size or molecular induction pathway is asserted. Strain provenance remains unresolved; this is qualified phenotype evidence, not a natural canonical exemplar.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,7 @@

    Discussions and Knowledge Gaps (3)

    mechanism it concerns.

    -

    Live NCBI https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=47266 resolves Dactylellina cionopaga at species rank, with Monacrosporium cionopagum and Dactylella cionopaga synonyms. It does not identify YMF1.01472 as a strain accession or establish its origin. The 2020 paper's cionopagum spelling and experimental strain must be reconciled before a canonical example is added; do not conflate strains across these papers. Formation, adhesion, capture, penetration and digestion are separate endpoints; formation alone does not guarantee capture in every condition. Protein-resolved causal graphs require column-specific perturbation/complementation evidence and taxon-paired accessions. Sequence features and expression correlations are not validated phenotype predictors. No mechanism is transferred from nets, knobs or rings; mechanism is deferred, not claimed absent.

    +

    Live NCBI https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=47266 resolves Dactylellina cionopaga at species rank, with Monacrosporium cionopagum and Dactylella cionopaga synonyms. It does not identify YMF1.01472 as a strain accession or establish its origin. The 2020 paper's cionopagum spelling and experimental strain must be reconciled before a canonical example is added; do not conflate strains across these papers. Formation, adhesion, capture, penetration and digestion are separate endpoints; formation alone does not guarantee capture in every condition. Protein-resolved causal graphs require column-specific perturbation/complementation evidence and taxon-paired accessions. Sequence features and expression correlations are not validated phenotype predictors. No mechanism is transferred from nets, knobs or rings; mechanism is deferred, not claimed absent.

    @@ -365,7 +366,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -394,12 +404,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-13 13:33 UTC diff --git a/pages/traits/morphology/fungal_adhesive_knob_trap_formation.html b/pages/traits/morphology/fungal_adhesive_knob_trap_formation.html index fa613081cb4..dcf26afde78 100644 --- a/pages/traits/morphology/fungal_adhesive_knob_trap_formation.html +++ b/pages/traits/morphology/fungal_adhesive_knob_trap_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1128/AEM.01390-13
    The trap of M. haptotylum consists of a unicellular structure called a knob that develops at the apex of a hypha.
    -

    Andersson et al. (2013), scientific Abstract; primary publisher HTML https://journals.asm.org/doi/10.1128/AEM.01390-13. Introduction, Culture Methods, relevant Results/Discussion and Conclusion, and actual Figure 1 were inspected. CBS 200.50 formed knobs in aerated liquid culture. Figure 1 shows residual attached knobs and isolated knobs after filtration, not a capture time course. Detachment is a culture observation, not a defining requirement. Proteomic and transcript changes do not establish causal functions of individual proteins; WSC adhesion roles remain hypotheses. Supplements were not used to assert protein mechanisms.

    +

    Andersson et al. (2013), scientific Abstract; primary publisher HTML https://journals.asm.org/doi/10.1128/AEM.01390-13. Introduction, Culture Methods, relevant Results/Discussion and Conclusion, and actual Figure 1 were inspected. CBS 200.50 formed knobs in aerated liquid culture. Figure 1 shows residual attached knobs and isolated knobs after filtration, not a capture time course. Detachment is a culture observation, not a defining requirement. Proteomic and transcript changes do not establish causal functions of individual proteins; WSC adhesion roles remain hypotheses. Supplements were not used to assert protein mechanisms.

  • DOI:10.1016/j.femsle.2005.02.027
    The adhesive knobs were produced frequently on nutritional agar plates even in the absence of challenging nematodes.
    -

    Liu, Liu and Zhuang (2005), scientific Abstract, directly retrieved from the primary publisher https://academic.oup.com/femsle/article/245/1/99/483775 (minimal-article redirect). Abstract-only access: full Methods and figures were not retrieved. Orbilia querci material came from rotten Quercus wood in Huai-rou County, Beijing, and pure culture from ascospores. The authors report nematode capture with adhesive stalked knobs. Formation without added prey under these conditions excludes an obligatory prey-induction definition; neither medium nor stalk length is universal. The reported Dactylellina querci anamorph name is source terminology, not an independently verified current taxonomic equivalence.

    +

    Liu, Liu and Zhuang (2005), scientific Abstract, directly retrieved from the primary publisher https://academic.oup.com/femsle/article/245/1/99/483775 (minimal-article redirect). Abstract-only access: full Methods and figures were not retrieved. Orbilia querci material came from rotten Quercus wood in Huai-rou County, Beijing, and pure culture from ascospores. The authors report nematode capture with adhesive stalked knobs. Formation without added prey under these conditions excludes an obligatory prey-induction definition; neither medium nor stalk length is universal. The reported Dactylellina querci anamorph name is source terminology, not an independently verified current taxonomic equivalence.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Canonical examples DOI:10.1128/AEM.01390-13 - Source-named Monacrosporium haptotylum CBS 200.50. Live NCBI https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=1284197 resolves rank strain, the exact label Dactylellina haptotyla CBS 200.50 and the historical name. Zhou et al. (2018), DOI:10.1080/23802359.2018.1507650, body paragraph 2, directly read primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7801010/fullTextXML, reports collection from a decaying leaf in a pond at Chelsea Physic Garden, London, by M.P. Peach in 1948. That genome study is strain-provenance support, not an independent knob-formation experiment. The unperturbed natural-origin strain example is qualified by the 2013 culture conditions, not every isolate or field biocontrol efficacy. + Source-named Monacrosporium haptotylum CBS 200.50. Live NCBI https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=1284197 resolves rank strain, the exact label Dactylellina haptotyla CBS 200.50 and the historical name. Zhou et al. (2018), DOI:10.1080/23802359.2018.1507650, body paragraph 2, directly read primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7801010/fullTextXML, reports collection from a decaying leaf in a pond at Chelsea Physic Garden, London, by M.P. Peach in 1948. That genome study is strain-provenance support, not an independent knob-formation experiment. The unperturbed natural-origin strain example is qualified by the 2013 culture conditions, not every isolate or field biocontrol efficacy. @@ -304,7 +305,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed fungal adhesive-knob trap formation -

      Created traitmech:000679 with primary DOI:10.1128/AEM.01390-13 and DOI:10.1016/j.femsle.2005.02.027, contiguous scientific-abstract snippets, and NCBITaxon:1284197 Dactylellina haptotyla CBS 200.50. ASM HTML and actual Figure 1 read; 2005 evidence is abstract-only. DOI:10.1080/23802359.2018.1507650 primary XML supports natural strain provenance, not a third phenotype replication. Kept morphology, detachment, prey induction and sequence-derived mechanism claims separate; closer parent and molecular mechanism remain open. Ignored-and-hidden whole-root and complete open-PR snapshot checks support local ID, cohort v555 and whole METPO block 1063200-1063299. Guarded writer dry-run and 20 focused tests passed; both snippets VERIFIED by the maintained live resolver. Broader validation results will be recorded in the PR. Existing trait YAMLs and protected spore_germination remain unchanged.

    +

    Created traitmech:000679 with primary DOI:10.1128/AEM.01390-13 and DOI:10.1016/j.femsle.2005.02.027, contiguous scientific-abstract snippets, and NCBITaxon:1284197 Dactylellina haptotyla CBS 200.50. ASM HTML and actual Figure 1 read; 2005 evidence is abstract-only. DOI:10.1080/23802359.2018.1507650 primary XML supports natural strain provenance, not a third phenotype replication. Kept morphology, detachment, prey induction and sequence-derived mechanism claims separate; closer parent and molecular mechanism remain open. Ignored-and-hidden whole-root and complete open-PR snapshot checks support local ID, cohort v555 and whole METPO block 1063200-1063299. Guarded writer dry-run and 20 focused tests passed; both snippets VERIFIED by the maintained live resolver. Broader validation results will be recorded in the PR. Existing trait YAMLs and protected spore_germination remain unchanged.

    • Read this curation session
  • @@ -342,7 +343,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -371,12 +381,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-13 13:33 UTC diff --git a/pages/traits/morphology/fungal_adhesive_net_trap_formation.html b/pages/traits/morphology/fungal_adhesive_net_trap_formation.html index e4656c450bc..7552d9a182e 100644 --- a/pages/traits/morphology/fungal_adhesive_net_trap_formation.html +++ b/pages/traits/morphology/fungal_adhesive_net_trap_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1371/journal.ppat.1002179
    A. oligospora forms adhesive networks to capture nematodes
    -

    Yang et al. (2011), Author Summary, not the scientific abstract; primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3164635/fullTextXML. Introduction, trap-formation Results, strain/proteomics Methods, actual Figure 1 and relevant Text S1 supplemental Methods were inspected. Figure 1I shows connected hyphal loops; the paper describes complex three-dimensional networks. ATCC 24927 is the reference strain. Supplemental Methods distinguish nematode-extract induction on vegetative hyphae from subsequent live-nematode interaction assays. Formation, adhesion, capture, penetration and digestion are separate observations. No universal induction medium, prey species or capture efficacy is inferred. Proteomic correlations are not treated as a causal gene requirement.

    +

    Yang et al. (2011), Author Summary, not the scientific abstract; primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3164635/fullTextXML. Introduction, trap-formation Results, strain/proteomics Methods, actual Figure 1 and relevant Text S1 supplemental Methods were inspected. Figure 1I shows connected hyphal loops; the paper describes complex three-dimensional networks. ATCC 24927 is the reference strain. Supplemental Methods distinguish nematode-extract induction on vegetative hyphae from subsequent live-nematode interaction assays. Formation, adhesion, capture, penetration and digestion are separate observations. No universal induction medium, prey species or capture efficacy is inferred. Proteomic correlations are not treated as a causal gene requirement.

  • DOI:10.3390/jof8070671
    Captures nematodes with adhesive networks.
    -

    Zhang et al. (2022; published 26 June), Results 3.2 Taxonomy, Arthrobotrys eryuanensis description; primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9317614/fullTextXML. Isolation/observation Methods, all six species descriptions and actual Figure 2 were inspected. Figure 2i shows the adhesive network, not time-resolved capture or adhesion kinetics. Holotype CGMCC3.19715 (Figure 2) and ex-type culture DLUCC 14-1 are distinguished by the authors. The material originated from freshwater sediment at Xihu Lake, Eryuan, Yunnan, China, collected 20 June 2014. Repeated spore transfers established pure cultures; corn meal agar observation at 26 degrees C with Panagrellus redivivus induced traps. These are study conditions, not universal requirements. The other newly described soil/sediment taxa provide context, not a universal genus-level phenotype assertion.

    +

    Zhang et al. (2022; published 26 June), Results 3.2 Taxonomy, Arthrobotrys eryuanensis description; primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9317614/fullTextXML. Isolation/observation Methods, all six species descriptions and actual Figure 2 were inspected. Figure 2i shows the adhesive network, not time-resolved capture or adhesion kinetics. Holotype CGMCC3.19715 (Figure 2) and ex-type culture DLUCC 14-1 are distinguished by the authors. The material originated from freshwater sediment at Xihu Lake, Eryuan, Yunnan, China, collected 20 June 2014. Repeated spore transfers established pure cultures; corn meal agar observation at 26 degrees C with Panagrellus redivivus induced traps. These are study conditions, not universal requirements. The other newly described soil/sediment taxa provide context, not a universal genus-level phenotype assertion.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Canonical examples DOI:10.1371/journal.ppat.1002179 - Source-named Arthrobotrys oligospora ATCC 24927. Yang et al. Methods identify the purchased ATCC strain as originally isolated from soil in Sweden. Live https://www.atcc.org/products/24927 independently confirms environmental soil origin and Sweden; it lists Arthrobotrys oligospora as the former name. Live NCBI https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=756982 resolves rank strain with the exact label Orbilia oligospora ATCC 24927. This unperturbed natural-origin reference strain is qualified by the reported induction conditions, not every isolate or field biocontrol efficacy. The 2011 paper's O. auricolor teleomorph wording is not imported as a current taxonomic equivalence or synonym. + Source-named Arthrobotrys oligospora ATCC 24927. Yang et al. Methods identify the purchased ATCC strain as originally isolated from soil in Sweden. Live https://www.atcc.org/products/24927 independently confirms environmental soil origin and Sweden; it lists Arthrobotrys oligospora as the former name. Live NCBI https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=756982 resolves rank strain with the exact label Orbilia oligospora ATCC 24927. This unperturbed natural-origin reference strain is qualified by the reported induction conditions, not every isolate or field biocontrol efficacy. The 2011 paper's O. auricolor teleomorph wording is not imported as a current taxonomic equivalence or synonym. @@ -342,7 +343,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -371,12 +381,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-13 13:33 UTC diff --git a/pages/traits/morphology/fungal_appressorium_formation.html b/pages/traits/morphology/fungal_appressorium_formation.html index bd24f2efb1d..2b083bee312 100644 --- a/pages/traits/morphology/fungal_appressorium_formation.html +++ b/pages/traits/morphology/fungal_appressorium_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.3390/jof5030072
    Here, we report on the ability of many saprotrophs from a large range of taxa to produce appressoria on cellophane.
    -

    Demoor, Silar and Brun (2019), PMID:31382649, PMC6787622; scientific abstract retrieved as full-text XML. Introduction, Methods, Results and the broad-definition Discussion paragraph were read; actual Figures 2 and 6 and supplementary Table S1 were inspected. The authors explicitly include structures previously called appressorium-like under a broad penetration-structure usage, including unicellular and compound forms. The principal assay used mycelial implants on cellophane over M2 medium at 27 C, with observations after 3-15 days. It is not an in-host assay or a universal fungal prevalence estimate. Contact and growth reorientation without penetration were distinguished from appressoria. Negative results apply to the tested conditions, not to entire clades. Table S1 identifies strains but does not independently establish natural provenance for all of them; they are not added as canonical examples.

    +

    Demoor, Silar and Brun (2019), PMID:31382649, PMC6787622; scientific abstract retrieved as full-text XML. Introduction, Methods, Results and the broad-definition Discussion paragraph were read; actual Figures 2 and 6 and supplementary Table S1 were inspected. The authors explicitly include structures previously called appressorium-like under a broad penetration-structure usage, including unicellular and compound forms. The principal assay used mycelial implants on cellophane over M2 medium at 27 C, with observations after 3-15 days. It is not an in-host assay or a universal fungal prevalence estimate. Contact and growth reorientation without penetration were distinguished from appressoria. Negative results apply to the tested conditions, not to entire clades. Table S1 identifies strains but does not independently establish natural provenance for all of them; they are not added as canonical examples.

  • DOI:10.1371/journal.ppat.1002514
    an appressorium is already developing in Guy11 strain whereas no infection cell development occurs in an isogenic Δpmk1 mutant
    -

    Soanes et al. (2012), PMID:22346750, PMC3276559; Results describing Figure 1B, not the Author Summary. Actual Figure 1 and the fungal-strain/growth Methods were inspected. Wild-type Guy11 and the deletion mutant were compared at four hours; the Guy11 series also includes 6, 8, 14 and 16 hours. The Methods describe plastic coverslips and 1,16-hexadecanediol, whereas the Results describing Figure 1A name a hydrophobic glass slide. This within-article surface discrepancy is unresolved; neither description is silently substituted for the other or treated as a universal surface requirement. Natural-isolate provenance is checked separately in the canonical-example note. The observed formation phenotype is not inferred from RNA expression. Neither these transcript profiles nor one deletion establish a universal protein-resolved mechanism across fungi. Other figures and transcript-data supplements were not inspected.

    +

    Soanes et al. (2012), PMID:22346750, PMC3276559; Results describing Figure 1B, not the Author Summary. Actual Figure 1 and the fungal-strain/growth Methods were inspected. Wild-type Guy11 and the deletion mutant were compared at four hours; the Guy11 series also includes 6, 8, 14 and 16 hours. The Methods describe plastic coverslips and 1,16-hexadecanediol, whereas the Results describing Figure 1A name a hydrophobic glass slide. This within-article surface discrepancy is unresolved; neither description is silently substituted for the other or treated as a universal surface requirement. Natural-isolate provenance is checked separately in the canonical-example note. The observed formation phenotype is not inferred from RNA expression. Neither these transcript profiles nor one deletion establish a universal protein-resolved mechanism across fungi. Other figures and transcript-data supplements were not inspected.

  • DOI:10.1186/1741-7007-6-9
    blocking of the cell cycle did not prevent spore germination and appressoria formation.
    -

    Nesher, Barhoom and Sharon (2008), PMID:18275611, PMC2276476; scientific abstract Results, read directly in full-text XML. The Methods name Colletotrichum gloeosporioides f. sp. aeschynomene 3.1.3 wild-type and transgenic strains; germination and onion-epidermis assays were read. This result separates formation from a universal mitosis requirement. It does not show unrestricted post-penetration growth under cell-cycle inhibition. Full result figures, natural strain provenance and current species-complex assignment were not inspected or resolved, so this is qualified evidence, not a canonical taxon assignment or a universal autophagy/cell-cycle claim.

    +

    Nesher, Barhoom and Sharon (2008), PMID:18275611, PMC2276476; scientific abstract Results, read directly in full-text XML. The Methods name Colletotrichum gloeosporioides f. sp. aeschynomene 3.1.3 wild-type and transgenic strains; germination and onion-epidermis assays were read. This result separates formation from a universal mitosis requirement. It does not show unrestricted post-penetration growth under cell-cycle inhibition. Full result figures, natural strain provenance and current species-complex assignment were not inspected or resolved, so this is qualified evidence, not a canonical taxon assignment or a universal autophagy/cell-cycle claim.

  • DOI:10.1111/nph.13931
    Here we identify an appressorium‐like structure, which we call an expressorium
    -

    Becker et al. (2016), PMID:26991322, PMC5069595; the article's scientific Summary and the Results paragraph distinguishing intrinsecus/extrinsecus terminology were read directly in full-text XML. The internal structure enables Epichloe festucae to exit a leaf. The authors propose expressorium to distinguish it from an external appressorium, while noting an intrinsecus-appressorium convention. This is terminology-boundary evidence, not an asserted exact synonym or additional canonical example. Figures, movies, supplements and strain provenance were not inspected; no Nox mechanism or turgor measurement is inferred from this quotation.

    +

    Becker et al. (2016), PMID:26991322, PMC5069595; the article's scientific Summary and the Results paragraph distinguishing intrinsecus/extrinsecus terminology were read directly in full-text XML. The internal structure enables Epichloe festucae to exit a leaf. The authors propose expressorium to distinguish it from an external appressorium, while noting an intrinsecus-appressorium convention. This is terminology-boundary evidence, not an asserted exact synonym or additional canonical example. Figures, movies, supplements and strain provenance were not inspected; no Nox mechanism or turgor measurement is inferred from this quotation.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Canonical examples DOI:10.1371/journal.ppat.1002514 - Wild-type Guy11 in Soanes et al. (2012), Figure 1A-B and Methods, directly forms appressoria under the tested in-vitro induction conditions. NCBI Taxonomy resolves Pyricularia oryzae at species rank and lists the paper's Magnaporthe oryzae name as a synonym. Independent primary population-study Methods at https://doi.org/10.5423/PPJ.NT.04.2013.0042 (PMID:25288972, PMC4174813) explicitly identify Guy11 as a rice-pathogenic isolate from French Guiana and distinguish it from laboratory crossing derivatives. That passage was read directly; its cited original 1988 isolation study was not retrieved. This provenance citation is not counted as an independent appressorium observation. The example concerns Guy11, not its engineered deletion mutant, strain 70-15, every strain, or every environmental condition. + Wild-type Guy11 in Soanes et al. (2012), Figure 1A-B and Methods, directly forms appressoria under the tested in-vitro induction conditions. NCBI Taxonomy resolves Pyricularia oryzae at species rank and lists the paper's Magnaporthe oryzae name as a synonym. Independent primary population-study Methods at https://doi.org/10.5423/PPJ.NT.04.2013.0042 (PMID:25288972, PMC4174813) explicitly identify Guy11 as a rice-pathogenic isolate from French Guiana and distinguish it from laboratory crossing derivatives. That passage was read directly; its cited original 1988 isolation study was not retrieved. This provenance citation is not counted as an independent appressorium observation. The example concerns Guy11, not its engineered deletion mutant, strain 70-15, every strain, or every environmental condition. @@ -352,7 +353,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -381,12 +391,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 05:47 UTC diff --git a/pages/traits/morphology/fungal_arbuscule_formation.html b/pages/traits/morphology/fungal_arbuscule_formation.html index c09f1d840e1..b1a654456cc 100644 --- a/pages/traits/morphology/fungal_arbuscule_formation.html +++ b/pages/traits/morphology/fungal_arbuscule_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1104/pp.109.141879
    In the arbuscular mycorrhizal symbiosis, the fungal symbiont colonizes root cortical cells, where it establishes differentiated hyphae called arbuscules.
    -

    Pumplin and Harrison (2009), PMID:19692536, PMC2754618; scientific-abstract sentence checked against Europe PMC and https://academic.oup.com/plphys/article/151/2/809/6108581. Main text, Figures 1-7 and supplementary Figures S1-S9 were inspected; Figure 7 is a model. The supplementary movie was not viewed. Glomus versiforme colonized transgenic Medicago truncatula A17 roots. Host fluorescent markers distinguish periarbuscular membrane domains; they are not fungal protein anchors or nutrient-flux measurements. The host-derived membrane separates fungal branches from host cytoplasm. Fungal isolate provenance was not established, so this experiment is not a natural canonical example.

    +

    Pumplin and Harrison (2009), PMID:19692536, PMC2754618; scientific-abstract sentence checked against Europe PMC and https://academic.oup.com/plphys/article/151/2/809/6108581. Main text, Figures 1-7 and supplementary Figures S1-S9 were inspected; Figure 7 is a model. The supplementary movie was not viewed. Glomus versiforme colonized transgenic Medicago truncatula A17 roots. Host fluorescent markers distinguish periarbuscular membrane domains; they are not fungal protein anchors or nutrient-flux measurements. The host-derived membrane separates fungal branches from host cytoplasm. Fungal isolate provenance was not established, so this experiment is not a natural canonical example.

  • DOI:10.3390/plants8060142
    All AMF strains formed arbuscules in the parenchyma cells of the mycothalli
    -

    Kobae et al. (2019), PMID:31151150, PMC6631804; Results 2.2 clause. Primary text and Figures 1-4 on pages 1-11 of https://rakuno.repo.nii.ac.jp/record/6472/files/R-2020-321_kobae.pdf and all four supplementary pages were inspected. Liverwort Marchantia paleacea thallus observations support plant-cell, not root-only, scope. Methods 3.2 and Figure S1 identify cultures separately from unidentified field-root trapping. For DAOM197198, Results 2.2 reports arbuscules at 18 dps and none until 14 dps; S2A instead describes rhizoid-only hyphae at 18 dps and S2B arbuscules at 28 dps. Onset remains unresolved. Pigmentation alone is insufficient. Figure 4C shows root arbuscules, although Results points to 4B and uses dps instead of the caption's dpi. Figure 3 and Methods 3.6 disagree on phylogenetic method; no independent fungal species assignment from mixed rDNA is asserted.

    +

    Kobae et al. (2019), PMID:31151150, PMC6631804; Results 2.2 clause. Primary text and Figures 1-4 on pages 1-11 of https://rakuno.repo.nii.ac.jp/record/6472/files/R-2020-321_kobae.pdf and all four supplementary pages were inspected. Liverwort Marchantia paleacea thallus observations support plant-cell, not root-only, scope. Methods 3.2 and Figure S1 identify cultures separately from unidentified field-root trapping. For DAOM197198, Results 2.2 reports arbuscules at 18 dps and none until 14 dps; S2A instead describes rhizoid-only hyphae at 18 dps and S2B arbuscules at 28 dps. Onset remains unresolved. Pigmentation alone is insufficient. Figure 4C shows root arbuscules, although Results points to 4B and uses dps instead of the caption's dpi. Figure 3 and Methods 3.6 disagree on phylogenetic method; no independent fungal species assignment from mixed rDNA is asserted.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Canonical examples DOI:10.3390/plants8060142 - MAFF520053 (H1-1), reported as Claroideoglomus etunicatum in Methods 3.2 and actual Figure S1, forms arbuscules in Marchantia paleacea thallus cells. NARO's collection record https://www.gene.affrc.go.jp/databases-micro_search_detail_en.php?maff=520053 lists soybean-field soil, Tokyo, October 1987, H. Hirata; it was deposited as Glomus etunicatum. These separate fields support this culture's field-isolate origin, not a trait evidence snippet. NCBI Taxonomy resolves species 937382 to Entrophospora etunicata, with Claroideoglomus etunicatum as a homotypic synonym; name correspondence is not independent reidentification of the culture. + MAFF520053 (H1-1), reported as Claroideoglomus etunicatum in Methods 3.2 and actual Figure S1, forms arbuscules in Marchantia paleacea thallus cells. NARO's collection record https://www.gene.affrc.go.jp/databases-micro_search_detail_en.php?maff=520053 lists soybean-field soil, Tokyo, October 1987, H. Hirata; it was deposited as Glomus etunicatum. These separate fields support this culture's field-isolate origin, not a trait evidence snippet. NCBI Taxonomy resolves species 937382 to Entrophospora etunicata, with Claroideoglomus etunicatum as a homotypic synonym; name correspondence is not independent reidentification of the culture. @@ -296,7 +297,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add fungal arbuscule formation with root and thallus evidence -

      Added traitmech:000664 as PROPOSED with DOI:10.1104/pp.109.141879 and DOI:10.3390/plants8060142, two directly checked verbatim snippets, a provenance-qualified MAFF520053 example and explicit ontology, host-marker and timing limits. Reserved v540 and METPO:1061700 within 1061700-1061799 after ignored-and-hidden main/worktree/open-PR checks. Writer dry run and 27 focused tests passed; broad validation and review remain pending. No causal graph is asserted.

    +

    Added traitmech:000664 as PROPOSED with DOI:10.1104/pp.109.141879 and DOI:10.3390/plants8060142, two directly checked verbatim snippets, a provenance-qualified MAFF520053 example and explicit ontology, host-marker and timing limits. Reserved v540 and METPO:1061700 within 1061700-1061799 after ignored-and-hidden main/worktree/open-PR checks. Writer dry run and 27 focused tests passed; broad validation and review remain pending. No causal graph is asserted.

    • Read this curation session @@ -328,7 +329,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -357,12 +367,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 13:25 UTC diff --git a/pages/traits/morphology/fungal_auxiliary_cell_formation.html b/pages/traits/morphology/fungal_auxiliary_cell_formation.html index 6da1017940e..d529d123198 100644 --- a/pages/traits/morphology/fungal_auxiliary_cell_formation.html +++ b/pages/traits/morphology/fungal_auxiliary_cell_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -61,13 +62,13 @@

    Trait evidence (3)

    DOI:10.1111/j.1469-8137.2007.02345.x
    In G. margarita, auxiliary cells were formed on germ tubes
    -

    Kuga et al. (2008), PMID:18194149; Results clause before Elemental analyses, directly read in publisher full text. Methods identify MAFF520054. The Results point to Figure 3a/i; captions were read but actual paper images and supplements were not inspected. The HTML temperature glyph renders as 25×C and remains unresolved rather than normalized to degrees. Organelle localization and nonspecific DAPI fluorescence do not establish a formation mechanism or a universal storage function.

    +

    Kuga et al. (2008), PMID:18194149; Results clause before Elemental analyses, directly read in publisher full text. Methods identify MAFF520054. The Results point to Figure 3a/i; captions were read but actual paper images and supplements were not inspected. The HTML temperature glyph renders as 25×C and remains unresolved rather than normalized to degrees. Organelle localization and nonspecific DAPI fluorescence do not establish a formation mechanism or a universal storage function.

  • DOI:10.1017/S0953756203008761
    Isolated auxiliary cells were shown to exhibit hyphal re-growth, but not root colonization, either in situ or in vitro.
    -

    Declerck et al. (2004), PMID:15035509; scientific abstract retrieved directly from Europe PMC. It follows extraradical mycelium, auxiliary cells and spores of Scutellospora reticulata in root-organ culture. Ri T-DNA transformation concerns carrot roots, not an engineered fungus. Regrowth without root colonization is conditional on the tested assays, not universal noninfectivity. Resource reallocation is the authors' interpretation, not a direct flux measurement. Full paper, images and isolate provenance were not inspected; no additional canonical culture is assigned.

    +

    Declerck et al. (2004), PMID:15035509; scientific abstract retrieved directly from Europe PMC. It follows extraradical mycelium, auxiliary cells and spores of Scutellospora reticulata in root-organ culture. Ri T-DNA transformation concerns carrot roots, not an engineered fungus. Regrowth without root colonization is conditional on the tested assays, not universal noninfectivity. Resource reallocation is the authors' interpretation, not a direct flux measurement. Full paper, images and isolate provenance were not inspected; no additional canonical culture is assigned.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1111/j.1469-8137.2007.02345.x - MAFF520054, Results and Fungal materials of Kuga et al. (2008): auxiliary cells on germ tubes. Methods describe white-clover propagation, membranes over 1% soil agar, 10 days in darkness and a separate nutrient-agar staining treatment; cultivation duration is not formation onset. The temperature glyph and actual Figure 3 images remain unverified. The directly retrieved NARO record https://www.gene.affrc.go.jp/databases-micro_search_detail_en.php?maff=520054 lists designation C, soybean-field soil, Saitama Japan, isolator S. Ban and depositor/identifier M. Saito as separate fields. These establish field-isolate provenance, not a composite quote or independent trait evidence. NCBI Taxonomy resolves species 4874, not culture reidentification. Table 1 of DOI:10.1264/jsme2.ME25040 retains C/520054; primer-dependent ASVs, including above-genus assignments, are not culture counts or proof of contamination, identity or this phenotype. Its figures and supplements were not inspected. This example does not assert the response of all strains or conditions. + MAFF520054, Results and Fungal materials of Kuga et al. (2008): auxiliary cells on germ tubes. Methods describe white-clover propagation, membranes over 1% soil agar, 10 days in darkness and a separate nutrient-agar staining treatment; cultivation duration is not formation onset. The temperature glyph and actual Figure 3 images remain unverified. The directly retrieved NARO record https://www.gene.affrc.go.jp/databases-micro_search_detail_en.php?maff=520054 lists designation C, soybean-field soil, Saitama Japan, isolator S. Ban and depositor/identifier M. Saito as separate fields. These establish field-isolate provenance, not a composite quote or independent trait evidence. NCBI Taxonomy resolves species 4874, not culture reidentification. Table 1 of DOI:10.1264/jsme2.ME25040 retains C/520054; primer-dependent ASVs, including above-genus assignments, are not culture counts or proof of contamination, identity or this phenotype. Its figures and supplements were not inspected. This example does not assert the response of all strains or conditions. @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-08 02:08 UTC diff --git a/pages/traits/morphology/fungal_branched_absorbing_structure_formation.html b/pages/traits/morphology/fungal_branched_absorbing_structure_formation.html index 6c3602874cf..ccb689713bb 100644 --- a/pages/traits/morphology/fungal_branched_absorbing_structure_formation.html +++ b/pages/traits/morphology/fungal_branched_absorbing_structure_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -61,7 +62,7 @@

    Trait evidence (2)

    DOI:10.1093/pcp/pcz122
    highly branched hyphae called branched absorbing structures (BAS) differentiate on the runner hyphae
    -

    Kameoka et al. (2019), PMID:31241164; Introduction clause before the Figure 1 citation, exact-matched in directly retrieved publisher HTML. Abstract, Introduction, Results, Discussion and Methods were read. Actual Figure 1C/G and its caption were inspected: six-week Rhizophagus irregularis DAOM197198 carrot hairy-root cocultures supply direct BAS morphology evidence. The RNA-seq comparison is not a direct uptake assay or causal perturbation. Runner-hypha and spore samples contained some BAS; negligible contamination influence was the authors' inference, not measured absence. Their historical no-direct-uptake-evidence statement is not a present-day knowledge claim. Remaining figure images and supplementary spreadsheet contents were not inspected.

    +

    Kameoka et al. (2019), PMID:31241164; Introduction clause before the Figure 1 citation, exact-matched in directly retrieved publisher HTML. Abstract, Introduction, Results, Discussion and Methods were read. Actual Figure 1C/G and its caption were inspected: six-week Rhizophagus irregularis DAOM197198 carrot hairy-root cocultures supply direct BAS morphology evidence. The RNA-seq comparison is not a direct uptake assay or causal perturbation. Runner-hypha and spore samples contained some BAS; negligible contamination influence was the authors' inference, not measured absence. Their historical no-direct-uptake-evidence statement is not a present-day knowledge claim. Remaining figure images and supplementary spreadsheet contents were not inspected.

    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Canonical examples DOI:10.1093/pcp/pcz122 - DAOM197198 from Premier Tech in six-week carrot hairy-root coculture, Methods and actual Figure 1C/G. The Canadian GINCO catalogue https://agriculture.canada.ca/en/agricultural-science-and-innovation/agriculture-and-agri-food-research-centres-and-collections/glomeromycota-vitro-collection-ginco/catalogue-arbuscular-mycorrhizal-fungi-strains-available-glomeromycetes-vitro-collection lists DAOMC197198, herbarium DAOM197198/181602, MUCL43194, Pont-Rouge in Quebec, a tree plantation, and collectors/isolators C. Plenchette and V. Furlan. These collection fields support field-isolate origin and are not a synthesized evidence snippet. NCBI Taxonomy confirms species 588596 and its strain 747089, Rhizophagus irregularis DAOM 181602=DAOM 197198. The transformed carrot host does not imply an engineered fungus. This is a culture-qualified observation, not independent reidentification or evidence for every strain and condition. + DAOM197198 from Premier Tech in six-week carrot hairy-root coculture, Methods and actual Figure 1C/G. The Canadian GINCO catalogue https://agriculture.canada.ca/en/agricultural-science-and-innovation/agriculture-and-agri-food-research-centres-and-collections/glomeromycota-vitro-collection-ginco/catalogue-arbuscular-mycorrhizal-fungi-strains-available-glomeromycetes-vitro-collection lists DAOMC197198, herbarium DAOM197198/181602, MUCL43194, Pont-Rouge in Quebec, a tree plantation, and collectors/isolators C. Plenchette and V. Furlan. These collection fields support field-isolate origin and are not a synthesized evidence snippet. NCBI Taxonomy confirms species 588596 and its strain 747089, Rhizophagus irregularis DAOM 181602=DAOM 197198. The transformed carrot host does not imply an engineered fungus. This is a culture-qualified observation, not independent reidentification or evidence for every strain and condition. @@ -264,7 +265,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Absorbing is the established structure name, not a required flux measurement. Do not infer mineral uptake, obligatory host contact, universal timing, inevitable degeneration or sporulation from morphology. Bago et al.'s host-dependence interpretation describes their tested media; later asymbiotic growth work DOI:10.1073/pnas.2006948117 remains a BAS-specific full-text/figure follow-up, not counted BAS evidence here. Transcriptional associations in Kameoka et al. do not identify a causal formation pathway. Their in vitro host system also does not establish expression patterns in soil-grown intact plants. A protein-resolved graph is deferred pending direct perturbation evidence and authority-verified protein anchors; it is not claimed biologically absent.

    +

    Absorbing is the established structure name, not a required flux measurement. Do not infer mineral uptake, obligatory host contact, universal timing, inevitable degeneration or sporulation from morphology. Bago et al.'s host-dependence interpretation describes their tested media; later asymbiotic growth work DOI:10.1073/pnas.2006948117 remains a BAS-specific full-text/figure follow-up, not counted BAS evidence here. Transcriptional associations in Kameoka et al. do not identify a causal formation pathway. Their in vitro host system also does not establish expression patterns in soil-grown intact plants. A protein-resolved graph is deferred pending direct perturbation evidence and authority-verified protein anchors; it is not claimed biologically absent.

    @@ -296,7 +297,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add source-qualified fungal BAS formation -

      Added traitmech:000665 as PROPOSED MORPHOLOGY with primary DOI:10.1046/j.1469-8137.1998.00199.x and DOI:10.1093/pcp/pcz122 snippets, and a DAOM197198 culture-qualified Rhizophagus irregularis example supported by inspected microscopy, collection provenance and NCBI taxonomy. Reserved v541/METPO:1061800 in 1061800-1061899 after ignored-and-hidden current-main/worktree and paginated immutable-head PR checks. Kept uptake, universal host dependence and protein mechanisms out of the definition; two discussions remain OPEN. Writer dry run and all 20 focused writer tests passed before application. No existing trait was edited.

    +

    Added traitmech:000665 as PROPOSED MORPHOLOGY with primary DOI:10.1046/j.1469-8137.1998.00199.x and DOI:10.1093/pcp/pcz122 snippets, and a DAOM197198 culture-qualified Rhizophagus irregularis example supported by inspected microscopy, collection provenance and NCBI taxonomy. Reserved v541/METPO:1061800 in 1061800-1061899 after ignored-and-hidden current-main/worktree and paginated immutable-head PR checks. Kept uptake, universal host dependence and protein mechanisms out of the definition; two discussions remain OPEN. Writer dry run and all 20 focused writer tests passed before application. No existing trait was edited.

    • Read this curation session @@ -328,7 +329,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -357,12 +367,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 14:24 UTC diff --git a/pages/traits/morphology/fungal_chlamydospore_formation.html b/pages/traits/morphology/fungal_chlamydospore_formation.html index b80a1cc5674..180d1ad3ac9 100644 --- a/pages/traits/morphology/fungal_chlamydospore_formation.html +++ b/pages/traits/morphology/fungal_chlamydospore_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (6)

    DOI:10.1038/s41467-020-20010-9
    Chlamydospores are enlarged thick-walled cells produced within hyphae or at hyphal tips
    -

    Hernandez-Cervantes et al. (2020), PMID:33277479, PMC7718266, Introduction; this contiguous clause supplies morphological terminology, not independent experimental replication across all fungi. Abstract, Introduction and selected Methods were read directly. Mechanistic panels and supplementary strain tables were not inspected, so no universal Rme1 dependence or protein-resolved causal graph is asserted. The definition does not impose a survival function.

    +

    Hernandez-Cervantes et al. (2020), PMID:33277479, PMC7718266, Introduction; this contiguous clause supplies morphological terminology, not independent experimental replication across all fungi. Abstract, Introduction and selected Methods were read directly. Mechanistic panels and supplementary strain tables were not inspected, so no universal Rme1 dependence or protein-resolved causal graph is asserted. The definition does not impose a survival function.

  • DOI:10.1099/13500872-141-7-1507
    These organisms were germ-tube-positive and produced abundant chlamydospores which were frequently arranged in triplets or in contiguous pairs.
    -

    Sullivan et al. (1995), PMID:7551019, original Candida dubliniensis description; scientific abstract retrieved directly from Europe PMC. These organisms refers to the recovered oral clinical isolates. This is primary phenotype and natural-isolate provenance at cohort level, not evidence that chlamydospores were observed in patient tissue. Full Methods and strain tables were not inspected; no named culture, universal arrangement or response of every strain is inferred.

    +

    Sullivan et al. (1995), PMID:7551019, original Candida dubliniensis description; scientific abstract retrieved directly from Europe PMC. These organisms refers to the recovered oral clinical isolates. This is primary phenotype and natural-isolate provenance at cohort level, not evidence that chlamydospores were observed in patient tissue. Full Methods and strain tables were not inspected; no named culture, universal arrangement or response of every strain is inferred.

  • DOI:10.3389/fmicb.2016.01697
    Both species produced typically high amounts of chlamydospores on rice and CM agar (chlamydospore index [CI] 3).
    -

    Bottcher et al. (2016), PMID:27833594, PMC5081361, Figure 1 caption. Actual Figure 1 micrographs, Methods and Tables 1-2 were inspected. The strains are C. albicans SC5314 and C. dubliniensis Wu284, rendered with an umlaut in the source; CM means corn meal. Cultures were examined after seven days at 27 C in darkness. CI is an ordinal 0-3 score, not a cell percentage. Nutrient effects differ by strain and medium; no universal starvation or darkness requirement is inferred. Independent provenance of these laboratory strains was not checked, so they are not the canonical example.

    +

    Bottcher et al. (2016), PMID:27833594, PMC5081361, Figure 1 caption. Actual Figure 1 micrographs, Methods and Tables 1-2 were inspected. The strains are C. albicans SC5314 and C. dubliniensis Wu284, rendered with an umlaut in the source; CM means corn meal. Cultures were examined after seven days at 27 C in darkness. CI is an ordinal 0-3 score, not a cell percentage. Nutrient effects differ by strain and medium; no universal starvation or darkness requirement is inferred. Independent provenance of these laboratory strains was not checked, so they are not the canonical example.

  • DOI:10.1111/j.1567-1364.2009.00533.x
    Mycelium-attached and purified chlamydospores rapidly lost their viability in water and when subjected to dry stress
    -

    Citiulo et al. (2009), PMID:19538507, scientific abstract retrieved directly from Europe PMC and checked against publisher text. The complete result clause is quoted before the authors' interpretation about long-term storage. It argues against assuming durable dormancy for these Candida cells, not against survival roles in every fungus. The publisher Introduction and selected Methods were also read; the Introduction calls Candida budding blastic conidiogenesis and explains chlamydoconidia terminology. Formation is kept separate from subsequent germination and viability.

    +

    Citiulo et al. (2009), PMID:19538507, scientific abstract retrieved directly from Europe PMC and checked against publisher text. The complete result clause is quoted before the authors' interpretation about long-term storage. It argues against assuming durable dormancy for these Candida cells, not against survival roles in every fungus. The publisher Introduction and selected Methods were also read; the Introduction calls Candida budding blastic conidiogenesis and explains chlamydoconidia terminology. Formation is kept separate from subsequent germination and viability.

  • @@ -85,7 +86,7 @@

    Trait evidence (6)

    DOI:10.1007/s10886-012-0171-1
    two species of Fusarium formed chlamydospores from hyphae, germ tubes, or inside the conidia within 2 days.
    -

    Li et al. (2012), PMID:22932866, scientific abstract retrieved directly from Europe PMC. This result concerns sub-MIC FA17 fengycin treatment of two Fusarium species, not untreated formation in every fungus. It establishes a conidial route excluded by the initial hypha-only draft definition (#1772). The abstract separately calls structures in 17 other fungi chlamydospore-like; those are not promoted to equivalent phenotypes. Full Methods, figures and strain provenance were not inspected, so no additional canonical strain or causal chemical mapping is asserted.

    +

    Li et al. (2012), PMID:22932866, scientific abstract retrieved directly from Europe PMC. This result concerns sub-MIC FA17 fengycin treatment of two Fusarium species, not untreated formation in every fungus. It establishes a conidial route excluded by the initial hypha-only draft definition (#1772). The abstract separately calls structures in 17 other fungi chlamydospore-like; those are not promoted to equivalent phenotypes. Full Methods, figures and strain provenance were not inspected, so no additional canonical strain or causal chemical mapping is asserted.

    • @@ -137,7 +138,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,7 @@

    Canonical examples DOI:10.1099/13500872-141-7-1507 - Species-level example from naturally recovered oral clinical isolates in the original 1995 description. The primary scientific abstract at https://doi.org/10.1099/13500872-141-7-1507 reports abundant chlamydospore production. This supports cohort-level isolate provenance, not a particular named laboratory culture, an inferred wild-type or GMO status, or chlamydospores in patient tissue. Full strain tables and Methods were not inspected; the observation is not assigned to CD36 or to every strain or condition. + Species-level example from naturally recovered oral clinical isolates in the original 1995 description. The primary scientific abstract at https://doi.org/10.1099/13500872-141-7-1507 reports abundant chlamydospore production. This supports cohort-level isolate provenance, not a particular named laboratory culture, an inferred wild-type or GMO status, or chlamydospores in patient tissue. Full strain tables and Methods were not inspected; the observation is not assigned to CD36 or to every strain or condition. @@ -258,7 +259,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Retain phenotype METPO:1000059. Sporulation METPO:1000870 and spore forming METPO:1000871 explicitly concern endospores. Citiulo et al. (2009) call Candida chlamydospore budding blastic conidiogenesis; that source-attributed usage does not settle whether this broader fungal class should be below fungal conidiation traitmech:000657. Do not equate it with ordinary pseudohyphal growth or any hyphal swelling. Closed upstream issue https://github.com/berkeleybop/metpo/issues/67 suggested chlamydospores under resting spores; the Candida viability evidence does not support that as a universal function. GO:0001410 was resolved through QuickGO: it is a biological process and its survival/endogenous-formation wording also needs scope review. Leave exact synonyms and xrefs unset rather than asserting equivalence. The four obsolete METPO chlamydospore terms are material classes, not active organismal phenotypes.

    +

    Retain phenotype METPO:1000059. Sporulation METPO:1000870 and spore forming METPO:1000871 explicitly concern endospores. Citiulo et al. (2009) call Candida chlamydospore budding blastic conidiogenesis; that source-attributed usage does not settle whether this broader fungal class should be below fungal conidiation traitmech:000657. Do not equate it with ordinary pseudohyphal growth or any hyphal swelling. Closed upstream issue https://github.com/berkeleybop/metpo/issues/67 suggested chlamydospores under resting spores; the Candida viability evidence does not support that as a universal function. GO:0001410 was resolved through QuickGO: it is a biological process and its survival/endogenous-formation wording also needs scope review. Leave exact synonyms and xrefs unset rather than asserting equivalence. The four obsolete METPO chlamydospore terms are material classes, not active organismal phenotypes.

    @@ -288,7 +289,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Wall thickening alone does not establish long-term survival, dormancy, infectivity or a dispersal function. Preserve species-, strain-, age- and medium-specific endpoints. Do not require one arrangement, nucleus count, nutrient trigger or illumination regime. The USDA Phytophthora report documents a nonfungal terminology boundary, not additional fungal replication. Formation and later germination are different observations. A causal graph is deferred pending reconciliation of primary perturbations and supplementary strain identities with natural-host provenance and taxon-paired protein accessions. Gene possession alone is not a chlamydospore phenotype. Li et al. (2012), PMID:22932866, report formation inside conidia as well as from hyphae and germ tubes under the tested treatment. Issue #1772 corrected the initial hypha-only restriction; retain formation-site neutrality and do not promote the separately reported chlamydospore-like structures to confirmed chlamydospores.

    +

    Wall thickening alone does not establish long-term survival, dormancy, infectivity or a dispersal function. Preserve species-, strain-, age- and medium-specific endpoints. Do not require one arrangement, nucleus count, nutrient trigger or illumination regime. The USDA Phytophthora report documents a nonfungal terminology boundary, not additional fungal replication. Formation and later germination are different observations. A causal graph is deferred pending reconciliation of primary perturbations and supplementary strain identities with natural-host provenance and taxon-paired protein accessions. Gene possession alone is not a chlamydospore phenotype. Li et al. (2012), PMID:22932866, report formation inside conidia as well as from hyphae and germ tubes under the tested treatment. Issue #1772 corrected the initial hypha-only restriction; retain formation-site neutrality and do not promote the separately reported chlamydospore-like structures to confirmed chlamydospores.

    @@ -332,7 +333,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Remove hypha-only chlamydospore formation restriction -

      Addressed #1772 with directly retrieved Li et al. 2012 evidence, DOI:10.1007/s10886-012-0171-1, PMID:22932866: Fusarium can form chlamydospores inside conidia under the tested treatment. Broadened the definition, added a sixth exact snippet and source-access/treatment limits, and preserved the initial curation event and canonical example. The earlier CREATE record 2026-10-07T042707Z-codex-070b8d.yaml remains unchanged; this EDIT documents its pre-merge scope correction. Interrupted pre-fix validation is not counted as a successful final run.

    +

    Addressed #1772 with directly retrieved Li et al. 2012 evidence, DOI:10.1007/s10886-012-0171-1, PMID:22932866: Fusarium can form chlamydospores inside conidia under the tested treatment. Broadened the definition, added a sixth exact snippet and source-access/treatment limits, and preserved the initial curation event and canonical example. The earlier CREATE record 2026-10-07T042707Z-codex-070b8d.yaml remains unchanged; this EDIT documents its pre-merge scope correction. Interrupted pre-fix validation is not counted as a successful final run.

    • Read this curation session @@ -364,7 +365,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -393,12 +403,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 04:36 UTC diff --git a/pages/traits/morphology/fungal_conidiation.html b/pages/traits/morphology/fungal_conidiation.html index fc8c460fd00..a227faf9855 100644 --- a/pages/traits/morphology/fungal_conidiation.html +++ b/pages/traits/morphology/fungal_conidiation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (4)

    DOI:10.2336/nishinihonhifu.40.1083
    produce asexual, nonmotile and usually deciduous propagules (conidia) by de novo growth from, or conversion of a fertile hypha (conidiogenous cell).
    -

    Cole (1978), publisher abstract directly retrieved at https://www.jstage.jst.go.jp/article/nishinihonhifu/40/6/40_6_1083/_article/-char/en. The article is labeled Mini Review and supports terminology, not independent experimental replication. Its historical Deuteromycetes classification is not imposed on the trait. Both new outgrowth and conversion of existing cells are retained; detached spores, an aerial stalk and one spore shape are not universal requirements. The exact DOI query returned no Europe PMC records. Full text and figures were not inspected.

    +

    Cole (1978), publisher abstract directly retrieved at https://www.jstage.jst.go.jp/article/nishinihonhifu/40/6/40_6_1083/_article/-char/en. The article is labeled Mini Review and supports terminology, not independent experimental replication. Its historical Deuteromycetes classification is not imposed on the trait. Both new outgrowth and conversion of existing cells are retained; detached spores, an aerial stalk and one spore shape are not universal requirements. The exact DOI query returned no Europe PMC records. Full text and figures were not inspected.

  • DOI:10.1101/gad.3.4.559
    The filamentous fungus Neurospora crassa responds to nutrient deprivation and dessication by producing asexual spores, or conidia.
    -

    Springer and Yanofsky (1989), PMID:2524423, scientific abstract retrieved directly from Europe PMC. The source spelling dessication is preserved. Primary scanning-electron microscopy and fluorescent-probe study of wild-type and morphological mutants: the abstract describes apical proconidial budding, septation and disarticulation. Early chains can return to hyphal growth; later chains are committed. These are source-reported observations, not personally inspected figures. Full Methods, figures and independent strain provenance were not read, so no canonical Neurospora strain or universal nutrient/stress requirement is asserted.

    +

    Springer and Yanofsky (1989), PMID:2524423, scientific abstract retrieved directly from Europe PMC. The source spelling dessication is preserved. Primary scanning-electron microscopy and fluorescent-probe study of wild-type and morphological mutants: the abstract describes apical proconidial budding, septation and disarticulation. Early chains can return to hyphal growth; later chains are committed. These are source-reported observations, not personally inspected figures. Full Methods, figures and independent strain provenance were not read, so no canonical Neurospora strain or universal nutrient/stress requirement is asserted.

  • DOI:10.1016/j.simyco.2017.09.001
    H–I. Conidiophores, conidiogenous cells and conidia.
    -

    Woudenberg et al. (2017), PMID:29158610, PMC5679026, Figure 7 caption, Cephalotrichum lignatile CBS 209.63. The actual panels were inspected together with Taxonomy and Methods. H-I show the named structures; J shows conidia. The description reports conidia in basipetal chains. Microscopic descriptions use SNA cultures after 14 days at 25 C in darkness; A-C instead show OA, MEA and DG18 colonies. These are descriptive morphology observations, not time-lapse proof of each developmental transition.

    +

    Woudenberg et al. (2017), PMID:29158610, PMC5679026, Figure 7 caption, Cephalotrichum lignatile CBS 209.63. The actual panels were inspected together with Taxonomy and Methods. H-I show the named structures; J shows conidia. The description reports conidia in basipetal chains. Microscopic descriptions use SNA cultures after 14 days at 25 C in darkness; A-C instead show OA, MEA and DG18 colonies. These are descriptive morphology observations, not time-lapse proof of each developmental transition.

  • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Canonical examples DOI:10.1016/j.simyco.2017.09.001 - Ex-type culture CBS 209.63. Figure 7H-J and the primary taxonomic description document conidiogenous structures and conidia in basipetal chains. Microscopic descriptions use SNA after 14 days at 25 C in darkness. Specimen examined and Table 1 at https://pmc.ncbi.nlm.nih.gov/articles/PMC5679026/ identify Hennebert's 1959 isolate from timber in a cave at Han-sur-Lesse, Belgium. This is primary isolate provenance, not an inferred wild-type or GMO status. The observation does not imply production at every life stage or condition. + Ex-type culture CBS 209.63. Figure 7H-J and the primary taxonomic description document conidiogenous structures and conidia in basipetal chains. Microscopic descriptions use SNA after 14 days at 25 C in darkness. Specimen examined and Table 1 at https://pmc.ncbi.nlm.nih.gov/articles/PMC5679026/ identify Hennebert's 1959 isolate from timber in a cave at Han-sur-Lesse, Belgium. This is primary isolate provenance, not an inferred wild-type or GMO status. The observation does not imply production at every life stage or condition.

    • @@ -246,7 +247,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Retain phenotype METPO:1000059. Sporulation METPO:1000870 and spore forming METPO:1000871 concern endospores, whereas mycelial growth traitmech:000074 concerns bacterial hyphae. The four obsolete METPO conidium/conidia classes denote material entities, not an active organismal phenotype. PMID:9199700 documents bacterial conidium usage, so the fungal qualifier is intentional. Synnema formation traitmech:000656 is stalk aggregation and includes sporeless forms; neither trait is imposed as the other's is-a parent. Pseudohyphal growth traitmech:000653 is a cell arrangement, not equivalent to conidial production. Leave exact synonyms and xrefs unset pending authority and scope review; process ontology classes need not be exact organismal phenotypes.

    +

    Retain phenotype METPO:1000059. Sporulation METPO:1000870 and spore forming METPO:1000871 concern endospores, whereas mycelial growth traitmech:000074 concerns bacterial hyphae. The four obsolete METPO conidium/conidia classes denote material entities, not an active organismal phenotype. PMID:9199700 documents bacterial conidium usage, so the fungal qualifier is intentional. Synnema formation traitmech:000656 is stalk aggregation and includes sporeless forms; neither trait is imposed as the other's is-a parent. Pseudohyphal growth traitmech:000653 is a cell arrangement, not equivalent to conidial production. Leave exact synonyms and xrefs unset pending authority and scope review; process ontology classes need not be exact organismal phenotypes.

    @@ -340,7 +341,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -369,12 +379,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 03:33 UTC diff --git a/pages/traits/morphology/fungal_constricting_ring_formation.html b/pages/traits/morphology/fungal_constricting_ring_formation.html index c1d02116461..ad01c35c7e9 100644 --- a/pages/traits/morphology/fungal_constricting_ring_formation.html +++ b/pages/traits/morphology/fungal_constricting_ring_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1038/s41467-023-43235-w
    The R3 cell fuses with the S2 and R1 cells to complete CR formation
    -

    Chen et al. (2023), Results, Morphogenesis and development of CR; primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10651832/fullTextXML and actual Figure 1 inspected. CR means constricting ring; R1-R3 are ring cells and S1-S2 stalk cells. Wild-type Drechslerella dactyloides strain 29 (CGMCC3.20198) forms complete rings before becoming inflation-competent. Methods use water agar at 25 degrees C with Caenorhabditis elegans for induction, and nematodes or 55-degree-C water for inflation assays; a separate horse-serum protocol is also described. These are distinct assay conditions, not universal requirements. Figure 1 separates immature-ring escape from mature-ring capture. Neither formation alone nor a circular outline proves immediate capture competence.

    +

    Chen et al. (2023), Results, Morphogenesis and development of CR; primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10651832/fullTextXML and actual Figure 1 inspected. CR means constricting ring; R1-R3 are ring cells and S1-S2 stalk cells. Wild-type Drechslerella dactyloides strain 29 (CGMCC3.20198) forms complete rings before becoming inflation-competent. Methods use water agar at 25 degrees C with Caenorhabditis elegans for induction, and nematodes or 55-degree-C water for inflation assays; a separate horse-serum protocol is also described. These are distinct assay conditions, not universal requirements. Figure 1 separates immature-ring escape from mature-ring capture. Neither formation alone nor a circular outline proves immediate capture competence.

  • DOI:10.3897/BDJ.10.e96642
    Both of them produce constricting rings to capture nematodes.
    -

    Zhang et al. (2022; published 16 December), scientific abstract, New information; primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9836436/fullTextXML. The two taxa are Drechslerella daliensis and D. xiaguanensis. Methods, taxon descriptions and actual Figure 1e were inspected. Soil isolates were purified by single-spore transfers; trapping structures were induced on corn meal agar observation plates at 26 degrees C using Panagrellus redivivus. Descriptions distinguish three-celled constricting rings from adhesive trapping devices. Figure 1e shows an uninflated ring, not time-resolved inflation. The taxon-name validity caveat is retained in the example.

    +

    Zhang et al. (2022; published 16 December), scientific abstract, New information; primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9836436/fullTextXML. The two taxa are Drechslerella daliensis and D. xiaguanensis. Methods, taxon descriptions and actual Figure 1e were inspected. Soil isolates were purified by single-spore transfers; trapping structures were induced on corn meal agar observation plates at 26 degrees C using Panagrellus redivivus. Descriptions distinguish three-celled constricting rings from adhesive trapping devices. Figure 1e shows an uninflated ring, not time-resolved inflation. The taxon-name validity caveat is retained in the example.

  • DOI:10.1016/j.devcel.2014.04.021
    Cytokinesis involves constriction of a contractile actomyosin ring.
    -

    Stachowiak et al. (2014), scientific abstract retrieved from Europe PMC for PMID:24914559, and primary article https://pmc.ncbi.nlm.nih.gov/articles/PMC4137230/. Results explicitly use constricting-ring terminology for intracellular actomyosin rings in fission-yeast protoplasts. This is terminology-boundary evidence, not another positive nematode-trap observation. The trap qualifier excludes this unrelated cellular structure; no cytokinesis mechanism, protein grounding or canonical example is transferred.

    +

    Stachowiak et al. (2014), scientific abstract retrieved from Europe PMC for PMID:24914559, and primary article https://pmc.ncbi.nlm.nih.gov/articles/PMC4137230/. Results explicitly use constricting-ring terminology for intracellular actomyosin rings in fission-yeast protoplasts. This is terminology-boundary evidence, not another positive nematode-trap observation. The trap qualifier excludes this unrelated cellular structure; no cytokinesis mechanism, protein grounding or canonical example is transferred.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.3897/BDJ.10.e96642 - Source-named D. daliensis, holotype culture CGMCC3.20131, isolated from burned forest soil at Cangshan Mountain, Dali, Yunnan, China, collected 25 July 2017. The primary taxon treatment and Figure 1e directly document three-celled constricting rings. Morphology and ITS, TEF1-alpha and RPB2 analyses support the study's identification. Live NCBI https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=2743661 resolves rank species but retains the nomenclatural qualifier nom. inval.; this is not a claim that the fungal name is validly published. The example is restricted to the observed culture and induction conditions, not every isolate or successful field biocontrol. + Source-named D. daliensis, holotype culture CGMCC3.20131, isolated from burned forest soil at Cangshan Mountain, Dali, Yunnan, China, collected 25 July 2017. The primary taxon treatment and Figure 1e directly document three-celled constricting rings. Morphology and ITS, TEF1-alpha and RPB2 analyses support the study's identification. Live NCBI https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=2743661 resolves rank species but retains the nomenclatural qualifier nom. inval.; this is not a claim that the fungal name is validly published. The example is restricted to the observed culture and induction conditions, not every isolate or successful field biocontrol. @@ -240,7 +241,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Parent phenotype METPO:1000059 is broader than this multicellular differentiation phenotype. Ring shaped METPO:1000680 denotes individual cell geometry, not a three-cell trapping apparatus. Mycelial growth and hyphal anastomosis alone do not define this trap. Exclude adhesive non-constricting rings, adhesive nets and generic nematophagy; neither a taxonomic genus nor prey capture by any mechanism is an exact synonym. Formation includes morphologically complete immature rings, not only already inflated traps. Do not infer that every formed ring immediately inflates. No xrefs, synonyms, SSSOM mappings or organism-level disjointness are asserted; closer hierarchy remains open. Stachowiak et al. (2014), DOI:10.1016/j.devcel.2014.04.021, also use constricting-ring terminology for fission-yeast cytokinesis. The trap-qualified label explicitly excludes those intracellular actomyosin rings; they are not synonyms or phenotype evidence here.

    +

    Parent phenotype METPO:1000059 is broader than this multicellular differentiation phenotype. Ring shaped METPO:1000680 denotes individual cell geometry, not a three-cell trapping apparatus. Mycelial growth and hyphal anastomosis alone do not define this trap. Exclude adhesive non-constricting rings, adhesive nets and generic nematophagy; neither a taxonomic genus nor prey capture by any mechanism is an exact synonym. Formation includes morphologically complete immature rings, not only already inflated traps. Do not infer that every formed ring immediately inflates. No xrefs, synonyms, SSSOM mappings or organism-level disjointness are asserted; closer hierarchy remains open. Stachowiak et al. (2014), DOI:10.1016/j.devcel.2014.04.021, also use constricting-ring terminology for fission-yeast cytokinesis. The trap-qualified label explicitly excludes those intracellular actomyosin rings; they are not synonyms or phenotype evidence here.

    @@ -322,7 +323,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Qualify constricting-ring trap label after adversarial review -

      Addressed #1823 by adding trap to the label and explicit exclusion of intracellular actomyosin rings. Added DOI:10.1016/j.devcel.2014.04.021 with a verified scientific-abstract snippet as terminology-boundary evidence, not a third positive trap study. Preserved the original CREATE record history/records/fungal_constricting_ring_formation/2026-10-08T085642Z-codex-ff4ed3.yaml and initial TraitRecord event; appended the correction. Definition, ID, natural example, parent and block reservation unchanged.

    +

    Addressed #1823 by adding trap to the label and explicit exclusion of intracellular actomyosin rings. Added DOI:10.1016/j.devcel.2014.04.021 with a verified scientific-abstract snippet as terminology-boundary evidence, not a third positive trap study. Preserved the original CREATE record history/records/fungal_constricting_ring_formation/2026-10-08T085642Z-codex-ff4ed3.yaml and initial TraitRecord event; appended the correction. Definition, ID, natural example, parent and block reservation unchanged.

    • Read this curation session
  • @@ -360,7 +361,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -389,12 +399,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-13 13:33 UTC diff --git a/pages/traits/morphology/fungal_hartig_net_formation.html b/pages/traits/morphology/fungal_hartig_net_formation.html index 2bba4169e91..d7b373dac31 100644 --- a/pages/traits/morphology/fungal_hartig_net_formation.html +++ b/pages/traits/morphology/fungal_hartig_net_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -61,13 +62,13 @@

    Trait evidence (3)

    DOI:10.1111/nph.15113
    a loose hyphal weft has been formed between two rhizodermal cells to differentiate an intraradicular hyphal network, the so-called Hartig net
    -

    Zhang et al. (2018), Introduction, printed/physical p. 1, early-view author PDF: https://ri.conicet.gov.ar/bitstream/handle/11336/117651/CONICET_Digital_Nro.2f10e756-314d-4409-8829-81a4798588b0_A.pdf?isAllowed=y&sequence=2 The contiguous clause was exact-matched after joining PDF line wraps and hyphenated line breaks, and visually checked. Main text and actual Figure 2 on p. 7 were inspected. Panel d shows wild-type S238N root sections; panel c retains a thinner RNAi A4 network, not its absence. Other images and supplementary contents were not inspected.

    +

    Zhang et al. (2018), Introduction, printed/physical p. 1, early-view author PDF: https://ri.conicet.gov.ar/bitstream/handle/11336/117651/CONICET_Digital_Nro.2f10e756-314d-4409-8829-81a4798588b0_A.pdf?isAllowed=y&sequence=2 The contiguous clause was exact-matched after joining PDF line wraps and hyphenated line breaks, and visually checked. Main text and actual Figure 2 on p. 7 were inspected. Panel d shows wild-type S238N root sections; panel c retains a thinner RNAi A4 network, not its absence. Other images and supplementary contents were not inspected.

  • DOI:10.1007/s00572-014-0590-7
    Hartig net around epidermal cells para-epidermal in one row; hyphal cells roundish to cylindrical.
    -

    Kuehdorf et al. (2015; online 2014), Results, Anatomical characters of longitudinal section, printed p. 112 / physical p. 4: https://d-nb.info/1192098684/34 Complete contiguous descriptive sentence, exact-matched and visually checked. Main text through Discussion and actual Figure 3 on p. 114 were read. Panels e-f distinguish the Hartig net from intracellular hyphae in field-collected Leotia cf. lubrica-Comarostaphylis arbutoides roots. Anatomy was restricted to subgroup e; it does not identify every Leotia sample or the separately observed fruit bodies. No species-level canonical example or nutrient flux is inferred. Other figure images were not inspected.

    +

    Kuehdorf et al. (2015; online 2014), Results, Anatomical characters of longitudinal section, printed p. 112 / physical p. 4: https://d-nb.info/1192098684/34 Complete contiguous descriptive sentence, exact-matched and visually checked. Main text through Discussion and actual Figure 3 on p. 114 were read. Panels e-f distinguish the Hartig net from intracellular hyphae in field-collected Leotia cf. lubrica-Comarostaphylis arbutoides roots. Anatomy was restricted to subgroup e; it does not identify every Leotia sample or the separately observed fruit bodies. No species-level canonical example or nutrient flux is inferred. Other figure images were not inspected.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1111/nph.15113 - Wild-type S238N, not an RNAi line or its haploid S238N-H82 progeny. Zhang (2018) Figure 2d documents the Hartig net in hybrid poplar INRA 717-1-B4 roots three weeks after contact; Methods specifies low-glucose Pachlewski medium. The laboratory provenance page https://mycor.iam.inrae.fr/IAM/?page_id=4555 traces S238N to a 1976 Crater Lake, Oregon fruitbody collection under Tsuga mertensiana. NCBI EFetch confirms species 29883 and child strain 486041 S238N-H82; the child is not substituted for the experimental culture. This qualified example is not independent reidentification or evidence for all strains and conditions. + Wild-type S238N, not an RNAi line or its haploid S238N-H82 progeny. Zhang (2018) Figure 2d documents the Hartig net in hybrid poplar INRA 717-1-B4 roots three weeks after contact; Methods specifies low-glucose Pachlewski medium. The laboratory provenance page https://mycor.iam.inrae.fr/IAM/?page_id=4555 traces S238N to a 1976 Crater Lake, Oregon fruitbody collection under Tsuga mertensiana. NCBI EFetch confirms species 29883 and child strain 486041 S238N-H82; the child is not substituted for the experimental culture. This qualified example is not independent reidentification or evidence for all strains and conditions. @@ -240,7 +241,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Use active phenotype METPO:1000059 under quality METPO:1000188. METPO:1000198 mycorrhization is obsolete. Branched shaped METPO:1000687 concerns cell shape; mycelial growth traitmech:000074 is explicitly bacterial. Arbuscule formation 000664 and peloton formation 000666 concern intracellular architectures; BAS formation 000665 is extraradical. Haustorium formation 000663 is not asserted exact, broader or disjoint. Ecological symbiosis, mutualism and endosymbiosis are not this network morphology. Arbutoid usage is directly supported above. The directly retrieved PubMed abstract for DOI:10.1007/s00572-004-0305-6 (PMID:15490255) also describes paraepidermal Hartig nets in field-collected Monotropa uniflora and Pterospora andromedea roots; its full text and figures remain unread, and no fungal taxon is inferred. The label is not restricted to one mycorrhizal category, root cell layer or host species. No exact synonyms, structure xrefs or SSSOM equivalences are asserted; a bare Hartig net names a structure, not its formation.

    +

    Use active phenotype METPO:1000059 under quality METPO:1000188. METPO:1000198 mycorrhization is obsolete. Branched shaped METPO:1000687 concerns cell shape; mycelial growth traitmech:000074 is explicitly bacterial. Arbuscule formation 000664 and peloton formation 000666 concern intracellular architectures; BAS formation 000665 is extraradical. Haustorium formation 000663 is not asserted exact, broader or disjoint. Ecological symbiosis, mutualism and endosymbiosis are not this network morphology. Arbutoid usage is directly supported above. The directly retrieved PubMed abstract for DOI:10.1007/s00572-004-0305-6 (PMID:15490255) also describes paraepidermal Hartig nets in field-collected Monotropa uniflora and Pterospora andromedea roots; its full text and figures remain unread, and no fungal taxon is inferred. The label is not restricted to one mycorrhizal category, root cell layer or host species. No exact synonyms, structure xrefs or SSSOM equivalences are asserted; a bare Hartig net names a structure, not its formation.

    @@ -270,7 +271,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    No universal nutrient-transfer rate, mutualistic outcome or cell-wall mechanism is part of the definition. Native RNAi perturbations are evidence leads, not proof that the entire network is absent; heterologous and purified-protein assays are separate. DOI:10.1111/nph.18358, directly read main text and actual Figures 3 and 8, reports shallower RNAi networks and deeper overexpression networks despite lower overall ectomycorrhizal frequency. Its T89 host is not INRA 717-1-B4, and Figure 8a/c are schematics. A causal graph is deferred pending authority-verified proteins and sequence-to-culture links, not because mechanisms are biologically absent. Keep S238N distinct from H82 reference/progeny material. The laboratory history calls an Oregon-derived antecedent S238-O, whereas DOI:10.7150/jgen.130158 assigns S238O to Quebec; those source-specific aliases are not silently equated.

    +

    No universal nutrient-transfer rate, mutualistic outcome or cell-wall mechanism is part of the definition. Native RNAi perturbations are evidence leads, not proof that the entire network is absent; heterologous and purified-protein assays are separate. DOI:10.1111/nph.18358, directly read main text and actual Figures 3 and 8, reports shallower RNAi networks and deeper overexpression networks despite lower overall ectomycorrhizal frequency. Its T89 host is not INRA 717-1-B4, and Figure 8a/c are schematics. A causal graph is deferred pending authority-verified proteins and sequence-to-culture links, not because mechanisms are biologically absent. Keep S238N distinct from H82 reference/progeny material. The laboratory history calls an Oregon-derived antecedent S238-O, whereas DOI:10.7150/jgen.130158 assigns S238O to Quebec; those source-specific aliases are not silently equated.

    @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 18:23 UTC diff --git a/pages/traits/morphology/fungal_internal_mycorrhizal_vesicle_formation.html b/pages/traits/morphology/fungal_internal_mycorrhizal_vesicle_formation.html index 903858fbce8..d1ec92147dd 100644 --- a/pages/traits/morphology/fungal_internal_mycorrhizal_vesicle_formation.html +++ b/pages/traits/morphology/fungal_internal_mycorrhizal_vesicle_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -61,13 +62,13 @@

    Trait evidence (3)

    DOI:10.1139/m75-258
    Mature vesicles were engorged with lipid droplets, possessed a trilaminate wall and were also enclosed by host wall material and cytoplasm.
    -

    Kinden and Brown (1975), PMID:172206; directly retrieved scientific abstract from Europe PMC. Electron microscopy of yellow-poplar mycorrhizal roots supports intracellular vesicles and lipid accumulation. Full text and actual micrographs were not inspected; the abstract does not name the fungus, so no taxon is inferred from historical MeSH. Trilaminate walls are this observation, not a universal definition. Nutrient release after degeneration is the authors' hypothesis, not measured transfer.

    +

    Kinden and Brown (1975), PMID:172206; directly retrieved scientific abstract from Europe PMC. Electron microscopy of yellow-poplar mycorrhizal roots supports intracellular vesicles and lipid accumulation. Full text and actual micrographs were not inspected; the abstract does not name the fungus, so no taxon is inferred from historical MeSH. Trilaminate walls are this observation, not a universal definition. Nutrient release after degeneration is the authors' hypothesis, not measured transfer.

  • DOI:10.3390/plants8060142
    C. etunicatum and R. intraradices formed vesicles at 25 days post-sowing (dps)
    -

    Kobae et al. (2019), PMID:31151150, PMC6631804; Results 2.2 clause checked against the primary full-text XML and https://rakuno.repo.nii.ac.jp/record/6472/files/R-2020-321_kobae.pdf. Methods 3.1-3.3 and actual supplementary Figure S1 were inspected. The top two S1 panels separately label vesicles and arbuscules in young Marchantia paleacea thalli for MAFF520053 and MAFF520059, with 20-micrometer bars. WGA-HRP and DAB visualize fungal cell walls, not lipid chemistry. This is direct vesicle morphology, not an independent lipid assay or universal 25-day onset. The other panels' missing vesicle labels do not establish absence. The paper's DAOM197198 arbuscule-timing discrepancy concerns a separate culture and readout, not a resolved vesicle onset.

    +

    Kobae et al. (2019), PMID:31151150, PMC6631804; Results 2.2 clause checked against the primary full-text XML and https://rakuno.repo.nii.ac.jp/record/6472/files/R-2020-321_kobae.pdf. Methods 3.1-3.3 and actual supplementary Figure S1 were inspected. The top two S1 panels separately label vesicles and arbuscules in young Marchantia paleacea thalli for MAFF520053 and MAFF520059, with 20-micrometer bars. WGA-HRP and DAB visualize fungal cell walls, not lipid chemistry. This is direct vesicle morphology, not an independent lipid assay or universal 25-day onset. The other panels' missing vesicle labels do not establish absence. The paper's DAOM197198 arbuscule-timing discrepancy concerns a separate culture and readout, not a resolved vesicle onset.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.3390/plants8060142 - MAFF520053 (H1-1), reported as Claroideoglomus etunicatum, forms vesicles in Marchantia paleacea thalli (Results 2.2; actual Figure S1). Methods 3.2 uses 1 g MAFF inoculum below approximately 100 gemmae per pot, at 26 C with 16 h light/day; Results reports 25 days post-sowing. The directly checked NARO collection record https://www.gene.affrc.go.jp/databases-micro_search_detail_en.php?maff=520053 lists soybean-field soil, Tokyo, October 1987 and H. Hirata as separate fields, and deposition as Glomus etunicatum. These are provenance, not a composite quote or independent trait evidence. NCBI Taxonomy resolves 937382 to Entrophospora etunicata with Claroideoglomus etunicatum as a homotypic synonym. Name correspondence is not reidentification. The directly read Table 1 and Results of DOI:10.1264/jsme2.ME25040 retain H1-1/520053; primer-dependent ASV resolution does not independently prove every culture's identity or a vesicle phenotype. Its figures and supplements were not inspected. The example is culture- and condition-qualified, not an assertion about all strains. + MAFF520053 (H1-1), reported as Claroideoglomus etunicatum, forms vesicles in Marchantia paleacea thalli (Results 2.2; actual Figure S1). Methods 3.2 uses 1 g MAFF inoculum below approximately 100 gemmae per pot, at 26 C with 16 h light/day; Results reports 25 days post-sowing. The directly checked NARO collection record https://www.gene.affrc.go.jp/databases-micro_search_detail_en.php?maff=520053 lists soybean-field soil, Tokyo, October 1987 and H. Hirata as separate fields, and deposition as Glomus etunicatum. These are provenance, not a composite quote or independent trait evidence. NCBI Taxonomy resolves 937382 to Entrophospora etunicata with Claroideoglomus etunicatum as a homotypic synonym. Name correspondence is not reidentification. The directly read Table 1 and Results of DOI:10.1264/jsme2.ME25040 retain H1-1/520053; primer-dependent ASV resolution does not independently prove every culture's identity or a vesicle phenotype. Its figures and supplements were not inspected. The example is culture- and condition-qualified, not an assertion about all strains. @@ -302,7 +303,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add source-qualified fungal internal mycorrhizal vesicle formation -

      Minted traitmech:000670, PROPOSED MORPHOLOGY, and v546 block 1062300-1062399. Two primary DOI sources (10.1139/m75-258 and 10.3390/plants8060142), attributed Brundrett terminology and three verbatim snippets support plant-tissue vesicle formation. Direct S1 microscopy and separately verified NARO/NCBI provenance qualify MAFF520053 under NCBITaxon:937382; the 2025 identification study supplies provenance context, not trait evidence. Internal does not mean root-only, intercellular-only or membrane vesicles. No exact mappings or protein mechanism are asserted. Ignored/hidden searches cover all worktrees, current main, complete pending PR heads and CommunityMech; neighboring definitions were reviewed. Existing trait records remain unchanged. Initial writer dry run and 20 focused writer tests passed; broader gates pending.

    +

    Minted traitmech:000670, PROPOSED MORPHOLOGY, and v546 block 1062300-1062399. Two primary DOI sources (10.1139/m75-258 and 10.3390/plants8060142), attributed Brundrett terminology and three verbatim snippets support plant-tissue vesicle formation. Direct S1 microscopy and separately verified NARO/NCBI provenance qualify MAFF520053 under NCBITaxon:937382; the 2025 identification study supplies provenance context, not trait evidence. Internal does not mean root-only, intercellular-only or membrane vesicles. No exact mappings or protein mechanism are asserted. Ignored/hidden searches cover all worktrees, current main, complete pending PR heads and CommunityMech; neighboring definitions were reviewed. Existing trait records remain unchanged. Initial writer dry run and 20 focused writer tests passed; broader gates pending.

    • Read this curation session @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 23:14 UTC diff --git a/pages/traits/morphology/fungal_mycelial_cord_formation.html b/pages/traits/morphology/fungal_mycelial_cord_formation.html index f5f126040cd..fa124e04995 100644 --- a/pages/traits/morphology/fungal_mycelial_cord_formation.html +++ b/pages/traits/morphology/fungal_mycelial_cord_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1007/s10267-008-0450-4
    the whole organ does not extend apically; rather, it develops behind a mycelial margin of diffuse hyphae
    -

    Boddy et al. (2009), Introduction, printed p. 10; contiguous clause whose antecedent is mature mycelial cords. Directly read and visually checked in the author PDF: https://markfricker.org/wp-content/uploads/2015/12/boddy_et_al-2009-mycoscience-50-9.pdf This review supplies the operational terminology adopted here, not independent experimental replication. First three pages and Figure 1 were inspected; remaining figures and supplements were not.

    +

    Boddy et al. (2009), Introduction, printed p. 10; contiguous clause whose antecedent is mature mycelial cords. Directly read and visually checked in the author PDF: https://markfricker.org/wp-content/uploads/2015/12/boddy_et_al-2009-mycoscience-50-9.pdf This review supplies the operational terminology adopted here, not independent experimental replication. First three pages and Figure 1 were inspected; remaining figures and supplements were not.

  • DOI:10.1099/00221287-132-1-203
    Both fungi grew out radially from the inoculum blocks in the form of networks of mycelial cords.
    -

    Dowson, Rayner and Boddy (1986), complete abstract sentence, visually verified in the original-paper reprint: https://www.davidmoore.org.uk/21st_century_guidebook_to_fungi_platinum/REPRINT_collection/Dowson_etal_mycelia_cord-forming_basidiomycetes.pdf All nine pages of text and actual Figures 1 and 3 were inspected. The Introduction describes predominantly parallel, longitudinally aligned hyphal aggregates. Underside photocopies show network development, not microscopic proof of internal anatomy. Inoculum size and culture age are confounded. Other figure images were not inspected.

    +

    Dowson, Rayner and Boddy (1986), complete abstract sentence, visually verified in the original-paper reprint: https://www.davidmoore.org.uk/21st_century_guidebook_to_fungi_platinum/REPRINT_collection/Dowson_etal_mycelia_cord-forming_basidiomycetes.pdf All nine pages of text and actual Figures 1 and 3 were inspected. The Introduction describes predominantly parallel, longitudinally aligned hyphal aggregates. Underside photocopies show network development, not microscopic proof of internal anatomy. Inoculum size and culture age are confounded. Other figure images were not inspected.

  • DOI:10.1016/j.mycres.2006.05.013
    After 99 d, all systems had produced distinct mycelial cords
    -

    Wood et al. (2006), PMID:16891104; contiguous scientific-abstract clause retrieved directly through Europe PMC. The following clause describes regression of diffuse mycelium and thinner cords. This soil-microcosm experiment supports formation and remodeling, not a universal 99-day onset. Full text, figures and strain provenance were not inspected; no additional canonical isolate is inferred.

    +

    Wood et al. (2006), PMID:16891104; contiguous scientific-abstract clause retrieved directly through Europe PMC. The following clause describes regression of diffuse mycelium and thinner cords. This soil-microcosm experiment supports formation and remodeling, not a universal 99-day onset. Full text, figures and strain provenance were not inspected; no additional canonical isolate is inferred.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1099/00221287-132-1-203 - The unnumbered isolate in Dowson et al. (1986), Methods p. 204 at https://doi.org/10.1099/00221287-132-1-203, originated from decayed Fagus sylvatica wood at Farleigh Hungerford Woods, Wiltshire, UK (ST795563). Colonized beech blocks produced cords on moist unsterile sandy loam at 20 C in darkness; actual Figure 1d-f shows controls at 8, 12 and 44 days. NCBI EFetch confirms species 194680. No later collection number or all-strain claim is inferred. + The unnumbered isolate in Dowson et al. (1986), Methods p. 204 at https://doi.org/10.1099/00221287-132-1-203, originated from decayed Fagus sylvatica wood at Farleigh Hungerford Woods, Wiltshire, UK (ST795563). Colonized beech blocks produced cords on moist unsterile sandy loam at 20 C in darkness; actual Figure 1d-f shows controls at 8, 12 and 44 days. NCBI EFetch confirms species 194680. No later collection number or all-strain claim is inferred. @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 22:18 UTC diff --git a/pages/traits/morphology/fungal_nematode_trap_formation.html b/pages/traits/morphology/fungal_nematode_trap_formation.html index 03b342221d8..b4f5dd72f21 100644 --- a/pages/traits/morphology/fungal_nematode_trap_formation.html +++ b/pages/traits/morphology/fungal_nematode_trap_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.1016/j.isci.2020.101057
    Nematode-trapping fungi (NTF) can switch to pathogens by producing various trapping devices to capture nematodes.
    -

    Ji et al. 2020, scientific Summary; PMID:32339992. Direct primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7186526/fullTextXML and actual Figure 1 inspected. Introduction and Results group constricting rings, adhesive networks, columns and knobs as four representative devices, not an exhaustive taxonomy. Selected Transparent Methods and actual PDF pages 8, 11, 12, 15 and 16 were inspected; not every supplement figure or dataset. The main Introduction describes serial column cells while PDF 12 allows one or more; that narrower child-scope question remains open. Adhesion-gene expansion and expression correlations do not establish a universal molecular mechanism or sequence-only phenotype prediction. Native abstract verifier: VERIFIED.

    +

    Ji et al. 2020, scientific Summary; PMID:32339992. Direct primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7186526/fullTextXML and actual Figure 1 inspected. Introduction and Results group constricting rings, adhesive networks, columns and knobs as four representative devices, not an exhaustive taxonomy. Selected Transparent Methods and actual PDF pages 8, 11, 12, 15 and 16 were inspected; not every supplement figure or dataset. The main Introduction describes serial column cells while PDF 12 allows one or more; that narrower child-scope question remains open. Adhesion-gene expansion and expression correlations do not establish a universal molecular mechanism or sequence-only phenotype prediction. Native abstract verifier: VERIFIED.

  • DOI:10.1371/journal.ppat.1002179
    A. oligospora forms adhesive networks to capture nematodes
    -

    Yang et al. 2011, Author Summary, not the scientific abstract; PMID:21909256. Direct primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3164635/fullTextXML and actual Figure 1 inspected. Panel I shows interconnected loops; the caption distinguishes formation, attraction, adhesion, capture, penetration and digestion. These are separate endpoints, not automatic consequences of an observed shape. This parent curation did not renew the full Methods/supplement audit retained by the net child. The old teleomorph wording is not imported as a current taxonomic equivalence. Shares authors with Ji 2020, not independent-laboratory replication. Native verifier: NOT_IN_ABSTRACT; the Author Summary span matches directly.

    +

    Yang et al. 2011, Author Summary, not the scientific abstract; PMID:21909256. Direct primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3164635/fullTextXML and actual Figure 1 inspected. Panel I shows interconnected loops; the caption distinguishes formation, attraction, adhesion, capture, penetration and digestion. These are separate endpoints, not automatic consequences of an observed shape. This parent curation did not renew the full Methods/supplement audit retained by the net child. The old teleomorph wording is not imported as a current taxonomic equivalence. Shares authors with Ji 2020, not independent-laboratory replication. Native verifier: NOT_IN_ABSTRACT; the Author Summary span matches directly.

  • DOI:10.1038/s41467-023-43235-w
    CRs differentiate from hyphae and develop two basal stalk cells (S1 and S2) and three distal ring cells (R1, R2, and R3)
    -

    Chen et al. 2023, Results, Morphogenesis and development of CR; PMID:37968349. CR means constricting ring. Primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10651832/fullTextXML, relevant formation/inflation Methods and actual Figure 1 inspected. Strain 29 (CGMCC3.20198) forms morphologically complete rings before inflation competence; panels l/m contrast immature-ring escape with mature-ring capture. Water-agar induction with C. elegans, horse-serum formation and hot-water inflation are distinct assays, not universal requirements. Later protein-mechanism figures and supplements were not fully audited; the incomplete supplementary ZIP is not evidence. No universal SNARE dependency or natural-strain exemplar is inferred. Native verifier: NOT_IN_ABSTRACT; the Results span matches directly.

    +

    Chen et al. 2023, Results, Morphogenesis and development of CR; PMID:37968349. CR means constricting ring. Primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10651832/fullTextXML, relevant formation/inflation Methods and actual Figure 1 inspected. Strain 29 (CGMCC3.20198) forms morphologically complete rings before inflation competence; panels l/m contrast immature-ring escape with mature-ring capture. Water-agar induction with C. elegans, horse-serum formation and hot-water inflation are distinct assays, not universal requirements. Later protein-mechanism figures and supplements were not fully audited; the incomplete supplementary ZIP is not evidence. No universal SNARE dependency or natural-strain exemplar is inferred. Native verifier: NOT_IN_ABSTRACT; the Results span matches directly.

  • DOI:10.1007/s102670200061
    A nonconstricting ring (arrow) is capturing a nematode (asterisk).
    -

    Saikawa and Takahashi 2002, Figure 8 caption, page 418. All three pages and actual Figures 1-20 inspected at https://www.jstage.jst.go.jp/article/mycosci/43/5/43_MYC43417/_pdf. Figures 8-14 and 15-20 document nonconstricting rings in source-named Dactylella leptospora and Dactylaria candida; Figures 1-7 show the constricting comparator. Curved hyphal branches form the traps. The observations support inclusion of nonconstricting rings, not universal stalk lengths, culture conditions or adhesion proteins. Adhesive ultrastructure is attributed to earlier work, not newly imaged here. DOI/title reconciled against Crossref. Native verifier: UNRESOLVED with no result for that exact DOI query; the caption matches directly. This does not assert that the paper is unindexed everywhere.

    +

    Saikawa and Takahashi 2002, Figure 8 caption, page 418. All three pages and actual Figures 1-20 inspected at https://www.jstage.jst.go.jp/article/mycosci/43/5/43_MYC43417/_pdf. Figures 8-14 and 15-20 document nonconstricting rings in source-named Dactylella leptospora and Dactylaria candida; Figures 1-7 show the constricting comparator. Curved hyphal branches form the traps. The observations support inclusion of nonconstricting rings, not universal stalk lengths, culture conditions or adhesion proteins. Adhesive ultrastructure is attributed to earlier work, not newly imaged here. DOI/title reconciled against Crossref. Native verifier: UNRESOLVED with no result for that exact DOI query; the caption matches directly. This does not assert that the paper is unindexed everywhere.

    • @@ -142,7 +143,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -332,7 +333,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -361,12 +371,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-13 13:33 UTC diff --git a/pages/traits/morphology/fungal_nonconstricting_ring_trap_formation.html b/pages/traits/morphology/fungal_nonconstricting_ring_trap_formation.html index a5c50843c43..89421f63a51 100644 --- a/pages/traits/morphology/fungal_nonconstricting_ring_trap_formation.html +++ b/pages/traits/morphology/fungal_nonconstricting_ring_trap_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1007/s102670200061
    A nonconstricting ring (arrow) is capturing a nematode (asterisk).
    -

    Saikawa and Takahashi (2002), Figure 8 caption, page 418; all three pages and actual Figures 1-20 directly inspected at https://www.jstage.jst.go.jp/article/mycosci/43/5/43_MYC43417/_pdf. Time-lapse microscopy distinguishes noninflating three-cell rings in Dactylella leptospora and Dactylaria candida from the inflating Arthrobotrys dactyloides comparator. Figures 8-14 and 15-20 show the former taxa; Figures 1-7 show the comparator. Hook-tip fusion lacks the opposing bud seen in that comparator; stalk lengths vary. Adhesive ultrastructure is attributed to Saikawa (1985), not newly imaged here. These morphological observations do not identify causal proteins.

    +

    Saikawa and Takahashi (2002), Figure 8 caption, page 418; all three pages and actual Figures 1-20 directly inspected at https://www.jstage.jst.go.jp/article/mycosci/43/5/43_MYC43417/_pdf. Time-lapse microscopy distinguishes noninflating three-cell rings in Dactylella leptospora and Dactylaria candida from the inflating Arthrobotrys dactyloides comparator. Figures 8-14 and 15-20 show the former taxa; Figures 1-7 show the comparator. Hook-tip fusion lacks the opposing bud seen in that comparator; stalk lengths vary. Adhesive ultrastructure is attributed to Saikawa (1985), not newly imaged here. These morphological observations do not identify causal proteins.

  • DOI:10.1016/j.mycres.2006.04.011
    D. varietas forms both adhesive knobs and non-constricting rings
    -

    Li et al. (2006), scientific Abstract, directly retrieved as published abstract XML for PMID:16876699 at https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=16876699&retmode=xml. Abstract-only access: full Methods and figures were not retrieved. The independent description of Dactylellina sichuanensis and D. varietas from China reports capture with knobs and nonconstricting rings. The quoted clause contrasts D. varietas with nontrapping Dactylella oxyspora. Co-occurring trap types are not disjoint organism categories. The sequence analyses concern taxonomy, not a sequence-predicted trapping phenotype; no current taxonomic equivalence for those new taxa is asserted.

    +

    Li et al. (2006), scientific Abstract, directly retrieved as published abstract XML for PMID:16876699 at https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=16876699&retmode=xml. Abstract-only access: full Methods and figures were not retrieved. The independent description of Dactylellina sichuanensis and D. varietas from China reports capture with knobs and nonconstricting rings. The quoted clause contrasts D. varietas with nontrapping Dactylella oxyspora. Co-occurring trap types are not disjoint organism categories. The sequence analyses concern taxonomy, not a sequence-predicted trapping phenotype; no current taxonomic equivalence for those new taxa is asserted.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Canonical examples DOI:10.1007/s102670200061 - Source-named Dactylella leptospora, natural TGU orchard-soil isolate collected June 1998. Observed on water agar at 18-22 degrees C with Rhabditis sp.; Figures 8-14 document capture and ring development. Live NCBI https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=430499 resolves rank species, exact label Dactylellina leptospora and synonym Dactylella leptospora. This is not a strain accession or an assertion about every isolate, universal culture conditions or field biocontrol. + Source-named Dactylella leptospora, natural TGU orchard-soil isolate collected June 1998. Observed on water agar at 18-22 degrees C with Rhabditis sp.; Figures 8-14 document capture and ring development. Live NCBI https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=430499 resolves rank species, exact label Dactylellina leptospora and synonym Dactylella leptospora. This is not a strain accession or an assertion about every isolate, universal culture conditions or field biocontrol. @@ -304,7 +305,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed fungal nonconstricting-ring trap formation -

      Added traitmech:000680 as a PROPOSED morphology class with Saikawa and Takahashi 2002 DOI:10.1007/s102670200061 and Li et al. 2006 DOI:10.1016/j.mycres.2006.04.011. Directly read the three-page primary microscopy paper and all figures; the second study is explicitly abstract-only. Added contiguous caption and abstract snippets, qualified natural TGU isolate example NCBITaxon:430499 at species rank, and open scope/parent and mechanism discussions. Kept formation, noninflating capture and molecular mechanism separate. Writer defaults to dry-run, validates before writing and refuses changed parent/target/proposal preimages; 20 focused tests passed. Ignored-and-hidden main, all worktrees, CommunityMech and complete paginated open-PR checks support local ID000680, cohort v556 and full METPO1063300-1063399 block. Prior records untouched. METPO placeholder is not a released term.

    +

    Added traitmech:000680 as a PROPOSED morphology class with Saikawa and Takahashi 2002 DOI:10.1007/s102670200061 and Li et al. 2006 DOI:10.1016/j.mycres.2006.04.011. Directly read the three-page primary microscopy paper and all figures; the second study is explicitly abstract-only. Added contiguous caption and abstract snippets, qualified natural TGU isolate example NCBITaxon:430499 at species rank, and open scope/parent and mechanism discussions. Kept formation, noninflating capture and molecular mechanism separate. Writer defaults to dry-run, validates before writing and refuses changed parent/target/proposal preimages; 20 focused tests passed. Ignored-and-hidden main, all worktrees, CommunityMech and complete paginated open-PR checks support local ID000680, cohort v556 and full METPO1063300-1063399 block. Prior records untouched. METPO placeholder is not a released term.

    • Read this curation session
  • @@ -342,7 +343,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -371,12 +381,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-13 13:33 UTC diff --git a/pages/traits/morphology/fungal_peloton_formation.html b/pages/traits/morphology/fungal_peloton_formation.html index 32f06ecef21..0dac5cc8e12 100644 --- a/pages/traits/morphology/fungal_peloton_formation.html +++ b/pages/traits/morphology/fungal_peloton_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1111/nph.14279
    In the colonised protocorm cells, ORM fungi form coiled hyphae, known as pelotons
    -

    Fochi et al. (2017), author final manuscript, Discussion, Nitrogen transfer inside the mycorrhizal orchid protocorm, printed p. 15 / physical p. 17, line 465: https://iris.unito.it/retrieve/e27ce429-fbc3-2581-e053-d805fe0acbaa/N_metabolism_ORM_rev10_4aperto.pdf Contiguous clause matched after removing standalone line numbers and joining PDF line wraps, and visually checked. The maintained resolver returned NOT_IN_ABSTRACT; this is a manual full-text check, not a resolver VERIFIED result. Main text through Conclusions and actual Figure 5 were inspected. Figure 5 shows intact and collapsed pelotons in Serapias vomeracea 30 days after sowing with Tulasnella calospora. The manuscript's title wording and GEO(XXXX) placeholder differ from final metadata; no dataset accession is inferred. Other figure images and supplementary contents were not inspected. Transcript patterns and heterologous yeast assays are not causal tests of native peloton formation.

    +

    Fochi et al. (2017), author final manuscript, Discussion, Nitrogen transfer inside the mycorrhizal orchid protocorm, printed p. 15 / physical p. 17, line 465: https://iris.unito.it/retrieve/e27ce429-fbc3-2581-e053-d805fe0acbaa/N_metabolism_ORM_rev10_4aperto.pdf Contiguous clause matched after removing standalone line numbers and joining PDF line wraps, and visually checked. The maintained resolver returned NOT_IN_ABSTRACT; this is a manual full-text check, not a resolver VERIFIED result. Main text through Conclusions and actual Figure 5 were inspected. Figure 5 shows intact and collapsed pelotons in Serapias vomeracea 30 days after sowing with Tulasnella calospora. The manuscript's title wording and GEO(XXXX) placeholder differ from final metadata; no dataset accession is inferred. Other figure images and supplementary contents were not inspected. Transcript patterns and heterologous yeast assays are not causal tests of native peloton formation.

  • DOI:10.1111/1365-2745.70188
    Ericoid hyphal coils (also called pelotons) are specific structures formed by ericoid fungi in root epidermal cells
    -

    Meyers et al. (2025), Table 1 continued, CCI row, Relevance column, p. 3681 / physical p. 4. The complete morphology clause was exact-matched and visually checked in the public publisher PDF deposited at https://freidok.uni-freiburg.de/data/273892; its SHA256 matches the repository checksum. This directly read usage supports ericoid scope, not an orchid-only definition. Methods 2.4 scores Vaccinium myrtillus root intersects, distinguishing coils from other intracellular hyphae; CCI is not a fungal cell fraction or measured nutrient flux. No fungal species was identified for a canonical example. Actual supplementary Figure S3 was not inspected. The resolver returned UNRESOLVED; an exact Europe PMC DOI query returned no hit and Crossref confirmed the exact DOI/title. Manual PDF verification does not change that resolver verdict.

    +

    Meyers et al. (2025), Table 1 continued, CCI row, Relevance column, p. 3681 / physical p. 4. The complete morphology clause was exact-matched and visually checked in the public publisher PDF deposited at https://freidok.uni-freiburg.de/data/273892; its SHA256 matches the repository checksum. This directly read usage supports ericoid scope, not an orchid-only definition. Methods 2.4 scores Vaccinium myrtillus root intersects, distinguishing coils from other intracellular hyphae; CCI is not a fungal cell fraction or measured nutrient flux. No fungal species was identified for a canonical example. Actual supplementary Figure S3 was not inspected. The resolver returned UNRESOLVED; an exact Europe PMC DOI query returned no hit and Crossref confirmed the exact DOI/title. Manual PDF verification does not change that resolver verdict.

  • DOI:10.1111/nph.19338
    tightly coiled intracellular fungal hyphae (i.e. pelotons) are a constant feature of OrM
    -

    Perotto and Balestrini, Viewpoint, online 2023, institutional early-view PDF: https://iris.unito.it/retrieve/b44ea427-adb1-4f5b-a5b6-cc876e060f2f/New%20Phytologist%20-%202023%20-%20Perotto%20-%20At%20the%20core%20of%20the%20endomycorrhizal%20symbioses%20intracellular%20fungal%20structures%20in%20orchid.pdf Printed/physical p. 2, The peloton: a constant feature in orchid mycorrhiza. Main text and actual Figures 1-3 were read; the contiguous clause was visually checked. This is review terminology, not independent experimental replication. The same page describes Paris-type AM coils as resembling orchid pelotons and discusses a continuum with arbusculate coils; resemblance is not exact equivalence. Figure 2 has inconsistent panel/scale labels, so no panel-specific dimensions are adopted. Its hypothesis of plant-driven development is not an established formation mechanism. The orchid discussion does not erase the separate ericoid usage in Meyers et al.

    +

    Perotto and Balestrini, Viewpoint, online 2023, institutional early-view PDF: https://iris.unito.it/retrieve/b44ea427-adb1-4f5b-a5b6-cc876e060f2f/New%20Phytologist%20-%202023%20-%20Perotto%20-%20At%20the%20core%20of%20the%20endomycorrhizal%20symbioses%20intracellular%20fungal%20structures%20in%20orchid.pdf Printed/physical p. 2, The peloton: a constant feature in orchid mycorrhiza. Main text and actual Figures 1-3 were read; the contiguous clause was visually checked. This is review terminology, not independent experimental replication. The same page describes Paris-type AM coils as resembling orchid pelotons and discusses a continuum with arbusculate coils; resemblance is not exact equivalence. Figure 2 has inconsistent panel/scale labels, so no panel-specific dimensions are adopted. Its hypothesis of plant-driven development is not an established formation mechanism. The orchid discussion does not erase the separate ericoid usage in Meyers et al.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1111/nph.14279 - AL13/4D = MUT4182 in Serapias vomeracea protocorms, oat medium, 20 C in darkness; actual Figure 5 documents pelotons 30 days after sowing. Fochi Methods, printed p. 4 / physical p. 6, https://iris.unito.it/retrieve/e27ce429-fbc3-2581-e053-d805fe0acbaa/N_metabolism_ORM_rev10_4aperto.pdf reports isolation from Anacamptis laxiflora mycorrhizal roots in northern Italy and deposition as MUT4182 (citing Girlanda et al. 2011, DOI:10.3732/ajb.1000486; that original isolation paper was not read). NCBI EFetch confirms species 156515 and child strain 1051891, Tulasnella calospora MUT 4182, with equivalent name Tulasnella calospora AL13/4D. The paper's engineered yeast complementation assay is a separate experiment, not an engineered fungal exemplar. This culture-qualified example is not independent taxonomic reidentification or evidence for every strain and condition. + AL13/4D = MUT4182 in Serapias vomeracea protocorms, oat medium, 20 C in darkness; actual Figure 5 documents pelotons 30 days after sowing. Fochi Methods, printed p. 4 / physical p. 6, https://iris.unito.it/retrieve/e27ce429-fbc3-2581-e053-d805fe0acbaa/N_metabolism_ORM_rev10_4aperto.pdf reports isolation from Anacamptis laxiflora mycorrhizal roots in northern Italy and deposition as MUT4182 (citing Girlanda et al. 2011, DOI:10.3732/ajb.1000486; that original isolation paper was not read). NCBI EFetch confirms species 156515 and child strain 1051891, Tulasnella calospora MUT 4182, with equivalent name Tulasnella calospora AL13/4D. The paper's engineered yeast complementation assay is a separate experiment, not an engineered fungal exemplar. This culture-qualified example is not independent taxonomic reidentification or evidence for every strain and condition. @@ -240,7 +241,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Use phenotype METPO:1000059. Spiral shaped METPO:1000684, branched shaped METPO:1000687 and filament shaped METPO:1000674 concern cell shape. Mycelial growth traitmech:000074 is explicitly bacterial. Fungal arbuscule formation traitmech:000664 concerns branched intracellular structures; hyphal anastomosis traitmech:000605 is fusion, pseudohyphal growth traitmech:000653 budding-cell chains, and haustorium formation traitmech:000663 a specialized host interface. None is an exact duplicate or settled closer parent. Fochi's orchid usage and Meyers' ericoid usage both inform the unqualified label. The review's Paris-type AM comparison does not make every intracellular coil a peloton or establish disjoint organisms. No exact synonyms, structure xrefs or SSSOM equivalences are asserted. Liverwort terminology in DOI:10.1098/rstb.2000.0617 remains an abstract-only analogy lead; its full text and figures were not inspected.

    +

    Use phenotype METPO:1000059. Spiral shaped METPO:1000684, branched shaped METPO:1000687 and filament shaped METPO:1000674 concern cell shape. Mycelial growth traitmech:000074 is explicitly bacterial. Fungal arbuscule formation traitmech:000664 concerns branched intracellular structures; hyphal anastomosis traitmech:000605 is fusion, pseudohyphal growth traitmech:000653 budding-cell chains, and haustorium formation traitmech:000663 a specialized host interface. None is an exact duplicate or settled closer parent. Fochi's orchid usage and Meyers' ericoid usage both inform the unqualified label. The review's Paris-type AM comparison does not make every intracellular coil a peloton or establish disjoint organisms. No exact synonyms, structure xrefs or SSSOM equivalences are asserted. Liverwort terminology in DOI:10.1098/rstb.2000.0617 remains an abstract-only analogy lead; its full text and figures were not inspected.

    @@ -270,7 +271,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    The phenotype does not require a measured nutrient flux, exclusive mutualism, a universal lifespan, or a specific plant-driven mechanism. Transcript associations and isolated transporter complementation do not establish the native formation pathway. Nutrient transfer before or during coil degeneration is a separate question from morphogenesis. A protein-resolved causal graph is deferred pending direct formation perturbations and authority-verified protein anchors; a mechanism is not claimed biologically absent. Keep the example's MUT4182 separate from Tulasnella sp. SV6 (MUT4178) studied in DOI:10.1186/s43008-024-00165-6: that paper uses AL13/4D as a reference genome, not as its culture.

    +

    The phenotype does not require a measured nutrient flux, exclusive mutualism, a universal lifespan, or a specific plant-driven mechanism. Transcript associations and isolated transporter complementation do not establish the native formation pathway. Nutrient transfer before or during coil degeneration is a separate question from morphogenesis. A protein-resolved causal graph is deferred pending direct formation perturbations and authority-verified protein anchors; a mechanism is not claimed biologically absent. Keep the example's MUT4182 separate from Tulasnella sp. SV6 (MUT4178) studied in DOI:10.1186/s43008-024-00165-6: that paper uses AL13/4D as a reference genome, not as its culture.

    @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 15:44 UTC diff --git a/pages/traits/morphology/fungal_rhizomorph_formation.html b/pages/traits/morphology/fungal_rhizomorph_formation.html index 99f0ae6303c..632eed57c1d 100644 --- a/pages/traits/morphology/fungal_rhizomorph_formation.html +++ b/pages/traits/morphology/fungal_rhizomorph_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.1016/j.fgb.2009.04.005
    Rhizomorphs of wood-decay basidiomycetes are root-like structures produced by the coordinated growth of thousands of hyphae.
    -

    Yafetto, Davis and Money (2009), PMID:19427390; scientific abstract retrieved directly through Europe PMC. The naming sentence supports the formation phenotype, not a universal hyphal-count threshold. Armillaria gallica cultures were tested in media of different gel strengths. The reported 760 kPa is an osmolality-derived turgor estimate, whereas 40-300 kPa describes pressure corresponding to measured tip forces. These are distinct readouts, not trait thresholds. Full text, figures, supplements and isolate provenance were not inspected; no canonical example is inferred from this abstract.

    +

    Yafetto, Davis and Money (2009), PMID:19427390; scientific abstract retrieved directly through Europe PMC. The naming sentence supports the formation phenotype, not a universal hyphal-count threshold. Armillaria gallica cultures were tested in media of different gel strengths. The reported 760 kPa is an osmolality-derived turgor estimate, whereas 40-300 kPa describes pressure corresponding to measured tip forces. These are distinct readouts, not trait thresholds. Full text, figures, supplements and isolate provenance were not inspected; no canonical example is inferred from this abstract.

  • DOI:10.1016/j.mycres.2005.09.006
    Air pores develop near the inoculum plug shortly after inoculation, arising directly from the mycelium, and rhizomorphs are initiated from them.
    -

    Pareek, Allaway and Ashford (2006), PMID:16376531; scientific abstract checked against the directly retrieved PDF and Europe PMC abstract. Methods, Results, Discussion, Table 1 and actual Figures 9-17 were inspected. Results place first tips on day 6, but Table 1 reports tips on day 5; no exact onset is asserted. Table 1 counts tips and air pores on five plates, not organisms. The main oxygen-conductance assay used cut rhizomorph ends; it does not establish intact-rind permeability or universal oxygen adaptation. Air pores and rhizomorphs are distinct structures. Remaining figure images and supplements were not inspected.

    +

    Pareek, Allaway and Ashford (2006), PMID:16376531; scientific abstract checked against the directly retrieved PDF and Europe PMC abstract. Methods, Results, Discussion, Table 1 and actual Figures 9-17 were inspected. Results place first tips on day 6, but Table 1 reports tips on day 5; no exact onset is asserted. Table 1 counts tips and air pores on five plates, not organisms. The main oxygen-conductance assay used cut rhizomorph ends; it does not establish intact-rind permeability or universal oxygen adaptation. Air pores and rhizomorphs are distinct structures. Remaining figure images and supplements were not inspected.

  • DOI:10.1186/s12862-017-0877-3
    All armillarioid species have the capacity to form rhizomorphs in culture, but only the later diverging lineages have been observed to form them in nature
    -

    Koch et al. (2017), PMID:28122504, PMC5264464; directly retrieved full-text XML, Discussion subsection The rise of rhizomorphs and Table 2. The quoted clause precedes a parenthetical figure/table citation. This is the authors' comparative summary, partly based on earlier literature, not a new formation experiment on every species. They explicitly describe unmelanized rhizomorphs in culture. Field non-observation is not biological absence; the summary does not establish expression in every strain or condition. Full Methods, actual figures, supplements and additional isolate provenance were not inspected.

    +

    Koch et al. (2017), PMID:28122504, PMC5264464; directly retrieved full-text XML, Discussion subsection The rise of rhizomorphs and Table 2. The quoted clause precedes a parenthetical figure/table citation. This is the authors' comparative summary, partly based on earlier literature, not a new formation experiment on every species. They explicitly describe unmelanized rhizomorphs in culture. Field non-observation is not biological absence; the summary does not establish expression in every strain or condition. Full Methods, actual figures, supplements and additional isolate provenance were not inspected.

  • DOI:10.3114/fuse.2024.14.03
    Many rhizomorph-forming fungi occur in the litter on the forest floor (ground species), while other species make aerial rhizomorph networks (epiphytic species).
    -

    Oliveira et al. (2024), PMID:39830290, PMC11739697; Introduction read directly in PMC HTML after the Europe PMC XML endpoint failed. This terminology passage supports not restricting formation to underground growth. These authors adopt a narrow melanized, differentiated, organized-tip concept and contrast Singer's white rhizomorph usage with mycelial cords. That is their attributed account; the original Singer/Rayner sources were not retrieved. Abstract, Introduction and selected taxonomic text/captions were read, but actual figures, supplements and the full Methods were not inspected. No additional canonical taxon or exact cord synonym is asserted.

    +

    Oliveira et al. (2024), PMID:39830290, PMC11739697; Introduction read directly in PMC HTML after the Europe PMC XML endpoint failed. This terminology passage supports not restricting formation to underground growth. These authors adopt a narrow melanized, differentiated, organized-tip concept and contrast Singer's white rhizomorph usage with mycelial cords. That is their attributed account; the original Singer/Rayner sources were not retrieved. Abstract, Introduction and selected taxonomic text/captions were read, but actual figures, supplements and the full Methods were not inspected. No additional canonical taxon or exact cord synonym is asserted.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Canonical examples DOI:10.1016/j.mycres.2005.09.006 - Isolate 930199KGS in Pareek et al. (2006), Fungal material and culture conditions, Results and Figures 9-17. Primary Methods at https://doi.org/10.1016/j.mycres.2005.09.006 identify the University of Western Sydney collection culture as originating from fruit bodies collected at Gore Hill Park, North Sydney, in June 1993. Rhizomorph development was observed on malt-marmite agar in darkness at 23 C. The Methods provenance and actual images were inspected; natural origin is not inferred from a wild-type label. NCBI Taxonomy confirms the species ID, label and rank. This is a qualified culture observation, not evidence for every strain or condition. + Isolate 930199KGS in Pareek et al. (2006), Fungal material and culture conditions, Results and Figures 9-17. Primary Methods at https://doi.org/10.1016/j.mycres.2005.09.006 identify the University of Western Sydney collection culture as originating from fruit bodies collected at Gore Hill Park, North Sydney, in June 1993. Rhizomorph development was observed on malt-marmite agar in darkness at 23 C. The Methods provenance and actual images were inspected; natural origin is not inferred from a wild-type label. NCBI Taxonomy confirms the species ID, label and rank. This is a qualified culture observation, not evidence for every strain or condition. @@ -246,7 +247,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Use phenotype METPO:1000059. Mycelial growth traitmech:000074 is explicitly bacterial; filament shaped METPO:1000674 is a cell-shape class; rhizoid colony METPO:1007068 and filamentous colony METPO:1007066 concern colony outlines. None is an exact fungal multihyphal formation record. Hyphal anastomosis traitmech:000605 denotes fusion and fungal sclerotium formation traitmech:000660 denotes compact resting bodies. Koch et al. (2017) use rhizomorph for unmelanized culture structures, whereas Oliveira et al. (2024) adopt the narrower melanized, organized-tip sense and distinguish mycelial cords. The broad formation definition does not settle that anatomical boundary: retain the source attribution and do not assert exact cord/strand synonyms, a universal pigment requirement or an underground-only habitat. A closer fungal growth-form parent and external equivalences require upstream review; no xrefs or SSSOM mappings are asserted. Fungal mycelial cord formation traitmech:000669 now represents the diffuse-front aggregation sense defined by Boddy et al. (2009), DOI:10.1007/s10267-008-0450-4, rather than silently equating the two names. Its experimental examples do not resolve all historical usage. Keep this terminology/hierarchy question OPEN: neither equivalence, a parent-child relationship nor organism-level disjointness is asserted.

    +

    Use phenotype METPO:1000059. Mycelial growth traitmech:000074 is explicitly bacterial; filament shaped METPO:1000674 is a cell-shape class; rhizoid colony METPO:1007068 and filamentous colony METPO:1007066 concern colony outlines. None is an exact fungal multihyphal formation record. Hyphal anastomosis traitmech:000605 denotes fusion and fungal sclerotium formation traitmech:000660 denotes compact resting bodies. Koch et al. (2017) use rhizomorph for unmelanized culture structures, whereas Oliveira et al. (2024) adopt the narrower melanized, organized-tip sense and distinguish mycelial cords. The broad formation definition does not settle that anatomical boundary: retain the source attribution and do not assert exact cord/strand synonyms, a universal pigment requirement or an underground-only habitat. A closer fungal growth-form parent and external equivalences require upstream review; no xrefs or SSSOM mappings are asserted. Fungal mycelial cord formation traitmech:000669 now represents the diffuse-front aggregation sense defined by Boddy et al. (2009), DOI:10.1007/s10267-008-0450-4, rather than silently equating the two names. Its experimental examples do not resolve all historical usage. Keep this terminology/hierarchy question OPEN: neither equivalence, a parent-child relationship nor organism-level disjointness is asserted.

    @@ -352,7 +353,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -381,12 +391,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 22:18 UTC diff --git a/pages/traits/morphology/fungal_root_mantle_formation.html b/pages/traits/morphology/fungal_root_mantle_formation.html index f82114338ac..aff78ce8117 100644 --- a/pages/traits/morphology/fungal_root_mantle_formation.html +++ b/pages/traits/morphology/fungal_root_mantle_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -67,7 +68,7 @@

    Trait evidence (3)

    DOI:10.3390/microorganisms9122612
    Three weeks post-inoculation, fungal hyphae formed a thinner but denser mantle.
    -

    Ruytinx et al. (2021), Results 3.3, complete sentence, exact-matched in primary full-text XML. Main text and actual Figure 2 on PDF p. 8 were inspected: https://pure.mpg.de/rest/items/item_3375108_1/component/file_3400121/content The 21-day state follows the reported thick, dense 14-day mantle, not loss of the sheath. Methods 2.6 names WGA-Alexa 488 whereas the Figure 2 caption names WGA-oregon green; the discrepancy is retained, not resolved by inference. Other figure images and supplements were not inspected.

    +

    Ruytinx et al. (2021), Results 3.3, complete sentence, exact-matched in primary full-text XML. Main text and actual Figure 2 on PDF p. 8 were inspected: https://pure.mpg.de/rest/items/item_3375108_1/component/file_3400121/content The 21-day state follows the reported thick, dense 14-day mantle, not loss of the sheath. Methods 2.6 names WGA-Alexa 488 whereas the Figure 2 caption names WGA-oregon green; the discrepancy is retained, not resolved by inference. Other figure images and supplements were not inspected.

    @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.3390/microorganisms9122612 - Reference culture S238N, not haploid S238N-H82. Ruytinx (2021), Methods 2.1/2.3 and Results 3.3 with Figure 2B-C, documents a mantle around Populus tremula x alba 717-1B4 lateral roots in P20 sandwich coculture, including the 14- and 21-day states. The laboratory history at https://mycor.iam.inrae.fr/IAM/?page_id=4555 traces S238N to a 1976 Crater Lake, Oregon fruitbody collection under Tsuga mertensiana. NCBI EFetch confirms species 29883 and separate child strain 486041 S238N-H82; the genome strain is not substituted for the experimental culture. This is culture-qualified evidence, not independent reidentification or a claim for all strains. + Reference culture S238N, not haploid S238N-H82. Ruytinx (2021), Methods 2.1/2.3 and Results 3.3 with Figure 2B-C, documents a mantle around Populus tremula x alba 717-1B4 lateral roots in P20 sandwich coculture, including the 14- and 21-day states. The laboratory history at https://mycor.iam.inrae.fr/IAM/?page_id=4555 traces S238N to a 1976 Crater Lake, Oregon fruitbody collection under Tsuga mertensiana. NCBI EFetch confirms species 29883 and separate child strain 486041 S238N-H82; the genome strain is not substituted for the experimental culture. This is culture-qualified evidence, not independent reidentification or a claim for all strains. @@ -270,7 +271,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    A protein-resolved causal graph is deferred pending authority-verified proteins, sequence-to-culture links and inspection of the relevant perturbation images, not because mechanisms are absent. DOI:10.1128/AEM.01991-15 reports a thicker mantle in native ald1 overexpression; it does not establish an obligatory universal pathway. Its mte1 evidence is heterologous yeast growth rescue, not a native mantle-formation knockout. Keep increased thickness, first sheath formation, branching and plant responses separate. DOI:10.3390/microorganisms9122612 uses an EcM transcriptomic sample containing all fungal and mixed plant-fungal material within 0.5 cm of a root. Coexpression in that bulk sample is not mantle-specific localization or functional validation. The paper explicitly presents working models for future experimental tests.

    +

    A protein-resolved causal graph is deferred pending authority-verified proteins, sequence-to-culture links and inspection of the relevant perturbation images, not because mechanisms are absent. DOI:10.1128/AEM.01991-15 reports a thicker mantle in native ald1 overexpression; it does not establish an obligatory universal pathway. Its mte1 evidence is heterologous yeast growth rescue, not a native mantle-formation knockout. Keep increased thickness, first sheath formation, branching and plant responses separate. DOI:10.3390/microorganisms9122612 uses an EcM transcriptomic sample containing all fungal and mixed plant-fungal material within 0.5 cm of a root. Coexpression in that bulk sample is not mantle-specific localization or functional validation. The paper explicitly presents working models for future experimental tests.

    @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 19:56 UTC diff --git a/pages/traits/morphology/fungal_sclerotium_formation.html b/pages/traits/morphology/fungal_sclerotium_formation.html index 2faede5093e..ad40bd979ab 100644 --- a/pages/traits/morphology/fungal_sclerotium_formation.html +++ b/pages/traits/morphology/fungal_sclerotium_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,31 +56,31 @@

    Trait evidence (5)

    DOI:10.1128/AEM.00565-08
    Aspergillus flavus differentiates to produce asexual dispersing spores (conidia) or overwintering survival structures called sclerotia.
    -

    Horowitz Brown et al. (2008), PMID:18658287, PMC2547031; scientific abstract retrieved through Europe PMC and checked against publisher/PMC HTML. The XML endpoint failed; full text was read as HTML. Introduction, growth/density Methods, first Results subsection, Table 1 and actual Figure 1 were inspected. NRRL 3357 was tested at 29 C for seven days in darkness on glucose minimal medium with sorbitol. Figure 1A reports log10 sclerotial dry mass per plate, not raw body counts despite the abstract's number wording. Density association does not identify the proposed quorum factor. Other figures, supplements and natural strain provenance were not inspected; no additional canonical example or universal LOX mechanism is inferred.

    +

    Horowitz Brown et al. (2008), PMID:18658287, PMC2547031; scientific abstract retrieved through Europe PMC and checked against publisher/PMC HTML. The XML endpoint failed; full text was read as HTML. Introduction, growth/density Methods, first Results subsection, Table 1 and actual Figure 1 were inspected. NRRL 3357 was tested at 29 C for seven days in darkness on glucose minimal medium with sorbitol. Figure 1A reports log10 sclerotial dry mass per plate, not raw body counts despite the abstract's number wording. Density association does not identify the proposed quorum factor. Other figures, supplements and natural strain provenance were not inspected; no additional canonical example or universal LOX mechanism is inferred.

  • DOI:10.3390/jof9070737
    WT and ΔSSA-178C formed black mature sclerotia on the colonies and at the rim of the Petri dishes
    -

    Wang et al. (2023), PMID:37504726, PMC10381867; full-text XML, Results 3.3. Methods 2.1/2.6, Discussion and actual Figures 3-4 were inspected. WT 1980 was observed on PDA at 20 C after 10/15 days and on autoclaved carrot slices after 20 days. Colony photographs are Figure 3A; the Results' Figure 3B pointers for maturation are misplaced because 3B plots growth. Figure 4C/D report bodies and total air-dried mass per flask, not mass per body. Delayed maturation is not complete loss of formation; do not infer rescue of every cortex measurement or survival duration. Other figures and supplements were not inspected.

    +

    Wang et al. (2023), PMID:37504726, PMC10381867; full-text XML, Results 3.3. Methods 2.1/2.6, Discussion and actual Figures 3-4 were inspected. WT 1980 was observed on PDA at 20 C after 10/15 days and on autoclaved carrot slices after 20 days. Colony photographs are Figure 3A; the Results' Figure 3B pointers for maturation are misplaced because 3B plots growth. Figure 4C/D report bodies and total air-dried mass per flask, not mass per body. Delayed maturation is not complete loss of formation; do not infer rescue of every cortex measurement or survival duration. Other figures and supplements were not inspected.

  • DOI:10.1016/j.micres.2019.126326
    there are no structural differences in the three stages of formation of melanized and non-melanized sclerotium.
    -

    2019 microscopy study, PMID:31493702; directly retrieved Europe PMC scientific abstract only. The authors report development on PDA and compare melanized/non-melanized Sclerotinia sclerotiorum structures by microscopy and histochemistry. This supports not requiring melanization in the definition; the quoted observation is not a claim of identical composition or preserved function in every respect. Full text, figures, supplements, the treatment producing non-melanized structures and strain provenance were not inspected. No canonical example or transcript-inferred biochemical pathway is asserted.

    +

    2019 microscopy study, PMID:31493702; directly retrieved Europe PMC scientific abstract only. The authors report development on PDA and compare melanized/non-melanized Sclerotinia sclerotiorum structures by microscopy and histochemistry. This supports not requiring melanization in the definition; the quoted observation is not a claim of identical composition or preserved function in every respect. Full text, figures, supplements, the treatment producing non-melanized structures and strain provenance were not inspected. No canonical example or transcript-inferred biochemical pathway is asserted.

  • DOI:10.1128/spectrum.02084-21
    There are different types of sclerotia-like fungal structures, such as the true sclerotia, the pseudosclerotia, the small sclerotia, and the microsclerotia.
    -

    2022 primary study, PMID:35080446, PMC8791194; Introduction read directly as full-text XML. This passage is a terminology classification, not a new experimental observation. The authors distinguish tissue organization, host-material incorporation and developmental origins across these forms. Preserve that attributed distinction rather than imposing one size, three-layer anatomy or pure-fungal composition on every usage. Detailed equivalence/subclass mapping remains unresolved. Experimental Results, figures, supplements and strain provenance were not inspected; no universal ROS mechanism or additional canonical example is claimed.

    +

    2022 primary study, PMID:35080446, PMC8791194; Introduction read directly as full-text XML. This passage is a terminology classification, not a new experimental observation. The authors distinguish tissue organization, host-material incorporation and developmental origins across these forms. Preserve that attributed distinction rather than imposing one size, three-layer anatomy or pure-fungal composition on every usage. Detailed equivalence/subclass mapping remains unresolved. Experimental Results, figures, supplements and strain provenance were not inspected; no universal ROS mechanism or additional canonical example is claimed.

  • DOI:10.2478/s11658-007-0047-5
    Sclerotization only took place when the plasmodia were starved and very slowly dried.
    -

    Krzywda et al. (2008; online 2007), PMID:17965965, PMC6275577; scientific abstract read directly in full-text XML. Fuligo septica forms a dormant plasmodial state also called a sclerotium. This nonfungal usage motivates the explicit fungal scope; it is not a mycelial exemplar or an exact synonym of this trait. The reported dehydration conditions and pigment/viability observations are not transferred to fungi. Methods, figures and natural-isolate provenance were not inspected.

    +

    Krzywda et al. (2008; online 2007), PMID:17965965, PMC6275577; scientific abstract read directly in full-text XML. Fuligo septica forms a dormant plasmodial state also called a sclerotium. This nonfungal usage motivates the explicit fungal scope; it is not a mycelial exemplar or an exact synonym of this trait. The reported dehydration conditions and pigment/viability observations are not transferred to fungi. Methods, figures and natural-isolate provenance were not inspected.

    • @@ -131,7 +132,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -220,7 +221,7 @@

    Canonical examples DOI:10.3390/jof9070737 - Wild-type strain 1980 in Wang et al. (2023), Methods 2.1/2.6, Results 3.3 and actual Figures 3A/4, forms sclerotia under the tested PDA/carrot conditions. NCBI Taxonomy confirms the species label and rank. Independent primary Methods at https://doi.org/10.1128/AEM.67.1.75-81.2001 (PMID:11133430, PMC92519) explicitly identify isolate 1980 as originating from dry bean culls in western Nebraska, supplied by J. R. Steadman. That passage was read directly in PMC HTML; its cited original 1990 study was not retrieved. This URL supports provenance, not an extra formation observation. The example is not an SSA disruption/complementary mutant and does not assert the phenotype for every strain or condition. + Wild-type strain 1980 in Wang et al. (2023), Methods 2.1/2.6, Results 3.3 and actual Figures 3A/4, forms sclerotia under the tested PDA/carrot conditions. NCBI Taxonomy confirms the species label and rank. Independent primary Methods at https://doi.org/10.1128/AEM.67.1.75-81.2001 (PMID:11133430, PMC92519) explicitly identify isolate 1980 as originating from dry bean culls in western Nebraska, supplied by J. R. Steadman. That passage was read directly in PMC HTML; its cited original 1990 study was not retrieved. This URL supports provenance, not an extra formation observation. The example is not an SSA disruption/complementary mutant and does not assert the phenotype for every strain or condition. @@ -352,7 +353,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -381,12 +391,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 06:51 UTC diff --git a/pages/traits/morphology/fusiform_shaped.html b/pages/traits/morphology/fusiform_shaped.html index e04e0d536a3..2206427f3ab 100644 --- a/pages/traits/morphology/fusiform_shaped.html +++ b/pages/traits/morphology/fusiform_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -311,7 +312,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • fusiform RELATED_SYNONYM · metpo.owl
      • +
    • fusiform RELATED_SYNONYM · metpo.owl
    @@ -327,7 +328,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -621,7 +622,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -985,12 +995,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/gas_vesicle.html b/pages/traits/morphology/gas_vesicle.html index 62f25989cf6..dfb1642ccf7 100644 --- a/pages/traits/morphology/gas_vesicle.html +++ b/pages/traits/morphology/gas_vesicle.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,10 +97,10 @@

    Edge evidence

  • gas vesicle - traitmech:000070 + traitmech:000070 confers cellular buoyancy - traitmech:000528 + traitmech:000528 METPO:2007700

    Internal gas-filled vesicles lower effective density and provide buoyancy.

      @@ -115,7 +116,7 @@

      Edge evidence

    • cellular buoyancy - traitmech:000528 + traitmech:000528 enables water-column positioning @@ -251,7 +252,7 @@

      Edge evidence

      GO:0033172 part of gas vesicle - traitmech:000070 + traitmech:000070 biolink:part_of

      The gas-filled compartment and its protein shell constitute the gas-vesicle structure.

        @@ -270,7 +271,7 @@

        Edge evidence

        negatively regulates gas vesicle - traitmech:000070 + traitmech:000070 RO:0002212

        Irreversible pressure collapse eliminates the intact gas-vesicle structural state.

          @@ -289,7 +290,7 @@

          Edge evidence

          negatively regulates gas vesicle - traitmech:000070 + traitmech:000070 RO:0002212

          GvpD inhibits formation of the gas-vesicle structure under the reviewed regulatory model.

            @@ -345,8 +346,8 @@

            Protein and taxon examples

    		•  - Microcystis aeruginosa NIES-843 -
    NCBITaxon:449447 + Microcystis aeruginosa NIES-843 +
    NCBITaxon:449447         		REVIEWED
    @@ -412,7 +413,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • gas vacuole RELATED_SYNONYM · DOI:10.1038/nrmicro2834
      • +
    • gas vacuole RELATED_SYNONYM · DOI:10.1038/nrmicro2834
    @@ -435,7 +436,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -759,7 +760,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1123,12 +1133,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/gliding.html b/pages/traits/morphology/gliding.html index 51e89df3c7b..1886822736a 100644 --- a/pages/traits/morphology/gliding.html +++ b/pages/traits/morphology/gliding.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -301,8 +302,8 @@

    Protein and taxon examples

    		 - Myxococcus xanthus DK1622 -
    NCBITaxon:246197 + Myxococcus xanthus DK1622 +
    NCBITaxon:246197         		REVIEWED
    @@ -375,7 +376,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000706 [-1.115, +0.741, -2.784, -0.615, …]
      • +
    • gliding METPO:1000706 [-1.115, +0.741, -2.784, -0.615, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -690,7 +691,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1054,12 +1064,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/gram_negative.html b/pages/traits/morphology/gram_negative.html index daca4cdf6d1..5a2a8eb478a 100644 --- a/pages/traits/morphology/gram_negative.html +++ b/pages/traits/morphology/gram_negative.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -368,9 +369,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • G_negative RELATED_SYNONYM · metpo.owl
      • +
    • G_negative RELATED_SYNONYM · metpo.owl
      • -
    • negative RELATED_SYNONYM · metpo.owl
      • +
    • negative RELATED_SYNONYM · metpo.owl
    @@ -386,7 +387,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000699 [+365.243, +263.306, -35.927, -345.448, …]
      • +
    • gram negative METPO:1000699 [+365.243, +263.306, -35.927, -345.448, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -680,7 +681,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1044,12 +1054,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/gram_positive.html b/pages/traits/morphology/gram_positive.html index c53ef602737..f2879184e42 100644 --- a/pages/traits/morphology/gram_positive.html +++ b/pages/traits/morphology/gram_positive.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -349,9 +350,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • G_positive RELATED_SYNONYM · metpo.owl
      • +
    • G_positive RELATED_SYNONYM · metpo.owl
      • -
    • positive RELATED_SYNONYM · metpo.owl
      • +
    • positive RELATED_SYNONYM · metpo.owl
    @@ -367,7 +368,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000698 [+104.737, -799.711, +133.158, -97.829, …]
      • +
    • gram positive METPO:1000698 [+104.737, -799.711, +133.158, -97.829, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -637,7 +638,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1001,12 +1011,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/gram_stain.html b/pages/traits/morphology/gram_stain.html index 87d036e2c83..deba75c9709 100644 --- a/pages/traits/morphology/gram_stain.html +++ b/pages/traits/morphology/gram_stain.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -299,9 +300,9 @@

    Children (3)

    Synonyms (2)

      -
    • Morphology.cell morphology.gram stain RELATED_SYNONYM · metpo.owl
      • +
    • Morphology.cell morphology.gram stain RELATED_SYNONYM · metpo.owl
      • -
    • gram_stain RELATED_SYNONYM · metpo.owl
      • +
    • gram_stain RELATED_SYNONYM · metpo.owl
    @@ -317,7 +318,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000697 [-2.552, -2.118, -3.376, -0.738, …]
      • +
    • gram stain METPO:1000697 [-2.552, -2.118, -3.376, -0.738, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -557,7 +558,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 2 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; PMID:9278503), Bacillus subtilis (NCBITaxon:1423; PMID:9384377). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 2 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; PMID:9278503), Bacillus subtilis (NCBITaxon:1423; PMID:9384377). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  • @@ -611,7 +612,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -975,12 +985,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-07 02:20 UTC diff --git a/pages/traits/morphology/gram_variable.html b/pages/traits/morphology/gram_variable.html index cd5f19ec92e..fe9b7be7a2d 100644 --- a/pages/traits/morphology/gram_variable.html +++ b/pages/traits/morphology/gram_variable.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -286,7 +287,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • variable RELATED_SYNONYM · metpo.owl
      • +
    • variable RELATED_SYNONYM · metpo.owl
    @@ -302,7 +303,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -605,7 +606,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -969,12 +979,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/green_pigmented.html b/pages/traits/morphology/green_pigmented.html index 6ee0718da92..4893676b024 100644 --- a/pages/traits/morphology/green_pigmented.html +++ b/pages/traits/morphology/green_pigmented.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -343,7 +344,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Pigment_green RELATED_SYNONYM · metpo.owl
      • +
    • Pigment_green RELATED_SYNONYM · metpo.owl
    @@ -359,7 +360,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -674,7 +675,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1038,12 +1048,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/helical_shaped.html b/pages/traits/morphology/helical_shaped.html index 753cd0a9e7c..3dc0c08a66d 100644 --- a/pages/traits/morphology/helical_shaped.html +++ b/pages/traits/morphology/helical_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -305,7 +306,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • helical-shaped RELATED_SYNONYM · metpo.owl
      • +
    • helical-shaped RELATED_SYNONYM · metpo.owl
    @@ -321,7 +322,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -597,7 +598,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -961,12 +971,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/heterocyst.html b/pages/traits/morphology/heterocyst.html index 59792c338c5..bb96af11f0e 100644 --- a/pages/traits/morphology/heterocyst.html +++ b/pages/traits/morphology/heterocyst.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    GO:0030154 confers heterocyst - traitmech:000073 + traitmech:000073 METPO:2007700

    Cyanobacterial cell differentiation realizes the thick-walled heterocyst.

      @@ -115,7 +116,7 @@

      Edge evidence

    • heterocyst - traitmech:000073 + traitmech:000073 causes microoxic intracellular environment @@ -270,7 +271,7 @@

      Edge evidence

      contributes to heterocyst - traitmech:000073 + traitmech:000073 RO:0002326

      HetR is the central positive regulator of heterocyst development and contributes to realization of the differentiated cell trait.

        @@ -326,8 +327,8 @@

        Protein and taxon examples

    		 - Nostoc sp. PCC 7120 -
    NCBITaxon:103690 + Nostoc sp. PCC 7120 +
    NCBITaxon:103690         		REVIEWED
    @@ -393,7 +394,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -409,7 +410,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -652,7 +653,7 @@

    Curation history

  • · CONNECT_CAUSAL_GRAPH_COMPONENTS · codex -

    Resolved issue #183 graph fragmentation (4 components to 1) using 2 source- and verbatim-snippet-backed connector(s). Removed the isolated FurC/hetR-promoter branch: its primary source states that more studies are required to understand the regulation exerted by FurC on hetR expression (DOI:10.1371/journal.pone.0289761), so no directional bridge was asserted. No paid research service was called.

    +

    Resolved issue #183 graph fragmentation (4 components to 1) using 2 source- and verbatim-snippet-backed connector(s). Removed the isolated FurC/hetR-promoter branch: its primary source states that more studies are required to understand the regulation exerted by FurC on hetR expression (DOI:10.1371/journal.pone.0289761), so no directional bridge was asserted. No paid research service was called.

  • @@ -700,7 +701,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1064,12 +1074,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/holdfast.html b/pages/traits/morphology/holdfast.html index 196a518330c..783e4c138c8 100644 --- a/pages/traits/morphology/holdfast.html +++ b/pages/traits/morphology/holdfast.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,7 +113,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • holdfast adhesin RELATED_SYNONYM · DOI:10.1128/jb.00276-19
      • +
    • holdfast adhesin RELATED_SYNONYM · DOI:10.1128/jb.00276-19
    @@ -128,7 +129,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -278,7 +279,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries polar adhesin function and monosaccharide-composition snippets in Caulobacterales (DOI:10.1128/jb.00276-19, DOI:10.1128/jb.00273-22) without biosynthetic or anchoring protein quotes.

    +

    The current record carries polar adhesin function and monosaccharide-composition snippets in Caulobacterales (DOI:10.1128/jb.00276-19, DOI:10.1128/jb.00273-22) without biosynthetic or anchoring protein quotes.

    @@ -360,7 +361,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -389,12 +399,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/morphology/hormogonium_formation.html b/pages/traits/morphology/hormogonium_formation.html index 7a706dd7dd2..6e399381e71 100644 --- a/pages/traits/morphology/hormogonium_formation.html +++ b/pages/traits/morphology/hormogonium_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -61,13 +62,13 @@

    Trait evidence (3)

    DOI:10.1128/aem.55.1.125-131.1989
    motile (gliding) filaments lacking heterocysts and with distinctly smaller cells than those of vegetative filaments
    -

    PMID:16347816, PMC184065. Scientific Abstract directly read on PubMed and through the Europe PMC core API. Campbell and Meeks (1989) observed induced hormogonia in symbiotically competent Nostoc cultures. The quoted morphology describes those cultures, not every hormogonium. Strain 7801 underwent conversion in Anthoceros punctatus-conditioned medium under the tested conditions and later reverted to vegetative growth. The reported loss and recovery of acetylene reduction are stage-dependent readouts, not a definition requiring nitrogen fixation or plant symbiosis. Full text and panels were not read.

    +

    PMID:16347816, PMC184065. Scientific Abstract directly read on PubMed and through the Europe PMC core API. Campbell and Meeks (1989) observed induced hormogonia in symbiotically competent Nostoc cultures. The quoted morphology describes those cultures, not every hormogonium. Strain 7801 underwent conversion in Anthoceros punctatus-conditioned medium under the tested conditions and later reverted to vegetative growth. The reported loss and recovery of acetylene reduction are stage-dependent readouts, not a definition requiring nitrogen fixation or plant symbiosis. Full text and panels were not read.

  • DOI:10.1128/mSphere.00231-19
    both sigC and sigJ may be required for an early stage in hormogonium development, while sigF is late acting.
    -

    PMID:31043519, PMC6495340. Direct Europe PMC full-text XML: scientific ABSTRACT, first RESULTS subsection, and MATERIALS AND METHODS subsections Strains and culture conditions and Plasmid and strain construction were read. The snippet is from Results, not the separate precis/IMPORTANCE text. Wild-type Nostoc punctiforme formed shorter, morphologically distinct filaments after induction. In-frame sigF deletion abolished motility but retained morphological differentiation and heterocyst loss; sigC and sigJ deletions lacked those morphological markers. This separates development from locomotion experimentally. Complementation restored motility in the assay, not necessarily wild-type levels. These are strain- and assay-qualified results, not a universal sigma-factor rule inferred from sequence. Actual panels, movies and the strain-table supplement were not inspected; no panel-level or numerical claim is made.

    +

    PMID:31043519, PMC6495340. Direct Europe PMC full-text XML: scientific ABSTRACT, first RESULTS subsection, and MATERIALS AND METHODS subsections Strains and culture conditions and Plasmid and strain construction were read. The snippet is from Results, not the separate precis/IMPORTANCE text. Wild-type Nostoc punctiforme formed shorter, morphologically distinct filaments after induction. In-frame sigF deletion abolished motility but retained morphological differentiation and heterocyst loss; sigC and sigJ deletions lacked those morphological markers. This separates development from locomotion experimentally. Complementation restored motility in the assay, not necessarily wild-type levels. These are strain- and assay-qualified results, not a universal sigma-factor rule inferred from sequence. Actual panels, movies and the strain-table supplement were not inspected; no panel-level or numerical claim is made.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 22:10 UTC diff --git a/pages/traits/morphology/intracellular_inclusion.html b/pages/traits/morphology/intracellular_inclusion.html index 29867d15928..7f574f444fe 100644 --- a/pages/traits/morphology/intracellular_inclusion.html +++ b/pages/traits/morphology/intracellular_inclusion.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -96,7 +97,7 @@

    Edge evidence

  • intracellular inclusion - traitmech:000066 + traitmech:000066 manifests as cytoplasmic compartmentalization @@ -118,8 +119,8 @@

    Edge evidence

    GO:0031469 example of intracellular inclusion - traitmech:000066 - rdfs:subClassOf + traitmech:000066 + rdfs:subClassOf

    Bacterial microcompartments are protein-bounded inclusion organelles.

      @@ -213,7 +214,7 @@

      Edge evidence

      GO:0031411 confers buoyancy - traitmech:000528 + traitmech:000528 METPO:2007700

      Gas vesicles confer buoyancy enabling positioning in the water column.

        @@ -334,7 +335,7 @@

        Children (8)

        Synonyms (1)

          -
        • cytoplasmic inclusion RELATED_SYNONYM · DOI:10.1038/s41579-020-0413-0
          • +
        • cytoplasmic inclusion RELATED_SYNONYM · DOI:10.1038/s41579-020-0413-0
    • @@ -350,7 +351,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -677,7 +678,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1041,12 +1051,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 22:50 UTC diff --git a/pages/traits/morphology/irregular_shaped.html b/pages/traits/morphology/irregular_shaped.html index e5b00050aa3..5ca46586fdb 100644 --- a/pages/traits/morphology/irregular_shaped.html +++ b/pages/traits/morphology/irregular_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -311,7 +312,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • irregular RELATED_SYNONYM · metpo.owl
      • +
    • irregular RELATED_SYNONYM · metpo.owl
    @@ -327,7 +328,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -558,7 +559,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Corynebacterium glutamicum (NCBITaxon:1718; DOI:10.1111/j.1574-6976.2011.00298.x). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Corynebacterium glutamicum (NCBITaxon:1718; DOI:10.1111/j.1574-6976.2011.00298.x). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -591,7 +592,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -955,12 +965,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/morphology/lateral_flagellation.html b/pages/traits/morphology/lateral_flagellation.html index 7dd2e7401fd..a60e1f0007f 100644 --- a/pages/traits/morphology/lateral_flagellation.html +++ b/pages/traits/morphology/lateral_flagellation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -88,7 +89,7 @@

    Trait evidence (4)

    Inducible proton-driven lateral flagella and surface swarming

    Evidence-backed causal sketch linking proton-driven lateral flagella to the lateral flagellation morphology and surface swarming motility.

    -

    NONMECHANISTIC · Morphological arrangement descriptor spanning multiple bacterial lineages (DOI:10.1111/j.1574-6968.2006.00403.x, DOI:10.1128/jb.167.1.210-218.1986, DOI:10.1128/jb.185.15.4508-4518.2003); the record's verbatim evidence quotes characterize organelle-level lateral flagellation and proton-driven swarming without naming individual protein subunits.

    +

    NONMECHANISTIC · Morphological arrangement descriptor spanning multiple bacterial lineages (DOI:10.1111/j.1574-6968.2006.00403.x, DOI:10.1128/jb.167.1.210-218.1986, DOI:10.1128/jb.185.15.4508-4518.2003); the record's verbatim evidence quotes characterize organelle-level lateral flagellation and proton-driven swarming without naming individual protein subunits.

    Loading graph…

    @@ -216,7 +217,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -375,7 +376,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -739,12 +749,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 21:12 UTC diff --git a/pages/traits/morphology/lophotrichous.html b/pages/traits/morphology/lophotrichous.html index 332aece04cf..1261057d2f5 100644 --- a/pages/traits/morphology/lophotrichous.html +++ b/pages/traits/morphology/lophotrichous.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -105,7 +106,7 @@

    Edge evidence

    GO:0009288 defines lophotrichous - traitmech:000058 + traitmech:000058 METPO:2007500

    A tuft of flagella at one pole defines the lophotrichous arrangement.

      @@ -121,7 +122,7 @@

      Edge evidence

    • lophotrichous - traitmech:000058 + traitmech:000058 associated with polar tuft placement @@ -200,7 +201,7 @@

      Edge evidence

      required for lophotrichous - traitmech:000058 + traitmech:000058

      FipA is required for normal FlhF activity and polar flagellar synthesis.

        @@ -305,7 +306,7 @@

        kg-microbe context

        via parent_proxy.

        512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

        @@ -542,7 +543,7 @@

        Curation history

      • · REPAIR_CANONICAL_CITATION_SCOPE_1626 · codex -

        Resolved issue 1626 by replacing the mismatched bipolar example note and compound PMID:16561638 (DOI:10.1128/jb.57.1.111-118.1949) citation with a life-stage-qualified, one-bundle example from Swan 1982 (DOI:10.1128/jb.150.1.377-380.1982; PMID:7061399; PMC220122). This is an explicit source and scope correction, not a PMID-to-DOI normalization: Pijper's original PMID and DOI identify the same 1949 paper. Source-native scans distinguish recently divided unipolar ATCC 19554 cells from older bipolar cells. Added the exact methods snippet and bounded interpretation; retained NCBITaxon:968 and the independently checked NCBI label. The definition, hierarchy, graph, other example and existing amphitrichous record are unchanged.

        +

        Resolved issue 1626 by replacing the mismatched bipolar example note and compound PMID:16561638 (DOI:10.1128/jb.57.1.111-118.1949) citation with a life-stage-qualified, one-bundle example from Swan 1982 (DOI:10.1128/jb.150.1.377-380.1982; PMID:7061399; PMC220122). This is an explicit source and scope correction, not a PMID-to-DOI normalization: Pijper's original PMID and DOI identify the same 1949 paper. Source-native scans distinguish recently divided unipolar ATCC 19554 cells from older bipolar cells. Added the exact methods snippet and bounded interpretation; retained NCBITaxon:968 and the independently checked NCBI label. The definition, hierarchy, graph, other example and existing amphitrichous record are unchanged.

      • @@ -554,7 +555,7 @@

        Curation history

      • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

        Added verified verbatim snippet from DOI:10.1093/femsre/fuv034 (already present on sibling record polar_flagellation.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-016 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

        +

        Added verified verbatim snippet from DOI:10.1093/femsre/fuv034 (already present on sibling record polar_flagellation.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-016 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

        • @@ -564,7 +565,7 @@

        Recorded curation sessions

      • · codex
        • EDIT — Correct the Spirillum canonical example to naturally unipolar division-stage cells -

          Replaced the compound Pijper 1949 reference and mismatched bipolar-tufts note with Swan 1982 DOI:10.1128/jb.150.1.377-380.1982 (PMID:7061399, PMC220122). PubMed/Europe PMC confirm the original PMID:16561638 and DOI:10.1128/jb.57.1.111-118.1949 identify the same paper; this change is an explicit source/scope replacement, not normalization. Source-native scans of Swan p.377 establish recently divided, naturally unipolar ATCC 19554 cells grown at 30 C in ATCC medium 234, distinct from older bipolar cells. Retained NCBITaxon:968 with its live NCBI label. Added a verbatim methods snippet and notes; no definition, hierarchy, graph, other example, mapping status or amphitrichous record changed. Guarded mutator prevalidates all three issue targets before live writes and preserves unrelated fields. All 47 new writer tests plus 44 citation-rendering tests pass; full downstream checks and independent review remain required.

        +

        Replaced the compound Pijper 1949 reference and mismatched bipolar-tufts note with Swan 1982 DOI:10.1128/jb.150.1.377-380.1982 (PMID:7061399, PMC220122). PubMed/Europe PMC confirm the original PMID:16561638 and DOI:10.1128/jb.57.1.111-118.1949 identify the same paper; this change is an explicit source/scope replacement, not normalization. Source-native scans of Swan p.377 establish recently divided, naturally unipolar ATCC 19554 cells grown at 30 C in ATCC medium 234, distinct from older bipolar cells. Retained NCBITaxon:968 with its live NCBI label. Added a verbatim methods snippet and notes; no definition, hierarchy, graph, other example, mapping status or amphitrichous record changed. Guarded mutator prevalidates all three issue targets before live writes and preserves unrelated fields. All 47 new writer tests plus 44 citation-rendering tests pass; full downstream checks and independent review remain required.

      Read this curation session
    • @@ -602,7 +603,16 @@

      Identifier

      Term kind
      CLASS
      Status
      -
      REVIEWED
      +
      REVIEWED + + +
      + What this status means +

      Curator has signed off on label / definition / parents.

      +

      Quoted from the schema's status definitions.

      +
      + +
    @@ -966,12 +976,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/morphology/magnetosome.html b/pages/traits/morphology/magnetosome.html index ebe2c3ef0de..8aaef40a9c8 100644 --- a/pages/traits/morphology/magnetosome.html +++ b/pages/traits/morphology/magnetosome.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    located in magnetosome - traitmech:000071 + traitmech:000071 biolink:located_in

    The magnetic mineral crystal sits inside the magnetosome membrane.

      @@ -115,10 +116,10 @@

      Edge evidence

    • magnetosome - traitmech:000071 + traitmech:000071 enables magnetotaxis - traitmech:000176 + traitmech:000176 RO:0002327

      Chains of magnetosomes act as a cellular compass, aligning the organism with geomagnetic field lines.

        @@ -175,7 +176,7 @@

        Edge evidence

        enables magnetotaxis - traitmech:000176 + traitmech:000176 RO:0002327

        Chain assembly of magnetosomes underlies the cellular compass enabling magnetotaxis.

          @@ -308,7 +309,7 @@

          Edge evidence

          located in magnetosome - traitmech:000071 + traitmech:000071 biolink:located_in

          Magnetite is one mineral-crystal form contained by magnetosomes.

            @@ -327,7 +328,7 @@

            Edge evidence

            located in magnetosome - traitmech:000071 + traitmech:000071 biolink:located_in

            Greigite is one mineral-crystal form contained by magnetosomes.

              @@ -364,8 +365,8 @@

              Protein and taxon examples

    		 - Magnetospirillum gryphiswaldense MSR-1 -
    NCBITaxon:431944 + Magnetospirillum gryphiswaldense MSR-1 +
    NCBITaxon:431944         		REVIEWED
    @@ -445,7 +446,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -742,7 +743,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1106,12 +1116,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/microbial_haustorium_formation.html b/pages/traits/morphology/microbial_haustorium_formation.html index f4f951c64fe..b0163be3e58 100644 --- a/pages/traits/morphology/microbial_haustorium_formation.html +++ b/pages/traits/morphology/microbial_haustorium_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.1016/j.fgb.2014.08.006
    The haustorium is separated from the extrahaustorial membrane (em) by the extrahaustorial matrix (emx).
    -

    Martinez-Cruz et al. (2014), PMID:25151531; primary PDF at https://powderymildew.ucr.edu/wp-content/uploads/2017/04/MPM14.pdf. Abstract, Introduction, Methods and main text were read; actual Figures 2-4 and complete pages 24-26 were visually inspected. The quote is from Figure 3's caption. Podosphaera xanthii isolate 2086 forms haustoria within melon epidermal cells. This supports the fungal formation phenotype and this interface anatomy, not a universal membrane arrangement. Callose correlates with maturity; functional partitioning of lobes and putative exosomes remains an interpretation. Remaining actual figures and supplements were not inspected. Initial natural-isolation provenance for 2086 was not established, so it is not used as a canonical example.

    +

    Martinez-Cruz et al. (2014), PMID:25151531; primary PDF at https://powderymildew.ucr.edu/wp-content/uploads/2017/04/MPM14.pdf. Abstract, Introduction, Methods and main text were read; actual Figures 2-4 and complete pages 24-26 were visually inspected. The quote is from Figure 3's caption. Podosphaera xanthii isolate 2086 forms haustoria within melon epidermal cells. This supports the fungal formation phenotype and this interface anatomy, not a universal membrane arrangement. Callose correlates with maturity; functional partitioning of lobes and putative exosomes remains an interpretation. Remaining actual figures and supplements were not inspected. Initial natural-isolation provenance for 2086 was not established, so it is not used as a canonical example.

  • DOI:10.1080/00275514.1994.12026373
    A single micropore connected the cytoplasm of the haustorial filament with that of the host cell.
    -

    Zugmaier, Bauer and Oberwinkler (1994), Mycologia 86:49-56; all eight pages and actual Figures 1-16 directly inspected at https://dr-franz.oberwinkler.de/wp-content/uploads/Tremella_mycoparasitism.pdf. The snippet is from the scientific abstract on page 49, visually checked because OCR is poor. Crossref confirms this DOI, title, authors and 1994 print date; its 2018 online date is not the study year. Field and culture observations distinguish tremelloid haustorial cells, filaments and host-dependent micropores. Membrane continuity was visible only under optimal sectioning; some captions say probably or presumed. Some tested hosts had attached filaments without an observed continuous micropore. Static microscopy is not a nutrient-flux assay, and formation does not guarantee a successful feeding connection.

    +

    Zugmaier, Bauer and Oberwinkler (1994), Mycologia 86:49-56; all eight pages and actual Figures 1-16 directly inspected at https://dr-franz.oberwinkler.de/wp-content/uploads/Tremella_mycoparasitism.pdf. The snippet is from the scientific abstract on page 49, visually checked because OCR is poor. Crossref confirms this DOI, title, authors and 1994 print date; its 2018 online date is not the study year. Field and culture observations distinguish tremelloid haustorial cells, filaments and host-dependent micropores. Membrane continuity was visible only under optimal sectioning; some captions say probably or presumed. Some tested hosts had attached filaments without an observed continuous micropore. Static microscopy is not a nutrient-flux assay, and formation does not guarantee a successful feeding connection.

  • DOI:10.1111/mpp.13072
    We transformed P. kernoviae to express green fluorescent protein (GFP) and demonstrated that it forms haustoria within infected N. benthamiana cells.
    -

    Wang et al. (2021), PMID:34018655, PMC8295517; scientific abstract, Results 2.1, Figure 1 caption and Methods 4.1, 4.6 and 4.7 read in directly retrieved full-text XML. The quoted abstract sentence explicitly identifies transformation. Imaging used engineered GFP line PkGFP8 derived from SCRP1055 and transgenic Nicotiana benthamiana membrane markers. Results call the projections likely biotrophic haustoria; the caption says they appeared in natural hosts without membrane markers. Those hosts are not unmodified-pathogen controls. Actual figures, supplements and complete remaining Methods were not inspected. This supports oomycete scope with engineering qualifiers, not a natural canonical example or a requirement for lifelong obligate biotrophy.

    +

    Wang et al. (2021), PMID:34018655, PMC8295517; scientific abstract, Results 2.1, Figure 1 caption and Methods 4.1, 4.6 and 4.7 read in directly retrieved full-text XML. The quoted abstract sentence explicitly identifies transformation. Imaging used engineered GFP line PkGFP8 derived from SCRP1055 and transgenic Nicotiana benthamiana membrane markers. Results call the projections likely biotrophic haustoria; the caption says they appeared in natural hosts without membrane markers. Those hosts are not unmodified-pathogen controls. Actual figures, supplements and complete remaining Methods were not inspected. This supports oomycete scope with engineering qualifiers, not a natural canonical example or a requirement for lifelong obligate biotrophy.

  • DOI:10.1104/pp.18.00979
    Biotrophic and hemibiotrophic oomycetes form intimate associations with their hosts using haustoria
    -

    Judelson and Ah-Fong (2019), PMID:30538168, PMC6446794; publisher HTML at https://academic.oup.com/plphys/article/179/4/1198/6116504 read directly after PMC and Europe PMC access failed. The clause precedes a figure citation in HAUSTORIA REPRESENT A SPECIALIZED INTERFACE. This is a review, not another formation experiment. Its interface and nutrient-acquisition passages distinguish demonstrated effector secretion from then-unproven nutritional importance in oomycetes. Neither a universal transport mechanism nor a present-day absence of such evidence is inferred. Actual figures and cited underlying experiments were not inspected.

    +

    Judelson and Ah-Fong (2019), PMID:30538168, PMC6446794; publisher HTML at https://academic.oup.com/plphys/article/179/4/1198/6116504 read directly after PMC and Europe PMC access failed. The clause precedes a figure citation in HAUSTORIA REPRESENT A SPECIALIZED INTERFACE. This is a review, not another formation experiment. Its interface and nutrient-acquisition passages distinguish demonstrated effector secretion from then-unproven nutritional importance in oomycetes. Neither a universal transport mechanism nor a present-day absence of such evidence is inferred. Actual figures and cited underlying experiments were not inspected.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Canonical examples DOI:10.1080/00275514.1994.12026373 - Field-collected material in Zugmaier et al. (1994), Methods page 51, field Results page 53 and Figures 1-9. Collections from Haldenwald near Sonnenberg, Stuttgart, Germany, on Carpinus betulus adjacent to Peniophora laeta include 8 June 1987 and 20 November 1989, W. Zugmaier 97 and 158. The authors observed tremelloid haustorial cells and filaments in contact with P. laeta and micropore connections. Figures are not assigned individually to one voucher; no such match is invented. Their separate laboratory culture was obtained by crossing monospore cultures from different basidiomata and is not equated to an unmodified field isolate. NCBI Taxonomy confirms ID 5217, label and species rank; the field material is not identified as NCBI type strain CBS 6973. The directly inspected primary PDF is https://dr-franz.oberwinkler.de/wp-content/uploads/Tremella_mycoparasitism.pdf. + Field-collected material in Zugmaier et al. (1994), Methods page 51, field Results page 53 and Figures 1-9. Collections from Haldenwald near Sonnenberg, Stuttgart, Germany, on Carpinus betulus adjacent to Peniophora laeta include 8 June 1987 and 20 November 1989, W. Zugmaier 97 and 158. The authors observed tremelloid haustorial cells and filaments in contact with P. laeta and micropore connections. Figures are not assigned individually to one voucher; no such match is invented. Their separate laboratory culture was obtained by crossing monospore cultures from different basidiomata and is not equated to an unmodified field isolate. NCBI Taxonomy confirms ID 5217, label and species rank; the field material is not identified as NCBI type strain CBS 6973. The directly inspected primary PDF is https://dr-franz.oberwinkler.de/wp-content/uploads/Tremella_mycoparasitism.pdf. @@ -352,7 +353,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -381,12 +391,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 13:25 UTC diff --git a/pages/traits/morphology/monotrichous.html b/pages/traits/morphology/monotrichous.html index 72c55a0e5f1..13b73fd2eaf 100644 --- a/pages/traits/morphology/monotrichous.html +++ b/pages/traits/morphology/monotrichous.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    GO:0009288 defines monotrichous - traitmech:000057 + traitmech:000057 METPO:2007500

    A single polar flagellum defines the monotrichous arrangement.

      @@ -115,7 +116,7 @@

      Edge evidence

    • monotrichous - traitmech:000057 + traitmech:000057 associated with polar single-flagellum placement @@ -299,7 +300,7 @@

      kg-microbe context

      via parent_proxy.

      512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

      @@ -539,7 +540,7 @@

      Curation history

    • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

      Added verified verbatim snippet from DOI:10.1093/femsre/fuv034 (already present on sibling record polar_flagellation.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-017 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

      +

      Added verified verbatim snippet from DOI:10.1093/femsre/fuv034 (already present on sibling record polar_flagellation.yaml evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-017 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

      • @@ -572,7 +573,16 @@

      Identifier

      Term kind
      CLASS
      Status
      -
      REVIEWED
      +
      REVIEWED + + +
      + What this status means +

      Curator has signed off on label / definition / parents.

      +

      Quoted from the schema's status definitions.

      +
      + +
    @@ -936,12 +946,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/morphology/motile.html b/pages/traits/morphology/motile.html index d364a8f5478..ca396f14236 100644 --- a/pages/traits/morphology/motile.html +++ b/pages/traits/morphology/motile.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -478,8 +479,8 @@

    Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -594,7 +595,7 @@

    Children (21)

    Synonyms (1)

      -
    • yes RELATED_SYNONYM · metpo.owl
      • +
    • yes RELATED_SYNONYM · metpo.owl
    @@ -610,7 +611,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -994,7 +995,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1358,12 +1368,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/motility.html b/pages/traits/morphology/motility.html index 648d81e8a72..dbf11af6a0b 100644 --- a/pages/traits/morphology/motility.html +++ b/pages/traits/morphology/motility.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -354,7 +355,7 @@

    Children (2)

    Synonyms (1)

      -
    • Morphology.cell morphology.motility RELATED_SYNONYM · metpo.owl
      • +
    • Morphology.cell morphology.motility RELATED_SYNONYM · metpo.owl
    @@ -370,7 +371,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000701 [-1.722, -3.036, -3.705, +0.093, …]
      • +
    • motility METPO:1000701 [-1.722, -3.036, -3.705, +0.093, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -465,7 +466,7 @@

    Deep research

    ### Operational definition -The supplied definition is consistent with current mechanistic understanding: an organism has motility when it can move independently through its environment using a biological propulsion apparatus. Active bacterial movement includes flagellar swimming/swarming and T4P twitching, whereas passive movement can arise from rainfall, protists, nematodes, or hitchhiking on another microbe’s appendage (Alexandre, October 2025; DOI URL: https://doi.org/10.1128/aem.00246-25). (alexandre2025movementofbacteria pages 1-2) +The supplied definition is consistent with current mechanistic understanding: an organism has motility when it can move independently through its environment using a biological propulsion apparatus. Active bacterial movement includes flagellar swimming/swarming and T4P twitching, whereas passive movement can arise from rainfall, protists, nematodes, or hitchhiking on another microbe’s appendage (Alexandre, October 2025; DOI URL: https://doi.org/10.1128/aem.00246-25). (alexandre2025movementofbacteria pages 1-2) ### Included phenotypes @@ -477,7 +478,7 @@

    Deep research

    ### Excluded or separately modeled boundary cases -- **Chemotaxis/taxis:** chemotaxis is “the ability to sense chemical gradients and actively direct motility along them,” so it controls direction rather than establishing propulsion capacity. Surface twitching *Pseudomonas aeruginosa* can use spatial sensing, whereas canonical swimming bacteria generally use temporal sensing. These should be regulatory edges, not synonyms for motility (Wheeler et al., published 2 September 2024; https://doi.org/10.1038/s41564-024-01729-3). (wheeler2024individualbacterialcells pages 1-2) +- **Chemotaxis/taxis:** chemotaxis is “the ability to sense chemical gradients and actively direct motility along them,” so it controls direction rather than establishing propulsion capacity. Surface twitching *Pseudomonas aeruginosa* can use spatial sensing, whereas canonical swimming bacteria generally use temporal sensing. These should be regulatory edges, not synonyms for motility (Wheeler et al., published 2 September 2024; https://doi.org/10.1038/s41564-024-01729-3). (wheeler2024individualbacterialcells pages 1-2) - **Passive transport:** advection, rainfall, sediment movement, vectors, or hitchhiking do not demonstrate independent locomotion. (alexandre2025movementofbacteria pages 1-2) - **Growth and colony expansion:** increased colony diameter may reflect growth, sliding, wetting, or active motility. A growth control and/or single-cell tracking is required. - **Biofilm formation and adhesion:** these are associated functions or consequences of motility machines, not motility itself. @@ -709,7 +710,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1073,12 +1083,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 19:05 UTC diff --git a/pages/traits/morphology/mycelial_growth.html b/pages/traits/morphology/mycelial_growth.html index 0668693d26e..7892c15661d 100644 --- a/pages/traits/morphology/mycelial_growth.html +++ b/pages/traits/morphology/mycelial_growth.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    confers mycelial growth - traitmech:000074 + traitmech:000074 METPO:2007700

    Sustained apical extension and branching realize mycelial growth.

      @@ -115,7 +116,7 @@

      Edge evidence

    • mycelial growth - traitmech:000074 + traitmech:000074 develops into aerial hyphae and spore differentiation @@ -311,9 +312,9 @@

      Parent traits (1)

      Synonyms (2)

        -
      • mycelium-forming RELATED_SYNONYM · DOI:10.1038/nrmicro1968
        • +
      • mycelium-forming RELATED_SYNONYM · DOI:10.1038/nrmicro1968
        • -
      • hyphal growth RELATED_SYNONYM · DOI:10.1038/nrmicro3178
        • +
      • hyphal growth RELATED_SYNONYM · DOI:10.1038/nrmicro3178
    @@ -329,7 +330,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -575,7 +576,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -939,12 +949,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/necridium_formation.html b/pages/traits/morphology/necridium_formation.html index d116ee53680..5a5e48f0e9d 100644 --- a/pages/traits/morphology/necridium_formation.html +++ b/pages/traits/morphology/necridium_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (3)

    DOI:10.1127/1864-1318/2005/0117-0239
    Trichome breakage and hormogonia liberation were caused by the disintegration of such necridia
    -

    Hernandez-Marine and Roldan (2005), scientific abstract on article page 239, visually checked in the published article reproduced in Roldan's university thesis: https://diposit.ub.edu/server/api/core/bitstreams/6ce8a85f-d68f-402d-8c13-882f128e4a7f/content (PDF page 106). Article pages 239-247, including Methods, Results, Discussion and actual Figures 1-4, were inspected. Natural cave/catacomb biofilms contain Leptolyngbya and Scytonema; microscopy associates cell degeneration with fragmentation and terminal polysaccharide pads. The proposed adhesive function is not a demonstrated universal requirement. No exact strain exemplar is assigned from these mixed samples.

    +

    Hernandez-Marine and Roldan (2005), scientific abstract on article page 239, visually checked in the published article reproduced in Roldan's university thesis: https://diposit.ub.edu/server/api/core/bitstreams/6ce8a85f-d68f-402d-8c13-882f128e4a7f/content (PDF page 106). Article pages 239-247, including Methods, Results, Discussion and actual Figures 1-4, were inspected. Natural cave/catacomb biofilms contain Leptolyngbya and Scytonema; microscopy associates cell degeneration with fragmentation and terminal polysaccharide pads. The proposed adhesive function is not a demonstrated universal requirement. No exact strain exemplar is assigned from these mixed samples.

  • DOI:10.1111/mmi.12506
    Necridia formation inhibits further molecular exchange, determining the fate of a branch likely to become a hormogonium.
    -

    Nurnberg et al. (2014), scientific abstract directly retrieved from DOI-matched Europe PMC record PMID:24383541. Publisher full-text Results and Methods were read; actual Figures 5-6 were inspected in the accepted manuscript at https://idus.us.es/bitstreams/05b873c9-9775-45f4-a6d6-2b6c54f97978/download (PDF pages 41-42), with final publisher captions cross-checked. Figure 5 follows 5-CFDA fluorescence for 24 seconds across a necridium; this is not proof of permanent exclusion of every molecule. Figure 6 shows terminal cell remnants and sealed neighboring membranes. Supplements were not inspected.

    +

    Nurnberg et al. (2014), scientific abstract directly retrieved from DOI-matched Europe PMC record PMID:24383541. Publisher full-text Results and Methods were read; actual Figures 5-6 were inspected in the accepted manuscript at https://idus.us.es/bitstreams/05b873c9-9775-45f4-a6d6-2b6c54f97978/download (PDF pages 41-42), with final publisher captions cross-checked. Figure 5 follows 5-CFDA fluorescence for 24 seconds across a necridium; this is not proof of permanent exclusion of every molecule. Figure 6 shows terminal cell remnants and sealed neighboring membranes. Supplements were not inspected.

  • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1111/mmi.12506 - Necridium-forming stage of the study strain, not a claim that every cell is a necridium. Methods report Castenholz D liquid culture at 40 degrees C under constant white light and fresh medium growth before communication assays. Natural origin from an Icelandic thermal spring in 1967 is independently confirmed by the culture collection at https://sagdb.uni-goettingen.de/detailedList.php?str_number=4.84. NCBI Taxonomy efetch for 447715 confirms this current name and rank strain. These authorities support identity/provenance, not additional phenotype experiments. + Necridium-forming stage of the study strain, not a claim that every cell is a necridium. Methods report Castenholz D liquid culture at 40 degrees C under constant white light and fresh medium growth before communication assays. Natural origin from an Icelandic thermal spring in 1967 is independently confirmed by the culture collection at https://sagdb.uni-goettingen.de/detailedList.php?str_number=4.84. NCBI Taxonomy efetch for 447715 confirms this current name and rank strain. These authorities support identity/provenance, not additional phenotype experiments.

    • @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-08 05:32 UTC diff --git a/pages/traits/morphology/non_motile.html b/pages/traits/morphology/non_motile.html index f8d45ebee09..c6e03d9415b 100644 --- a/pages/traits/morphology/non_motile.html +++ b/pages/traits/morphology/non_motile.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -311,9 +312,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • no RELATED_SYNONYM · metpo.owl
      • +
    • no RELATED_SYNONYM · metpo.owl
      • -
    • non-motile RELATED_SYNONYM · metpo.owl
      • +
    • non-motile RELATED_SYNONYM · metpo.owl
    @@ -329,7 +330,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000703 [+135.175, -208.275, +67.323, -38.317, …]
      • +
    • non motile METPO:1000703 [+135.175, -208.275, +67.323, -38.317, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -614,7 +615,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -978,12 +988,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/non_spore_forming.html b/pages/traits/morphology/non_spore_forming.html index 89fb0f7eb9c..349bd7fb051 100644 --- a/pages/traits/morphology/non_spore_forming.html +++ b/pages/traits/morphology/non_spore_forming.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -240,7 +241,7 @@

    Edge evidence

  • DOI:10.1038/s41522-024-00594-6 - Reduced phosphate flow to Spo0A in the sporulation phosphorelay (corroborated by DOI:10.3390/microorganisms11081928). + Reduced phosphate flow to Spo0A in the sporulation phosphorelay (corroborated by DOI:10.3390/microorganisms11081928).
    • @@ -330,9 +331,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • no RELATED_SYNONYM · metpo.owl
      • +
    • no RELATED_SYNONYM · metpo.owl
      • -
    • no_spore RELATED_SYNONYM · metpo.owl
      • +
    • no_spore RELATED_SYNONYM · metpo.owl
    @@ -348,7 +349,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -627,7 +628,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -991,12 +1001,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/orange_pigmented.html b/pages/traits/morphology/orange_pigmented.html index 3acdb005b5e..1bf060a2603 100644 --- a/pages/traits/morphology/orange_pigmented.html +++ b/pages/traits/morphology/orange_pigmented.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -362,7 +363,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Pigment_orange RELATED_SYNONYM · metpo.owl
      • +
    • Pigment_orange RELATED_SYNONYM · metpo.owl
    @@ -378,7 +379,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -660,7 +661,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Replaced elliptical record-level evidence[0].snippet on DOI:10.1080/1040841X.2025.2526423 with contiguous verbatim snippet already present on parent record carotenoid_pigmentation.yaml and sibling records pink_pigmented.yaml and yellow_pigmented.yaml evidence[0] (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-006 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Replaced elliptical record-level evidence[0].snippet on DOI:10.1080/1040841X.2025.2526423 with contiguous verbatim snippet already present on parent record carotenoid_pigmentation.yaml and sibling records pink_pigmented.yaml and yellow_pigmented.yaml evidence[0] (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-006 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -693,7 +694,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1057,12 +1067,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/morphology/oval_shaped.html b/pages/traits/morphology/oval_shaped.html index 196a774f461..e4640a3de98 100644 --- a/pages/traits/morphology/oval_shaped.html +++ b/pages/traits/morphology/oval_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -320,8 +321,8 @@

    Protein and taxon examples

    		 - Streptococcus pneumoniae R6 -
    NCBITaxon:171101 + Streptococcus pneumoniae R6 +
    NCBITaxon:171101         		REVIEWED
    @@ -387,7 +388,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • oval-shaped RELATED_SYNONYM · metpo.owl
      • +
    • oval-shaped RELATED_SYNONYM · metpo.owl
    @@ -403,7 +404,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000678 [-12.940, -17.188, -48.453, +20.919, …]
      • +
    • oval shaped METPO:1000678 [-12.940, -17.188, -48.453, +20.919, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -697,7 +698,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1061,12 +1071,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/ovoid_shaped.html b/pages/traits/morphology/ovoid_shaped.html index f02f6496ca7..a5ada76f555 100644 --- a/pages/traits/morphology/ovoid_shaped.html +++ b/pages/traits/morphology/ovoid_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -339,8 +340,8 @@

    Protein and taxon examples

    		 - Streptococcus pneumoniae R6 -
    NCBITaxon:171101 + Streptococcus pneumoniae R6 +
    NCBITaxon:171101         		REVIEWED
    @@ -406,9 +407,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • S_ovoid RELATED_SYNONYM · metpo.owl
      • +
    • S_ovoid RELATED_SYNONYM · metpo.owl
      • -
    • ovoid-shaped RELATED_SYNONYM · metpo.owl
      • +
    • ovoid-shaped RELATED_SYNONYM · metpo.owl
    @@ -424,7 +425,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -700,7 +701,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1064,12 +1074,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/palmelloid_formation.html b/pages/traits/morphology/palmelloid_formation.html index a0d6fc2ae2d..70a0cddfada 100644 --- a/pages/traits/morphology/palmelloid_formation.html +++ b/pages/traits/morphology/palmelloid_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.3390/ijms24098374
    the cells continue to divide within the mother cell, i.e., they are unable to separate and remain encased in a single membrane.
    -

    Suwannachuen et al. (2023), PMID:37176080, PMC10179368, Discussion 3.3. The quote is the authors' interpretation of enclosed dividing cells, not an abstract quote or a specific molecular mechanism. Results 2.5 and actual Figure 10 show CC-4414 palmelloids after high-light exposure in TAP medium. Methods 4.2 defines the percentage as palmelloid area divided by total cell area, not an individual-cell count. Larger aggregates are distinguished from palmelloids. CC-4414 provenance remains qualified in the discussion below.

    +

    Suwannachuen et al. (2023), PMID:37176080, PMC10179368, Discussion 3.3. The quote is the authors' interpretation of enclosed dividing cells, not an abstract quote or a specific molecular mechanism. Results 2.5 and actual Figure 10 show CC-4414 palmelloids after high-light exposure in TAP medium. Methods 4.2 defines the percentage as palmelloid area divided by total cell area, not an individual-cell count. Larger aggregates are distinguished from palmelloids. CC-4414 provenance remains qualified in the discussion below.

  • DOI:10.3389/fpls.2022.911035
    a morphological state characterized by multiple, single cells encased in an outer limiting membrane
    -

    Szyszka-Mroz et al. (2022), PMID:36119589, PMC9470844, Introduction. The scientific abstract, growth Methods, morphology Results and actual Figure 1 were inspected. Palmelloids occur alongside single cells at permissive 8 C; stress is not a necessary condition. Internal cells may retain flagella. Shared enclosure does not establish a particular membrane chemistry or universal cytokinesis defect.

    +

    Szyszka-Mroz et al. (2022), PMID:36119589, PMC9470844, Introduction. The scientific abstract, growth Methods, morphology Results and actual Figure 1 were inspected. Palmelloids occur alongside single cells at permissive 8 C; stress is not a necessary condition. Internal cells may retain flagella. Shared enclosure does not establish a particular membrane chemistry or universal cytokinesis defect.

  • DOI:10.1038/s41598-019-39558-8
    the production of a gelatinous material that is secreted extracellularly, resulting in adhesion among cells and/or colonies
    -

    Herron et al. (2019), PMID:30787483, PMC6382799, Discussion. Directly retrieved full text explicitly uses palmelloid for both mother-wall retention and extracellular-material-mediated adhesion. This quote supports the second sense. The adjacent text describes palmelloids as nonmotile. This is terminology evidence, not a claim that the selected evolved isolates are natural canonical examples. The narrower enclosed-cell usage in the 2022/2023 sources is retained with its source attribution.

    +

    Herron et al. (2019), PMID:30787483, PMC6382799, Discussion. Directly retrieved full text explicitly uses palmelloid for both mother-wall retention and extracellular-material-mediated adhesion. This quote supports the second sense. The adjacent text describes palmelloids as nonmotile. This is terminology evidence, not a claim that the selected evolved isolates are natural canonical examples. The narrower enclosed-cell usage in the 2022/2023 sources is retained with its source attribution.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -300,7 +301,7 @@

    Discussions and Knowledge Gaps (3)

    mechanism it concerns.

    -

    The 2023 paper and Chlamydomonas Resource Center describe CC-4414/DN2 as a field isolate: https://www.chlamycollection.org/product/cc-4414-wild-type-mt-dn2/ . However, Flowers et al. (2015), Results accompanying Figure 2, reports extensive identity-by-descent with laboratory strains and raises possible cross-contamination while retaining a distinct chromosome-16 segment: https://academic.oup.com/plcell/article/27/9/2353/6206349 . Both primary passages were directly read. This is a provenance uncertainty, not proof of engineering or contamination in the 2023 experimental stock. Preserve the observed high-light phenotype as qualified evidence, but omit CC-4414 from canonical examples pending reconciliation.

    +

    The 2023 paper and Chlamydomonas Resource Center describe CC-4414/DN2 as a field isolate: https://www.chlamycollection.org/product/cc-4414-wild-type-mt-dn2/ . However, Flowers et al. (2015), Results accompanying Figure 2, reports extensive identity-by-descent with laboratory strains and raises possible cross-contamination while retaining a distinct chromosome-16 segment: https://academic.oup.com/plcell/article/27/9/2353/6206349 . Both primary passages were directly read. This is a provenance uncertainty, not proof of engineering or contamination in the 2023 experimental stock. Preserve the observed high-light phenotype as qualified evidence, but omit CC-4414 from canonical examples pending reconciliation.

    @@ -328,7 +329,7 @@

    Curation history

  • · CORRECTED_DEFINITION_SCOPE · codex -

    Addressed issue #1767: the unqualified palmelloid label was narrower than documented usage. Added DOI:10.1038/s41598-019-39558-8 and its verified snippet, broadened the definition to include extracellular-material adhesion, and retained source-specific scope and mechanism distinctions. Canonical example unchanged.

    +

    Addressed issue #1767: the unqualified palmelloid label was narrower than documented usage. Added DOI:10.1038/s41598-019-39558-8 and its verified snippet, broadened the definition to include extracellular-material adhesion, and retained source-specific scope and mechanism distinctions. Canonical example unchanged.

    • @@ -344,7 +345,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Correct palmelloid definition to cover both documented senses -

      Addresses issue #1767. The initial unqualified definition covered only mother-wall retention. Directly retrieved Herron et al. (2019), DOI:10.1038/s41598-019-39558-8, Discussion explicitly also includes extracellular gelatinous material causing adhesion. Broadened the definition and v530 proposal, added a verified 17-word snippet, and revised scope/mechanism discussions while retaining the qualified Antarctic canonical example. The guarded writer preserves the first curation event and appends CORRECTED_DEFINITION_SCOPE. The original CREATE record history/records/palmelloid_formation/2026-10-07T004714Z-codex-8e7daa.yaml remains accurate about the initial state and is unchanged. Twenty-four revised writer tests and dry run passed; final artifact regeneration, corpus validation and PR review remain pending. The obsolete validation process was deliberately terminated and is not claimed as a complete pass.

    +

    Addresses issue #1767. The initial unqualified definition covered only mother-wall retention. Directly retrieved Herron et al. (2019), DOI:10.1038/s41598-019-39558-8, Discussion explicitly also includes extracellular gelatinous material causing adhesion. Broadened the definition and v530 proposal, added a verified 17-word snippet, and revised scope/mechanism discussions while retaining the qualified Antarctic canonical example. The guarded writer preserves the first curation event and appends CORRECTED_DEFINITION_SCOPE. The original CREATE record history/records/palmelloid_formation/2026-10-07T004714Z-codex-8e7daa.yaml remains accurate about the initial state and is unchanged. Twenty-four revised writer tests and dry run passed; final artifact regeneration, corpus validation and PR review remain pending. The obsolete validation process was deliberately terminated and is not claimed as a complete pass.

    • Read this curation session @@ -376,7 +377,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -405,12 +415,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 00:59 UTC diff --git a/pages/traits/morphology/peritrichous.html b/pages/traits/morphology/peritrichous.html index e017b6403ad..82acf3792a1 100644 --- a/pages/traits/morphology/peritrichous.html +++ b/pages/traits/morphology/peritrichous.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    GO:0009288 defines peritrichous - traitmech:000060 + traitmech:000060 METPO:2007500

    Flagella distributed over the cell surface define the peritrichous arrangement.

      @@ -115,7 +116,7 @@

      Edge evidence

    • peritrichous - traitmech:000060 + traitmech:000060 associated with surface-distributed placement @@ -153,7 +154,7 @@

      Edge evidence

    • peritrichous - traitmech:000060 + traitmech:000060 distinguished from polar flagellar arrangement @@ -299,7 +300,7 @@

      kg-microbe context

      via parent_proxy.

      512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

      @@ -512,7 +513,7 @@

      Curation history

    • · ENRICH_CAUSAL_GRAPH · codex -

      Replaced a polar-flagellation FlhG claim and an unrelated carbon-limitation island with the taxon-scoped B. subtilis rod/peptidoglycan mechanism supported by DOI:10.1128/mbio.00530-25. Connected the filament-number branch with a weak association rather than treating flagellar count as diagnostic; the graph is now one connected component.

      +

      Replaced a polar-flagellation FlhG claim and an unrelated carbon-limitation island with the taxon-scoped B. subtilis rod/peptidoglycan mechanism supported by DOI:10.1128/mbio.00530-25. Connected the filament-number branch with a weak association rather than treating flagellar count as diagnostic; the graph is now one connected component.

    • @@ -524,7 +525,7 @@

      Curation history

    • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

      Added verified verbatim snippet from DOI:10.1093/femsre/fuv034 (already present on causal_graphs[0].edges[2].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-003 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

      +

      Added verified verbatim snippet from DOI:10.1093/femsre/fuv034 (already present on causal_graphs[0].edges[2].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-003 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

      • @@ -534,7 +535,7 @@

      Recorded curation sessions

    • · codex
      • EDIT — Apply verified peritrichous graph research -

        Verified the historical enrichment lead against the current trait and primary sources. Removed a polar-specific FlhG branch and an unrelated carbon-limitation island, added the taxon-scoped Bacillus subtilis flagellar-rod and peptidoglycan-pore patterning mechanism from DOI:10.1128/mbio.00530-25, and connected the filament-number branch with a deliberately weak association. The graph moved from four components to one, reducing the corpus baseline by one fragmented graph and six unreachable nodes without introducing predicate-domain or evidence-snippet debt.

      +

      Verified the historical enrichment lead against the current trait and primary sources. Removed a polar-specific FlhG branch and an unrelated carbon-limitation island, added the taxon-scoped Bacillus subtilis flagellar-rod and peptidoglycan-pore patterning mechanism from DOI:10.1128/mbio.00530-25, and connected the filament-number branch with a deliberately weak association. The graph moved from four components to one, reducing the corpus baseline by one fragmented graph and six unreachable nodes without introducing predicate-domain or evidence-snippet debt.

    Read this curation session @@ -566,7 +567,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -930,12 +940,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/morphology/pigmentation.html b/pages/traits/morphology/pigmentation.html index 2f3e1f4b125..04f08e0e15c 100644 --- a/pages/traits/morphology/pigmentation.html +++ b/pages/traits/morphology/pigmentation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -227,7 +228,7 @@

    Edge evidence

    is a carotenoid biosynthesis GO:0016117 - rdfs:subClassOf + rdfs:subClassOf

    Beta-carotene biosynthesis is a specific carotenoid biosynthetic route.

      @@ -418,7 +419,7 @@

      kg-microbe context

      via direct_metpo.

      512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

      @@ -685,7 +686,7 @@

      Curation history

    • · ADD_CANONICAL_EXAMPLES · codex -

      Added Serratia marcescens as a directly observed pigmentation example using wild-type SCQ1 red-colony prodigiosin evidence from DOI:10.3389/fmicb.2021.793202; verified the current species taxon and label through NCBI Taxonomy.

      +

      Added Serratia marcescens as a directly observed pigmentation example using wild-type SCQ1 red-colony prodigiosin evidence from DOI:10.3389/fmicb.2021.793202; verified the current species taxon and label through NCBI Taxonomy.

    • @@ -724,7 +725,16 @@

      Identifier

      Term kind
      CLASS
      Status
      -
      REVIEWED
      +
      REVIEWED + + +
      + What this status means +

      Curator has signed off on label / definition / parents.

      +

      Quoted from the schema's status definitions.

      +
      + +
    @@ -1088,12 +1098,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 17:46 UTC diff --git a/pages/traits/morphology/pink_pigmented.html b/pages/traits/morphology/pink_pigmented.html index 9f39b18edd4..a8ad5ca4e60 100644 --- a/pages/traits/morphology/pink_pigmented.html +++ b/pages/traits/morphology/pink_pigmented.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -343,7 +344,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Pigment_pink RELATED_SYNONYM · metpo.owl
      • +
    • Pigment_pink RELATED_SYNONYM · metpo.owl
    @@ -359,7 +360,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -662,7 +663,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1026,12 +1036,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/pleomorphic_shaped.html b/pages/traits/morphology/pleomorphic_shaped.html index 1ae11e829fd..96badd5b334 100644 --- a/pages/traits/morphology/pleomorphic_shaped.html +++ b/pages/traits/morphology/pleomorphic_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -311,11 +312,11 @@

    Parent traits (1)

    Synonyms (3)

      -
    • S_star_dumbbell_pleomorphic RELATED_SYNONYM · metpo.owl
      • +
    • S_star_dumbbell_pleomorphic RELATED_SYNONYM · metpo.owl
      • -
    • pleomorphic RELATED_SYNONYM · metpo.owl
      • +
    • pleomorphic RELATED_SYNONYM · metpo.owl
      • -
    • pleomorphic-shaped RELATED_SYNONYM · metpo.owl
      • +
    • pleomorphic-shaped RELATED_SYNONYM · metpo.owl
    @@ -331,7 +332,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -423,8 +424,8 @@

    Deep research

    | module | causal chain | strongest source DOI/year | confidence | principal caveat | |---|---|---|---|---| -| **Bacillus subtilis L-form route** | PG precursor synthesis inhibition (e.g., D-cycloserine or glmM repression) → residual **aPBP** synthesis or enhanced **RodA** pathway + **LytE/CwlO** autolysis → wall lesions and often bulging → wall-free L-form state → loss of rigid wall-based shape constraint → pleomorphic/irregular morphology; in parallel, **excess membrane synthesis** increases surface area-to-volume ratio → blebbing/tubulation/scission for FtsZ-independent proliferation; **ROS reduction** supports survival/proliferation but is not evidenced as the direct cause of pleomorphic shape (kawai2023dissectingtheroles pages 7-9, kawai2023dissectingtheroles pages 1-2, kawai2023dissectingtheroles pages 5-7, mercier2013excessmembranesynthesis pages 7-8, kawai2015cellgrowthof pages 1-3, kawai2015cellgrowthof pages 5-6, tian2024implementationoffluorescentproteinbased pages 4-6) | 10.3389/fmicb.2023.1204979 (2023); 10.1016/j.cell.2013.01.043 (2013); 10.1016/j.cub.2015.04.031 (2015) | High | Strongly supported for **B. subtilis** under osmoprotective experimental conditions; pleomorphism is largely inferred from wall-loss/irregular L-form morphology and should not be overgeneralized to all bacteria or all wall-deficient states. | -| **Haloferax volcanii shape-plasticity route** | Growth phase/state cues → **RdfA/Sph3/CetZ1** rod-promoting program versus **DdfA/volactin** disk-promoting program → rods in early-log/swimming states and disks in mid/late-log or other states → population/time-dependent coexistence of multiple morphologies consistent with pleomorphic shape plasticity (schiller2024identificationofstructural pages 1-2, schiller2024identificationofstructural pages 6-7, schiller2024identificationofstructural pages 3-5, schiller2024identificationofstructural pages 5-5, schiller2024identificationofstructural pages 7-9, schiller2024identificationofstructural pages 2-3) | 10.1038/s41467-024-45196-0 (2024) | Moderate-High | Evidence is strongest for regulated **rod↔disk transitions** in a specific haloarchaeon; this supports shape plasticity/pleomorphism at the population or temporal level, but not a generic archaeal pleomorphism mechanism, and some cited determinants are shape-state specific rather than direct causes of irregular morphology. | +| **Bacillus subtilis L-form route** | PG precursor synthesis inhibition (e.g., D-cycloserine or glmM repression) → residual **aPBP** synthesis or enhanced **RodA** pathway + **LytE/CwlO** autolysis → wall lesions and often bulging → wall-free L-form state → loss of rigid wall-based shape constraint → pleomorphic/irregular morphology; in parallel, **excess membrane synthesis** increases surface area-to-volume ratio → blebbing/tubulation/scission for FtsZ-independent proliferation; **ROS reduction** supports survival/proliferation but is not evidenced as the direct cause of pleomorphic shape (kawai2023dissectingtheroles pages 7-9, kawai2023dissectingtheroles pages 1-2, kawai2023dissectingtheroles pages 5-7, mercier2013excessmembranesynthesis pages 7-8, kawai2015cellgrowthof pages 1-3, kawai2015cellgrowthof pages 5-6, tian2024implementationoffluorescentproteinbased pages 4-6) | 10.3389/fmicb.2023.1204979 (2023); 10.1016/j.cell.2013.01.043 (2013); 10.1016/j.cub.2015.04.031 (2015) | High | Strongly supported for **B. subtilis** under osmoprotective experimental conditions; pleomorphism is largely inferred from wall-loss/irregular L-form morphology and should not be overgeneralized to all bacteria or all wall-deficient states. | +| **Haloferax volcanii shape-plasticity route** | Growth phase/state cues → **RdfA/Sph3/CetZ1** rod-promoting program versus **DdfA/volactin** disk-promoting program → rods in early-log/swimming states and disks in mid/late-log or other states → population/time-dependent coexistence of multiple morphologies consistent with pleomorphic shape plasticity (schiller2024identificationofstructural pages 1-2, schiller2024identificationofstructural pages 6-7, schiller2024identificationofstructural pages 3-5, schiller2024identificationofstructural pages 5-5, schiller2024identificationofstructural pages 7-9, schiller2024identificationofstructural pages 2-3) | 10.1038/s41467-024-45196-0 (2024) | Moderate-High | Evidence is strongest for regulated **rod↔disk transitions** in a specific haloarchaeon; this supports shape plasticity/pleomorphism at the population or temporal level, but not a generic archaeal pleomorphism mechanism, and some cited determinants are shape-state specific rather than direct causes of irregular morphology. | *Table: This table summarizes two evidence-supported mechanistic routes linked to METPO:1000679 using only gathered evidence. It is useful for deciding which causal chains are strong enough for TraitMech curation and where taxon or assay caveats remain.* @@ -583,7 +584,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -947,12 +957,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/polar_flagellation.html b/pages/traits/morphology/polar_flagellation.html index d8d3a4c87fa..335fda9ce0a 100644 --- a/pages/traits/morphology/polar_flagellation.html +++ b/pages/traits/morphology/polar_flagellation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -180,8 +181,8 @@

    Protein and taxon examples

    		 - Vibrio alginolyticus -
    NCBITaxon:663 + Vibrio alginolyticus +
    NCBITaxon:663         		UNREVIEWED
    @@ -210,8 +211,8 @@

    Protein and taxon examples

    		 - Vibrio alginolyticus -
    NCBITaxon:663 + Vibrio alginolyticus +
    NCBITaxon:663         		UNREVIEWED
    @@ -277,7 +278,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • flagellum arrangement RELATED_SYNONYM · metpo.owl
      • +
    • flagellum arrangement RELATED_SYNONYM · metpo.owl
    @@ -293,7 +294,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -452,7 +453,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -816,12 +826,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 21:12 UTC diff --git a/pages/traits/morphology/polyhydroxyalkanoate_granule.html b/pages/traits/morphology/polyhydroxyalkanoate_granule.html index af87b96c861..d8ed7fe9eed 100644 --- a/pages/traits/morphology/polyhydroxyalkanoate_granule.html +++ b/pages/traits/morphology/polyhydroxyalkanoate_granule.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    located in polyhydroxyalkanoate granule - traitmech:000067 + traitmech:000067 biolink:located_in

    PHA polymer accumulates inside cytoplasmic granules.

      @@ -115,7 +116,7 @@

      Edge evidence

    • polyhydroxyalkanoate granule - traitmech:000067 + traitmech:000067 enables carbon and energy storage @@ -308,7 +309,7 @@

      Edge evidence

      contributes to polyhydroxyalkanoate granule - traitmech:000067 + traitmech:000067 RO:0002326

      Intracellular accumulation of amorphous PHA produces the polymer body represented by the granule trait.

        @@ -383,8 +384,8 @@

        Protein and taxon examples

    		 - Cupriavidus necator H16 -
    NCBITaxon:381666 + Cupriavidus necator H16 +
    NCBITaxon:381666         		REVIEWED
    @@ -450,11 +451,11 @@

    Parent traits (1)

    Synonyms (3)

    @@ -477,7 +478,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -759,7 +760,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1123,12 +1133,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/polyphosphate_granule.html b/pages/traits/morphology/polyphosphate_granule.html index d61805312fe..28c97b790bf 100644 --- a/pages/traits/morphology/polyphosphate_granule.html +++ b/pages/traits/morphology/polyphosphate_granule.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    located in polyphosphate granule - traitmech:000068 + traitmech:000068 biolink:located_in

    Inorganic polyphosphate accumulates as granules in the cytoplasm.

      @@ -115,7 +116,7 @@

      Edge evidence

    • polyphosphate granule - traitmech:000068 + traitmech:000068 contributes to phosphate / energy reserve @@ -231,8 +232,8 @@

      Protein and taxon examples

    		 - Microlunatus phosphovorus NM-1 -
    NCBITaxon:1032480 + Microlunatus phosphovorus NM-1 +
    NCBITaxon:1032480         		UNREVIEWED
    @@ -298,9 +299,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -316,7 +317,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -595,7 +596,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -959,12 +969,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/polytrichous_flagellation.html b/pages/traits/morphology/polytrichous_flagellation.html index 2fdd16ce840..17866809831 100644 --- a/pages/traits/morphology/polytrichous_flagellation.html +++ b/pages/traits/morphology/polytrichous_flagellation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -76,7 +77,7 @@

    Trait evidence (2)

    Polytrichous multi-flagellar tuft arrangement and swimming motility

    Evidence-backed morphology sketch linking monopolar or bipolar multi-flagellar tufts to polytrichous flagellation and swimming locomotion.

    -

    NONMECHANISTIC · Morphological arrangement sketch backed by DOI:10.1128/AEM.64.10.3576-3583.1998 and DOI:10.1128/AEM.68.12.6310-6320.2002; specific flagellar structural or placement proteins in Thermocrinis ruber are not identified in the cited electron-microscopy and motility sources.

    +

    NONMECHANISTIC · Morphological arrangement sketch backed by DOI:10.1128/AEM.64.10.3576-3583.1998 and DOI:10.1128/AEM.68.12.6310-6320.2002; specific flagellar structural or placement proteins in Thermocrinis ruber are not identified in the cited electron-microscopy and motility sources.

    Loading graph…

    @@ -178,7 +179,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • polytrichous EXACT_SYNONYM · metpo.owl
      • +
    • polytrichous EXACT_SYNONYM · metpo.owl
    @@ -194,7 +195,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -321,7 +322,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add polytrichous flagellation trait -

      Seeded METPO:1007006 as a morphology TraitRecord, replaced the duplicate upstream METPO:1007005 parent with the reviewed local flagellar-arrangement parent traitmech:000056, added DOI:10.1128/AEM.64.10.3576-3583.1998 and DOI:10.1128/AEM.68.12.6310-6320.2002 evidence, and added Thermocrinis ruber NCBITaxon:75906 as a canonical example. No causal graph was added because the reusable placement trait has direct morphology evidence but published FlhF/FlhG placement programs are organism-specific.

    +

    Seeded METPO:1007006 as a morphology TraitRecord, replaced the duplicate upstream METPO:1007005 parent with the reviewed local flagellar-arrangement parent traitmech:000056, added DOI:10.1128/AEM.64.10.3576-3583.1998 and DOI:10.1128/AEM.68.12.6310-6320.2002 evidence, and added Thermocrinis ruber NCBITaxon:75906 as a canonical example. No causal graph was added because the reusable placement trait has direct morphology evidence but published FlhF/FlhG placement programs are organism-specific.

    • Read this curation session @@ -353,7 +354,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -717,12 +727,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 21:12 UTC diff --git a/pages/traits/morphology/prosthecate.html b/pages/traits/morphology/prosthecate.html index 806aabfa3f3..9db38fa9e4d 100644 --- a/pages/traits/morphology/prosthecate.html +++ b/pages/traits/morphology/prosthecate.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    confers prosthecate - traitmech:000065 + traitmech:000065 METPO:2007700

    Regulated stalk-extension elongation realizes the prosthecate phenotype.

      @@ -115,7 +116,7 @@

      Edge evidence

    • prosthecate - traitmech:000065 + traitmech:000065 contributes to nutrient-uptake surface area @@ -229,7 +230,7 @@

      Edge evidence

    • prosthecate - traitmech:000065 + traitmech:000065 facilitates nutrient-uptake surface area @@ -292,9 +293,9 @@

      Parent traits (1)

      Synonyms (2)

    @@ -310,7 +311,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -580,7 +581,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -944,12 +954,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/pseudohyphal_growth.html b/pages/traits/morphology/pseudohyphal_growth.html index 6c86b182148..7cdf3e415f9 100644 --- a/pages/traits/morphology/pseudohyphal_growth.html +++ b/pages/traits/morphology/pseudohyphal_growth.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1590/S1517-83822013005000056
    pseudohyphae formed branched chains of elongated blastoconidial cells retaining constrictions at the septal junctions
    -

    Staniszewska et al. (2013), PMID:24516422, PMC3910194, Results subsection Pseudohyphae. Full-text XML, strain/culture Methods, Table 1 and actual Figure 4 were inspected. Clinical isolate 82 forms pseudohyphae mixed with true hyphae after six hours in serum; later hyphal predominance is not a contradictory same-time observation. The quote is from Results, not the abstract. Numerical morphology indices and serum induction conditions are study-specific, not universal trait thresholds.

    +

    Staniszewska et al. (2013), PMID:24516422, PMC3910194, Results subsection Pseudohyphae. Full-text XML, strain/culture Methods, Table 1 and actual Figure 4 were inspected. Clinical isolate 82 forms pseudohyphae mixed with true hyphae after six hours in serum; later hyphal predominance is not a contradictory same-time observation. The quote is from Results, not the abstract. Numerical morphology indices and serum induction conditions are study-specific, not universal trait thresholds.

  • DOI:10.1016/0092-8674(92)90079-r
    Cells become long and thin and form pseudohyphae that grow away from the colony and invade the agar medium.
    -

    Gimeno et al. (1992), PMID:1547504, scientific abstract directly retrieved through Europe PMC. Diploid Saccharomyces cerevisiae under nitrogen starvation changes morphology and budding pattern. The abstract also reports RAS2, SHR3 and RSR1/BUD1 perturbations. Full text and figures were not verified. Diploidy, nitrogen starvation and agar invasion describe this study, not necessary conditions for every pseudohyphal yeast.

    +

    Gimeno et al. (1992), PMID:1547504, scientific abstract directly retrieved through Europe PMC. Diploid Saccharomyces cerevisiae under nitrogen starvation changes morphology and budding pattern. The abstract also reports RAS2, SHR3 and RSR1/BUD1 perturbations. Full text and figures were not verified. Diploidy, nitrogen starvation and agar invasion describe this study, not necessary conditions for every pseudohyphal yeast.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -296,7 +297,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed pseudohyphal growth -

      Created traitmech:000653 with DOI:10.1590/S1517-83822013005000056 and DOI:10.1016/0092-8674(92)90079-r, two directly checked snippets, and a condition-qualified Candida albicans clinical-isolate example resolved as NCBITaxon:5476. Ignored-and-hidden novelty searches and a fresh structured METPO frontier audit found no exact record. Added two scope/mechanism discussions and a v529 proposal reserving METPO:1060600. Existing records remain unchanged. The guarded writer dry run and 20 focused tests passed; corpus validation, generated artifacts and PR review remain pending at this event.

    +

    Created traitmech:000653 with DOI:10.1590/S1517-83822013005000056 and DOI:10.1016/0092-8674(92)90079-r, two directly checked snippets, and a condition-qualified Candida albicans clinical-isolate example resolved as NCBITaxon:5476. Ignored-and-hidden novelty searches and a fresh structured METPO frontier audit found no exact record. Added two scope/mechanism discussions and a v529 proposal reserving METPO:1060600. Existing records remain unchanged. The guarded writer dry run and 20 focused tests passed; corpus validation, generated artifacts and PR review remain pending at this event.

    • Read this curation session @@ -328,7 +329,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -357,12 +367,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 23:56 UTC diff --git a/pages/traits/morphology/red_pigmented.html b/pages/traits/morphology/red_pigmented.html index 02731e564d0..d705e980e11 100644 --- a/pages/traits/morphology/red_pigmented.html +++ b/pages/traits/morphology/red_pigmented.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -324,7 +325,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Pigment_red RELATED_SYNONYM · metpo.owl
      • +
    • Pigment_red RELATED_SYNONYM · metpo.owl
    @@ -340,7 +341,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -451,16 +452,16 @@

    Deep research

    | subject | predicate | object | taxon/strain | evidence type | confidence | DOI | |---|---|---|---|---|---|---| -| pigABCDEFGHIJKLMN operon | enables biosynthesis of | prodigiosin | *Serratia marcescens* ATCC 274; JNB5-1 | operon/genetic evidence, transcriptional response (esteves2024serratiamarcescensatcc pages 1-2, pan2021regulatorrcsbcontrols pages 7-10) | High | 10.1038/s41598-024-68747-3; 10.1128/AEM.02052-20 | -| MAP precursor branch + MBC precursor branch | are condensed by | PigC to form prodigiosin | *Serratia* spp. / prodigiosin pathway literature | pathway/mechanistic review summarized from primary studies (esteves2024serratiamarcescensatcc pages 11-12, sun2020improvedprodigiosinproduction pages 1-2) | High | 10.1038/nrmicro1531; 10.3389/fbioe.2020.00344 | -| prodigiosin | causes | red pigmented phenotype | *Serratia marcescens* ATCC 274; OK482790 | phenotype-chemistry association, pigment characterization (esteves2024serratiamarcescensatcc pages 1-2, hamada2024characterizationofserratia pages 8-9) | High | 10.1038/s41598-024-68747-3; 10.1186/s12866-024-03634-5 | -| Chi phage infection | increases transcription of | pig operon | *Serratia marcescens* ATCC 274 | primary infection/reporter assay (esteves2024serratiamarcescensatcc pages 1-2) | High | 10.1038/s41598-024-68747-3 | -| Chi phage infection | increases production of | prodigiosin | *Serratia marcescens* ATCC 274 | primary infection/phenotype assay (esteves2024serratiamarcescensatcc pages 1-2) | High | 10.1038/s41598-024-68747-3 | -| CpxR | directly represses transcription of | pig gene cluster promoter | *Serratia marcescens* JNB5-1 | primary EMSA + mutant analysis (sun2020improvedprodigiosinproduction pages 1-2) | High | 10.3389/fbioe.2020.00344 | -| MetR | directly represses transcription of | pigP | *Serratia marcescens* | primary EMSA + RT-qPCR/transcriptomics (pan2020lysrtypetranscriptionalregulator pages 1-2) | High | 10.1128/AEM.02241-19 | -| PigP | positively regulates | pig operon | *Serratia marcescens* | regulator linkage from direct MetR→pigP repression and pigP as positive regulator (pan2020lysrtypetranscriptionalregulator pages 1-2) | High | 10.1128/AEM.02241-19 | -| RcsB | binds promoter of and negatively regulates | flhDC | *Serratia marcescens* JNB5-1 | primary EMSA + expression analysis (pan2021regulatorrcsbcontrols pages 10-12, pan2021regulatorrcsbcontrols pages 46-48) | High | 10.1128/AEM.02052-20 | -| FlhDC | activates biosynthesis of | prodigiosin | *Serratia marcescens* JNB5-1 | primary regulatory genetics downstream of RcsB (pan2021regulatorrcsbcontrols pages 10-12, pan2021regulatorrcsbcontrols pages 1-3) | High | 10.1128/AEM.02052-20 | +| pigABCDEFGHIJKLMN operon | enables biosynthesis of | prodigiosin | *Serratia marcescens* ATCC 274; JNB5-1 | operon/genetic evidence, transcriptional response (esteves2024serratiamarcescensatcc pages 1-2, pan2021regulatorrcsbcontrols pages 7-10) | High | 10.1038/s41598-024-68747-3; 10.1128/AEM.02052-20 | +| MAP precursor branch + MBC precursor branch | are condensed by | PigC to form prodigiosin | *Serratia* spp. / prodigiosin pathway literature | pathway/mechanistic review summarized from primary studies (esteves2024serratiamarcescensatcc pages 11-12, sun2020improvedprodigiosinproduction pages 1-2) | High | 10.1038/nrmicro1531; 10.3389/fbioe.2020.00344 | +| prodigiosin | causes | red pigmented phenotype | *Serratia marcescens* ATCC 274; OK482790 | phenotype-chemistry association, pigment characterization (esteves2024serratiamarcescensatcc pages 1-2, hamada2024characterizationofserratia pages 8-9) | High | 10.1038/s41598-024-68747-3; 10.1186/s12866-024-03634-5 | +| Chi phage infection | increases transcription of | pig operon | *Serratia marcescens* ATCC 274 | primary infection/reporter assay (esteves2024serratiamarcescensatcc pages 1-2) | High | 10.1038/s41598-024-68747-3 | +| Chi phage infection | increases production of | prodigiosin | *Serratia marcescens* ATCC 274 | primary infection/phenotype assay (esteves2024serratiamarcescensatcc pages 1-2) | High | 10.1038/s41598-024-68747-3 | +| CpxR | directly represses transcription of | pig gene cluster promoter | *Serratia marcescens* JNB5-1 | primary EMSA + mutant analysis (sun2020improvedprodigiosinproduction pages 1-2) | High | 10.3389/fbioe.2020.00344 | +| MetR | directly represses transcription of | pigP | *Serratia marcescens* | primary EMSA + RT-qPCR/transcriptomics (pan2020lysrtypetranscriptionalregulator pages 1-2) | High | 10.1128/AEM.02241-19 | +| PigP | positively regulates | pig operon | *Serratia marcescens* | regulator linkage from direct MetR→pigP repression and pigP as positive regulator (pan2020lysrtypetranscriptionalregulator pages 1-2) | High | 10.1128/AEM.02241-19 | +| RcsB | binds promoter of and negatively regulates | flhDC | *Serratia marcescens* JNB5-1 | primary EMSA + expression analysis (pan2021regulatorrcsbcontrols pages 10-12, pan2021regulatorrcsbcontrols pages 46-48) | High | 10.1128/AEM.02052-20 | +| FlhDC | activates biosynthesis of | prodigiosin | *Serratia marcescens* JNB5-1 | primary regulatory genetics downstream of RcsB (pan2021regulatorrcsbcontrols pages 10-12, pan2021regulatorrcsbcontrols pages 1-3) | High | 10.1128/AEM.02052-20 | *Table: This table summarizes the strongest, most curation-ready causal edges for the red pigmented trait METPO:1003028, emphasizing direct genetic and regulatory evidence in Serratia prodigiosin systems. It is useful as a compact starting point for building a TraitMech YAML graph while preserving taxon specificity and confidence.* @@ -634,7 +635,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -998,12 +1008,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/ring_shaped.html b/pages/traits/morphology/ring_shaped.html index 12e293d80ae..f06e509f67d 100644 --- a/pages/traits/morphology/ring_shaped.html +++ b/pages/traits/morphology/ring_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -305,11 +306,11 @@

    Parent traits (1)

    Synonyms (3)

    @@ -332,7 +333,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -653,7 +654,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1017,12 +1027,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-07 20:05 UTC diff --git a/pages/traits/morphology/rod_shaped.html b/pages/traits/morphology/rod_shaped.html index 6fa56b2212d..c4d5e00b08e 100644 --- a/pages/traits/morphology/rod_shaped.html +++ b/pages/traits/morphology/rod_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -349,9 +350,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • S_rod RELATED_SYNONYM · metpo.owl
      • +
    • S_rod RELATED_SYNONYM · metpo.owl
      • -
    • rod-shaped RELATED_SYNONYM · metpo.owl
      • +
    • rod-shaped RELATED_SYNONYM · metpo.owl
    @@ -367,7 +368,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000681 [+3.060, +7.761, -10.358, +10.121, …]
      • +
    • rod shaped METPO:1000681 [+3.060, +7.761, -10.358, +10.121, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -703,7 +704,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1067,12 +1077,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/rosette_cell_arrangement.html b/pages/traits/morphology/rosette_cell_arrangement.html index 35f60fe6fe8..5a63dccca02 100644 --- a/pages/traits/morphology/rosette_cell_arrangement.html +++ b/pages/traits/morphology/rosette_cell_arrangement.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.7554/eLife.41482
    all cells are oriented with their basal poles toward the rosette center and their apical flagella extending out from the rosette surface
    -

    Wetzel et al. (2018), PMID:30556809, PMC6322860, first Results subsection; full-text XML and Figure 1 directly inspected. Wild-type Salpingoeca rosetta rosettes have organized polarity, unlike disordered clumps in the four Class C mutants. Methods identify wild type as SrEpac and use Algoriphagus-derived rosette-inducing factors. The three-cell minimum after vortexing is this study's scoring rule, not a universal definition. Clonal development rather than aggregation is specific to S. rosetta here. The Results quote is not the scientific abstract or editorial digest.

    +

    Wetzel et al. (2018), PMID:30556809, PMC6322860, first Results subsection; full-text XML and Figure 1 directly inspected. Wild-type Salpingoeca rosetta rosettes have organized polarity, unlike disordered clumps in the four Class C mutants. Methods identify wild type as SrEpac and use Algoriphagus-derived rosette-inducing factors. The three-cell minimum after vortexing is this study's scoring rule, not a universal definition. Clonal development rather than aggregation is specific to S. rosetta here. The Results quote is not the scientific abstract or editorial digest.

  • DOI:10.1128/jb.00064-19
    form multicellular rosettes by adhering to each other through the polar polysaccharide, or holdfast.
    -

    Fiebig (2019), PMID:31010900, PMC6707911, Results subsection Holdfasts are prominent in the pellicle. Publisher HTML, growth/sampling/microscopy Methods, and Figure 4 were directly inspected. Static CB15 cultures form rosettes with holdfast-rich cores. The Results describe both radial and oblong rosettes; not every core is a single attachment point. Supplemental Figure S2's text was accessible but its image was not verified. Pellicle dependence on holdfast is not a universal rosette mechanism. The Discussion leaves the field relevance of thick Caulobacter pellicles unresolved; laboratory observations are not evidence that these structures occur in every habitat.

    +

    Fiebig (2019), PMID:31010900, PMC6707911, Results subsection Holdfasts are prominent in the pellicle. Publisher HTML, growth/sampling/microscopy Methods, and Figure 4 were directly inspected. Static CB15 cultures form rosettes with holdfast-rich cores. The Results describe both radial and oblong rosettes; not every core is a single attachment point. Supplemental Figure S2's text was accessible but its image was not verified. Pellicle dependence on holdfast is not a universal rosette mechanism. The Discussion leaves the field relevance of thick Caulobacter pellicles unresolved; laboratory observations are not evidence that these structures occur in every habitat.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Canonical examples DOI:10.7554/eLife.41482 - Wild-type SrEpac (ATCC PRA-390) in rosette-inducing-factor cultures, not every life stage. Natural-isolate provenance was checked in Levin and King's Experimental Procedures: https://doi.org/10.1016/j.cub.2013.08.061. SrEpac is isolate C, derived from Px1 by feeder replacement, antibiotic treatment and clonal isolation; Px1 derives from environmental rosette isolate ATCC 50818. It is not the EMS-mutagenized isolate B. The provenance citation is not counted as independent trait evidence. NCBI Taxonomy resolves the species ID and label. + Wild-type SrEpac (ATCC PRA-390) in rosette-inducing-factor cultures, not every life stage. Natural-isolate provenance was checked in Levin and King's Experimental Procedures: https://doi.org/10.1016/j.cub.2013.08.061. SrEpac is isolate C, derived from Px1 by feeder replacement, antibiotic treatment and clonal isolation; Px1 derives from environmental rosette isolate ATCC 50818. It is not the EMS-mutagenized isolate B. The provenance citation is not counted as independent trait evidence. NCBI Taxonomy resolves the species ID and label. @@ -296,7 +297,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed rosette cell arrangement -

      Added traitmech:000652 as PROPOSED MORPHOLOGY with DOI:10.7554/eLife.41482 and DOI:10.1128/jb.00064-19 Results snippets, a provenance-qualified Salpingoeca rosetta NCBITaxon:946362 example, and two OPEN scope/mechanism discussions. SrEpac provenance was directly checked in DOI:10.1016/j.cub.2013.08.061; this is not counted as independent trait evidence. Ignored-and-hidden novelty and identifier searches plus fresh seed, release/review, RDF and pinned-template audits found no exact record or collision. Reserved METPO:1060500 in v528. Writer dry run and 20 focused tests passed; full validation, artifact generation and PR review were pending at this event. No existing trait was edited.

    +

    Added traitmech:000652 as PROPOSED MORPHOLOGY with DOI:10.7554/eLife.41482 and DOI:10.1128/jb.00064-19 Results snippets, a provenance-qualified Salpingoeca rosetta NCBITaxon:946362 example, and two OPEN scope/mechanism discussions. SrEpac provenance was directly checked in DOI:10.1016/j.cub.2013.08.061; this is not counted as independent trait evidence. Ignored-and-hidden novelty and identifier searches plus fresh seed, release/review, RDF and pinned-template audits found no exact record or collision. Reserved METPO:1060500 in v528. Writer dry run and 20 focused tests passed; full validation, artifact generation and PR review were pending at this event. No existing trait was edited.

    • Read this curation session @@ -328,7 +329,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -357,12 +367,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 23:08 UTC diff --git a/pages/traits/morphology/s_layer.html b/pages/traits/morphology/s_layer.html index 80be2c79c11..8984c19a371 100644 --- a/pages/traits/morphology/s_layer.html +++ b/pages/traits/morphology/s_layer.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    confers S-layer - traitmech:000064 + traitmech:000064 METPO:2007700

    Completed 2D assembly realizes the S-layer surface coating.

      @@ -197,7 +198,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • surface layer RELATED_SYNONYM · DOI:10.1038/nrmicro3213
        • +
      • surface layer RELATED_SYNONYM · DOI:10.1038/nrmicro3213
    @@ -213,7 +214,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -453,7 +454,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -817,12 +827,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/sarcina_arrangement.html b/pages/traits/morphology/sarcina_arrangement.html index f920126d2c0..8dbab7885e1 100644 --- a/pages/traits/morphology/sarcina_arrangement.html +++ b/pages/traits/morphology/sarcina_arrangement.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    causes sarcina arrangement - traitmech:000120 + traitmech:000120 biolink:causes

    Three perpendicular division planes with incomplete separation yield cubic eight-cell packets.

      @@ -118,7 +119,7 @@

      Edge evidence

      GO:0051301 confers sarcina arrangement - traitmech:000120 + traitmech:000120 METPO:2007700

      Bacterial cell division underlies sarcina packet formation.

        @@ -311,7 +312,7 @@

        Parent traits (1)

        Synonyms (1)

          -
        • cubic packet cocci RELATED_SYNONYM · DOI:10.1128/MMBR.00001-06
          • +
        • cubic packet cocci RELATED_SYNONYM · DOI:10.1128/MMBR.00001-06
    @@ -327,7 +328,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]
      • +
    • cell shape METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -591,7 +592,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -955,12 +965,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/sphere_shaped.html b/pages/traits/morphology/sphere_shaped.html index 99868869285..dbbdb13a817 100644 --- a/pages/traits/morphology/sphere_shaped.html +++ b/pages/traits/morphology/sphere_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -324,9 +325,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • S_sphere RELATED_SYNONYM · metpo.owl
      • +
    • S_sphere RELATED_SYNONYM · metpo.owl
      • -
    • sphere-shaped RELATED_SYNONYM · metpo.owl
      • +
    • sphere-shaped RELATED_SYNONYM · metpo.owl
    @@ -342,7 +343,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -645,7 +646,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1009,12 +1019,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/spindle_shaped.html b/pages/traits/morphology/spindle_shaped.html index 2f4bd227263..e540353f468 100644 --- a/pages/traits/morphology/spindle_shaped.html +++ b/pages/traits/morphology/spindle_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -229,7 +230,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • spindle RELATED_SYNONYM · metpo.owl
      • +
    • spindle RELATED_SYNONYM · metpo.owl
    @@ -245,7 +246,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -515,7 +516,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -879,12 +889,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/spiral_shaped.html b/pages/traits/morphology/spiral_shaped.html index 0a25a1a8cae..82a4eee2e8e 100644 --- a/pages/traits/morphology/spiral_shaped.html +++ b/pages/traits/morphology/spiral_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -324,11 +325,11 @@

    Parent traits (1)

    Synonyms (3)

      -
    • S_curved_spiral RELATED_SYNONYM · metpo.owl
      • +
    • S_curved_spiral RELATED_SYNONYM · metpo.owl
      • -
    • spiral RELATED_SYNONYM · metpo.owl
      • +
    • spiral RELATED_SYNONYM · metpo.owl
      • -
    • spiral-shaped RELATED_SYNONYM · metpo.owl
      • +
    • spiral-shaped RELATED_SYNONYM · metpo.owl
    @@ -344,7 +345,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -626,7 +627,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -990,12 +1000,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/spirochete_shaped.html b/pages/traits/morphology/spirochete_shaped.html index 5f8c0814235..688513126b1 100644 --- a/pages/traits/morphology/spirochete_shaped.html +++ b/pages/traits/morphology/spirochete_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -343,7 +344,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • spirochete RELATED_SYNONYM · metpo.owl
      • +
    • spirochete RELATED_SYNONYM · metpo.owl
    @@ -359,7 +360,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -614,7 +615,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Replaced elliptical record-level evidence[0].snippet on DOI:10.1073/pnas.200221797 with contiguous verbatim snippet already present on causal_graphs[0].edges[3].evidence[0] (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-007 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Replaced elliptical record-level evidence[0].snippet on DOI:10.1073/pnas.200221797 with contiguous verbatim snippet already present on causal_graphs[0].edges[3].evidence[0] (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-007 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -647,7 +648,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1011,12 +1021,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/morphology/spore_forming.html b/pages/traits/morphology/spore_forming.html index 0c3918ab3d7..846c4f176dc 100644 --- a/pages/traits/morphology/spore_forming.html +++ b/pages/traits/morphology/spore_forming.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -383,8 +384,8 @@

    Protein and taxon examples

    		 - Bacillus subtilis 168 -
    NCBITaxon:224308 + Bacillus subtilis 168 +
    NCBITaxon:224308         		REVIEWED
    @@ -450,9 +451,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • spore RELATED_SYNONYM · metpo.owl
      • +
    • spore RELATED_SYNONYM · metpo.owl
      • -
    • yes RELATED_SYNONYM · metpo.owl
      • +
    • yes RELATED_SYNONYM · metpo.owl
    @@ -468,7 +469,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -804,7 +805,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1168,12 +1178,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/spore_shaped.html b/pages/traits/morphology/spore_shaped.html index fbde4acb099..fa6f8d0c499 100644 --- a/pages/traits/morphology/spore_shaped.html +++ b/pages/traits/morphology/spore_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -434,8 +435,8 @@

    Protein and taxon examples

    		 - Bacillus subtilis 168 -
    NCBITaxon:224308 + Bacillus subtilis 168 +
    NCBITaxon:224308         		REVIEWED
    @@ -501,7 +502,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • spore-shaped RELATED_SYNONYM · metpo.owl
      • +
    • spore-shaped RELATED_SYNONYM · metpo.owl
    @@ -517,7 +518,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -814,7 +815,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1178,12 +1188,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/sporulation.html b/pages/traits/morphology/sporulation.html index 4d6b7d5b32a..19db244f6b7 100644 --- a/pages/traits/morphology/sporulation.html +++ b/pages/traits/morphology/sporulation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -453,8 +454,8 @@

    Protein and taxon examples

    		 - Bacillus subtilis 168 -
    NCBITaxon:224308 + Bacillus subtilis 168 +
    NCBITaxon:224308         		REVIEWED
    @@ -483,8 +484,8 @@

    Protein and taxon examples

    		 - Bacillus subtilis 168 -
    NCBITaxon:224308 + Bacillus subtilis 168 +
    NCBITaxon:224308         		REVIEWED
    @@ -513,8 +514,8 @@

    Protein and taxon examples

    		 - Bacillus subtilis 168 -
    NCBITaxon:224308 + Bacillus subtilis 168 +
    NCBITaxon:224308         		REVIEWED
    @@ -543,8 +544,8 @@

    Protein and taxon examples

    		 - Bacillus subtilis 168 -
    NCBITaxon:224308 + Bacillus subtilis 168 +
    NCBITaxon:224308         		REVIEWED
    @@ -573,8 +574,8 @@

    Protein and taxon examples

    		 - Bacillus subtilis 168 -
    NCBITaxon:224308 + Bacillus subtilis 168 +
    NCBITaxon:224308         		REVIEWED
    @@ -651,9 +652,9 @@

    Children (2)

    Synonyms (2)

      -
    • General.keywords RELATED_SYNONYM · metpo.owl
      • +
    • General.keywords RELATED_SYNONYM · metpo.owl
      • -
    • Physiology and metabolism.spore formation.spore formation RELATED_SYNONYM · metpo.owl
      • +
    • Physiology and metabolism.spore formation.spore formation RELATED_SYNONYM · metpo.owl
    @@ -669,7 +670,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -984,7 +985,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Added reviewed B. subtilis 168 sporulation sigma-factor protein_examples UniProtKB:P07860 (SigF, v175), UniProtKB:P06222 (SigE, v173), UniProtKB:P19940 (SigG, v166), and UniProtKB:P12254 (SigK, v158) across sigma_f, sigma_e, sigma_g, and sigma_k (DOI:10.1038/s41467-024-51654-6), updated scope_notes, and refreshed UniProtKB:P21458 entry_version 156 -> 157 on spoiiie_translocase.

    +

    Added reviewed B. subtilis 168 sporulation sigma-factor protein_examples UniProtKB:P07860 (SigF, v175), UniProtKB:P06222 (SigE, v173), UniProtKB:P19940 (SigG, v166), and UniProtKB:P12254 (SigK, v158) across sigma_f, sigma_e, sigma_g, and sigma_k (DOI:10.1038/s41467-024-51654-6), updated scope_notes, and refreshed UniProtKB:P21458 entry_version 156 -> 157 on spoiiie_translocase.

    • @@ -1026,7 +1027,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1390,12 +1400,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/square_shaped.html b/pages/traits/morphology/square_shaped.html index edde5851e19..9bb7bacced8 100644 --- a/pages/traits/morphology/square_shaped.html +++ b/pages/traits/morphology/square_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -273,7 +274,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • square RELATED_SYNONYM · metpo.owl
      • +
    • square RELATED_SYNONYM · metpo.owl
    @@ -289,7 +290,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -553,7 +554,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -917,12 +927,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/staphylococcus_arrangement.html b/pages/traits/morphology/staphylococcus_arrangement.html index d5d8332b929..16f6b5d749b 100644 --- a/pages/traits/morphology/staphylococcus_arrangement.html +++ b/pages/traits/morphology/staphylococcus_arrangement.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    causes staphylococcus arrangement - traitmech:000118 + traitmech:000118 biolink:causes

    Multi-plane non-orthogonal division with incomplete separation generates 3D coccal clusters.

      @@ -118,7 +119,7 @@

      Edge evidence

      GO:0051301 confers staphylococcus arrangement - traitmech:000118 + traitmech:000118 METPO:2007700

      Bacterial cell division underlies coccal cluster formation.

        @@ -273,7 +274,7 @@

        Parent traits (1)

        Synonyms (1)

          -
        • cluster-forming cocci RELATED_SYNONYM · DOI:10.1128/MMBR.00001-06
          • +
        • cluster-forming cocci RELATED_SYNONYM · DOI:10.1128/MMBR.00001-06
    @@ -289,7 +290,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]
      • +
    • cell shape METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -559,7 +560,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -923,12 +933,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/star_shaped.html b/pages/traits/morphology/star_shaped.html index f45d5c73116..5957c143859 100644 --- a/pages/traits/morphology/star_shaped.html +++ b/pages/traits/morphology/star_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -311,13 +312,13 @@

    Parent traits (1)

    Synonyms (4)

      -
    • S_star_dumbbell_pleomorphic RELATED_SYNONYM · metpo.owl
      • +
    • S_star_dumbbell_pleomorphic RELATED_SYNONYM · metpo.owl
      • -
    • star RELATED_SYNONYM · metpo.owl
      • +
    • star RELATED_SYNONYM · metpo.owl
      • -
    • star-shaped RELATED_SYNONYM · metpo.owl
      • +
    • star-shaped RELATED_SYNONYM · metpo.owl
      • -
    • stellate EXACT_SYNONYM · http://purl.obolibrary.org/obo/pato/releases/2025-05-14/pato.obo
      • +
    • stellate EXACT_SYNONYM · http://purl.obolibrary.org/obo/pato/releases/2025-05-14/pato.obo
    @@ -340,7 +341,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -616,7 +617,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -980,12 +990,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 06:15 UTC diff --git a/pages/traits/morphology/streptococcus_arrangement.html b/pages/traits/morphology/streptococcus_arrangement.html index 9b97f2ceca1..4f9ea4d6b3f 100644 --- a/pages/traits/morphology/streptococcus_arrangement.html +++ b/pages/traits/morphology/streptococcus_arrangement.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    causes streptococcus arrangement - traitmech:000117 + traitmech:000117 biolink:causes

    Parallel successive division planes with incomplete daughter separation produce coccal chains.

      @@ -118,7 +119,7 @@

      Edge evidence

      GO:0051301 confers streptococcus arrangement - traitmech:000117 + traitmech:000117 METPO:2007700

      Bacterial cell division underlies coccal chain formation.

        @@ -232,7 +233,7 @@

        Edge evidence

        prevents streptococcus arrangement - traitmech:000117 + traitmech:000117 RO:0002212

        Complete daughter-cell separation prevents chain formation; its failure produces chains.

          @@ -311,7 +312,7 @@

          Parent traits (1)

          Synonyms (1)

            -
          • chain-forming cocci RELATED_SYNONYM · DOI:10.1128/MMBR.00001-06
            • +
          • chain-forming cocci RELATED_SYNONYM · DOI:10.1128/MMBR.00001-06
    @@ -327,7 +328,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]
      • +
    • cell shape METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -579,7 +580,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -943,12 +953,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/subpolar_flagellation.html b/pages/traits/morphology/subpolar_flagellation.html index 841b7d45078..7867fa558eb 100644 --- a/pages/traits/morphology/subpolar_flagellation.html +++ b/pages/traits/morphology/subpolar_flagellation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -76,7 +77,7 @@

    Trait evidence (2)

    Subpolar flagellar assembly and cell-surface placement

    Evidence-backed morphology sketch linking cell-surface assembly of subpolar flagella to the subpolar flagellation phenotype.

    -

    NONMECHANISTIC · Morphological placement sketch backed by DOI:10.1128/JB.01405-06 and DOI:10.3390/biom10050774; strain-matched UniProtKB protein examples for the Bradyrhizobium diazoefficiens USDA 110 subpolar flagellin or placement factors remain to be curated.

    +

    NONMECHANISTIC · Morphological placement sketch backed by DOI:10.1128/JB.01405-06 and DOI:10.3390/biom10050774; strain-matched UniProtKB protein examples for the Bradyrhizobium diazoefficiens USDA 110 subpolar flagellin or placement factors remain to be curated.

    Loading graph…

    @@ -185,7 +186,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -344,7 +345,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -708,12 +718,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 21:12 UTC diff --git a/pages/traits/morphology/sulfur_globule.html b/pages/traits/morphology/sulfur_globule.html index 2a4f6ffbc81..7c32dcfb3e8 100644 --- a/pages/traits/morphology/sulfur_globule.html +++ b/pages/traits/morphology/sulfur_globule.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    CHEBI:26833 located in sulfur globule - traitmech:000069 + traitmech:000069 biolink:located_in

    The deposited elemental sulfur forms a globule inclusion.

      @@ -175,7 +176,7 @@

      Edge evidence

      precursor of sulfur globule - traitmech:000069 + traitmech:000069

      Polysulfide/sulfane sulfur spontaneously generates S8 that aggregates into sulfur globules.

        @@ -273,7 +274,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -289,7 +290,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -508,7 +509,7 @@

    Curation history

  • · ENRICH_CAUSAL_GRAPH · claude -

    Added 1 evidence-backed edge attaching the stranded PDO/sulfite branch to the pathway the rest of the graph models (issue 183): persulfide_dioxygenase participates in oxidative_sulfur_metabolism, grounded biolink:participates_in. The snippet is verbatim from PMID:35653932, checked against the PubMed abstract. Resolves this graph's FRAGMENTED_GRAPH and its 2 UNREACHABLE_FROM_TRAIT findings.

    +

    Added 1 evidence-backed edge attaching the stranded PDO/sulfite branch to the pathway the rest of the graph models (issue 183): persulfide_dioxygenase participates in oxidative_sulfur_metabolism, grounded biolink:participates_in. The snippet is verbatim from PMID:35653932, checked against the PubMed abstract. Resolves this graph's FRAGMENTED_GRAPH and its 2 UNREACHABLE_FROM_TRAIT findings.

  • @@ -536,7 +537,7 @@

    Recorded curation sessions

  • · claude-code
    • EDIT — Attach the stranded PDO/sulfite branch to the sulfide-oxidation pathway -

      persulfide_dioxygenase -> sulfite was a correct enzymatic fact with no undirected path to sulfur_globule_trait. PDO acts downstream of SQR in the same sulfide-oxidation pathway this graph already models, so it now participates in oxidative_sulfur_metabolism (biolink:participates_in). The snippet is verbatim from PMID:35653932, checked against the PubMed abstract in the same run. Resolves this graph's FRAGMENTED_GRAPH and 2 UNREACHABLE_FROM_TRAIT findings. Scope caveat recorded in issue 297: the quote covers heterotrophic bacteria and human mitochondria rather than the Thiomargarita/Beggiatoa exemplars, so it supports the generic pathway claim the object node makes and no more.

    +

    persulfide_dioxygenase -> sulfite was a correct enzymatic fact with no undirected path to sulfur_globule_trait. PDO acts downstream of SQR in the same sulfide-oxidation pathway this graph already models, so it now participates in oxidative_sulfur_metabolism (biolink:participates_in). The snippet is verbatim from PMID:35653932, checked against the PubMed abstract in the same run. Resolves this graph's FRAGMENTED_GRAPH and 2 UNREACHABLE_FROM_TRAIT findings. Scope caveat recorded in issue 297: the quote covers heterotrophic bacteria and human mitochondria rather than the Thiomargarita/Beggiatoa exemplars, so it supports the generic pathway claim the object node makes and no more.

    • Read this curation session @@ -568,7 +569,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -932,12 +942,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/swarming_motility.html b/pages/traits/morphology/swarming_motility.html index 2d0c16559ae..670f6ec1d5b 100644 --- a/pages/traits/morphology/swarming_motility.html +++ b/pages/traits/morphology/swarming_motility.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    GO:0009288 confers swarming motility - traitmech:000062 + traitmech:000062 METPO:2007700

    Hyperflagellation provides the propulsive machinery for swarming.

      @@ -118,7 +119,7 @@

      Edge evidence

      confers swarming motility - traitmech:000062 + traitmech:000062 METPO:2007700

      Secreted wetting surfactant supports multicellular surface spreading.

        @@ -134,7 +135,7 @@

        Edge evidence

      • swarming motility - traitmech:000062 + traitmech:000062 participates in bacterial flagellum-dependent cell motility GO:0071973 @@ -254,7 +255,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -270,7 +271,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -522,7 +523,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -886,12 +896,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/swimming_motility.html b/pages/traits/morphology/swimming_motility.html index 5f6c00d8ca0..24ea210e735 100644 --- a/pages/traits/morphology/swimming_motility.html +++ b/pages/traits/morphology/swimming_motility.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1038/s41467-020-18253-7
    Their swimming direction is stabilised by their flagella (archaella)
    -

    Thornton et al. 2020, PMID:32901025, PMC7478972, scientific abstract. Qualified MED identity, title and DOI checked. Results, Swimming behaviour in three dimensions, and Methods on culture and holographic reconstruction directly support liquid swimming by environmental Haloferax sp. Boulby Mine and Haloarcula sp. Great Salt Lake isolates. Mean-squared displacement separated swimming from diffusion. Figure 2 was visually inspected; Supplementary Note 1 describes sampling locations. Methods explicitly leave exact species unresolved. Cultures were grown in 25% dissolved-salt MGM to early exponential phase. The measured trajectories, not merely genes or simulations, support the phenotype. Chemotactic efficiency simulations do not define swimming or establish a universal speed optimum. Raw movies were not reanalyzed. MED, Crossref and the retrieved publisher page exposed no linked correction or retraction at the check. Source: https://www.nature.com/articles/s41467-020-18253-7.

    +

    Thornton et al. 2020, PMID:32901025, PMC7478972, scientific abstract. Qualified MED identity, title and DOI checked. Results, Swimming behaviour in three dimensions, and Methods on culture and holographic reconstruction directly support liquid swimming by environmental Haloferax sp. Boulby Mine and Haloarcula sp. Great Salt Lake isolates. Mean-squared displacement separated swimming from diffusion. Figure 2 was visually inspected; Supplementary Note 1 describes sampling locations. Methods explicitly leave exact species unresolved. Cultures were grown in 25% dissolved-salt MGM to early exponential phase. The measured trajectories, not merely genes or simulations, support the phenotype. Chemotactic efficiency simulations do not define swimming or establish a universal speed optimum. Raw movies were not reanalyzed. MED, Crossref and the retrieved publisher page exposed no linked correction or retraction at the check. Source: https://www.nature.com/articles/s41467-020-18253-7.

  • DOI:10.1038/s41467-018-07802-w
    However, the free-swimming capability of the different strains did not correlate well to the spreading capability in soft agar.
    -

    Kuhn et al. 2018, PMID:30560868, PMC6299084, Results, Filament composition affects flagella-mediated swimming; quote checked directly in full-text XML, not the abstract. Qualified MED identity and DOI checked. Figure 3 and Supplementary Table 1 (printed p. 10, PDF p. 11) were visually inspected. Main Results describe a delta-flaA2B2 background, called wild type for the polar system. Supplementary Figure 11 (printed p. 7, PDF p. 8) instead retains both lateral flagellins for a separate soft-agar assay. Preserve this discrepancy; do not apply the main-text claim to every experiment. Methods distinguish three-dimensional cell tracking in regular or Ficoll-supplemented liquid from soft-agar spreading, and reject Brownian-only tracks. Thus liquid swimming is observed in engineered material; it is not inferred from agar halos or a sequence feature. Filament simulations are separate model evidence. Raw movies were not reanalyzed. MED, Crossref and the retrieved publisher page exposed no linked correction or retraction at the check. Source: https://www.nature.com/articles/s41467-018-07802-w.

    +

    Kuhn et al. 2018, PMID:30560868, PMC6299084, Results, Filament composition affects flagella-mediated swimming; quote checked directly in full-text XML, not the abstract. Qualified MED identity and DOI checked. Figure 3 and Supplementary Table 1 (printed p. 10, PDF p. 11) were visually inspected. Main Results describe a delta-flaA2B2 background, called wild type for the polar system. Supplementary Figure 11 (printed p. 7, PDF p. 8) instead retains both lateral flagellins for a separate soft-agar assay. Preserve this discrepancy; do not apply the main-text claim to every experiment. Methods distinguish three-dimensional cell tracking in regular or Ficoll-supplemented liquid from soft-agar spreading, and reject Brownian-only tracks. Thus liquid swimming is observed in engineered material; it is not inferred from agar halos or a sequence feature. Filament simulations are separate model evidence. Raw movies were not reanalyzed. MED, Crossref and the retrieved publisher page exposed no linked correction or retraction at the check. Source: https://www.nature.com/articles/s41467-018-07802-w.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-11 18:28 UTC diff --git a/pages/traits/morphology/synnema_formation.html b/pages/traits/morphology/synnema_formation.html index d1565e863ae..9648d6897f5 100644 --- a/pages/traits/morphology/synnema_formation.html +++ b/pages/traits/morphology/synnema_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1016/j.simyco.2017.09.001
    Hyphae of stipe parallel, 2–2.5 μm wide, pale-brown, slightly thick-walled.
    -

    Woudenberg et al. (2017), PMID:29158610, PMC5679026. Direct full-text Taxonomy, Cephalotrichum lignatile description; the snippet describes this species, not universal dimensions or pigmentation. Actual Figure 7D-F shows synnemata, G the stalk apex, and H-I conidiophores and conidiogenous cells. Methods describes microscopic structures from SNA cultures after 14 days at 25 C in darkness; Figure 7A-C instead shows colonies on OA, MEA and DG18. The paper also reports loosely attached stipe hyphae in C. domesticum, so tight fusion is not imposed on the class.

    +

    Woudenberg et al. (2017), PMID:29158610, PMC5679026. Direct full-text Taxonomy, Cephalotrichum lignatile description; the snippet describes this species, not universal dimensions or pigmentation. Actual Figure 7D-F shows synnemata, G the stalk apex, and H-I conidiophores and conidiogenous cells. Methods describes microscopic structures from SNA cultures after 14 days at 25 C in darkness; Figure 7A-C instead shows colonies on OA, MEA and DG18. The paper also reports loosely attached stipe hyphae in C. domesticum, so tight fusion is not imposed on the class.

  • DOI:10.3390/ijms21186660
    deletion of the brlA gene blocked conidiation but not the formation of synnemata formed by aggregation of hyphal mycelia.
    -

    Zetina-Serrano et al. (2020), PMID:32932988, PMC7555563, Introduction's summary of the authors' experiment. Direct Results 2.2.3 and actual Figure 4 were also inspected: after 30 days on apples at 25 C in darkness, the engineered Penicillium expansum brlA-null strain formed sporeless hyphal stalks lacking mature conidiophores; the wild-type strain formed conidiophores in coremia. This supports separating stalk formation from completed conidiation, not a universal BrlA requirement for synnemata. The mutant is qualified evidence, not a natural canonical example.

    +

    Zetina-Serrano et al. (2020), PMID:32932988, PMC7555563, Introduction's summary of the authors' experiment. Direct Results 2.2.3 and actual Figure 4 were also inspected: after 30 days on apples at 25 C in darkness, the engineered Penicillium expansum brlA-null strain formed sporeless hyphal stalks lacking mature conidiophores; the wild-type strain formed conidiophores in coremia. This supports separating stalk formation from completed conidiation, not a universal BrlA requirement for synnemata. The mutant is qualified evidence, not a natural canonical example.

  • DOI:10.1099/00221287-87-2-292
    Coremia of Penicillium claviforme develop in three stages; primordium formation, elongation, and sporulation.
    -

    Watkinson (1975), PMID:1141857, scientific abstract retrieved directly from Europe PMC. The publisher abstract agrees on the three stages but uses a colon where this indexed version has a semicolon. Only abstract-level developmental evidence is used; full text and figures were not inspected. Nutrient responses in this study do not define all synnemata. The historical species name is retained without a new taxon mapping or exact coremium/synnema synonym assertion.

    +

    Watkinson (1975), PMID:1141857, scientific abstract retrieved directly from Europe PMC. The publisher abstract agrees on the three stages but uses a colon where this indexed version has a semicolon. Only abstract-level developmental evidence is used; full text and figures were not inspected. Nutrient responses in this study do not define all synnemata. The historical species name is retained without a new taxon mapping or exact coremium/synnema synonym assertion.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1016/j.simyco.2017.09.001 - Ex-type culture CBS 209.63. The primary taxonomic description and Figure 7 directly document synnemata; microscopic descriptions use SNA after 14 days at 25 C in darkness. Specimen examined and Table 1 at https://pmc.ncbi.nlm.nih.gov/articles/PMC5679026/ identify Hennebert's 1959 isolate from timber in a cave at Han-sur-Lesse, Belgium. This is primary isolate provenance, not an inferred wild-type or GMO status. Synnemata production can vary with culture history; it is not asserted for every life stage or growth condition. + Ex-type culture CBS 209.63. The primary taxonomic description and Figure 7 directly document synnemata; microscopic descriptions use SNA after 14 days at 25 C in darkness. Specimen examined and Table 1 at https://pmc.ncbi.nlm.nih.gov/articles/PMC5679026/ identify Hennebert's 1959 isolate from timber in a cave at Han-sur-Lesse, Belgium. This is primary isolate provenance, not an inferred wild-type or GMO status. Synnemata production can vary with culture history; it is not asserted for every life stage or growth condition. @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 02:46 UTC diff --git a/pages/traits/morphology/tailed_shaped.html b/pages/traits/morphology/tailed_shaped.html index 9e2d2779c47..e96cd76f8a0 100644 --- a/pages/traits/morphology/tailed_shaped.html +++ b/pages/traits/morphology/tailed_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -307,8 +308,8 @@

    Protein and taxon examples

    		 - Caulobacter vibrioides NA1000 -
    NCBITaxon:565050 + Caulobacter vibrioides NA1000 +
    NCBITaxon:565050         		REVIEWED
    @@ -374,7 +375,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • tailed RELATED_SYNONYM · metpo.owl
      • +
    • tailed RELATED_SYNONYM · metpo.owl
    @@ -390,7 +391,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -696,7 +697,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1060,12 +1070,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/tetrad_arrangement.html b/pages/traits/morphology/tetrad_arrangement.html index 8cb6c4251ab..66cfb6f6e63 100644 --- a/pages/traits/morphology/tetrad_arrangement.html +++ b/pages/traits/morphology/tetrad_arrangement.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    causes tetrad arrangement - traitmech:000119 + traitmech:000119 biolink:causes

    Two perpendicular division planes with incomplete daughter separation yield four-cell tetrads.

      @@ -118,7 +119,7 @@

      Edge evidence

      GO:0051301 confers tetrad arrangement - traitmech:000119 + traitmech:000119 METPO:2007700

      Bacterial cell division underlies tetrad formation.

        @@ -194,7 +195,7 @@

        Edge evidence

        prevents tetrad arrangement - traitmech:000119 + traitmech:000119 RO:0002212

        Incomplete or delayed daughter-cell splitting after two-plane division leaves cells attached as four-cell tetrads.

          @@ -254,7 +255,7 @@

          Parent traits (1)

          Synonyms (1)

            -
          • tetrad-forming cocci RELATED_SYNONYM · DOI:10.1128/MMBR.00001-06
            • +
          • tetrad-forming cocci RELATED_SYNONYM · DOI:10.1128/MMBR.00001-06
    @@ -270,7 +271,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]
      • +
    • cell shape METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -537,7 +538,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -901,12 +911,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/triangular_shaped.html b/pages/traits/morphology/triangular_shaped.html index b24dc8b2665..057e578b5fa 100644 --- a/pages/traits/morphology/triangular_shaped.html +++ b/pages/traits/morphology/triangular_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -273,7 +274,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • triangular RELATED_SYNONYM · metpo.owl
      • +
    • triangular RELATED_SYNONYM · metpo.owl
    @@ -289,7 +290,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -553,7 +554,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -917,12 +927,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/twitching_motility.html b/pages/traits/morphology/twitching_motility.html index 1f78a1e39f4..6ef30ccebd1 100644 --- a/pages/traits/morphology/twitching_motility.html +++ b/pages/traits/morphology/twitching_motility.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    GO:0044096 confers twitching motility - traitmech:000061 + traitmech:000061 METPO:2007700

    Type IV pili are the molecular engines of twitching motility.

      @@ -118,7 +119,7 @@

      Edge evidence

      GO:0043107 confers twitching motility - traitmech:000061 + traitmech:000061 METPO:2007700

      Extension–attachment–retraction cycles pull the cell across the surface.

        @@ -175,7 +176,7 @@

        Edge evidence

        confers twitching motility - traitmech:000061 + traitmech:000061 METPO:2007700

        Pilus retraction pulls the cell across the surface, producing twitching translocation.

          @@ -307,8 +308,8 @@

          Protein and taxon examples

    		 - Pseudomonas aeruginosa PAO1 -
    NCBITaxon:208964 + Pseudomonas aeruginosa PAO1 +
    NCBITaxon:208964         		REVIEWED
    @@ -374,7 +375,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -390,7 +391,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -678,7 +679,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1042,12 +1052,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/morphology/type_iv_pilus.html b/pages/traits/morphology/type_iv_pilus.html index 6c1267fbc80..a25c6fef27c 100644 --- a/pages/traits/morphology/type_iv_pilus.html +++ b/pages/traits/morphology/type_iv_pilus.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -82,7 +83,7 @@

    Trait evidence (3)

    Type IV pilus cell-surface appendage and dynamic extension-retraction

    Evidence-backed morphology sketch linking cell-surface type IV pili fibers and their dynamic extension and retraction to the type IV pilus trait.

    -

    NONMECHANISTIC · Appendage-and-dynamics sketch backed by DOI:10.1093/femsre/fuab053 and DOI:10.1042/BST20160221; PilA/PilB/PilT protein nodes with strain-matched UniProtKB accessions for Pseudomonas aeruginosa PAO1 remain to be curated.

    +

    NONMECHANISTIC · Appendage-and-dynamics sketch backed by DOI:10.1093/femsre/fuab053 and DOI:10.1042/BST20160221; PilA/PilB/PilT protein nodes with strain-matched UniProtKB accessions for Pseudomonas aeruginosa PAO1 remain to be curated.

    Loading graph…

    @@ -105,7 +106,7 @@

    Edge evidence

    GO:0044096 confers type IV pilus - traitmech:000175 + traitmech:000175 METPO:2007700

    Production of type IV pili appendages confers the type IV pilus morphology trait.

      @@ -203,9 +204,9 @@

      Parent traits (1)

      Synonyms (2)

    @@ -228,7 +229,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -387,7 +388,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -751,12 +761,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 21:12 UTC diff --git a/pages/traits/morphology/vibrio_shaped.html b/pages/traits/morphology/vibrio_shaped.html index a8f8490c33d..37c1dd2aae7 100644 --- a/pages/traits/morphology/vibrio_shaped.html +++ b/pages/traits/morphology/vibrio_shaped.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -343,9 +344,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • vibrio RELATED_SYNONYM · metpo.owl
      • +
    • vibrio RELATED_SYNONYM · metpo.owl
      • -
    • vibrio-shaped RELATED_SYNONYM · metpo.owl
      • +
    • vibrio-shaped RELATED_SYNONYM · metpo.owl
    @@ -361,7 +362,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -625,7 +626,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -989,12 +999,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/morphology/white_pigmented.html b/pages/traits/morphology/white_pigmented.html index 394905ed2e9..31e8b7d593e 100644 --- a/pages/traits/morphology/white_pigmented.html +++ b/pages/traits/morphology/white_pigmented.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -324,7 +325,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Pigment_white RELATED_SYNONYM · metpo.owl
      • +
    • Pigment_white RELATED_SYNONYM · metpo.owl
    @@ -340,7 +341,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -625,7 +626,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Added a mutant-specific Serratia marcescens white-colony example from DOI:10.3389/fmicb.2021.793202, explicitly retaining SCQ1 delta-slyA context in the note; verified the current species taxon and label through NCBI Taxonomy.

    +

    Added a mutant-specific Serratia marcescens white-colony example from DOI:10.3389/fmicb.2021.793202, explicitly retaining SCQ1 delta-slyA context in the note; verified the current species taxon and label through NCBI Taxonomy.

    • @@ -658,7 +659,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1022,12 +1032,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 11:06 UTC diff --git a/pages/traits/morphology/yellow_pigmented.html b/pages/traits/morphology/yellow_pigmented.html index eccbd00a156..3c3efd75348 100644 --- a/pages/traits/morphology/yellow_pigmented.html +++ b/pages/traits/morphology/yellow_pigmented.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -381,7 +382,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • Pigment_yellow RELATED_SYNONYM · metpo.owl
      • +
    • Pigment_yellow RELATED_SYNONYM · metpo.owl
    @@ -397,7 +398,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -679,7 +680,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1043,12 +1053,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/observation/growth_nacl_observation.html b/pages/traits/observation/growth_nacl_observation.html index a3ef3eea62b..960cd405d6b 100644 --- a/pages/traits/observation/growth_nacl_observation.html +++ b/pages/traits/observation/growth_nacl_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/growth_oxygen_observation.html b/pages/traits/observation/growth_oxygen_observation.html index e80cb1451b3..f8e10c20437 100644 --- a/pages/traits/observation/growth_oxygen_observation.html +++ b/pages/traits/observation/growth_oxygen_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/growth_ph_observation.html b/pages/traits/observation/growth_ph_observation.html index 8f717866173..4f356fddcba 100644 --- a/pages/traits/observation/growth_ph_observation.html +++ b/pages/traits/observation/growth_ph_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/growth_temperature_observation.html b/pages/traits/observation/growth_temperature_observation.html index b43e4c9da2e..30ba092589d 100644 --- a/pages/traits/observation/growth_temperature_observation.html +++ b/pages/traits/observation/growth_temperature_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/nacl_delta_observation.html b/pages/traits/observation/nacl_delta_observation.html index 5f1b7403575..792d21fd0bb 100644 --- a/pages/traits/observation/nacl_delta_observation.html +++ b/pages/traits/observation/nacl_delta_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/nacl_observation.html b/pages/traits/observation/nacl_observation.html index 6952dc87b74..c0caae9b7bb 100644 --- a/pages/traits/observation/nacl_observation.html +++ b/pages/traits/observation/nacl_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/nacl_range_observation.html b/pages/traits/observation/nacl_range_observation.html index 82201fc00a9..672e404a44e 100644 --- a/pages/traits/observation/nacl_range_observation.html +++ b/pages/traits/observation/nacl_range_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/optimum_nacl_observation.html b/pages/traits/observation/optimum_nacl_observation.html index 0e7a3824eba..04d1028c745 100644 --- a/pages/traits/observation/optimum_nacl_observation.html +++ b/pages/traits/observation/optimum_nacl_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/optimum_oxygen_observation.html b/pages/traits/observation/optimum_oxygen_observation.html index e8715f78c82..c3234b5f63b 100644 --- a/pages/traits/observation/optimum_oxygen_observation.html +++ b/pages/traits/observation/optimum_oxygen_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/optimum_ph_observation.html b/pages/traits/observation/optimum_ph_observation.html index ac1f12a2ecb..855c7e8fb04 100644 --- a/pages/traits/observation/optimum_ph_observation.html +++ b/pages/traits/observation/optimum_ph_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/optimum_temperature_observation.html b/pages/traits/observation/optimum_temperature_observation.html index 99ab8eeea3a..35567943ff2 100644 --- a/pages/traits/observation/optimum_temperature_observation.html +++ b/pages/traits/observation/optimum_temperature_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/oxygen_delta_observation.html b/pages/traits/observation/oxygen_delta_observation.html index 52f24d1492e..42c1c98e027 100644 --- a/pages/traits/observation/oxygen_delta_observation.html +++ b/pages/traits/observation/oxygen_delta_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/oxygen_observation.html b/pages/traits/observation/oxygen_observation.html index 2096107a510..8e56d255847 100644 --- a/pages/traits/observation/oxygen_observation.html +++ b/pages/traits/observation/oxygen_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/oxygen_range_observation.html b/pages/traits/observation/oxygen_range_observation.html index 9c5eb88eb38..cdae5db5dff 100644 --- a/pages/traits/observation/oxygen_range_observation.html +++ b/pages/traits/observation/oxygen_range_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/ph_delta_observation.html b/pages/traits/observation/ph_delta_observation.html index d47b44b860b..34fb06ca29c 100644 --- a/pages/traits/observation/ph_delta_observation.html +++ b/pages/traits/observation/ph_delta_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/ph_observation.html b/pages/traits/observation/ph_observation.html index 66a257bbdf9..81e58673bdb 100644 --- a/pages/traits/observation/ph_observation.html +++ b/pages/traits/observation/ph_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/ph_range_observation.html b/pages/traits/observation/ph_range_observation.html index 7790e16536c..c10e581ac27 100644 --- a/pages/traits/observation/ph_range_observation.html +++ b/pages/traits/observation/ph_range_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/temperature_delta_observation.html b/pages/traits/observation/temperature_delta_observation.html index 0232dec1b62..5af4001b231 100644 --- a/pages/traits/observation/temperature_delta_observation.html +++ b/pages/traits/observation/temperature_delta_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/temperature_observation.html b/pages/traits/observation/temperature_observation.html index dc5fb83595c..46254f0d7c2 100644 --- a/pages/traits/observation/temperature_observation.html +++ b/pages/traits/observation/temperature_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/observation/temperature_range_observation.html b/pages/traits/observation/temperature_range_observation.html index 53126add381..ac20dd30bbc 100644 --- a/pages/traits/observation/temperature_range_observation.html +++ b/pages/traits/observation/temperature_range_observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -92,7 +93,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -224,7 +225,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -253,12 +263,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/other/catalase_negative.html b/pages/traits/other/catalase_negative.html index 1d87e73a176..f9a3b5ad703 100644 --- a/pages/traits/other/catalase_negative.html +++ b/pages/traits/other/catalase_negative.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,9 +107,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • catalase - EXACT_SYNONYM · metpo.owl
      • +
    • catalase - EXACT_SYNONYM · metpo.owl
      • -
    • catalase test negative EXACT_SYNONYM · metpo.owl
      • +
    • catalase test negative EXACT_SYNONYM · metpo.owl
    @@ -124,7 +125,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -274,7 +275,7 @@

    Discussions and Knowledge Gaps (2)

    -

    This record represents a negative catalase-test outcome phenotype; its evidence pairs an assay-foam snippet (DOI:10.1038/srep03081) with a single sentence noting that Enterococcus faecium is catalase negative (DOI:10.1128/iai.72.8.4512-4520.2004), which does not ground a multi-edge causal graph for the negative test state.

    +

    This record represents a negative catalase-test outcome phenotype; its evidence pairs an assay-foam snippet (DOI:10.1038/srep03081) with a single sentence noting that Enterococcus faecium is catalase negative (DOI:10.1128/iai.72.8.4512-4520.2004), which does not ground a multi-edge causal graph for the negative test state.

    @@ -374,7 +375,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -403,12 +413,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/catalase_test.html b/pages/traits/other/catalase_test.html index ef96a8cb940..9429be0aa03 100644 --- a/pages/traits/other/catalase_test.html +++ b/pages/traits/other/catalase_test.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,9 +116,9 @@

    Children (1)

    Synonyms (2)

      -
    • catalase activity test EXACT_SYNONYM · metpo.owl
      • +
    • catalase activity test EXACT_SYNONYM · metpo.owl
      • -
    • catalase assay EXACT_SYNONYM · metpo.owl
      • +
    • catalase assay EXACT_SYNONYM · metpo.owl
    @@ -133,7 +134,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -228,7 +229,7 @@

    Discussions and Knowledge Gaps (1)

    -

    METPO:1007080 represents a diagnostic biochemical test protocol (ASM catalase test protocol; DOI:10.1038/srep03081) rather than a cellular physiological pathway; the underlying H2O2 disproportionation mechanism is curated on catalase_positive.yaml.

    +

    METPO:1007080 represents a diagnostic biochemical test protocol (ASM catalase test protocol; DOI:10.1038/srep03081) rather than a cellular physiological pathway; the underlying H2O2 disproportionation mechanism is curated on catalase_positive.yaml.

    @@ -316,7 +317,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -345,12 +355,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/circular_colony.html b/pages/traits/other/circular_colony.html index a7ae6635fe6..cefaba7d526 100644 --- a/pages/traits/other/circular_colony.html +++ b/pages/traits/other/circular_colony.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • round colony EXACT_SYNONYM · metpo.owl
      • +
    • round colony EXACT_SYNONYM · metpo.owl
    @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -305,7 +306,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -334,12 +344,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/coagulase_negative.html b/pages/traits/other/coagulase_negative.html index 4f98c177bce..2a786af5b6a 100644 --- a/pages/traits/other/coagulase_negative.html +++ b/pages/traits/other/coagulase_negative.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,9 +107,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • coagulase - EXACT_SYNONYM · metpo.owl
      • +
    • coagulase - EXACT_SYNONYM · metpo.owl
      • -
    • coagulase test negative EXACT_SYNONYM · metpo.owl
      • +
    • coagulase test negative EXACT_SYNONYM · metpo.owl
    @@ -124,7 +125,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -244,7 +245,7 @@

    Discussions and Knowledge Gaps (1)

    -

    This record represents a negative diagnostic test-outcome phenotype uniting coagulase-negative staphylococci (DOI:10.3390/microorganisms9040830; NBK563240) by the absence of plasma clotting rather than an active multi-step biochemical pathway.

    +

    This record represents a negative diagnostic test-outcome phenotype uniting coagulase-negative staphylococci (DOI:10.3390/microorganisms9040830; NBK563240) by the absence of plasma clotting rather than an active multi-step biochemical pathway.

    @@ -332,7 +333,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -361,12 +371,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/coagulase_positive.html b/pages/traits/other/coagulase_positive.html index 3024d39827b..91bbf827284 100644 --- a/pages/traits/other/coagulase_positive.html +++ b/pages/traits/other/coagulase_positive.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -82,7 +83,7 @@

    Trait evidence (3)

    Coagulase-mediated prothrombin activation and plasma clotting

    Evidence-backed mechanism sketch linking bacterial prothrombin activation and plasma clotting to the coagulase positive test-outcome phenotype.

    -

    MECHANISTIC · Mechanistic graph backed by DOI:10.1371/journal.ppat.1001036; exemplified on coagulase_positive_coa with Staphylococcus aureus (NCBITaxon:1280) secreted staphylocoagulase Coa (UniProtKB:P07767).

    +

    MECHANISTIC · Mechanistic graph backed by DOI:10.1371/journal.ppat.1001036; exemplified on coagulase_positive_coa with Staphylococcus aureus (NCBITaxon:1280) secreted staphylocoagulase Coa (UniProtKB:P07767).

    Loading graph…

    @@ -180,8 +181,8 @@

    Protein and taxon examples

    		 - Staphylococcus aureus -
    NCBITaxon:1280 + Staphylococcus aureus +
    NCBITaxon:1280         		REVIEWED
    @@ -247,9 +248,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • coagulase + EXACT_SYNONYM · metpo.owl
      • +
    • coagulase + EXACT_SYNONYM · metpo.owl
      • -
    • coagulase test positive EXACT_SYNONYM · metpo.owl
      • +
    • coagulase test positive EXACT_SYNONYM · metpo.owl
    @@ -265,7 +266,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -385,7 +386,7 @@

    Discussions and Knowledge Gaps (1)

    -

    The record's primary literature (DOI:10.1099/mic.0.000019, DOI:10.1371/journal.ppat.1001036) establishes prothrombin activation by secreted coagulase (Coa) and plasma clotting in Staphylococcus aureus (NCBITaxon:1280), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    +

    The record's primary literature (DOI:10.1099/mic.0.000019, DOI:10.1371/journal.ppat.1001036) establishes prothrombin activation by secreted coagulase (Coa) and plasma clotting in Staphylococcus aureus (NCBITaxon:1280), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    @@ -404,7 +405,7 @@

    Evidence

    -

    Resolution: Promoted coagulase_positive_prothrombin_clotting_sketch to MECHANISTIC by adding InterPro:IPR001443-grounded GENE_OR_PROTEIN node coagulase_positive_coa with reviewed Staphylococcus aureus (NCBITaxon:1280) protein_examples UniProtKB:P07767 (Coa) backed by DOI:10.1371/journal.ppat.1001036.

    +

    Resolution: Promoted coagulase_positive_prothrombin_clotting_sketch to MECHANISTIC by adding InterPro:IPR001443-grounded GENE_OR_PROTEIN node coagulase_positive_coa with reviewed Staphylococcus aureus (NCBITaxon:1280) protein_examples UniProtKB:P07767 (Coa) backed by DOI:10.1371/journal.ppat.1001036.

    @@ -439,7 +440,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Promoted coagulase_positive_prothrombin_clotting_sketch to MECHANISTIC; added InterPro:IPR001443-grounded GENE_OR_PROTEIN node coagulase_positive_coa with reviewed Staphylococcus aureus (NCBITaxon:1280) protein_examples UniProtKB:P07767 (Coa) backed by DOI:10.1371/journal.ppat.1001036; resolved coagulase-positive-protein-example-gap.

    +

    Promoted coagulase_positive_prothrombin_clotting_sketch to MECHANISTIC; added InterPro:IPR001443-grounded GENE_OR_PROTEIN node coagulase_positive_coa with reviewed Staphylococcus aureus (NCBITaxon:1280) protein_examples UniProtKB:P07767 (Coa) backed by DOI:10.1371/journal.ppat.1001036; resolved coagulase-positive-protein-example-gap.

    • @@ -481,7 +482,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -845,12 +855,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 22:45 UTC diff --git a/pages/traits/other/colony_morphology.html b/pages/traits/other/colony_morphology.html index b1ee52a0ff0..d480b2c7fcf 100644 --- a/pages/traits/other/colony_morphology.html +++ b/pages/traits/other/colony_morphology.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -305,7 +306,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -334,12 +344,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/colony_shape.html b/pages/traits/other/colony_shape.html index aaa97a9af94..1f077b21394 100644 --- a/pages/traits/other/colony_shape.html +++ b/pages/traits/other/colony_shape.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -132,7 +133,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/epibiont_phenotype.html b/pages/traits/other/epibiont_phenotype.html index 9e0f7e63151..31c91225571 100644 --- a/pages/traits/other/epibiont_phenotype.html +++ b/pages/traits/other/epibiont_phenotype.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,9 +107,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • ectosymbiont EXACT_SYNONYM · metpo.owl
      • +
    • ectosymbiont EXACT_SYNONYM · metpo.owl
      • -
    • epibiont EXACT_SYNONYM · metpo.owl
      • +
    • epibiont EXACT_SYNONYM · metpo.owl
    @@ -124,7 +125,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -244,7 +245,7 @@

    Discussions and Knowledge Gaps (1)

    -

    The current record carries two strain-isolation habitat snippets from the surface of the marine alga Ulva australis (DOI:10.1099/ijs.0.042838-0; BacDive 24523) without molecular colonization or attachment mechanism quotes.

    +

    The current record carries two strain-isolation habitat snippets from the surface of the marine alga Ulva australis (DOI:10.1099/ijs.0.042838-0; BacDive 24523) without molecular colonization or attachment mechanism quotes.

    @@ -332,7 +333,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -361,12 +371,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/filamentous_colony.html b/pages/traits/other/filamentous_colony.html index 2c139d2a197..93cc22528f2 100644 --- a/pages/traits/other/filamentous_colony.html +++ b/pages/traits/other/filamentous_colony.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Discussions and Knowledge Gaps (1)

    -

    The current record carries a single general colony-morphology overview snippet (DOI:10.7759/cureus.374) without specific genetic or cellular morphogenesis quotes.

    +

    The current record carries a single general colony-morphology overview snippet (DOI:10.7759/cureus.374) without specific genetic or cellular morphogenesis quotes.

    @@ -258,7 +259,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add seeded filamentous colony trait -

      Added METPO:1007066 as data/traits/other/filamentous_colony.yaml from the METPO seed, preserving the OTHER category and colony shape parent. Enriched the record with stable OMP definition provenance and DOI:10.7759/cureus.374 evidence for filamentous as a bacterial colony shape after an exact duplicate search including ignored and hidden files found no existing live data/traits or history record.

    +

    Added METPO:1007066 as data/traits/other/filamentous_colony.yaml from the METPO seed, preserving the OTHER category and colony shape parent. Enriched the record with stable OMP definition provenance and DOI:10.7759/cureus.374 evidence for filamentous as a bacterial colony shape after an exact duplicate search including ignored and hidden files found no existing live data/traits or history record.

    • Read this curation session @@ -290,7 +291,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -319,12 +329,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/fried_egg_shaped_colony.html b/pages/traits/other/fried_egg_shaped_colony.html index 217b9ab4c0e..834c925ee64 100644 --- a/pages/traits/other/fried_egg_shaped_colony.html +++ b/pages/traits/other/fried_egg_shaped_colony.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • fried-egg colony EXACT_SYNONYM · metpo.owl
      • +
    • fried-egg colony EXACT_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -211,7 +212,7 @@

    Discussions and Knowledge Gaps (1)

    -

    The current record carries a single morphological description snippet (DOI:10.1371/journal.pone.0068373) describing the opaque center and translucent peripheral zone without molecular or cellular mechanism quotes.

    +

    The current record carries a single morphological description snippet (DOI:10.1371/journal.pone.0068373) describing the opaque center and translucent peripheral zone without molecular or cellular mechanism quotes.

    @@ -267,7 +268,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add seeded fried-egg-shaped colony trait -

      Added METPO:1007069 as data/traits/other/fried_egg_shaped_colony.yaml from the METPO seed, then enriched the record with stable MICRO definition provenance and DOI:10.1371/journal.pone.0068373 evidence for the opaque-center, translucent-periphery fried-egg colony appearance after an exact duplicate search including ignored and hidden files.

    +

    Added METPO:1007069 as data/traits/other/fried_egg_shaped_colony.yaml from the METPO seed, then enriched the record with stable MICRO definition provenance and DOI:10.1371/journal.pone.0068373 evidence for the opaque-center, translucent-periphery fried-egg colony appearance after an exact duplicate search including ignored and hidden files.

    • Read this curation session @@ -299,7 +300,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -328,12 +338,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/generalist.html b/pages/traits/other/generalist.html index 4faf7fea601..7cbeeec0913 100644 --- a/pages/traits/other/generalist.html +++ b/pages/traits/other/generalist.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1005040 [-2.687, -2.404, -3.843, +0.122, …]
      • +
    • generalist METPO:1005040 [-2.687, -2.404, -3.843, +0.122, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Discussions and Knowledge Gaps (1)

    -

    The current record carries two high-level ecological classification snippets (DOI:10.1093/femsec/fiaa240; DOI:10.1038/s41559-023-02027-7) contrasting niche breadth in generalists vs specialists without molecular mechanism quotes or a canonical example.

    +

    The current record carries two high-level ecological classification snippets (DOI:10.1093/femsec/fiaa240; DOI:10.1038/s41559-023-02027-7) contrasting niche breadth in generalists vs specialists without molecular mechanism quotes or a canonical example.

    @@ -296,7 +297,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -325,12 +335,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/hemolysis.html b/pages/traits/other/hemolysis.html index ac3de84c336..931a7112247 100644 --- a/pages/traits/other/hemolysis.html +++ b/pages/traits/other/hemolysis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -109,7 +110,7 @@

    Children (1)

    Synonyms (1)

      -
    • presence of hemolysis RELATED_SYNONYM · metpo.owl
      • +
    • presence of hemolysis RELATED_SYNONYM · metpo.owl
    @@ -125,7 +126,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1005025 [-3.115, -2.011, -3.899, -0.588, …]
      • +
    • hemolysis METPO:1005025 [-3.115, -2.011, -3.899, -0.588, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -245,7 +246,7 @@

    Discussions and Knowledge Gaps (1)

    -

    The current record carries a single 54-character phrase ('hemolysis to toxigenic substances secreted by S. aureus' in DOI:10.3390/toxins5061140); constructing a multi-edge graph from one short phrase would violate the snippet-diversity and anti-clause-splitting rules.

    +

    The current record carries a single 54-character phrase ('hemolysis to toxigenic substances secreted by S. aureus' in DOI:10.3390/toxins5061140); constructing a multi-edge graph from one short phrase would violate the snippet-diversity and anti-clause-splitting rules.

    @@ -333,7 +334,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -362,12 +372,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/hemolytic.html b/pages/traits/other/hemolytic.html index 4315e4a9b74..d47951d80eb 100644 --- a/pages/traits/other/hemolytic.html +++ b/pages/traits/other/hemolytic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1005026 [-3.020, -1.331, -3.251, -0.320, …]
      • +
    • hemolytic METPO:1005026 [-3.020, -1.331, -3.251, -0.320, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -227,7 +228,7 @@

    Discussions and Knowledge Gaps (1)

    -

    The current record carries a single 54-character phrase ('hemolysis to toxigenic substances secreted by S. aureus' in DOI:10.3390/toxins5061140); constructing a multi-edge graph from one short phrase would violate the snippet-diversity and anti-clause-splitting rules.

    +

    The current record carries a single 54-character phrase ('hemolysis to toxigenic substances secreted by S. aureus' in DOI:10.3390/toxins5061140); constructing a multi-edge graph from one short phrase would violate the snippet-diversity and anti-clause-splitting rules.

    @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/indole_test.html b/pages/traits/other/indole_test.html index 79e7854d18c..3e625a7b6d0 100644 --- a/pages/traits/other/indole_test.html +++ b/pages/traits/other/indole_test.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -124,7 +125,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -319,7 +320,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -348,12 +358,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/indole_test_negative.html b/pages/traits/other/indole_test_negative.html index 7214425c635..0dbcf4c82f7 100644 --- a/pages/traits/other/indole_test_negative.html +++ b/pages/traits/other/indole_test_negative.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -119,7 +120,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -271,7 +272,7 @@

    Discussions and Knowledge Gaps (2)

    -

    This record represents a negative diagnostic test-outcome phenotype (DOI:10.1128/AEM.02787-15; DOI:10.1128/JCM.00940-06) defined by the absence of indole production from tryptophan.

    +

    This record represents a negative diagnostic test-outcome phenotype (DOI:10.1128/AEM.02787-15; DOI:10.1128/JCM.00940-06) defined by the absence of indole production from tryptophan.

    @@ -419,7 +420,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -448,12 +458,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/indole_test_positive.html b/pages/traits/other/indole_test_positive.html index a0770daeed8..5e7096f21cb 100644 --- a/pages/traits/other/indole_test_positive.html +++ b/pages/traits/other/indole_test_positive.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -76,7 +77,7 @@

    Trait evidence (2)

    Bacterial L-tryptophan catabolism to indole

    Evidence-backed metabolic pathway sketch linking bacterial tryptophan catabolism and indole formation to the indole test positive phenotype.

    -

    NONMECHANISTIC · Pathway-and-metabolite sketch backed by DOI:10.1128/AEM.02787-15; strain-matched UniProtKB protein examples for Escherichia coli tryptophanase (TnaA) remain to be curated.

    +

    NONMECHANISTIC · Pathway-and-metabolite sketch backed by DOI:10.1128/AEM.02787-15; strain-matched UniProtKB protein examples for Escherichia coli tryptophanase (TnaA) remain to be curated.

    Loading graph…

    @@ -178,7 +179,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • indole test RELATED_SYNONYM · metpo.owl
      • +
    • indole test RELATED_SYNONYM · metpo.owl
    @@ -194,7 +195,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -346,7 +347,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The record's primary literature (DOI:10.1128/AEM.02787-15) establishes L-tryptophan degradation to indole in enterotoxigenic Escherichia coli strain H10407 (NCBITaxon:316401), but a verified UniProtKB accession for tryptophanase (TnaA) on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    +

    The record's primary literature (DOI:10.1128/AEM.02787-15) establishes L-tryptophan degradation to indole in enterotoxigenic Escherichia coli strain H10407 (NCBITaxon:316401), but a verified UniProtKB accession for tryptophanase (TnaA) on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    @@ -370,7 +371,7 @@

    Evidence

    Provenance -

    Cycle 3 Stage 3 UniProt audit: canonical_examples cites enterotoxigenic Escherichia coli strain H10407 (NCBITaxon:316401; DOI:10.1128/AEM.02787-15), an analytical indole-assay study whose text does not mention tnaA or tryptophanase and for which UniProtKB lacks a strain H10407 tnaA entry, whereas reviewed Swiss-Prot tryptophanase TnaA (UniProtKB:P0A853) is annotated on Escherichia coli K-12 (NCBITaxon:83333; UP000000625). Keeping graph NONMECHANISTIC and discussion OPEN until a K-12 tnaA primary source snippet and canonical_examples entry are added.

    +

    Cycle 3 Stage 3 UniProt audit: canonical_examples cites enterotoxigenic Escherichia coli strain H10407 (NCBITaxon:316401; DOI:10.1128/AEM.02787-15), an analytical indole-assay study whose text does not mention tnaA or tryptophanase and for which UniProtKB lacks a strain H10407 tnaA entry, whereas reviewed Swiss-Prot tryptophanase TnaA (UniProtKB:P0A853) is annotated on Escherichia coli K-12 (NCBITaxon:83333; UP000000625). Keeping graph NONMECHANISTIC and discussion OPEN until a K-12 tnaA primary source snippet and canonical_examples entry are added.

    @@ -409,7 +410,7 @@

    Curation history

  • · RECORD_CURATION_DISCUSSION · claude -

    Recorded Cycle 3 Stage 3 UniProtKB audit note on indole-test-positive-protein-example-gap documenting the source-snippet and strain-taxon blocker between Escherichia coli H10407 (NCBITaxon:316401; DOI:10.1128/AEM.02787-15) and Escherichia coli K-12 Swiss-Prot TnaA (UniProtKB:P0A853; NCBITaxon:83333).

    +

    Recorded Cycle 3 Stage 3 UniProtKB audit note on indole-test-positive-protein-example-gap documenting the source-snippet and strain-taxon blocker between Escherichia coli H10407 (NCBITaxon:316401; DOI:10.1128/AEM.02787-15) and Escherichia coli K-12 Swiss-Prot TnaA (UniProtKB:P0A853; NCBITaxon:83333).

    • @@ -419,7 +420,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add indole test positive TraitRecord -

      Seeded METPO:1005011 from data/raw/metpo.owl, enriched it with DOI:10.1128/AEM.02787-15 evidence for tryptophan-derived bacterial indole production, added Escherichia coli ETEC H10407 as a canonical example, and reparented the record from assay parent METPO:1005010 to METPO:1000059 with an open curation TODO for the missing non-assay parent.

    +

    Seeded METPO:1005011 from data/raw/metpo.owl, enriched it with DOI:10.1128/AEM.02787-15 evidence for tryptophan-derived bacterial indole production, added Escherichia coli ETEC H10407 as a canonical example, and reparented the record from assay parent METPO:1005010 to METPO:1000059 with an open curation TODO for the missing non-assay parent.

    • Read this curation session
  • @@ -457,7 +458,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -821,12 +831,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 22:45 UTC diff --git a/pages/traits/other/irregular_colony.html b/pages/traits/other/irregular_colony.html index 06561aaba57..47ec1c01e74 100644 --- a/pages/traits/other/irregular_colony.html +++ b/pages/traits/other/irregular_colony.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Discussions and Knowledge Gaps (1)

    -

    The current record carries a single general colony-morphology overview snippet (DOI:10.7759/cureus.374) without specific genetic or biophysical morphogenesis quotes.

    +

    The current record carries a single general colony-morphology overview snippet (DOI:10.7759/cureus.374) without specific genetic or biophysical morphogenesis quotes.

    @@ -258,7 +259,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add seeded irregular colony trait -

      Added METPO:1007065 as data/traits/other/irregular_colony.yaml from the METPO seed, preserving the OTHER category and colony shape parent. Enriched the record with DOI:10.7759/cureus.374 evidence for irregular as a bacterial colony shape after an exact duplicate search including ignored and hidden files found no existing live data/traits or history record.

    +

    Added METPO:1007065 as data/traits/other/irregular_colony.yaml from the METPO seed, preserving the OTHER category and colony shape parent. Enriched the record with DOI:10.7759/cureus.374 evidence for irregular as a bacterial colony shape after an exact duplicate search including ignored and hidden files found no existing live data/traits or history record.

    • Read this curation session @@ -290,7 +291,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -319,12 +329,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/methyl_red_test.html b/pages/traits/other/methyl_red_test.html index 0297524f7fe..4d81d4acff9 100644 --- a/pages/traits/other/methyl_red_test.html +++ b/pages/traits/other/methyl_red_test.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -130,7 +131,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -337,7 +338,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -366,12 +376,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/methyl_red_test_negative.html b/pages/traits/other/methyl_red_test_negative.html index e839271995e..92af49d8e91 100644 --- a/pages/traits/other/methyl_red_test_negative.html +++ b/pages/traits/other/methyl_red_test_negative.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -119,7 +120,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -271,7 +272,7 @@

    Discussions and Knowledge Gaps (2)

    -

    This record represents a negative diagnostic test-outcome phenotype supported by ASM protocol color-threshold and clinical panel reproducibility snippets (DOI:10.1128/JCM.42.8.3665-3669.2004) without enzymatic pathway quotes.

    +

    This record represents a negative diagnostic test-outcome phenotype supported by ASM protocol color-threshold and clinical panel reproducibility snippets (DOI:10.1128/JCM.42.8.3665-3669.2004) without enzymatic pathway quotes.

    @@ -395,7 +396,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -424,12 +434,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/methyl_red_test_positive.html b/pages/traits/other/methyl_red_test_positive.html index 2a9cb3ad5c4..26cf39964de 100644 --- a/pages/traits/other/methyl_red_test_positive.html +++ b/pages/traits/other/methyl_red_test_positive.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • methyl red test RELATED_SYNONYM · metpo.owl
      • +
    • methyl red test RELATED_SYNONYM · metpo.owl
    @@ -122,7 +123,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -274,7 +275,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record pairs an ASM pH-indicator color-change snippet with a clinical identification panel count snippet (DOI:10.1128/JCM.42.8.3665-3669.2004), lacking enzymatic or metabolic pathway quotes for the exemplar taxon.

    +

    The current record pairs an ASM pH-indicator color-change snippet with a clinical identification panel count snippet (DOI:10.1128/JCM.42.8.3665-3669.2004), lacking enzymatic or metabolic pathway quotes for the exemplar taxon.

    @@ -398,7 +399,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -427,12 +437,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/non_hemolytic.html b/pages/traits/other/non_hemolytic.html index a25461424aa..73b89c263ad 100644 --- a/pages/traits/other/non_hemolytic.html +++ b/pages/traits/other/non_hemolytic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -232,7 +233,7 @@

    Discussions and Knowledge Gaps (2)

    -

    This record represents a negative diagnostic phenotype (gamma-hemolysis / absence of red-blood-cell lysis in DOI:10.14202/vetworld.2025.3622-3630) supported by a single screening snippet without a canonical example.

    +

    This record represents a negative diagnostic phenotype (gamma-hemolysis / absence of red-blood-cell lysis in DOI:10.14202/vetworld.2025.3622-3630) supported by a single screening snippet without a canonical example.

    @@ -320,7 +321,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -349,12 +359,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/osmotic_tolerance.html b/pages/traits/other/osmotic_tolerance.html index 1fc1b689551..99b52ae022f 100644 --- a/pages/traits/other/osmotic_tolerance.html +++ b/pages/traits/other/osmotic_tolerance.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • osmophile EXACT_SYNONYM · metpo.owl
      • +
    • osmophile EXACT_SYNONYM · metpo.owl
    @@ -116,7 +117,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -211,7 +212,7 @@

    Discussions and Knowledge Gaps (1)

    -

    The current record carries a single 49-character snippet ('tolerance against hyperosmotic conditions (400 mM sorbitol)' in DOI:10.1128/mBio.00390-21) without a second mechanistic quote or canonical example.

    +

    The current record carries a single 49-character snippet ('tolerance against hyperosmotic conditions (400 mM sorbitol)' in DOI:10.1128/mBio.00390-21) without a second mechanistic quote or canonical example.

    @@ -267,7 +268,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add seeded osmotic tolerance trait -

      Added METPO:1007073 as data/traits/other/osmotic_tolerance.yaml from the METPO seed, preserving the OTHER category, phenotype parent, and osmophile exact synonym. Enriched the record with DOI:10.1128/mBio.00390-21 evidence for growth under a 400 mM sorbitol nonionic hyperosmotic challenge after exact duplicate searches including ignored and hidden files found no existing data/traits record.

    +

    Added METPO:1007073 as data/traits/other/osmotic_tolerance.yaml from the METPO seed, preserving the OTHER category, phenotype parent, and osmophile exact synonym. Enriched the record with DOI:10.1128/mBio.00390-21 evidence for growth under a 400 mM sorbitol nonionic hyperosmotic challenge after exact duplicate searches including ignored and hidden files found no existing data/traits record.

    • Read this curation session @@ -299,7 +300,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -328,12 +338,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/oxidase_negative.html b/pages/traits/other/oxidase_negative.html index 28902ba6706..e23ac5c4d57 100644 --- a/pages/traits/other/oxidase_negative.html +++ b/pages/traits/other/oxidase_negative.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,9 +113,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • oxidase - EXACT_SYNONYM · metpo.owl
      • +
    • oxidase - EXACT_SYNONYM · metpo.owl
      • -
    • oxidase test negative EXACT_SYNONYM · metpo.owl
      • +
    • oxidase test negative EXACT_SYNONYM · metpo.owl
    @@ -130,7 +131,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -225,7 +226,7 @@

    Discussions and Knowledge Gaps (1)

    -

    This record represents a negative diagnostic test-outcome phenotype (ASM oxidase test protocol; DOI:10.5812/chbs-160199) defined by the absence of cytochrome c oxidase indicator oxidation.

    +

    This record represents a negative diagnostic test-outcome phenotype (ASM oxidase test protocol; DOI:10.5812/chbs-160199) defined by the absence of cytochrome c oxidase indicator oxidation.

    @@ -313,7 +314,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -342,12 +352,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/oxidase_test.html b/pages/traits/other/oxidase_test.html index 6c075921268..4115ec9ed62 100644 --- a/pages/traits/other/oxidase_test.html +++ b/pages/traits/other/oxidase_test.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,9 +116,9 @@

    Children (1)

    Synonyms (2)

      -
    • cytochrome oxidase test EXACT_SYNONYM · metpo.owl
      • +
    • cytochrome oxidase test EXACT_SYNONYM · metpo.owl
      • -
    • oxidase activity test EXACT_SYNONYM · metpo.owl
      • +
    • oxidase activity test EXACT_SYNONYM · metpo.owl
    @@ -133,7 +134,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -228,7 +229,7 @@

    Discussions and Knowledge Gaps (1)

    -

    METPO:1007081 represents the diagnostic oxidase test protocol (ASM oxidase test protocol; DOI:10.5812/chbs-160199), whereas the cytochrome c oxidase respiratory mechanism is curated on oxidase_positive.yaml.

    +

    METPO:1007081 represents the diagnostic oxidase test protocol (ASM oxidase test protocol; DOI:10.5812/chbs-160199), whereas the cytochrome c oxidase respiratory mechanism is curated on oxidase_positive.yaml.

    @@ -316,7 +317,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -345,12 +355,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/punctiform_colony.html b/pages/traits/other/punctiform_colony.html index 2beaa2f02da..9530fb7aab4 100644 --- a/pages/traits/other/punctiform_colony.html +++ b/pages/traits/other/punctiform_colony.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Discussions and Knowledge Gaps (1)

    -

    The current record carries a single general colony-morphology overview snippet (DOI:10.7759/cureus.374) without specific genetic or physiological mechanism quotes.

    +

    The current record carries a single general colony-morphology overview snippet (DOI:10.7759/cureus.374) without specific genetic or physiological mechanism quotes.

    @@ -258,7 +259,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add seeded punctiform colony trait -

      Added METPO:1007067 as data/traits/other/punctiform_colony.yaml from the METPO seed, then enriched the record with stable OMP definition provenance and DOI:10.7759/cureus.374 evidence for pinpoint colony size after an exact duplicate search including ignored and hidden files.

    +

    Added METPO:1007067 as data/traits/other/punctiform_colony.yaml from the METPO seed, then enriched the record with stable OMP definition provenance and DOI:10.7759/cureus.374 evidence for pinpoint colony size after an exact duplicate search including ignored and hidden files.

    • Read this curation session @@ -290,7 +291,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -319,12 +329,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/rhizoid_colony.html b/pages/traits/other/rhizoid_colony.html index ee466e3515a..c54497af7fe 100644 --- a/pages/traits/other/rhizoid_colony.html +++ b/pages/traits/other/rhizoid_colony.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Discussions and Knowledge Gaps (1)

    -

    The current record carries a single general colony-morphology overview snippet (DOI:10.7759/cureus.374) without specific genetic or cellular morphogenesis quotes.

    +

    The current record carries a single general colony-morphology overview snippet (DOI:10.7759/cureus.374) without specific genetic or cellular morphogenesis quotes.

    @@ -258,7 +259,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add seeded rhizoid colony trait -

      Added METPO:1007068 as data/traits/other/rhizoid_colony.yaml from the METPO seed, preserving the OTHER category and colony shape parent. Enriched the record with stable OMP definition provenance and DOI:10.7759/cureus.374 evidence for rhizoid as a bacterial colony shape after an exact duplicate search including ignored and hidden files found no existing live data/traits or history record.

    +

    Added METPO:1007068 as data/traits/other/rhizoid_colony.yaml from the METPO seed, preserving the OTHER category and colony shape parent. Enriched the record with stable OMP definition provenance and DOI:10.7759/cureus.374 evidence for rhizoid as a bacterial colony shape after an exact duplicate search including ignored and hidden files found no existing live data/traits or history record.

    • Read this curation session @@ -290,7 +291,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -319,12 +329,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/specialist.html b/pages/traits/other/specialist.html index 03ee5007858..7ca8567ed5f 100644 --- a/pages/traits/other/specialist.html +++ b/pages/traits/other/specialist.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Discussions and Knowledge Gaps (1)

    -

    The current record carries two high-level ecological classification snippets (DOI:10.1093/femsec/fiaa240; DOI:10.1038/s41559-023-02027-7) contrasting niche breadth in generalists vs specialists without molecular mechanism quotes or a canonical example.

    +

    The current record carries two high-level ecological classification snippets (DOI:10.1093/femsec/fiaa240; DOI:10.1038/s41559-023-02027-7) contrasting niche breadth in generalists vs specialists without molecular mechanism quotes or a canonical example.

    @@ -290,7 +291,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -319,12 +329,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/urease_negative.html b/pages/traits/other/urease_negative.html index d7d7700706f..582c7ac70b0 100644 --- a/pages/traits/other/urease_negative.html +++ b/pages/traits/other/urease_negative.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,9 +107,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • urease - EXACT_SYNONYM · metpo.owl
      • +
    • urease - EXACT_SYNONYM · metpo.owl
      • -
    • urease test negative EXACT_SYNONYM · metpo.owl
      • +
    • urease test negative EXACT_SYNONYM · metpo.owl
    @@ -124,7 +125,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -219,7 +220,7 @@

    Discussions and Knowledge Gaps (1)

    -

    This record represents a negative diagnostic test-outcome phenotype supported by phenol-red urease medium indicator snippets (DOI:10.5812/chbs-160199) without a canonical example or active enzymatic pathway.

    +

    This record represents a negative diagnostic test-outcome phenotype supported by phenol-red urease medium indicator snippets (DOI:10.5812/chbs-160199) without a canonical example or active enzymatic pathway.

    @@ -307,7 +308,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -336,12 +346,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/urease_test.html b/pages/traits/other/urease_test.html index 07c10170181..ff67f13f372 100644 --- a/pages/traits/other/urease_test.html +++ b/pages/traits/other/urease_test.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,9 +116,9 @@

    Children (1)

    Synonyms (2)

      -
    • urea hydrolysis test EXACT_SYNONYM · metpo.owl
      • +
    • urea hydrolysis test EXACT_SYNONYM · metpo.owl
      • -
    • urease activity test EXACT_SYNONYM · metpo.owl
      • +
    • urease activity test EXACT_SYNONYM · metpo.owl
    @@ -133,7 +134,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -228,7 +229,7 @@

    Discussions and Knowledge Gaps (1)

    -

    METPO:1007082 represents the diagnostic urease test protocol (DOI:10.5812/chbs-160199), whereas the nickel-metalloenzyme urea hydrolysis mechanism is curated on urease_positive.yaml.

    +

    METPO:1007082 represents the diagnostic urease test protocol (DOI:10.5812/chbs-160199), whereas the nickel-metalloenzyme urea hydrolysis mechanism is curated on urease_positive.yaml.

    @@ -316,7 +317,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -345,12 +355,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/voges_proskauer_test.html b/pages/traits/other/voges_proskauer_test.html index 35907d1c2c9..f0ecb2fc717 100644 --- a/pages/traits/other/voges_proskauer_test.html +++ b/pages/traits/other/voges_proskauer_test.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -124,7 +125,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -307,7 +308,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -336,12 +346,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/voges_proskauer_test_negative.html b/pages/traits/other/voges_proskauer_test_negative.html index b6c42a97e88..3f5a643c7b4 100644 --- a/pages/traits/other/voges_proskauer_test_negative.html +++ b/pages/traits/other/voges_proskauer_test_negative.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -107,7 +108,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/other/voges_proskauer_test_positive.html b/pages/traits/other/voges_proskauer_test_positive.html index db7b69053c3..079a6122769 100644 --- a/pages/traits/other/voges_proskauer_test_positive.html +++ b/pages/traits/other/voges_proskauer_test_positive.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • voges-proskauer test RELATED_SYNONYM · metpo.owl
      • +
    • voges-proskauer test RELATED_SYNONYM · metpo.owl
    @@ -122,7 +123,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -274,7 +275,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record pairs an ASM KOH-oxidation reagent chemistry snippet with a clinical identification panel count snippet (DOI:10.1128/JCM.42.8.3665-3669.2004), lacking organismal enzymatic catalysis quotes for acetoin biosynthesis.

    +

    The current record pairs an ASM KOH-oxidation reagent chemistry snippet with a clinical identification panel count snippet (DOI:10.1128/JCM.42.8.3665-3669.2004), lacking organismal enzymatic catalysis quotes for acetoin biosynthesis.

    @@ -374,7 +375,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -403,12 +413,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 20:51 UTC diff --git a/pages/traits/physiology/acid_phosphatase_activity.html b/pages/traits/physiology/acid_phosphatase_activity.html index a625cbb5d54..d0ee65ff70f 100644 --- a/pages/traits/physiology/acid_phosphatase_activity.html +++ b/pages/traits/physiology/acid_phosphatase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -263,7 +264,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries one culture-filtrate detection snippet and one API ZYM profile snippet (DOI:10.1128/JB.182.23.6850-6853.2000, DOI:10.1155/2021/8888641) without distinct catalytic substrate/product quotes for a multi-edge graph.

    +

    The current record carries one culture-filtrate detection snippet and one API ZYM profile snippet (DOI:10.1128/JB.182.23.6850-6853.2000, DOI:10.1155/2021/8888641) without distinct catalytic substrate/product quotes for a multi-edge graph.

    @@ -345,7 +346,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -374,12 +384,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/acquired_stress_resistance_memory.html b/pages/traits/physiology/acquired_stress_resistance_memory.html index 42eb582eaf7..5621d7cdd25 100644 --- a/pages/traits/physiology/acquired_stress_resistance_memory.html +++ b/pages/traits/physiology/acquired_stress_resistance_memory.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1534/genetics.112.143016
    resistance persisted for four to five generations after cells were removed from the prior salt treatment
    -

    Guan et al. 2012, PMID:22851651, PMC3454879; scientific abstract, directly matched in publisher HTML and source-qualified MED. The resistance endpoint is H2O2 survival, not faster transcriptional reactivation. Relevant Methods, Results and actual Figure 1 and S1/S2 were inspected. BY4741-background cells received 0.7 M NaCl for 60 minutes, then grew in fresh stress-free YPD. Figure 1 describes three-to-four doublings over 360 minutes; four-to-five generations is the abstract statement. Methods specifies 11 peroxide doses plus control, whereas Figure 1A captions ten plotted doses. The normalized survival score is not a fraction of memory-bearing cells. S1 growth-arrest interventions and S2 engineered UCC8613 daughter marking are separate contexts. No natural canonical exemplar is asserted. The publisher's formula rendering differs from MED H(2)O(2); the selected span matches both without changing either source. Raw data were not independently reanalyzed.

    +

    Guan et al. 2012, PMID:22851651, PMC3454879; scientific abstract, directly matched in publisher HTML and source-qualified MED. The resistance endpoint is H2O2 survival, not faster transcriptional reactivation. Relevant Methods, Results and actual Figure 1 and S1/S2 were inspected. BY4741-background cells received 0.7 M NaCl for 60 minutes, then grew in fresh stress-free YPD. Figure 1 describes three-to-four doublings over 360 minutes; four-to-five generations is the abstract statement. Methods specifies 11 peroxide doses plus control, whereas Figure 1A captions ten plotted doses. The normalized survival score is not a fraction of memory-bearing cells. S1 growth-arrest interventions and S2 engineered UCC8613 daughter marking are separate contexts. No natural canonical exemplar is asserted. The publisher's formula rendering differs from MED H(2)O(2); the selected span matches both without changing either source. Raw data were not independently reanalyzed.

  • DOI:10.1371/journal.pbio.2003853
    the cells inheriting this ancestral PA displayed a significantly increased heat resistance compared to their isogenic, PA-free siblings.
    -

    Govers et al. 2018, PMID:30153247, PMC6112618; scientific abstract, not Author Summary, matched in primary XML and source-qualified MED. Relevant Results and Methods, actual Figure 4 and S6 were inspected. Engineered MG1655 IbpA-msfGFP reporters received 47 C for 15 minutes, recovered with growth, then faced 51 C for 7 minutes. Figure 4D compares aggregate-bearing and aggregate-free descendants; Figure 4C detects no improved population-average survival after pretreatment. Survival requires growth and division within eight hours. S6 detects no age-bin survival difference in this assay, not universal age independence. Reporter-induced clustering was separately tested in actual Figure 1, previously inspected for traitmech:000711; a monomeric label alone is not proof against artifacts. Synthetic induction experiments and their duration are not transferred to these heat-induced lineages. Raw data and all other memory-related figure images were not independently assessed.

    +

    Govers et al. 2018, PMID:30153247, PMC6112618; scientific abstract, not Author Summary, matched in primary XML and source-qualified MED. Relevant Results and Methods, actual Figure 4 and S6 were inspected. Engineered MG1655 IbpA-msfGFP reporters received 47 C for 15 minutes, recovered with growth, then faced 51 C for 7 minutes. Figure 4D compares aggregate-bearing and aggregate-free descendants; Figure 4C detects no improved population-average survival after pretreatment. Survival requires growth and division within eight hours. S6 detects no age-bin survival difference in this assay, not universal age independence. Reporter-induced clustering was separately tested in actual Figure 1, previously inspected for traitmech:000711; a monomeric label alone is not proof against artifacts. Synthetic induction experiments and their duration are not transferred to these heat-induced lineages. Raw data and all other memory-related figure images were not independently assessed.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -301,7 +302,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add memory of acquired stress resistance with primary evidence -

      Added a PROPOSED physiological class with Guan 2012 DOI:10.1534/genetics.112.143016 and Govers 2018 DOI:10.1371/journal.pbio.2003853, directly checked scientific-abstract snippets, inspected endpoint-specific figures, and explicit post-removal, transcription-versus-survival, cell-versus-population and reporter qualifications. Reserved traitmech:000712, v588 and 1066500-1066599 after ignored/hidden current-file, retained historical-tree, known independent-copy and pending-PR checks. Natural canonical taxa, exact external mappings and a shared causal mechanism are deferred. Existing TraitRecords and the pinned ontology are unchanged. Validation and adversarial review outcomes are recorded separately rather than claimed in advance.

    +

    Added a PROPOSED physiological class with Guan 2012 DOI:10.1534/genetics.112.143016 and Govers 2018 DOI:10.1371/journal.pbio.2003853, directly checked scientific-abstract snippets, inspected endpoint-specific figures, and explicit post-removal, transcription-versus-survival, cell-versus-population and reporter qualifications. Reserved traitmech:000712, v588 and 1066500-1066599 after ignored/hidden current-file, retained historical-tree, known independent-copy and pending-PR checks. Natural canonical taxa, exact external mappings and a shared causal mechanism are deferred. Existing TraitRecords and the pinned ontology are unchanged. Validation and adversarial review outcomes are recorded separately rather than claimed in advance.

    • Read this curation session @@ -333,7 +334,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -362,12 +372,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-12 21:04 UTC diff --git a/pages/traits/physiology/aerobic_anoxygenic_phototrophy.html b/pages/traits/physiology/aerobic_anoxygenic_phototrophy.html index ec43d6b30af..0da1af0954f 100644 --- a/pages/traits/physiology/aerobic_anoxygenic_phototrophy.html +++ b/pages/traits/physiology/aerobic_anoxygenic_phototrophy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -108,7 +109,7 @@

    Edge evidence

  • aerobic anoxygenic phototrophy - traitmech:000194 + traitmech:000194 has energy source light PATO:0001717 @@ -127,7 +128,7 @@

    Edge evidence

  • aerobic anoxygenic phototrophy - traitmech:000194 + traitmech:000194 has carbon source organic carbon CHEBI:50860 @@ -270,13 +271,13 @@

    Parent traits (3)

    Synonyms (4)

      -
    • aerobic anoxygenic phototroph EXACT_SYNONYM · DOI:10.1128/AEM.01747-12
      • +
    • aerobic anoxygenic phototroph EXACT_SYNONYM · DOI:10.1128/AEM.01747-12
      • -
    • aerobic anoxygenic phototrophic bacteria EXACT_SYNONYM · DOI:10.1186/s40168-024-01786-0
      • +
    • aerobic anoxygenic phototrophic bacteria EXACT_SYNONYM · DOI:10.1186/s40168-024-01786-0
      • -
    • AAP bacteria RELATED_SYNONYM · DOI:10.1186/s40168-024-01786-0
      • +
    • AAP bacteria RELATED_SYNONYM · DOI:10.1186/s40168-024-01786-0
      • -
    • aerobic_anoxygenic_phototrophy RELATED_SYNONYM · metpo.owl
      • +
    • aerobic_anoxygenic_phototrophy RELATED_SYNONYM · metpo.owl
    • @@ -292,7 +293,7 @@

    kg-microbe context

    via parent_proxy.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -477,7 +478,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -841,12 +851,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-14 23:14 UTC diff --git a/pages/traits/physiology/aerobic_overflow_metabolism.html b/pages/traits/physiology/aerobic_overflow_metabolism.html index 602dc8fd23f..60efc65a886 100644 --- a/pages/traits/physiology/aerobic_overflow_metabolism.html +++ b/pages/traits/physiology/aerobic_overflow_metabolism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1038/msb.2009.82
    S. cerevisiae and E. coli fully oxidize glucose at low concentrations and shift to overflow metabolism at high glucose concentrations.
    -

    Molenaar et al. 2009, PMID:19888218, PMC2795476; Current growth models and their limitations, not the abstract. The surrounding paragraph supplies the fully aerobic, incomplete-oxidation and retained respiratory-capacity differentia. This Perspective contains original modeling, not new experimental replication of the cited organisms. The terminology discussion also includes mixed-acid-to-lactate shifts; the qualified label here does not define every use of unqualified overflow metabolism.

    +

    Molenaar et al. 2009, PMID:19888218, PMC2795476; Current growth models and their limitations, not the abstract. The surrounding paragraph supplies the fully aerobic, incomplete-oxidation and retained respiratory-capacity differentia. This Perspective contains original modeling, not new experimental replication of the cited organisms. The terminology discussion also includes mixed-acid-to-lactate shifts; the qualified label here does not define every use of unqualified overflow metabolism.

  • DOI:10.1038/nature15765
    cells use fermentation instead of the more efficient respiration to generate energy, despite the availability of oxygen.
    -

    Basan et al. 2015, PMID:26632588, PMC4843128; scientific abstract. Relevant Results, growth Methods, model scope, Extended Data Table 1, actual Figure 1 and Extended Data Figure 2 were inspected through public XML and figure assets. Acetate excretion depends on growth conditions; the fitted threshold is not universal. The oxidative-fermentation accounting includes oxygen-dependent NADH oxidation. Net excretion does not exclude acetate reuptake. Proteome allocation is a tested model in this system, not a necessary mechanism for every member of the trait. Complete supplements, equations and referenced batch-culture methods were not independently reanalyzed. Publisher retrieval failed; the public full-text XML was accessible.

    +

    Basan et al. 2015, PMID:26632588, PMC4843128; scientific abstract. Relevant Results, growth Methods, model scope, Extended Data Table 1, actual Figure 1 and Extended Data Figure 2 were inspected through public XML and figure assets. Acetate excretion depends on growth conditions; the fitted threshold is not universal. The oxidative-fermentation accounting includes oxygen-dependent NADH oxidation. Net excretion does not exclude acetate reuptake. Proteome allocation is a tested model in this system, not a necessary mechanism for every member of the trait. Complete supplements, equations and referenced batch-culture methods were not independently reanalyzed. Publisher retrieval failed; the public full-text XML was accessible.

  • DOI:10.1111/febs.13019
    All fermenting yeasts exhibited significant ethanol formation within the first 20 min in response to a glucose pulse
    -

    Hagman et al. 2014, PMID:25161062, PMC4240471; Results and Discussion / Consumption of glucose and generation of biomass and ethanol, not the abstract. Introduction, relevant Results, Experimental procedures and actual Figures 1-2 were inspected. Glucose pulses into initially respiratory cultures produced ethanol in responsive yeasts while dissolved oxygen was controlled above 30% air saturation. The authors report no first-hour repression of respiration; Figure 2 does not establish monotonic or unchanged oxygen-consumption rates. Replication excludes V. polyspora; E. coryli received supplementation. This short-term Crabtree assay is not an exact synonym for the entire microbial phenotype. Supplemental time series and strain origins were not fully reviewed.

    +

    Hagman et al. 2014, PMID:25161062, PMC4240471; Results and Discussion / Consumption of glucose and generation of biomass and ethanol, not the abstract. Introduction, relevant Results, Experimental procedures and actual Figures 1-2 were inspected. Glucose pulses into initially respiratory cultures produced ethanol in responsive yeasts while dissolved oxygen was controlled above 30% air saturation. The authors report no first-hour repression of respiration; Figure 2 does not establish monotonic or unchanged oxygen-consumption rates. Replication excludes V. polyspora; E. coryli received supplementation. This short-term Crabtree assay is not an exact synonym for the entire microbial phenotype. Supplemental time series and strain origins were not fully reviewed.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -215,7 +216,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    The qualifier aerobic is deliberate. Unqualified overflow, Crabtree effect, respiro-fermentation and industrial aerobic fermentation are not asserted as exact synonyms. The local METPO:1002005 fermentation record is donor/acceptor-defined and excludes external electron acceptors; Basan's oxidative branch uses different accounting. https://github.com/berkeleybop/metpo/issues/468 discusses fermentation hierarchy, and the pinned ontology already differs from the retained local parent/definition. Neither that process nor METPO:1000060 metabolism is adopted as an is-a parent of this organismal phenotype. METPO:1000059 phenotype is used pending upstream hierarchy review. Product-specific ethanol/butanediol fermentation, aerotolerance, facultative anaerobiosis, copiotrophy and diauxic growth are not equivalent. Product detection or oxygen presence alone is insufficient: oxygen limitation must be excluded. No universal substrate, product, concentration, growth-rate threshold, complete respiratory shutdown or fixed molecular mechanism is required.

    +

    The qualifier aerobic is deliberate. Unqualified overflow, Crabtree effect, respiro-fermentation and industrial aerobic fermentation are not asserted as exact synonyms. The local METPO:1002005 fermentation record is donor/acceptor-defined and excludes external electron acceptors; Basan's oxidative branch uses different accounting. https://github.com/berkeleybop/metpo/issues/468 discusses fermentation hierarchy, and the pinned ontology already differs from the retained local parent/definition. Neither that process nor METPO:1000060 metabolism is adopted as an is-a parent of this organismal phenotype. METPO:1000059 phenotype is used pending upstream hierarchy review. Product-specific ethanol/butanediol fermentation, aerotolerance, facultative anaerobiosis, copiotrophy and diauxic growth are not equivalent. Product detection or oxygen presence alone is insufficient: oxygen limitation must be excluded. No universal substrate, product, concentration, growth-rate threshold, complete respiratory shutdown or fixed molecular mechanism is required.

    @@ -333,7 +334,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -362,12 +372,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-12 01:54 UTC diff --git a/pages/traits/physiology/aerotaxis.html b/pages/traits/physiology/aerotaxis.html index 72c3792d183..67f98185227 100644 --- a/pages/traits/physiology/aerotaxis.html +++ b/pages/traits/physiology/aerotaxis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1128/jb.169.7.3118-3123.1987
    at high concentrations, oxygen was a repellent of Salmonella typhimurium, Escherichia coli, and some bacilli
    -

    Abstract, exact-matched at Europe PMC (PMID:3036771); full text not inspected. The study contrasts high-oxygen repulsion with attraction at lower concentrations and reports temporal assays. This supports concentration-dependent response direction, not universal thresholds or a requirement that every organism exhibit both signs. The abstract's tentative receptor interpretation is not promoted to an established mechanism.

    +

    Abstract, exact-matched at Europe PMC (PMID:3036771); full text not inspected. The study contrasts high-oxygen repulsion with attraction at lower concentrations and reports temporal assays. This supports concentration-dependent response direction, not universal thresholds or a requirement that every organism exhibit both signs. The abstract's tentative receptor interpretation is not promoted to an established mechanism.

  • DOI:10.1128/jb.178.17.5199-5204.1996
    As a result of aerotaxis, the bacteria were attracted to a specific low concentration of oxygen (3 to 5 microM).
    -

    Abstract, exact-matched at Europe PMC (PMID:8752338); full text not inspected. Azospirillum brasilense forms a band in a spatial oxygen gradient and returns when swimming into higher or lower oxygen; temporal gradients corroborate the response. The preferred interval is experiment-specific. Proton motive force peaks in the same interval, but its proposed signaling role remains a hypothesis, not a protein-resolved causal edge. No strain-level canonical example is inferred from the abstract.

    +

    Abstract, exact-matched at Europe PMC (PMID:8752338); full text not inspected. Azospirillum brasilense forms a band in a spatial oxygen gradient and returns when swimming into higher or lower oxygen; temporal gradients corroborate the response. The preferred interval is experiment-specific. Proton motive force peaks in the same interval, but its proposed signaling role remains a hypothesis, not a protein-resolved causal edge. No strain-level canonical example is inferred from the abstract.

  • DOI:10.1103/PhysRevE.106.034404
    runs in the direction of the oxygen source (x < 0) are longer and more frequent.
    -

    Section II.B, page 3; published 2022-09-15. Published full text and Appendices A-E read at the author's institutional copy: https://www.fast.universite-paris-saclay.fr/~moisy/papers/2022_bouvard_pre.pdf. Figures 1-2 and the typeset x < 0 passage visually checked. Tracking in an oxygen-gradient capillary shows directional bias in Burkholderia contaminans; nonmotile cells are excluded with a 6 micrometre-per-second velocity threshold. The fitted response model does not identify a molecular receptor.

    +

    Section II.B, page 3; published 2022-09-15. Published full text and Appendices A-E read at the author's institutional copy: https://www.fast.universite-paris-saclay.fr/~moisy/papers/2022_bouvard_pre.pdf. Figures 1-2 and the typeset x < 0 passage visually checked. Tracking in an oxygen-gradient capillary shows directional bias in Burkholderia contaminans; nonmotile cells are excluded with a 6 micrometre-per-second velocity threshold. The fitted response model does not identify a molecular receptor.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 06:13 UTC diff --git a/pages/traits/physiology/aerotropism.html b/pages/traits/physiology/aerotropism.html index 859716d1a96..8cda0a4a8b5 100644 --- a/pages/traits/physiology/aerotropism.html +++ b/pages/traits/physiology/aerotropism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1016/S0168-6496(03)00161-2
    Conidia also germinated close to air-filled Teflon tubes and exhibited germ-tube tropism, but not as distinctly as on living reed roots.
    -

    Abstract, exact-matched at Europe PMC (PMID:19719598). Publisher HTML methods, results and discussion were read at https://academic.oup.com/femsec/article/45/3/293/549782. Section 3.2 reports Microdochium bolleyi germ-tube orientation toward air-filled Teflon root dummies (60% +/- 12%) and stronger orientation toward living roots. This is qualified supporting evidence: oxygen-dependent germination and root-derived chemicals complicate attribution, and the tube result alone does not establish significance against random orientation. Figure 3 measures germination, not orientation. Figures were not visually verified. No strain accession or molecular mechanism is asserted.

    +

    Abstract, exact-matched at Europe PMC (PMID:19719598). Publisher HTML methods, results and discussion were read at https://academic.oup.com/femsec/article/45/3/293/549782. Section 3.2 reports Microdochium bolleyi germ-tube orientation toward air-filled Teflon root dummies (60% +/- 12%) and stronger orientation toward living roots. This is qualified supporting evidence: oxygen-dependent germination and root-derived chemicals complicate attribution, and the tube result alone does not establish significance against random orientation. Figure 3 measures germination, not orientation. Figures were not visually verified. No strain accession or molecular mechanism is asserted.

  • DOI:10.1155/2012/517529
    C. albicans responds to other external stimuli in vitro, displaying aerotropism under hypoxic conditions and galvanotropism, where hyphae germinate and orient towards the cathode in an applied electric field (Figure 2(c)(iii)) [94, 97, 98].
    -

    Brand (2012), Hyphal Growth in Human Fungal Pathogens and Its Role in Virulence; published online in 2011, volume 2012. Review, not independent experimental replication. Full text directly retrieved as Europe PMC JATS XML (PMC3216317), https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3216317/fullTextXML. The complete sentence exact-matches the XML text and is quoted under its Creative Commons Attribution license. It supports use of aerotropism for hyphal responses under hypoxia, not a quantified oxygen-gradient experiment or a mechanism. The cathode and Figure 2(c)(iii) clauses describe galvanotropism, not aerotropism; no figure-based oxygen claim is made. Its cited Aoki paper remains an unverified primary-source lead in the discussion.

    +

    Brand (2012), Hyphal Growth in Human Fungal Pathogens and Its Role in Virulence; published online in 2011, volume 2012. Review, not independent experimental replication. Full text directly retrieved as Europe PMC JATS XML (PMC3216317), https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3216317/fullTextXML. The complete sentence exact-matches the XML text and is quoted under its Creative Commons Attribution license. It supports use of aerotropism for hyphal responses under hypoxia, not a quantified oxygen-gradient experiment or a mechanism. The cathode and Figure 2(c)(iii) clauses describe galvanotropism, not aerotropism; no figure-based oxygen claim is made. Its cited Aoki paper remains an unverified primary-source lead in the discussion.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -239,7 +240,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Unverified research leads: Aoki et al. (1998), DOI:10.1007/BF02464003, and Carlile and Tew (1988), DOI:10.1016/S0007-1536(88)80071-8. Crossref and Elsevier API retrievals confirmed metadata only; publisher retrieval returned 403. Search-index-limited summaries suggest positive Candida hyphal reorientation and negative aerotropism in Phytophthora germ tubes, respectively. Original wording, full text, figures and controls remain unverified. These are research leads, not definition authority or counted trait evidence (#1680, #1681). Inspect the older full texts and orientation readouts, and discriminate tip reorientation from preferential growth or survival in oxygen-rich regions. Resolve natural strain provenance and NCBI identity before canonical examples. The current evidence does not establish a universal oxygen sensor or a taxon-independent protein mechanism. Do not transfer pheromone chemotropism or aerotaxis mechanisms without direct evidence. Defer causal graphs until native causal evidence and taxon-paired protein accessions support them; NONMECHANISTIC is not a grounding bypass.

    +

    Unverified research leads: Aoki et al. (1998), DOI:10.1007/BF02464003, and Carlile and Tew (1988), DOI:10.1016/S0007-1536(88)80071-8. Crossref and Elsevier API retrievals confirmed metadata only; publisher retrieval returned 403. Search-index-limited summaries suggest positive Candida hyphal reorientation and negative aerotropism in Phytophthora germ tubes, respectively. Original wording, full text, figures and controls remain unverified. These are research leads, not definition authority or counted trait evidence (#1680, #1681). Inspect the older full texts and orientation readouts, and discriminate tip reorientation from preferential growth or survival in oxygen-rich regions. Resolve natural strain provenance and NCBI identity before canonical examples. The current evidence does not establish a universal oxygen sensor or a taxon-independent protein mechanism. Do not transfer pheromone chemotropism or aerotaxis mechanisms without direct evidence. Defer causal graphs until native causal evidence and taxon-paired protein accessions support them; NONMECHANISTIC is not a grounding bypass.

    @@ -307,7 +308,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Use directly read aerotropism evidence and definition authority -

      Addresses second review of PR #1677 (#1680, #1681). Damm replaces unread Aoki as definition_source. Unread Aoki/Carlile move from counted evidence to qualified discussion leads; negative response remains unverified. Brand 2012 review is added for terminology, explicitly not independent experimental replication. Its complete sentence exact-matches directly retrieved Europe PMC JATS (PMC3216317) under the stated Creative Commons Attribution license; cathode/figure clauses are explicitly galvanotropism. Guarded validated migration preserves all three prior per-record events. Corrects evidence-authority claims in 2026-10-04T173758Z-codex-bc6cda.yaml and 2026-10-04T180339Z-codex-a40156.yaml without editing either. No older trait YAML changed.

    +

    Addresses second review of PR #1677 (#1680, #1681). Damm replaces unread Aoki as definition_source. Unread Aoki/Carlile move from counted evidence to qualified discussion leads; negative response remains unverified. Brand 2012 review is added for terminology, explicitly not independent experimental replication. Its complete sentence exact-matches directly retrieved Europe PMC JATS (PMC3216317) under the stated Creative Commons Attribution license; cathode/figure clauses are explicitly galvanotropism. Guarded validated migration preserves all three prior per-record events. Corrects evidence-authority claims in 2026-10-04T173758Z-codex-bc6cda.yaml and 2026-10-04T180339Z-codex-a40156.yaml without editing either. No older trait YAML changed.

    • Read this curation session @@ -339,7 +340,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -368,12 +378,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 18:30 UTC diff --git a/pages/traits/physiology/aggrephagy.html b/pages/traits/physiology/aggrephagy.html index 6c310172458..ab02db8b2a8 100644 --- a/pages/traits/physiology/aggrephagy.html +++ b/pages/traits/physiology/aggrephagy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.1080/15548627.2026.2724473
    Our findings indicate that heat shock triggers the targeted degradation of ubiquitinated protein aggregates, mediated by the macroaggrephagy receptor Cue5.
    -

    PMID:42647820. Scientific abstract directly read in DOI-matched Europe PMC metadata, separately from Abbreviations. Supports selective macroautophagic aggregate degradation in Saccharomyces cerevisiae. In the same heat-stress context, Cct2 and polyQ-HTT vacuolar turnover is reported to be independent of canonical autophagy; that turnover is not positive aggrephagy evidence. Publisher full text returned HTTP 403; Methods, actual figures and strain provenance were not inspected.

    +

    PMID:42647820. Scientific abstract directly read in DOI-matched Europe PMC metadata, separately from Abbreviations. Supports selective macroautophagic aggregate degradation in Saccharomyces cerevisiae. In the same heat-stress context, Cct2 and polyQ-HTT vacuolar turnover is reported to be independent of canonical autophagy; that turnover is not positive aggrephagy evidence. Publisher full text returned HTTP 403; Methods, actual figures and strain provenance were not inspected.

  • DOI:10.1038/s44319-024-00275-7
    Deficiency in this interaction significantly weakens the association of Cct2 with Atg8.
    -

    PMID:39322741, PMC11549370. Scientific abstract and XML Introduction, Results Sec3-Sec7, Discussion Sec9 and yeast Methods Sec11 and Sec14-Sec16 were read. The quoted interaction is Atg11-Cct2. Yeast GFP-47Q cleavage and perturbations support solid-aggregate turnover; Ape1-P22L maturation alone is not complete cargo destruction. Synopsis S142 differs from scientific-abstract/Results S412; retain the discrepancy. Mammalian counterparts and phosphorylation sites are not interchangeable with yeast. Actual figures, supplements, Table EV1 and independent strain provenance were not inspected.

    +

    PMID:39322741, PMC11549370. Scientific abstract and XML Introduction, Results Sec3-Sec7, Discussion Sec9 and yeast Methods Sec11 and Sec14-Sec16 were read. The quoted interaction is Atg11-Cct2. Yeast GFP-47Q cleavage and perturbations support solid-aggregate turnover; Ape1-P22L maturation alone is not complete cargo destruction. Synopsis S142 differs from scientific-abstract/Results S412; retain the discrepancy. Mammalian counterparts and phosphorylation sites are not interchangeable with yeast. Actual figures, supplements, Table EV1 and independent strain provenance were not inspected.

  • DOI:10.1016/j.cell.2014.05.048
    We thus propose that CUET proteins play a critical and ancient role in autophagic clearance of cytotoxic protein aggregates.
    -

    PMID:25042851. Scientific abstract directly read in DOI-matched Europe PMC metadata. Yeast Cue5/Rsp5 perturbations and polyQ responses are separate from human Tollip experiments; do not transfer human rescue to yeast or equate toxicity alone with flux. Full text, actual figures and strain provenance were not inspected. Linked Comment-in articles are not counted as independent primary evidence.

    +

    PMID:25042851. Scientific abstract directly read in DOI-matched Europe PMC metadata. Yeast Cue5/Rsp5 perturbations and polyQ responses are separate from human Tollip experiments; do not transfer human rescue to yeast or equate toxicity alone with flux. Full text, actual figures and strain provenance were not inspected. Linked Comment-in articles are not counted as independent primary evidence.

  • DOI:10.1080/27694127.2023.2236407
    Interestingly, Cue5/Tollip, a known autophagy receptor for aggrephagy, is dispensable for this inclusion body autophagy.
    -

    PMID:37680383, PMC10482306. Scientific abstract directly read in DOI-matched Europe PMC metadata. Boundary evidence: the authors distinguish Htt103QP/A-beta42 inclusion-body clearance in budding yeast as IBophagy. Do not relabel it an unqualified Cue5-dependent aggrephagy observation. Complete full text and actual figures were not inspected; XML returned HTTP 500 and publisher access returned HTTP 403.

    +

    PMID:37680383, PMC10482306. Scientific abstract directly read in DOI-matched Europe PMC metadata. Boundary evidence: the authors distinguish Htt103QP/A-beta42 inclusion-body clearance in budding yeast as IBophagy. Do not relabel it an unqualified Cue5-dependent aggrephagy observation. Complete full text and actual figures were not inspected; XML returned HTTP 500 and publisher access returned HTTP 403.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -221,7 +222,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Autophagy traitmech:000638 is the broader phenotype. Protein aggregation, disaggregation, proteasomal proteolysis, puncta, toxicity reduction or vacuolar localization alone is not selective macroautophagic degradation. GO:0035973, directly resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0035973, is a nonobsolete biological process for selective protein-aggregate degradation by macroautophagy, not an exact organismal phenotype. Retain that route qualifier and omit exact xrefs and synonyms. The 2023 study explicitly separates IBophagy from aggrephagy; do not infer an exact synonym, disjointness or a separate TraitRecord solely from its receptor differences. Their potential broader/narrower relationship needs human review. Proteaphagy traitmech:000645 concerns proteasomes as cargo, not ordinary aggregate proteolysis.

    +

    Autophagy traitmech:000638 is the broader phenotype. Protein aggregation, disaggregation, proteasomal proteolysis, puncta, toxicity reduction or vacuolar localization alone is not selective macroautophagic degradation. GO:0035973, directly resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0035973, is a nonobsolete biological process for selective protein-aggregate degradation by macroautophagy, not an exact organismal phenotype. Retain that route qualifier and omit exact xrefs and synonyms. The 2023 study explicitly separates IBophagy from aggrephagy; do not infer an exact synonym, disjointness or a separate TraitRecord solely from its receptor differences. Their potential broader/narrower relationship needs human review. Proteaphagy traitmech:000645 concerns proteasomes as cargo, not ordinary aggregate proteolysis.

    @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 16:30 UTC diff --git a/pages/traits/physiology/alanine_arylamidase_activity.html b/pages/traits/physiology/alanine_arylamidase_activity.html index c4bc560ca95..30bdc74a9f4 100644 --- a/pages/traits/physiology/alanine_arylamidase_activity.html +++ b/pages/traits/physiology/alanine_arylamidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,11 +107,11 @@

    Parent traits (1)

    Synonyms (3)

    @@ -126,7 +127,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -276,7 +277,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record pairs one IUBMB EC 3.4.11.2 reaction snippet with a multi-enzyme API ZYM species-description list (DOI:10.1099/ijsem.0.006017), leaving only one mechanistic quote.

    +

    The current record pairs one IUBMB EC 3.4.11.2 reaction snippet with a multi-enzyme API ZYM species-description list (DOI:10.1099/ijsem.0.006017), leaving only one mechanistic quote.

    @@ -358,7 +359,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -387,12 +397,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/alkaline_phosphatase_activity.html b/pages/traits/physiology/alkaline_phosphatase_activity.html index feda87c90a9..b1e0a29e782 100644 --- a/pages/traits/physiology/alkaline_phosphatase_activity.html +++ b/pages/traits/physiology/alkaline_phosphatase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -263,7 +264,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries one constitutive-expression snippet and one API ZYM profile list (DOI:10.1128/JB.185.16.4983-4991.2003, DOI:10.1155/2021/8888641) without distinct catalytic reaction/product quotes for a multi-edge graph.

    +

    The current record carries one constitutive-expression snippet and one API ZYM profile list (DOI:10.1128/JB.185.16.4983-4991.2003, DOI:10.1155/2021/8888641) without distinct catalytic reaction/product quotes for a multi-edge graph.

    @@ -345,7 +346,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -374,12 +384,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/alpha_chymotrypsin_activity.html b/pages/traits/physiology/alpha_chymotrypsin_activity.html index 7dafff5b6b5..724a22c076c 100644 --- a/pages/traits/physiology/alpha_chymotrypsin_activity.html +++ b/pages/traits/physiology/alpha_chymotrypsin_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • alpha-chymotrypsin RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
      • +
    • alpha-chymotrypsin RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
    @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -272,7 +273,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record pairs one IUBMB EC 3.4.21.1 cleavage-specificity snippet with a multi-enzyme API ZYM species-description list (DOI:10.1099/ijsem.0.006017), leaving only one mechanistic quote.

    +

    The current record pairs one IUBMB EC 3.4.21.1 cleavage-specificity snippet with a multi-enzyme API ZYM species-description list (DOI:10.1099/ijsem.0.006017), leaving only one mechanistic quote.

    @@ -378,7 +379,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -407,12 +417,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/alpha_fucosidase_activity.html b/pages/traits/physiology/alpha_fucosidase_activity.html index 1556ef3b05b..8e2256aa2f9 100644 --- a/pages/traits/physiology/alpha_fucosidase_activity.html +++ b/pages/traits/physiology/alpha_fucosidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -263,7 +264,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record pairs one IUBMB EC 3.2.1.51 reaction snippet with a diagnostic assay-panel list (DOI:10.1128/jcm.22.3.333-335.1985), leaving only one mechanistic quote.

    +

    The current record pairs one IUBMB EC 3.2.1.51 reaction snippet with a diagnostic assay-panel list (DOI:10.1128/jcm.22.3.333-335.1985), leaving only one mechanistic quote.

    @@ -345,7 +346,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -374,12 +384,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/alpha_galactosidase_activity.html b/pages/traits/physiology/alpha_galactosidase_activity.html index 368dba3859b..2340f7c59c4 100644 --- a/pages/traits/physiology/alpha_galactosidase_activity.html +++ b/pages/traits/physiology/alpha_galactosidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -263,7 +264,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record pairs one EC 3.2.1.22 catalytic definition snippet (DOI:10.3109/07388551.2013.794124) with a diagnostic assay-panel list (DOI:10.1128/jcm.22.3.333-335.1985), leaving only one mechanistic quote.

    +

    The current record pairs one EC 3.2.1.22 catalytic definition snippet (DOI:10.3109/07388551.2013.794124) with a diagnostic assay-panel list (DOI:10.1128/jcm.22.3.333-335.1985), leaving only one mechanistic quote.

    @@ -345,7 +346,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -374,12 +384,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/alpha_glucosidase_activity.html b/pages/traits/physiology/alpha_glucosidase_activity.html index 02860edbfad..262587aee8d 100644 --- a/pages/traits/physiology/alpha_glucosidase_activity.html +++ b/pages/traits/physiology/alpha_glucosidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -263,7 +264,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two API ZYM enzyme-panel survey snippets (DOI:10.1371/journal.pone.0322500, DOI:10.3390/microorganisms13092005) without verbatim catalytic reaction or pathway quotes.

    +

    The current record carries two API ZYM enzyme-panel survey snippets (DOI:10.1371/journal.pone.0322500, DOI:10.3390/microorganisms13092005) without verbatim catalytic reaction or pathway quotes.

    @@ -345,7 +346,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -374,12 +384,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/alpha_mannosidase_activity.html b/pages/traits/physiology/alpha_mannosidase_activity.html index d46fa751bdf..d28bcdda415 100644 --- a/pages/traits/physiology/alpha_mannosidase_activity.html +++ b/pages/traits/physiology/alpha_mannosidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -263,7 +264,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record pairs one IUBMB EC 3.2.1.24 reaction snippet with a diagnostic strain-discrimination snippet (DOI:10.1128/jcm.32.3.854-855.1994), leaving only one mechanistic quote.

    +

    The current record pairs one IUBMB EC 3.2.1.24 reaction snippet with a diagnostic strain-discrimination snippet (DOI:10.1128/jcm.32.3.854-855.1994), leaving only one mechanistic quote.

    @@ -345,7 +346,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -374,12 +384,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/amylase_activity.html b/pages/traits/physiology/amylase_activity.html index ee32417e0cc..81964e9f101 100644 --- a/pages/traits/physiology/amylase_activity.html +++ b/pages/traits/physiology/amylase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -272,7 +273,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries one collective definition of amylolytic enzymes (DOI:10.3389/fbioe.2020.00871) and one short enzyme-naming phrase for BoGH13ASus (DOI:10.1007/s00018-023-04812-w) without catalytic reaction/product quotes.

    +

    The current record carries one collective definition of amylolytic enzymes (DOI:10.3389/fbioe.2020.00871) and one short enzyme-naming phrase for BoGH13ASus (DOI:10.1007/s00018-023-04812-w) without catalytic reaction/product quotes.

    @@ -354,7 +355,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -383,12 +393,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/anisogamy.html b/pages/traits/physiology/anisogamy.html index 475aab41d5b..daf85153ef2 100644 --- a/pages/traits/physiology/anisogamy.html +++ b/pages/traits/physiology/anisogamy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (4)

    DOI:10.1038/s42003-018-0019-5
    Male and female gametes differing in size—anisogamy—emerged independently from isogamous ancestors in various eukaryotic lineages
    -

    Hamaji et al. (2018), PMID:30271904, PMC6123790. Exact opening scientific-abstract clause checked in raw XML, not the separate editorial summary. Size dimorphism defines the phenotype; evolutionary origin is not part of this definition. Main text, Methods and captions were read and actual Figure 3 inspected: Eudorina gametes provide independent phenotype observations. Comparative MT architecture and RT-PCR expression do not demonstrate a gamete-size causal pathway. Results associate genomes with NIES-4100/4018, whereas Methods name NIES-3985/3984 for sequencing and the former sibling strains for other experiments. This unresolved discrepancy prevents strain-to-assembly inference here. Other actual figures and supplements remain unread.

    +

    Hamaji et al. (2018), PMID:30271904, PMC6123790. Exact opening scientific-abstract clause checked in raw XML, not the separate editorial summary. Size dimorphism defines the phenotype; evolutionary origin is not part of this definition. Main text, Methods and captions were read and actual Figure 3 inspected: Eudorina gametes provide independent phenotype observations. Comparative MT architecture and RT-PCR expression do not demonstrate a gamete-size causal pathway. Results associate genomes with NIES-4100/4018, whereas Methods name NIES-3985/3984 for sequencing and the former sibling strains for other experiments. This unresolved discrepancy prevents strain-to-assembly inference here. Other actual figures and supplements remain unread.

  • DOI:10.1186/1471-2148-14-37
    Obligately anisogamous conjugation between male and female motile gametes occurred outside the female colony (external fertilization during anisogamy).
    -

    Nozaki et al. (2014), PMID:24589311, PMC4015742. Exact scientific-abstract Results sentence verified in raw XML. Main text and captions, actual Figure 3, and Additional file 2 Information S1/Table S1 were inspected. Sexual reproduction was observed in C. charkowiensis, not C. angeleri. Male length was 5-10 micrometers; female diameter 13-17 micrometers. These different measurements do not establish a volume ratio. Other actual figures, Additional file 1 and the remainder of Additional file 2 remain uninspected. Proposed evolutionary intermediacy is not demonstrated ancestry.

    +

    Nozaki et al. (2014), PMID:24589311, PMC4015742. Exact scientific-abstract Results sentence verified in raw XML. Main text and captions, actual Figure 3, and Additional file 2 Information S1/Table S1 were inspected. Sexual reproduction was observed in C. charkowiensis, not C. angeleri. Male length was 5-10 micrometers; female diameter 13-17 micrometers. These different measurements do not establish a volume ratio. Other actual figures, Additional file 1 and the remainder of Additional file 2 remain uninspected. Proposed evolutionary intermediacy is not demonstrated ancestry.

  • DOI:10.1186/s12915-024-01878-1
    Oogamy constitutes a specialized form of anisogamy wherein small male gametes are motile and large female gametes are not
    -

    Lindsey et al. (2024), PMID:38600528, PMC11007952. Exact Background Sec1 clause before the parenthetical, checked in raw XML and publisher HTML. This supports broad terminology including oogamy, not a new gamete-fusion experiment. The scientific abstract and this scope paragraph were inspected; remaining analyses, actual figures and supplements were not audited. The quoted motility formulation is not imposed on all microbial anisogamy.

    +

    Lindsey et al. (2024), PMID:38600528, PMC11007952. Exact Background Sec1 clause before the parenthetical, checked in raw XML and publisher HTML. This supports broad terminology including oogamy, not a new gamete-fusion experiment. The scientific abstract and this scope paragraph were inspected; remaining analyses, actual figures and supplements were not audited. The quoted motility formulation is not imposed on all microbial anisogamy.

  • @@ -134,7 +135,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -223,7 +224,7 @@

    Canonical examples DOI:10.1186/1471-2148-14-37 - Source-observed reference example, not a claim about every strain. Figure 3 shows mixed 2013-0615-IC-3/4/7 cultures and male 2010-0713-E5; mating generally occurred after two days in nitrogen-deficient medium. Table S1 traces IC-3/4/7 to a natural water sample near Lake Isanuma. Collection provenance was checked at https://mcc.nbrp.jp/strainList.do?strainNumber=NIES-3388 (IC-7), https://mcc.nbrp.jp/strainList.do?strainNumber=NIES-3386 (IC-3) and https://mcc.nbrp.jp/strainList.do?strainNumber=NIES-3387 (IC-4). IC-3/4 collection and isolation dates conflict; no date is silently corrected. IC-7's 2018 axenic status is not projected onto 2014. Taxon label verified at https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=51706 on 2026-10-05. Collection fields support provenance, not independent experimental replication. + Source-observed reference example, not a claim about every strain. Figure 3 shows mixed 2013-0615-IC-3/4/7 cultures and male 2010-0713-E5; mating generally occurred after two days in nitrogen-deficient medium. Table S1 traces IC-3/4/7 to a natural water sample near Lake Isanuma. Collection provenance was checked at https://mcc.nbrp.jp/strainList.do?strainNumber=NIES-3388 (IC-7), https://mcc.nbrp.jp/strainList.do?strainNumber=NIES-3386 (IC-3) and https://mcc.nbrp.jp/strainList.do?strainNumber=NIES-3387 (IC-4). IC-3/4 collection and isolation dates conflict; no date is silently corrected. IC-7's 2018 axenic status is not projected onto 2014. Taxon label verified at https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=51706 on 2026-10-05. Collection fields support provenance, not independent experimental replication.

    • @@ -255,7 +256,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Use anisogamy in the broad size-dimorphism sense, including oogamy, as explicitly stated by Lindsey et al. (2024). Nozaki et al. (2014) instead distinguish anisogamy with flagellated female gametes from oogamy in their four-type classification. This is a terminology difference, not evidence that the phenotypes are disjoint. Motility of both gametes and external fertilization describe the canonical example, not universal requirements. The definition compares gamete types, not incidental size variation within a type, vegetative-versus-gamete size, or mating compatibility. Isogamy traitmech:000619, unisexual reproduction traitmech:000613 and fungal mating systems traitmech:000615 through traitmech:000618 describe distinct scopes. No numerical threshold or organism-level disjointness is asserted. Use phenotype METPO:1000059 pending a narrower reproductive-phenotype hierarchy; PHYSIOLOGY is a filesystem category. Oogamy traitmech:000621 now supplies the size-dimorphic child with large nonmotile female gametes. Its evidence explicitly preserves nonmotile male exceptions rather than imposing a universal motility convention. Verify lexical/external mappings and a narrower reproductive parent before adding them. Kaczmarska et al. (2017), DOI:10.1371/journal.pone.0181413, also use physiological/behavioural anisogamy for approximately equal-sized gametes in diatoms. That usage is not equivalent to the size-based sense selected here: behavioural or physiological differences alone do not establish gamete-type size dimorphism. Do not map that usage as an exact synonym or infer organism-level disjointness; its relationship needs separate scope review.

    +

    Use anisogamy in the broad size-dimorphism sense, including oogamy, as explicitly stated by Lindsey et al. (2024). Nozaki et al. (2014) instead distinguish anisogamy with flagellated female gametes from oogamy in their four-type classification. This is a terminology difference, not evidence that the phenotypes are disjoint. Motility of both gametes and external fertilization describe the canonical example, not universal requirements. The definition compares gamete types, not incidental size variation within a type, vegetative-versus-gamete size, or mating compatibility. Isogamy traitmech:000619, unisexual reproduction traitmech:000613 and fungal mating systems traitmech:000615 through traitmech:000618 describe distinct scopes. No numerical threshold or organism-level disjointness is asserted. Use phenotype METPO:1000059 pending a narrower reproductive-phenotype hierarchy; PHYSIOLOGY is a filesystem category. Oogamy traitmech:000621 now supplies the size-dimorphic child with large nonmotile female gametes. Its evidence explicitly preserves nonmotile male exceptions rather than imposing a universal motility convention. Verify lexical/external mappings and a narrower reproductive parent before adding them. Kaczmarska et al. (2017), DOI:10.1371/journal.pone.0181413, also use physiological/behavioural anisogamy for approximately equal-sized gametes in diatoms. That usage is not equivalent to the size-based sense selected here: behavioural or physiological differences alone do not establish gamete-type size dimorphism. Do not map that usage as an exact synonym or infer organism-level disjointness; its relationship needs separate scope review.

    @@ -329,13 +330,13 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed anisogamy with explicit size-based scope -

      Created traitmech:000620 as a PROPOSED PHYSIOLOGY class under METPO:1000059 with three DOI-backed sources (10.1038/s42003-018-0019-5, 10.1186/1471-2148-14-37, 10.1186/s12915-024-01878-1), exact raw-XML snippets and qualified Colemanosphaera charkowiensis NCBITaxon:51706 example. Retained broader versus motility-qualified terminology, strain/date discrepancies and unread-source limits; deferred mechanisms and mappings. Reserved METPO:1057400 in proposal v497. Whole-tree novelty/allocation searches included ignored and hidden files; fresh seed/release and open-PR checks found no exact conflict. Writer dry run/apply and eight regression tests passed. Maintained snippet resolver returned LIKELY_PARAPHRASE for the article-versus-abstract dash difference in 2018, VERIFIED for 2014 and NOT_IN_ABSTRACT for the 2024 Background quotation; all three independently match raw XML. Broader corpus, proposal, browser and CI validation remain pending at this history event.

    +

    Created traitmech:000620 as a PROPOSED PHYSIOLOGY class under METPO:1000059 with three DOI-backed sources (10.1038/s42003-018-0019-5, 10.1186/1471-2148-14-37, 10.1186/s12915-024-01878-1), exact raw-XML snippets and qualified Colemanosphaera charkowiensis NCBITaxon:51706 example. Retained broader versus motility-qualified terminology, strain/date discrepancies and unread-source limits; deferred mechanisms and mappings. Reserved METPO:1057400 in proposal v497. Whole-tree novelty/allocation searches included ignored and hidden files; fresh seed/release and open-PR checks found no exact conflict. Writer dry run/apply and eight regression tests passed. Maintained snippet resolver returned LIKELY_PARAPHRASE for the article-versus-abstract dash difference in 2018, VERIFIED for 2014 and NOT_IN_ABSTRACT for the 2024 Background quotation; all three independently match raw XML. Broader corpus, proposal, browser and CI validation remain pending at this history event.

    • Read this curation session
  • · codex
    • EDIT — Qualify anisogamy against behavioural-only diatom usage -

      Addressed review finding #1711 with DOI:10.1371/journal.pone.0181413, a 17-word contiguous Discussion snippet checked against publisher HTML and raw manuscript XML, and an explicit boundary distinguishing physiological/behavioural usage from the selected size-dimorphism sense. Preserved definition, canonical example and all earlier history. Updated the METPO proposal attribution and scope note. Guarded repair dry run/apply and 17 original/repair regression cases passed; derived regeneration and final broader validation remain pending at this event.

    +

    Addressed review finding #1711 with DOI:10.1371/journal.pone.0181413, a 17-word contiguous Discussion snippet checked against publisher HTML and raw manuscript XML, and an explicit boundary distinguishing physiological/behavioural usage from the selected size-dimorphism sense. Preserved definition, canonical example and all earlier history. Updated the METPO proposal attribution and scope note. Guarded repair dry run/apply and 17 original/repair regression cases passed; derived regeneration and final broader validation remain pending at this event.

    • Read this curation session
  • @@ -373,7 +374,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -402,12 +412,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 14:16 UTC diff --git a/pages/traits/physiology/antibiotic_resistance.html b/pages/traits/physiology/antibiotic_resistance.html index 291de5fc96b..e7b67d64d15 100644 --- a/pages/traits/physiology/antibiotic_resistance.html +++ b/pages/traits/physiology/antibiotic_resistance.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    confers antibiotic resistance - traitmech:000088 + traitmech:000088 METPO:2007700

    Drug efflux is one determinant enabling resistance.

      @@ -115,7 +116,7 @@

      Edge evidence

    • antibiotic resistance - traitmech:000088 + traitmech:000088 participates in response to antibiotic GO:0046677 @@ -251,7 +252,7 @@

      Edge evidence

      GO:0008800 confers antibiotic resistance - traitmech:000088 + traitmech:000088 METPO:2007700

      Beta-lactamase-mediated drug hydrolysis confers resistance to beta-lactam antibiotics.

        @@ -270,7 +271,7 @@

        Edge evidence

        confers antibiotic resistance - traitmech:000088 + traitmech:000088 METPO:2007700

        Resistance-associated QRDR mutations alter fluoroquinolone targets and confer the antibiotic-resistance phenotype.

          @@ -289,7 +290,7 @@

          Edge evidence

          confers antibiotic resistance - traitmech:000088 + traitmech:000088 METPO:2007700

          Methylation of the 23S rRNA drug-binding region confers macrolide resistance.

            @@ -326,8 +327,8 @@

            Protein and taxon examples

    		 - Staphylococcus aureus -
    NCBITaxon:1280 + Staphylococcus aureus +
    NCBITaxon:1280         		REVIEWED
    @@ -393,7 +394,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • antimicrobial resistance RELATED_SYNONYM · DOI:10.1038/nrmicro3380
      • +
    • antimicrobial resistance RELATED_SYNONYM · DOI:10.1038/nrmicro3380
    @@ -409,7 +410,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -718,7 +719,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1082,12 +1092,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/arginine_arylamidase_activity.html b/pages/traits/physiology/arginine_arylamidase_activity.html index 9c7938d9c36..dcef5a3aaee 100644 --- a/pages/traits/physiology/arginine_arylamidase_activity.html +++ b/pages/traits/physiology/arginine_arylamidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,15 +113,15 @@

    Parent traits (1)

    Synonyms (5)

    @@ -136,7 +137,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -286,7 +287,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record pairs one IUBMB EC 3.4.11.6 reaction snippet with two multi-enzyme diagnostic profile lists (DOI:10.3389/fgene.2023.1240581, DOI:10.1099/ijsem.0.006017), leaving only one mechanistic quote.

    +

    The current record pairs one IUBMB EC 3.4.11.6 reaction snippet with two multi-enzyme diagnostic profile lists (DOI:10.3389/fgene.2023.1240581, DOI:10.1099/ijsem.0.006017), leaving only one mechanistic quote.

    @@ -368,7 +369,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -397,12 +407,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/arginine_dihydrolase_activity.html b/pages/traits/physiology/arginine_dihydrolase_activity.html index 6b41a32bebb..2888e683f6f 100644 --- a/pages/traits/physiology/arginine_dihydrolase_activity.html +++ b/pages/traits/physiology/arginine_dihydrolase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    Trait evidence (5)

    Arginine deiminase (ADI) pathway conversion of L-arginine to citrulline and ornithine

    Evidence-backed physiological mechanism sketch linking arginine deiminase catalysis, L-citrulline and L-ornithine formation, and ADI pathway ATP generation to arginine dihydrolase activity.

    -

    MECHANISTIC · Mechanistic graph backed by EC 3.5.3.6, DOI:10.1016/j.fm.2010.11.016, DOI:10.1128/aem.07724-11, and DOI:10.1016/j.resmic.2012.11.004; exemplified on arginine_dihydrolase_arc_system with Latilactobacillus sakei (NCBITaxon:1599) arc operon enzymes ArcA (UniProtKB:O53088), ArcB (UniProtKB:O53089), and ArcC (UniProtKB:O53090).

    +

    MECHANISTIC · Mechanistic graph backed by EC 3.5.3.6, DOI:10.1016/j.fm.2010.11.016, DOI:10.1128/aem.07724-11, and DOI:10.1016/j.resmic.2012.11.004; exemplified on arginine_dihydrolase_arc_system with Latilactobacillus sakei (NCBITaxon:1599) arc operon enzymes ArcA (UniProtKB:O53088), ArcB (UniProtKB:O53089), and ArcC (UniProtKB:O53090).

    Loading graph…

    @@ -117,7 +118,7 @@

    Edge evidence

    GO:0019546 confers arginine dihydrolase activity - traitmech:000164 + traitmech:000164 METPO:2007700

    Arginine conversion through the arc-operon ADI pathway confers the arginine dihydrolase activity trait.

      @@ -211,8 +212,8 @@

      Protein and taxon examples

    		 - Latilactobacillus sakei -
    NCBITaxon:1599 + Latilactobacillus sakei +
    NCBITaxon:1599         		REVIEWED
    @@ -241,8 +242,8 @@

    Protein and taxon examples

    		 - Latilactobacillus sakei -
    NCBITaxon:1599 + Latilactobacillus sakei +
    NCBITaxon:1599         		REVIEWED
    @@ -271,8 +272,8 @@

    Protein and taxon examples

    		 - Latilactobacillus sakei -
    NCBITaxon:1599 + Latilactobacillus sakei +
    NCBITaxon:1599         		REVIEWED
    @@ -338,13 +339,13 @@

    Parent traits (1)

    Synonyms (4)

    @@ -360,7 +361,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -510,7 +511,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The record's primary literature (DOI:10.1016/j.fm.2010.11.016, DOI:10.1128/aem.07724-11, DOI:10.1016/j.resmic.2012.11.004) establishes arc-operon ADI pathway conversion of arginine to citrulline and ornithine in Latilactobacillus sakei (NCBITaxon:1599), but verified UniProtKB accessions must be curated on a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    +

    The record's primary literature (DOI:10.1016/j.fm.2010.11.016, DOI:10.1128/aem.07724-11, DOI:10.1016/j.resmic.2012.11.004) establishes arc-operon ADI pathway conversion of arginine to citrulline and ornithine in Latilactobacillus sakei (NCBITaxon:1599), but verified UniProtKB accessions must be curated on a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    @@ -529,7 +530,7 @@

    Evidence

    -

    Resolution: Promoted arginine_dihydrolase_adi_pathway_sketch to MECHANISTIC by adding InterPro:IPR003876-grounded GENE_OR_PROTEIN node arginine_dihydrolase_arc_system with reviewed Latilactobacillus sakei (NCBITaxon:1599) protein_examples UniProtKB:O53088 (ArcA), UniProtKB:O53089 (ArcB), and UniProtKB:O53090 (ArcC) backed by DOI:10.1016/j.resmic.2012.11.004 and DOI:10.1128/aem.07724-11.

    +

    Resolution: Promoted arginine_dihydrolase_adi_pathway_sketch to MECHANISTIC by adding InterPro:IPR003876-grounded GENE_OR_PROTEIN node arginine_dihydrolase_arc_system with reviewed Latilactobacillus sakei (NCBITaxon:1599) protein_examples UniProtKB:O53088 (ArcA), UniProtKB:O53089 (ArcB), and UniProtKB:O53090 (ArcC) backed by DOI:10.1016/j.resmic.2012.11.004 and DOI:10.1128/aem.07724-11.

    @@ -558,7 +559,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Promoted arginine_dihydrolase_adi_pathway_sketch to MECHANISTIC; added InterPro:IPR003876-grounded GENE_OR_PROTEIN node arginine_dihydrolase_arc_system with reviewed Latilactobacillus sakei (NCBITaxon:1599) protein_examples UniProtKB:O53088 (ArcA), UniProtKB:O53089 (ArcB), and UniProtKB:O53090 (ArcC) backed by DOI:10.1016/j.resmic.2012.11.004 and DOI:10.1128/aem.07724-11; resolved arginine-dihydrolase-activity-protein-example-gap.

    +

    Promoted arginine_dihydrolase_adi_pathway_sketch to MECHANISTIC; added InterPro:IPR003876-grounded GENE_OR_PROTEIN node arginine_dihydrolase_arc_system with reviewed Latilactobacillus sakei (NCBITaxon:1599) protein_examples UniProtKB:O53088 (ArcA), UniProtKB:O53089 (ArcB), and UniProtKB:O53090 (ArcC) backed by DOI:10.1016/j.resmic.2012.11.004 and DOI:10.1128/aem.07724-11; resolved arginine-dihydrolase-activity-protein-example-gap.

    • @@ -600,7 +601,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -964,12 +974,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 11:45 UTC diff --git a/pages/traits/physiology/autogamy.html b/pages/traits/physiology/autogamy.html index 1e70a6b671a..bbe56616738 100644 --- a/pages/traits/physiology/autogamy.html +++ b/pages/traits/physiology/autogamy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -61,19 +62,19 @@

    Trait evidence (4)

    DOI:10.1016/0014-4827(86)90492-1
    Autogamy is a process of meiosis and fertilization which takes place in unpaired Paramecium cells, and which is triggered by starvation.
    -

    Berger (1986), PMID:3743667, opening scientific-abstract sentence directly retrieved in Europe PMC core metadata. The complete abstract supports unpaired-cell meiosis/fertilization and a two-stage commitment response to nutritional down-shift. Starvation and cell-cycle timing concern the studied Paramecium system, not universal definition requirements. Full text, actual figures and strain provenance remain uninspected; no canonical example or protein-level causal mechanism is inferred from this abstract.

    +

    Berger (1986), PMID:3743667, opening scientific-abstract sentence directly retrieved in Europe PMC core metadata. The complete abstract supports unpaired-cell meiosis/fertilization and a two-stage commitment response to nutritional down-shift. Starvation and cell-cycle timing concern the studied Paramecium system, not universal definition requirements. Full text, actual figures and strain provenance remain uninspected; no canonical example or protein-level causal mechanism is inferred from this abstract.

  • DOI:10.1093/gbe/evaa052
    Autogamy in P. tetraurelia occurs in unpaired cells, is induced by starvation, and generates fully homozygous individuals
    -

    Thind et al. (2020), PMID:32163147, PMC7239694, Introduction sec1 clause before citations, checked in raw full-text XML. The scientific abstract, Introduction, strain/culture and autogamy-reactivity Methods, and survival-advantage Results were inspected. The scored autogamy readout was DAPI-visible macronuclear fragmentation, not direct gametic-nuclear fusion in every counted cell. Fully homozygous stock d12 mass cultures do not establish that every microbial autogamy event yields homozygosity. Survival associations and proposed heat-shock-protein models are not a validated causal pathway. Natural provenance of d12 remains unresolved; it is not a canonical example here. Actual figures, remaining sections and supplements were not audited.

    +

    Thind et al. (2020), PMID:32163147, PMC7239694, Introduction sec1 clause before citations, checked in raw full-text XML. The scientific abstract, Introduction, strain/culture and autogamy-reactivity Methods, and survival-advantage Results were inspected. The scored autogamy readout was DAPI-visible macronuclear fragmentation, not direct gametic-nuclear fusion in every counted cell. Fully homozygous stock d12 mass cultures do not establish that every microbial autogamy event yields homozygosity. Survival associations and proposed heat-shock-protein models are not a validated causal pathway. Natural provenance of d12 remains unresolved; it is not a canonical example here. Actual figures, remaining sections and supplements were not audited.

  • DOI:10.1080/0269249X.2013.791344
    Autogamy is a fusion of two gametic (haploid) nuclei within an undivided cell
    -

    Kaczmarska et al. (2013), p.271, section 5.2.2, opening clause directly read in the author-posted full text at https://www.researchgate.net/publication/259079699_Proposals_for_a_terminology_for_diatom_sexual_reproduction_auxospores_and_resting_stages. Sections 5.2.1-5.2.2 distinguish separate gamete fusion from undivided-cell nuclear fusion. This resolves the prior unread terminology lead; it is synthesis, not new ciliate replication. The following diatom-specific meiotic timing is not imposed on the ciliate definition, which allows postmeiotic mitosis as in Nobili and Luporini pp.35-37. Actual 2013 diagrams were not inspected.

    +

    Kaczmarska et al. (2013), p.271, section 5.2.2, opening clause directly read in the author-posted full text at https://www.researchgate.net/publication/259079699_Proposals_for_a_terminology_for_diatom_sexual_reproduction_auxospores_and_resting_stages. Sections 5.2.1-5.2.2 distinguish separate gamete fusion from undivided-cell nuclear fusion. This resolves the prior unread terminology lead; it is synthesis, not new ciliate replication. The following diatom-specific meiotic timing is not imposed on the ciliate definition, which allows postmeiotic mitosis as in Nobili and Luporini pp.35-37. Actual 2013 diagrams were not inspected.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Canonical examples DOI:10.1017/S0016672300010740 - Qualified A-25 example, named Euplotes minuta in the paper. Material and Methods p.36 traces it to coastal sand near Pisa, subsequently laboratory-maintained; no exact collection year is inferred from the relative date. Serial fixed-cell cytology supports the phenotype. Nonautogamic controls 5G/20 and hybrid offspring are not this example; A-25 also conjugates. NCBI https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=74792 and EFetch taxonomy XML checked on 2026-10-05 resolve Moneuplotes minuta with Euplotes minuta as a synonym. This species-name mapping does not authenticate a modern strain accession or reference genome. + Qualified A-25 example, named Euplotes minuta in the paper. Material and Methods p.36 traces it to coastal sand near Pisa, subsequently laboratory-maintained; no exact collection year is inferred from the relative date. Serial fixed-cell cytology supports the phenotype. Nonautogamic controls 5G/20 and hybrid offspring are not this example; A-25 also conjugates. NCBI https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=74792 and EFetch taxonomy XML checked on 2026-10-05 resolve Moneuplotes minuta with Euplotes minuta as a synonym. This species-name mapping does not authenticate a modern strain accession or reference genome. @@ -246,7 +247,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Use the unpaired-cell nuclear-fusion sense supported by the cited ciliate studies, not plant self-pollination or all selfing. The existing homothallism traitmech:000609, unisexual reproduction traitmech:000613 and primary homothallism traitmech:000614 definitions are explicitly fungal-scoped and are not exact parents or synonyms. Cytogamy traitmech:000623 involves paired cells without nuclear exchange in Nobili and Luporini p.39, unlike this unpaired-cell definition. Diller (1958), DOI:10.1111/j.1550-7408.1958.tb02567.x, uses double autogamy for the tentative paired-cell observation. That broader source terminology does not make cytogamy a child or exact synonym of this operationally unpaired-cell class. No universal genetic identity, complete homozygosity, starvation trigger, nuclear count, inability to outcross or gamete-size asymmetry is imposed. The parent gap is resolved by automixis traitmech:000625, whose single-meiotic-cell nuclear origin includes this operational scope. The broader terminology and mapping questions keep this discussion OPEN. Verify external equivalences and source-specific synonym scope before adding mappings. Paedogamy traitmech:000624 instead involves separate gametes formed within one gametangium. The clarified definition excludes their fusion, without forbidding later cell division or postmeiotic nuclear mitosis. These are event-level distinctions, not disjoint species.

    +

    Use the unpaired-cell nuclear-fusion sense supported by the cited ciliate studies, not plant self-pollination or all selfing. The existing homothallism traitmech:000609, unisexual reproduction traitmech:000613 and primary homothallism traitmech:000614 definitions are explicitly fungal-scoped and are not exact parents or synonyms. Cytogamy traitmech:000623 involves paired cells without nuclear exchange in Nobili and Luporini p.39, unlike this unpaired-cell definition. Diller (1958), DOI:10.1111/j.1550-7408.1958.tb02567.x, uses double autogamy for the tentative paired-cell observation. That broader source terminology does not make cytogamy a child or exact synonym of this operationally unpaired-cell class. No universal genetic identity, complete homozygosity, starvation trigger, nuclear count, inability to outcross or gamete-size asymmetry is imposed. The parent gap is resolved by automixis traitmech:000625, whose single-meiotic-cell nuclear origin includes this operational scope. The broader terminology and mapping questions keep this discussion OPEN. Verify external equivalences and source-specific synonym scope before adding mappings. Paedogamy traitmech:000624 instead involves separate gametes formed within one gametangium. The clarified definition excludes their fusion, without forbidding later cell division or postmeiotic nuclear mitosis. These are event-level distinctions, not disjoint species.

    @@ -276,7 +277,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    This is an organismal reproductive phenotype, not the literal mt marker locus or a heat-shock expression signature. Nuclear-selection inference, nutritional commitment and survival associations do not supply a universal protein-resolved mechanism. No causal graph bypasses missing accession-level and perturbation evidence. Keep macronuclear-fragmentation scoring separate from directly observed fusion. The earlier metadata-only lead DOI:10.1080/0269249X.2013.791344 is now resolved by direct reading of sections 5.2.1-5.2.2: paedogamy traitmech:000624 is distinct and automixis broader. Molecular mechanisms, wider taxon coverage and external equivalences remain open; the terminology source alone does not establish them. Preserve actual abstract-resolver verdicts separately from direct full-text checks.

    +

    This is an organismal reproductive phenotype, not the literal mt marker locus or a heat-shock expression signature. Nuclear-selection inference, nutritional commitment and survival associations do not supply a universal protein-resolved mechanism. No causal graph bypasses missing accession-level and perturbation evidence. Keep macronuclear-fragmentation scoring separate from directly observed fusion. The earlier metadata-only lead DOI:10.1080/0269249X.2013.791344 is now resolved by direct reading of sections 5.2.1-5.2.2: paedogamy traitmech:000624 is distinct and automixis broader. Molecular mechanisms, wider taxon coverage and external equivalences remain open; the terminology source alone does not establish them. Preserve actual abstract-resolver verdicts separately from direct full-text checks.

    @@ -344,7 +345,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Clarify autogamy versus separate-gamete fusion -

      Addressed issue 1719 by explicitly retaining nuclear fusion in an unpaired undivided cell and excluding fusion of separate gametes. Added directly read DOI:10.1080/0269249X.2013.791344 section 5.2.2 evidence and resolved the formerly unread terminology lead; linked paedogamy traitmech:000624. Preserved all prior evidence, the natural A-25 canonical example, parent, status and previous curation events. Did not impose universal immediate post-meiosis-II timing, forbid postmeiotic mitosis, or infer species disjointness. Updated the existing v498 template definition/citations in parity. Full-preimage guards, dry-run validation and 50 focused tests passed; broader gates follow.

    +

    Addressed issue 1719 by explicitly retaining nuclear fusion in an unpaired undivided cell and excluding fusion of separate gametes. Added directly read DOI:10.1080/0269249X.2013.791344 section 5.2.2 evidence and resolved the formerly unread terminology lead; linked paedogamy traitmech:000624. Preserved all prior evidence, the natural A-25 canonical example, parent, status and previous curation events. Did not impose universal immediate post-meiosis-II timing, forbid postmeiotic mitosis, or infer species disjointness. Updated the existing v498 template definition/citations in parity. Full-preimage guards, dry-run validation and 50 focused tests passed; broader gates follow.

    • Read this curation session
  • @@ -388,7 +389,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -417,12 +427,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 18:22 UTC diff --git a/pages/traits/physiology/automixis.html b/pages/traits/physiology/automixis.html index efef0fbcbd1..7eb914114ff 100644 --- a/pages/traits/physiology/automixis.html +++ b/pages/traits/physiology/automixis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -61,7 +62,7 @@

    Trait evidence (2)

    DOI:10.1186/s13059-021-02521-w
    Mating of gametes from the same meiotic event represents a particular type of inbreeding referred to as intratetrad mating or automixis
    -

    Papaioannou et al. (2021), PMID:34732243, PMC8567612, Background clause checked in publisher HTML and Europe PMC full-text XML. Scientific abstract, Results, Discussion and main Methods read; actual Figure 1 and all Table S1 pages visually inspected. Figure 1C depicts the automictic life cycle with NBRC 1722 and its diploid progenitor NBRC 1721. It is not a measured automixis rate. This fusion-based usage is narrower than Mogie's scope. Recombination experiments do not establish universal homozygosity or zero recombination. Other figures and detailed supplementary methods remain unread.

    +

    Papaioannou et al. (2021), PMID:34732243, PMC8567612, Background clause checked in publisher HTML and Europe PMC full-text XML. Scientific abstract, Results, Discussion and main Methods read; actual Figure 1 and all Table S1 pages visually inspected. Figure 1C depicts the automictic life cycle with NBRC 1722 and its diploid progenitor NBRC 1721. It is not a measured automixis rate. This fusion-based usage is narrower than Mogie's scope. Recombination experiments do not establish universal homozygosity or zero recombination. Other figures and detailed supplementary methods remain unread.

    @@ -126,7 +127,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -215,7 +216,7 @@

    Canonical examples DOI:10.1186/s13059-021-02521-w - Qualified NBRC 1721 strain-family example in Figure 1C; not a strain-specific automixis-frequency measurement. Table S1 p.1 and p.3 footnote 2 identify NBRC 1721 as a wild diploid isolate from grape must, Japan, 1964. NBRC 1722 is a single-spore descendant, not that wild parent or an engineered deletion strain. Provenance: https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs13059-021-02521-w/MediaObjects/13059_2021_2521_MOESM1_ESM.pdf. NCBI taxonomy EFetch on 2026-10-05 confirmed the species name at https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=36035; no genome accession is authenticated. + Qualified NBRC 1721 strain-family example in Figure 1C; not a strain-specific automixis-frequency measurement. Table S1 p.1 and p.3 footnote 2 identify NBRC 1721 as a wild diploid isolate from grape must, Japan, 1964. NBRC 1722 is a single-spore descendant, not that wild parent or an engineered deletion strain. Provenance: https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs13059-021-02521-w/MediaObjects/13059_2021_2521_MOESM1_ESM.pdf. NCBI taxonomy EFetch on 2026-10-05 confirmed the species name at https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=36035; no genome accession is authenticated. @@ -247,7 +248,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Mogie's broad reproductive class is not exclusively nuclear fusion or exclusively sexual reproduction. The operational autogamy traitmech:000622, cytogamy traitmech:000623 and paedogamy traitmech:000624 fit as narrower same-cell-origin routes; postmeiotic mitosis is allowed. Kaczmarska et al. DOI:10.1080/0269249X.2013.791344 section 5.2 directly names autogamy and paedogamy as automixis in diatoms. This does not make all botanical autogamy equivalent. Cytogamy's existing 1979 evidence supports same-parent meiotic origin despite cell pairing; cytoplasmic exchange is not nuclear outcrossing. Same-clone mating after different meioses is insufficient. Fungal homothallism, heterothallism and intratetrad mating are not exact synonyms of this broad class. External equivalences and narrower non-fusion microbial exemplars remain unresolved.

    +

    Mogie's broad reproductive class is not exclusively nuclear fusion or exclusively sexual reproduction. The operational autogamy traitmech:000622, cytogamy traitmech:000623 and paedogamy traitmech:000624 fit as narrower same-cell-origin routes; postmeiotic mitosis is allowed. Kaczmarska et al. DOI:10.1080/0269249X.2013.791344 section 5.2 directly names autogamy and paedogamy as automixis in diatoms. This does not make all botanical autogamy equivalent. Cytogamy's existing 1979 evidence supports same-parent meiotic origin despite cell pairing; cytoplasmic exchange is not nuclear outcrossing. Same-clone mating after different meioses is insufficient. Fungal homothallism, heterothallism and intratetrad mating are not exact synonyms of this broad class. External equivalences and narrower non-fusion microbial exemplars remain unresolved.

    @@ -341,7 +342,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -370,12 +380,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 18:22 UTC diff --git a/pages/traits/physiology/autophagic_glycogen_degradation.html b/pages/traits/physiology/autophagic_glycogen_degradation.html index e275cd9b357..bbed5706d98 100644 --- a/pages/traits/physiology/autophagic_glycogen_degradation.html +++ b/pages/traits/physiology/autophagic_glycogen_degradation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.4161/auto.6.4.11736
    Our results indicate that autophagy and Sga1 act cooperatively in vacuolar glycogen breakdown
    -

    PMID:20383057. DOI-matched scientific abstract directly read in Europe PMC metadata. Supports autophagy-associated vacuolar glycogen hydrolysis in Magnaporthe oryzae during asexual development. The reported breakdown supports conidia formation but is dispensable for pathogenicity. Cytoplasmic retargeting of GFP-Sga1 is an engineered rescue, not a natural vacuolar-flux exemplar. Full Methods, actual figures and independent strain provenance were not inspected.

    +

    PMID:20383057. DOI-matched scientific abstract directly read in Europe PMC metadata. Supports autophagy-associated vacuolar glycogen hydrolysis in Magnaporthe oryzae during asexual development. The reported breakdown supports conidia formation but is dispensable for pathogenicity. Cytoplasmic retargeting of GFP-Sga1 is an engineered rescue, not a natural vacuolar-flux exemplar. Full Methods, actual figures and independent strain provenance were not inspected.

  • DOI:10.3390/cells13060467
    vacuolar delivery of Glg1-GFP and its processing to free GFP were strictly dependent on autophagic machinery and vacuolar proteolysis.
    -

    PMID:38534311, PMC10969688. Scientific abstract, XML Methods 2.1, Results 3.2-3.4 and Discussion were read. The authors conclude nonselective glycogen autophagy in nitrogen-starved Komagataella phaffii using glycogen-bound, nonbinding and cytosolic reporters. Atg11 independence alone is not the selectivity argument. TCA extraction under-recovers the bound reporter; raw free-GFP/total-fusion ratios are unreliable. Reporter proteolysis is not a direct polymer-hydrolysis assay. Actual panels and independent strain provenance remain uninspected.

    +

    PMID:38534311, PMC10969688. Scientific abstract, XML Methods 2.1, Results 3.2-3.4 and Discussion were read. The authors conclude nonselective glycogen autophagy in nitrogen-starved Komagataella phaffii using glycogen-bound, nonbinding and cytosolic reporters. Atg11 independence alone is not the selectivity argument. TCA extraction under-recovers the bound reporter; raw free-GFP/total-fusion ratios are unreliable. Reporter proteolysis is not a direct polymer-hydrolysis assay. Actual panels and independent strain provenance remain uninspected.

  • DOI:10.3390/ijms252111772
    The K. phaffii Gsy1-GFP marked the GGs and reported on their autophagic degradation during nitrogen starvation, as expected.
    -

    PMID:39519320, PMC11546884. DOI-matched scientific abstract and XML Results 2.2-2.3 and Discussion were read. GGs means glycogen granules. This follow-up uses Gsy1 and CBM20 reporters to support neutral cargo behavior in nitrogen-starved K. phaffii; it is not independent-laboratory replication. Early Gsy1-GFP dot disappearance is autophagy-independent and is not positive flux evidence. A human STBD1 domain used as a reporter does not establish a native human mechanism in yeast. Complete Methods, actual panels and strain provenance were not inspected.

    +

    PMID:39519320, PMC11546884. DOI-matched scientific abstract and XML Results 2.2-2.3 and Discussion were read. GGs means glycogen granules. This follow-up uses Gsy1 and CBM20 reporters to support neutral cargo behavior in nitrogen-starved K. phaffii; it is not independent-laboratory replication. Early Gsy1-GFP dot disappearance is autophagy-independent and is not positive flux evidence. A human STBD1 domain used as a reporter does not establish a native human mechanism in yeast. Complete Methods, actual panels and strain provenance were not inspected.

  • DOI:10.1016/j.isci.2024.109810
    glycophagy may play a role in the suppression of glycogen consumption, rather than enhancing degradation.
    -

    PMID:38832010, PMC11145338. Exact XML Results sec2.7 span, not an abstract quote. Scientific Summary, Results, Discussion, Limitations and selected yeast, GFP-cleavage and glycogen-assay Methods were read. Boundary evidence: Atg45-dependent vacuolar delivery during Saccharomyces cerevisiae sporulation can preserve glycogen. Do not score that delivery alone as degradation. Receptor recruitment and prolonged-starvation reporter turnover do not make storage and hydrolysis interchangeable. Actual panels, supplements and independent strain provenance remain unread.

    +

    PMID:38832010, PMC11145338. Exact XML Results sec2.7 span, not an abstract quote. Scientific Summary, Results, Discussion, Limitations and selected yeast, GFP-cleavage and glycogen-assay Methods were read. Boundary evidence: Atg45-dependent vacuolar delivery during Saccharomyces cerevisiae sporulation can preserve glycogen. Do not score that delivery alone as degradation. Receptor recruitment and prolonged-starvation reporter turnover do not make storage and hydrolysis interchangeable. Actual panels, supplements and independent strain provenance remain unread.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -221,7 +222,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    The explicit degradative endpoint narrows autophagy traitmech:000638 without changing that parent's identity. This is intracellular cargo recycling, not growth on glycogen, extracellular amylolysis, granule possession or a gene inventory. The Cells paper introduces glycophagy as selective but reports nonselective K. phaffii turnover; the iScience paper also uses glycophagy for vacuolar preservation during sporulation. Those source-attributed usages are not exact synonyms of this endpoint-defined record. GO:0061723 was directly resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0061723 as a nonobsolete biological process for selective glycogen degradation by macroautophagy. It is narrower on selectivity and route, and is not an exact organismal phenotype. Omit exact xrefs and synonyms. Broader delivery/storage and selective subtype relationships require human review, not silent normalization of conflicting terminology.

    +

    The explicit degradative endpoint narrows autophagy traitmech:000638 without changing that parent's identity. This is intracellular cargo recycling, not growth on glycogen, extracellular amylolysis, granule possession or a gene inventory. The Cells paper introduces glycophagy as selective but reports nonselective K. phaffii turnover; the iScience paper also uses glycophagy for vacuolar preservation during sporulation. Those source-attributed usages are not exact synonyms of this endpoint-defined record. GO:0061723 was directly resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0061723 as a nonobsolete biological process for selective glycogen degradation by macroautophagy. It is narrower on selectivity and route, and is not an exact organismal phenotype. Omit exact xrefs and synonyms. Broader delivery/storage and selective subtype relationships require human review, not silent normalization of conflicting terminology.

    @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 17:29 UTC diff --git a/pages/traits/physiology/autophagy.html b/pages/traits/physiology/autophagy.html index 44f23b647a5..2cdc4fb1ceb 100644 --- a/pages/traits/physiology/autophagy.html +++ b/pages/traits/physiology/autophagy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,31 +56,31 @@

    Trait evidence (5)

    DOI:10.1083/jcb.119.2.301
    This is the first report that nutrient-deficient conditions induce extensive autophagic degradation of cytosolic components in the vacuoles of yeast cells.
    -

    PMID:1400575, PMC2289660. Scientific Abstract directly read in Europe PMC XML. Saccharomyces cerevisiae protease-deficient mutants and PMSF-treated reference cells accumulate bodies containing cytosol and organelles; bodies disappear after inhibitor removal. Sequestration and subsequent degradation, not inhibited-body accumulation alone, support the phenotype. The study's starvation conditions are not a universal trigger requirement. The XML body is sparse; full methods, actual figures and natural strain provenance were not inspected.

    +

    PMID:1400575, PMC2289660. Scientific Abstract directly read in Europe PMC XML. Saccharomyces cerevisiae protease-deficient mutants and PMSF-treated reference cells accumulate bodies containing cytosol and organelles; bodies disappear after inhibitor removal. Sequestration and subsequent degradation, not inhibited-body accumulation alone, support the phenotype. The study's starvation conditions are not a universal trigger requirement. The XML body is sparse; full methods, actual figures and natural strain provenance were not inspected.

  • DOI:10.1242/jcs.108.1.25
    there exist in P. pastoris at least two pathways for the sequestration of peroxisomes into the vacuole for degradation.
    -

    PMID:7738102. Scientific Abstract directly read in Europe PMC metadata and publisher HTML. In historically named Pichia pastoris, carbon-source adaptation elicits peroxisome turnover through macroautophagy-like wrapping or microautophagy-like vacuolar engulfment. Enzyme activities, morphology and mutants support route diversity; proteinase-deficient cells accumulate undegraded cargo. This supports selective organelle turnover without requiring starvation or a double-membrane intermediate for every route. Publisher full text requires access; methods, actual figures and strain-specific modern taxonomy were not inspected.

    +

    PMID:7738102. Scientific Abstract directly read in Europe PMC metadata and publisher HTML. In historically named Pichia pastoris, carbon-source adaptation elicits peroxisome turnover through macroautophagy-like wrapping or microautophagy-like vacuolar engulfment. Enzyme activities, morphology and mutants support route diversity; proteinase-deficient cells accumulate undegraded cargo. This supports selective organelle turnover without requiring starvation or a double-membrane intermediate for every route. Publisher full text requires access; methods, actual figures and strain-specific modern taxonomy were not inspected.

  • DOI:10.1073/pnas.0813319106
    In both organisms, genetic inactivation of the autophagy pathway increases bacterial intracellular replication, decreases animal lifespan, and results in apoptotic-independent death.
    -

    PMID:19667176, PMC2731839. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. The two models are Dictyostelium discoideum and Caenorhabditis elegans. Only the microbial amoeba's intracellular-infection phenotype is relevant here; the abstract's combined animal-lifespan wording and nematode insulin-signaling results are not transferred to the amoeba. Genetic perturbation supports an autophagy-associated host-defense role, not direct proof of completed cargo degradation by itself. Full text, actual figures and strain provenance were not accessible in this review.

    +

    PMID:19667176, PMC2731839. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. The two models are Dictyostelium discoideum and Caenorhabditis elegans. Only the microbial amoeba's intracellular-infection phenotype is relevant here; the abstract's combined animal-lifespan wording and nematode insulin-signaling results are not transferred to the amoeba. Genetic perturbation supports an autophagy-associated host-defense role, not direct proof of completed cargo degradation by itself. Full text, actual figures and strain provenance were not accessible in this review.

  • DOI:10.1371/journal.ppat.1006344
    Antagonistically, ESX-1 is also essential to block the autophagic flux and deplete the MCV of proteolytic activity.
    -

    PMID:28414774, PMC5407849. Scientific Abstract, distinct from the Author summary, directly read in Europe PMC XML and PLOS. The flux Results, flux-assay Methods and Discussion were read; Figure 6 and supplemental S6 Figure were visually inspected. Dictyostelium discoideum is the autophagic cell, not the infecting Mycobacterium marinum. Protease-inhibitor comparisons and GFP-Atg8 processing distinguish formation from degradation; the infection-associated block is partial, not a complete absence of flux. Free GFP reduction alone is ambiguous in this assay. The paper frames intracellular-pathogen digestion as xenophagy, but its blockade result is boundary evidence, not a positive completed-clearance observation. Other actual figures and supplements were not visually audited.

    +

    PMID:28414774, PMC5407849. Scientific Abstract, distinct from the Author summary, directly read in Europe PMC XML and PLOS. The flux Results, flux-assay Methods and Discussion were read; Figure 6 and supplemental S6 Figure were visually inspected. Dictyostelium discoideum is the autophagic cell, not the infecting Mycobacterium marinum. Protease-inhibitor comparisons and GFP-Atg8 processing distinguish formation from degradation; the infection-associated block is partial, not a complete absence of flux. Free GFP reduction alone is ambiguous in this assay. The paper frames intracellular-pathogen digestion as xenophagy, but its blockade result is boundary evidence, not a positive completed-clearance observation. Other actual figures and supplements were not visually audited.

  • DOI:10.1007/s00284-024-03838-y
    These results indicate that nuclei are engulfed in the autophagosomes as a whole and transported/released into the vacuolar lumen where they are degraded.
    -

    PMID:39162852, PMC11335778. Scientific Abstract directly read in Europe PMC with matching DOI. Selected XML Methods, Results and Discussion support including nuclear cargo within autophagy. The nucleophagy child retains the assay and access limits. This repairs cytoplasmic to intracellular in the parent definition (#1754), without imposing this macro route on all autophagy or changing its stable identity.

    +

    PMID:39162852, PMC11335778. Scientific Abstract directly read in Europe PMC with matching DOI. Selected XML Methods, Results and Discussion support including nuclear cargo within autophagy. The nucleophagy child retains the assay and access limits. This repairs cytoplasmic to intracellular in the parent definition (#1754), without imposing this macro route on all autophagy or changing its stable identity.

    • @@ -156,7 +157,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -252,7 +253,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    The phenotype belongs to the microbial cell doing the degradation, not to a bacterium merely eliciting an animal host response. Selective and bulk turnover, macro- and microautophagic routes, and intracellular non-self cargo are within scope; no universal starvation trigger, double-membrane intermediate or ATG gene inventory is asserted. ATG genes, puncta, autophagic-body accumulation, cell death or reduced pathogen replication alone do not establish completed degradative flux. Nondegradative membrane repair or ejection using autophagy machinery is not sufficient. Extracellular uptake and ordinary phagolysosomal digestion alone do not distinguish autophagy. Existing endocytosis, phagocytosis, phagotrophy and extracellular proteolysis records are not equivalent or broader parents; their co-occurrence is not prohibited. GO:0006914 was resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0006914 and includes self and non-self material, but denotes a biological process rather than an equivalent organismal phenotype. Keep METPO:1000059 as parent and omit exact xrefs and synonyms pending human scope review. Nuclear cargo is included: DOI:10.1007/s00284-024-03838-y supports whole-nucleus autophagy in Aspergillus oryzae. The former cytoplasmic-only wording was too narrow (#1754); intracellular corrects that wording, not the identity of autophagy. Nucleophagy traitmech:000643 is a cargo-defined child. The original definition source supports the retained vacuolar catabolic genus; the added evidence supports nuclear cargo.

    +

    The phenotype belongs to the microbial cell doing the degradation, not to a bacterium merely eliciting an animal host response. Selective and bulk turnover, macro- and microautophagic routes, and intracellular non-self cargo are within scope; no universal starvation trigger, double-membrane intermediate or ATG gene inventory is asserted. ATG genes, puncta, autophagic-body accumulation, cell death or reduced pathogen replication alone do not establish completed degradative flux. Nondegradative membrane repair or ejection using autophagy machinery is not sufficient. Extracellular uptake and ordinary phagolysosomal digestion alone do not distinguish autophagy. Existing endocytosis, phagocytosis, phagotrophy and extracellular proteolysis records are not equivalent or broader parents; their co-occurrence is not prohibited. GO:0006914 was resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0006914 and includes self and non-self material, but denotes a biological process rather than an equivalent organismal phenotype. Keep METPO:1000059 as parent and omit exact xrefs and synonyms pending human scope review. Nuclear cargo is included: DOI:10.1007/s00284-024-03838-y supports whole-nucleus autophagy in Aspergillus oryzae. The former cytoplasmic-only wording was too narrow (#1754); intracellular corrects that wording, not the identity of autophagy. Nucleophagy traitmech:000643 is a cargo-defined child. The original definition source supports the retained vacuolar catabolic genus; the added evidence supports nuclear cargo.

    @@ -326,7 +327,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Correct autophagy definition to include nuclear cargo -

      Changed cytoplasmic to intracellular in traitmech:000638 after directly reading DOI:10.1007/s00284-024-03838-y and current GO scope. Added a source-faithful snippet and clarified the existing scope discussion. Kept stable identity, prior evidence and history, existing parent, and route/flux limits. A whole-record preimage guard protects this repair and v519 supplies corrected proposal context without changing historical TSVs.

    +

    Changed cytoplasmic to intracellular in traitmech:000638 after directly reading DOI:10.1007/s00284-024-03838-y and current GO scope. Added a source-faithful snippet and clarified the existing scope discussion. Kept stable identity, prior evidence and history, existing parent, and route/flux limits. A whole-record preimage guard protects this repair and v519 supplies corrected proposal context without changing historical TSVs.

    • Read this curation session @@ -358,7 +359,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -387,12 +397,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 13:38 UTC diff --git a/pages/traits/physiology/autotrophic.html b/pages/traits/physiology/autotrophic.html index fad6549bab3..2032d4941c3 100644 --- a/pages/traits/physiology/autotrophic.html +++ b/pages/traits/physiology/autotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -182,7 +183,7 @@

    Edge evidence

    example of CO2-fixation pathway GO:0015977 - rdfs:subClassOf + rdfs:subClassOf

    The Calvin-Benson cycle is a major autotrophic CO2-fixation pathway.

      @@ -353,7 +354,7 @@

      Edge evidence

      example of CO2-fixation pathway GO:0015977 - rdfs:subClassOf + rdfs:subClassOf

      The Wood-Ljungdahl pathway is an autotrophic CO2-fixation pathway producing acetyl-CoA.

        @@ -480,8 +481,8 @@

        Protein and taxon examples

    		 - Cupriavidus necator H16 -
    NCBITaxon:381666 + Cupriavidus necator H16 +
    NCBITaxon:381666         		REVIEWED
    @@ -547,11 +548,11 @@

    Parent traits (1)

    Synonyms (3)

      -
    • TT_autotroph RELATED_SYNONYM · metpo.owl
      • +
    • TT_autotroph RELATED_SYNONYM · metpo.owl
      • -
    • autotroph RELATED_SYNONYM · metpo.owl
      • +
    • autotroph RELATED_SYNONYM · metpo.owl
      • -
    • autotrophy RELATED_SYNONYM · metpo.owl
      • +
    • autotrophy RELATED_SYNONYM · metpo.owl
    @@ -567,7 +568,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -978,7 +979,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1342,12 +1352,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/bacterial_flagellar_filament_internalization.html b/pages/traits/physiology/bacterial_flagellar_filament_internalization.html index c2a28f92d1e..745a8d90eb1 100644 --- a/pages/traits/physiology/bacterial_flagellar_filament_internalization.html +++ b/pages/traits/physiology/bacterial_flagellar_filament_internalization.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (2)

    DOI:10.1038/s41564-023-01401-2
    most or all of the filament was internalized to the periplasm
    -

    Kaplan et al. 2023, PMID:37349588, PMC11061892.1, Results S3, Attachment of B. bacteriovorus to prey, paragraph beginning In cells with larger portions. Direct manuscript JATS match; native NOT_IN_ABSTRACT retained. Source strain HD100 and frozen cryo-ET stages support partial through nearly complete withdrawal into the predator's own periplasm, not the prey's. Methods S8-S12 qualify minicell enrichment and possible physiology effects; the images contain no same-cell temporal information. Main Figure 3 and supplement PDF pages 1, 22-35, 66-67 were visually inspected. S20-S21 distinguish external and internal filament portions; S22 is a schematic, not a tracked trajectory. Table S2's 8/4/30 early/intermediate/late absorbed-flagellum observations are not culture replicates or a prevalence denominator. Publisher Figure 3's main scale bar is 100 nm, versus 50 nm in the manuscript caption; no dimension or rate is inferred. Main PDF, other actual main figures, unselected supplemental images and movies remain unread. Later breakage or degradation is not required by the definition.

    +

    Kaplan et al. 2023, PMID:37349588, PMC11061892.1, Results S3, Attachment of B. bacteriovorus to prey, paragraph beginning In cells with larger portions. Direct manuscript JATS match; native NOT_IN_ABSTRACT retained. Source strain HD100 and frozen cryo-ET stages support partial through nearly complete withdrawal into the predator's own periplasm, not the prey's. Methods S8-S12 qualify minicell enrichment and possible physiology effects; the images contain no same-cell temporal information. Main Figure 3 and supplement PDF pages 1, 22-35, 66-67 were visually inspected. S20-S21 distinguish external and internal filament portions; S22 is a schematic, not a tracked trajectory. Table S2's 8/4/30 early/intermediate/late absorbed-flagellum observations are not culture replicates or a prevalence denominator. Publisher Figure 3's main scale bar is 100 nm, versus 50 nm in the manuscript caption; no dimension or rate is inferred. Main PDF, other actual main figures, unselected supplemental images and movies remain unread. Later breakage or degradation is not required by the definition.

  • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -343,7 +344,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add bacterial flagellar filament internalization -

      Added one PROPOSED own-flagellar-filament withdrawal phenotype with primary DOI:10.1038/s41564-023-01401-2 and author-perspective DOI:10.1063/pt.nkma.bqid. Checked 11/13-word full-text excerpts; the perspective describes the same experiment, not independent replication. Kept DOI:10.1111/j.1365-2958.2006.05081.x and its 14-word excerpt as comparison context with NO_EVIDENCE, not a definition citation. Preserved native NOT_IN_ABSTRACT/UNRESOLVED/NOT_IN_ABSTRACT. Reserved traitmech:000735, v611 and full block 1068800-1068899 after ignored/hidden current-file, retained-history, complete-range and open/draft PR checks plus fresh state guard. Preserved partial-withdrawal, frozen-stage, scale-bar and preparation limits. No canonical taxon, exact synonym/xref or universal molecular graph is asserted. Per-record timestamp is the observed allocation decision, not source acquisition.

    +

    Added one PROPOSED own-flagellar-filament withdrawal phenotype with primary DOI:10.1038/s41564-023-01401-2 and author-perspective DOI:10.1063/pt.nkma.bqid. Checked 11/13-word full-text excerpts; the perspective describes the same experiment, not independent replication. Kept DOI:10.1111/j.1365-2958.2006.05081.x and its 14-word excerpt as comparison context with NO_EVIDENCE, not a definition citation. Preserved native NOT_IN_ABSTRACT/UNRESOLVED/NOT_IN_ABSTRACT. Reserved traitmech:000735, v611 and full block 1068800-1068899 after ignored/hidden current-file, retained-history, complete-range and open/draft PR checks plus fresh state guard. Preserved partial-withdrawal, frozen-stage, scale-bar and preparation limits. No canonical taxon, exact synonym/xref or universal molecular graph is asserted. Per-record timestamp is the observed allocation decision, not source acquisition.

    • Read this curation session @@ -375,7 +376,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -404,12 +414,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-16 01:43 UTC diff --git a/pages/traits/physiology/bacterial_polar_flagellar_ejection.html b/pages/traits/physiology/bacterial_polar_flagellar_ejection.html index 0f64e79d9b4..2e8f8b567ad 100644 --- a/pages/traits/physiology/bacterial_polar_flagellar_ejection.html +++ b/pages/traits/physiology/bacterial_polar_flagellar_ejection.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1371/journal.pbio.3000165
    Plesiomonas cells consistently lose their flagella at the base of the hook
    -

    Ferreira et al. 2019, PMID:30889173, PMC6424402. Results, Shed hook-filament structures accumulate in P. shigelloides supernatant, sole paragraph (HTML anchor article1.body1.sec2.sec4.p1; PDF pp. 4-5); Figure 1G. Direct publisher full-text match; native NOT_IN_ABSTRACT. Hook-bearing released structures, population counts and relic/assembly comparisons support ejection rather than daughter-cell dilution or passive midfilament breakage. Nutrient-depletion conditions vary among assays; minimal medium containing glucose is not complete carbon starvation. All 25 main PDF pages and six figures were inspected, not raw supplementary data. Energy conservation and leakage prevention are interpretations.

    +

    Ferreira et al. 2019, PMID:30889173, PMC6424402. Results, Shed hook-filament structures accumulate in P. shigelloides supernatant, sole paragraph (HTML anchor article1.body1.sec2.sec4.p1; PDF pp. 4-5); Figure 1G. Direct publisher full-text match; native NOT_IN_ABSTRACT. Hook-bearing released structures, population counts and relic/assembly comparisons support ejection rather than daughter-cell dilution or passive midfilament breakage. Nutrient-depletion conditions vary among assays; minimal medium containing glucose is not complete carbon starvation. All 25 main PDF pages and six figures were inspected, not raw supplementary data. Energy conservation and leakage prevention are interpretations.

  • DOI:10.1111/mmi.14511
    bacteria can actively abandon flagella after prolonged stationary culturing
    -

    Zhuang et al. 2020, PMID:32259388, scientific abstract, sentence beginning Interestingly. Direct MED/publisher match and native VERIFIED. Main publisher text and six figure captions were subsequently read, not the actual figures or supplement. Sections 2.4-2.7 separate daughter-cell dilution from stationary-phase shedding. OD times flagellated fraction is a population proxy, not a direct cell count. VIO5 and engineered EGFP-FliG strain NMB344 are distinct; red/green panels in Figure 3 are not the same cells. Two-color experiments in Figures 5-6 support basal release, but rod breakage is inferred, not a directly imaged cut. Surface immobilization and medium exchanges constrain the assay.

    +

    Zhuang et al. 2020, PMID:32259388, scientific abstract, sentence beginning Interestingly. Direct MED/publisher match and native VERIFIED. Main publisher text and six figure captions were subsequently read, not the actual figures or supplement. Sections 2.4-2.7 separate daughter-cell dilution from stationary-phase shedding. OD times flagellated fraction is a population proxy, not a direct cell count. VIO5 and engineered EGFP-FliG strain NMB344 are distinct; red/green panels in Figure 3 are not the same cells. Two-color experiments in Figures 5-6 support basal release, but rod breakage is inferred, not a directly imaged cut. Surface immobilization and medium exchanges constrain the assay.

  • DOI:10.1038/s41467-026-75593-6
    Nutrient depletion significantly increases the frequency of flagellar shedding and the accumulation of closed FOMCs
    -

    Guo et al. 2026, PMID:42660870, PMC13521929.1, Results, Two distinct in situ architectures of the flagellar motor in V. cholerae, and Supplementary Figure 4. Direct JATS match; native NOT_IN_ABSTRACT. FOMC denotes the flagellar outer membrane complex. The quoted experiment uses wild-type V. cholerae; delta-flhG structural samples are distinct. All 12 main PDF pages and six main figures were inspected, plus the actual supplementary Figure 4 and supplementary tables. Its 81/273 observations are cells in the figure caption and tomograms in Methods/Table 4, not biological replicates or ejection rates. The main-text Table 3 pointer instead corresponds to Table 4. Other supplements remain incompletely read.

    +

    Guo et al. 2026, PMID:42660870, PMC13521929.1, Results, Two distinct in situ architectures of the flagellar motor in V. cholerae, and Supplementary Figure 4. Direct JATS match; native NOT_IN_ABSTRACT. FOMC denotes the flagellar outer membrane complex. The quoted experiment uses wild-type V. cholerae; delta-flhG structural samples are distinct. All 12 main PDF pages and six main figures were inspected, plus the actual supplementary Figure 4 and supplementary tables. Its 81/273 observations are cells in the figure caption and tomograms in Methods/Table 4, not biological replicates or ejection rates. The main-text Table 3 pointer instead corresponds to Table 4. Other supplements remain incompletely read.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -381,7 +382,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -410,12 +420,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-15 13:10 UTC diff --git a/pages/traits/physiology/bacteriocin_production.html b/pages/traits/physiology/bacteriocin_production.html index ee5dc4b64fd..ff1e3f8eb65 100644 --- a/pages/traits/physiology/bacteriocin_production.html +++ b/pages/traits/physiology/bacteriocin_production.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -82,7 +83,7 @@

    Trait evidence (3)

    Ribosomal bacteriocin peptide production and antibacterial defense

    Evidence-backed physiological mechanism linking ribosomally synthesized bacteriocin peptides to the bacteriocin production trait and microbial defense against competing bacteria.

    -

    MECHANISTIC · Peptide-anchored mechanism backed by DOI:10.3389/fmicb.2016.00461 and DOI:10.1146/annurev.micro.56.012302.161024, with reviewed Lactococcus lactis subsp. lactis lantibiotic nisin-A (UniProtKB:P13068) curated on the InterPro:IPR006079 bacteriocin peptide node.

    +

    MECHANISTIC · Peptide-anchored mechanism backed by DOI:10.3389/fmicb.2016.00461 and DOI:10.1146/annurev.micro.56.012302.161024, with reviewed Lactococcus lactis subsp. lactis lantibiotic nisin-A (UniProtKB:P13068) curated on the InterPro:IPR006079 bacteriocin peptide node.

    Loading graph…

    @@ -105,7 +106,7 @@

    Edge evidence

    InterPro:IPR006079 confers bacteriocin production - traitmech:000183 + traitmech:000183 METPO:2007700

    Ribosomally synthesized antimicrobial bacteriocin peptides confer the bacteriocin production trait.

      @@ -161,8 +162,8 @@

      Protein and taxon examples

    		 - Lactococcus lactis subsp. lactis -
    NCBITaxon:1360 + Lactococcus lactis subsp. lactis +
    NCBITaxon:1360         		REVIEWED
    @@ -242,7 +243,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -401,7 +402,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -765,12 +775,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 21:12 UTC diff --git a/pages/traits/physiology/ballistospore_discharge.html b/pages/traits/physiology/ballistospore_discharge.html index eedfdc000b1..d81cf06afe9 100644 --- a/pages/traits/physiology/ballistospore_discharge.html +++ b/pages/traits/physiology/ballistospore_discharge.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1371/journal.pone.0004163
    At the moment of fusion, Buller's drop snaps from the hilar appendix onto the adjacent spore surface.
    -

    Stolze-Rybczynski et al. (2009), PMID:19129912, PMC2612744; Introduction, first paragraph, directly retrieved as publisher HTML and Europe PMC full-text XML. Abstract, Introduction, Results and Discussion, Table 1 and Methods were read. Seven basidiomycete species were analyzed by high-speed video; the yeast Sporobolomyces salmonicolor NPM01 had a measured mean launch speed of 1.42 +/- 0.12 m/s (s.e.m., six launches). Its 0.54 +/- 0.04 mm flight range is calculated, not a directly measured range. Drop geometry and flight range vary; a prominent lens-shaped adaxial drop is not universal. Figure captions were read, but image retrieval failed; actual figures, videos and supplements were not inspected.

    +

    Stolze-Rybczynski et al. (2009), PMID:19129912, PMC2612744; Introduction, first paragraph, directly retrieved as publisher HTML and Europe PMC full-text XML. Abstract, Introduction, Results and Discussion, Table 1 and Methods were read. Seven basidiomycete species were analyzed by high-speed video; the yeast Sporobolomyces salmonicolor NPM01 had a measured mean launch speed of 1.42 +/- 0.12 m/s (s.e.m., six launches). Its 0.54 +/- 0.04 mm flight range is calculated, not a directly measured range. Drop geometry and flight range vary; a prominent lens-shaped adaxial drop is not universal. Figure captions were read, but image retrieval failed; actual figures, videos and supplements were not inspected.

  • DOI:10.1371/journal.pone.0105147
    Ballistospores can be produced either asexually (ballistoconidia) or sexually (basidiospores).
    -

    Ianiri et al. (2014), PMID:25148260, PMC4141788; Introduction directly retrieved as full-text XML. This quotation supports terminology, not a new comparison of sexual and asexual development. Scientific abstract, strain table, mirror-assay Methods, initial mutant-screen Results and Discussion were also read. Of 18 mirror mutants, 17 had absent or reduced spore production; GI277 still formed abundant ballistospores but failed to release them. A failed mirror assay alone thus does not distinguish formation from discharge. PHS1 results concern delayed formation and broader cellular defects, not a demonstrated universal release motor. Actual figures, supplements and independent IAM 13481 provenance were not inspected; no canonical example is inferred from these mutants.

    +

    Ianiri et al. (2014), PMID:25148260, PMC4141788; Introduction directly retrieved as full-text XML. This quotation supports terminology, not a new comparison of sexual and asexual development. Scientific abstract, strain table, mirror-assay Methods, initial mutant-screen Results and Discussion were also read. Of 18 mirror mutants, 17 had absent or reduced spore production; GI277 still formed abundant ballistospores but failed to release them. A failed mirror assay alone thus does not distinguish formation from discharge. PHS1 results concern delayed formation and broader cellular defects, not a demonstrated universal release motor. Actual figures, supplements and independent IAM 13481 provenance were not inspected; no canonical example is inferred from these mutants.

  • DOI:10.1242/jeb.029975
    The fusion of the droplet onto the spore creates a momentum that propels the spore forward.
    -

    Noblin, Yang and Dumais (2009), PMID:19684219; scientific abstract retrieved directly through Europe PMC. The study reports high-speed observations in Auricularia auricula and Sporobolomyces yeasts, mechanical analysis and calibrated microcantilever measurements of detachment work. The artificial validation system is not a fungal exemplar. Predicted and observed velocities are distinct quantities. Full text, figures, supplements and strain provenance were not inspected; the abstract is not a complete mechanistic audit.

    +

    Noblin, Yang and Dumais (2009), PMID:19684219; scientific abstract retrieved directly through Europe PMC. The study reports high-speed observations in Auricularia auricula and Sporobolomyces yeasts, mechanical analysis and calibrated microcantilever measurements of detachment work. The artificial validation system is not a fungal exemplar. Predicted and observed velocities are distinct quantities. Full text, figures, supplements and strain provenance were not inspected; the abstract is not a complete mechanistic audit.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1371/journal.pone.0004163 - Strain NPM01. Table 1 reports high-speed-video launch measurements from six spores, with mean initial speed 1.42 +/- 0.12 m/s (s.e.m.); the listed flight distance is modeled, not directly measured. Organisms and culture methods at https://doi.org/10.1371/journal.pone.0004163 identify NPM01 as isolated from a contaminated manufacturing facility and report spore formation on potato dextrose agar within 24 h. That primary provenance passage was read directly; no engineered-strain origin is inferred. NCBI Taxonomy resolves the species ID and label. This example concerns NPM01 under the reported conditions, not every strain or life stage. + Strain NPM01. Table 1 reports high-speed-video launch measurements from six spores, with mean initial speed 1.42 +/- 0.12 m/s (s.e.m.); the listed flight distance is modeled, not directly measured. Organisms and culture methods at https://doi.org/10.1371/journal.pone.0004163 identify NPM01 as isolated from a contaminated manufacturing facility and report spore formation on potato dextrose agar within 24 h. That primary provenance passage was read directly; no engineered-strain origin is inferred. NCBI Taxonomy resolves the species ID and label. This example concerns NPM01 under the reported conditions, not every strain or life stage. @@ -270,7 +271,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    The cited studies support a surface-tension mechanism, not an unknown-mechanism claim. A causal graph is deferred until the full mechanical study and supplementary observations are inspected and the repository's protein-required MECHANISTIC graph convention is reconciled with a physical coalescence mechanism. Do not invent a protein motor or label a physical causal model NONMECHANISTIC merely to pass the audit. PHS1 possession or expression does not establish discharge; the 2014 formation-defect experiments do not isolate a universal ejection pathway. Negative mirror transfer can reflect impaired production, release or subsequent growth. The 2017 study at https://pmc.ncbi.nlm.nih.gov/articles/PMC5550963/ remains an unread research lead: PMC returned a challenge and two XML requests failed. It is not counted as verified evidence.

    +

    The cited studies support a surface-tension mechanism, not an unknown-mechanism claim. A causal graph is deferred until the full mechanical study and supplementary observations are inspected and the repository's protein-required MECHANISTIC graph convention is reconciled with a physical coalescence mechanism. Do not invent a protein motor or label a physical causal model NONMECHANISTIC merely to pass the audit. PHS1 possession or expression does not establish discharge; the 2014 formation-defect experiments do not isolate a universal ejection pathway. Negative mirror transfer can reflect impaired production, release or subsequent growth. The 2017 study at https://pmc.ncbi.nlm.nih.gov/articles/PMC5550963/ remains an unread research lead: PMC returned a challenge and two XML requests failed. It is not counted as verified evidence.

    @@ -308,13 +309,13 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add ballistospore discharge with source-bounded physical and developmental evidence -

      Added PROPOSED traitmech:000661 under phenotype METPO:1000059 using DOI:10.1371/journal.pone.0004163, DOI:10.1371/journal.pone.0105147 and DOI:10.1242/jeb.029975. All three snippets were matched to directly retrieved source text. Retained a provenance-qualified Sporobolomyces salmonicolor NPM01 example, separated measured velocity from modeled range and formation from discharge, and documented source access limits and deferred graph formalization. Ignored-and-hidden searches and structured METPO/seed review found no exact prior trait. Reserved METPO:1061400 in proposal v537. Writer dry run and 20 focused tests passed before application; broader validation and generated-artifact review remain subsequent steps. Existing traits, including protected spore germination, were not edited.

    +

    Added PROPOSED traitmech:000661 under phenotype METPO:1000059 using DOI:10.1371/journal.pone.0004163, DOI:10.1371/journal.pone.0105147 and DOI:10.1242/jeb.029975. All three snippets were matched to directly retrieved source text. Retained a provenance-qualified Sporobolomyces salmonicolor NPM01 example, separated measured velocity from modeled range and formation from discharge, and documented source access limits and deferred graph formalization. Ignored-and-hidden searches and structured METPO/seed review found no exact prior trait. Reserved METPO:1061400 in proposal v537. Writer dry run and 20 focused tests passed before application; broader validation and generated-artifact review remain subsequent steps. Existing traits, including protected spore germination, were not edited.

    • Read this curation session
  • · codex
    • EDIT — Replace subjectless discharge snippet with a complete source sentence -

      Corrected issue #1781 from PR #1780. Replaced the first DOI:10.1371/journal.pone.0004163 snippet with a 21-word complete Introduction sentence, exact-matched to the directly retrieved XML. Updated its section locator and appended CORRECTED_EVIDENCE_SNIPPET without altering the initial minting event. All other evidence, definition, hierarchy, example and discussion content remains unchanged. The guarded writer now accepts only the exact initial or corrected record; 23 focused tests and dry run passed before application. Initial full regression suite passed 3062 tests before this correction; post-correction validation follows.

    +

    Corrected issue #1781 from PR #1780. Replaced the first DOI:10.1371/journal.pone.0004163 snippet with a 21-word complete Introduction sentence, exact-matched to the directly retrieved XML. Updated its section locator and appended CORRECTED_EVIDENCE_SNIPPET without altering the initial minting event. All other evidence, definition, hierarchy, example and discussion content remains unchanged. The guarded writer now accepts only the exact initial or corrected record; 23 focused tests and dry run passed before application. Initial full regression suite passed 3062 tests before this correction; post-correction validation follows.

    • Read this curation session
  • @@ -352,7 +353,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -381,12 +391,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-07 09:12 UTC diff --git a/pages/traits/physiology/behavioral_habituation.html b/pages/traits/physiology/behavioral_habituation.html index 4a5e71187d9..c815240acf0 100644 --- a/pages/traits/physiology/behavioral_habituation.html +++ b/pages/traits/physiology/behavioral_habituation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.1098/rspb.2016.0446
    The Q and CAF slime moulds crossing a bridge containing quinine or caffeine for the sixth time showed reduced aversive behaviour.
    -

    Boisseau et al. 2016, PMID:27122563, PMC4855389; page 4, Results (b), Test phase 1. Q and CAF denote cultured Physarum polycephalum plasmodia repeatedly exposed to quinine or caffeine bridges. Five daily exposures precede same/alternate-repellent tests; two plain-agar days precede retesting. Contact latency, crossing time and shape are different readouts. Caffeine does not show every quinine effect: initial crossing time was not slower than control, and recovery was incomplete. Residual aversiveness remains. Alternate-repellent responses support stimulus specificity, not universal exclusion of every confound. Main Methods, Results, Discussion and all five figures were inspected in a public publisher-formatted PDF bearing a 2016 download stamp, not verified as the current corrected VoR. Supplementary statistics and raw data were not assessed. The contiguous quote crosses PDF columns; direct text and visual checks agree. Native abstract lookup: NOT_IN_ABSTRACT.

    +

    Boisseau et al. 2016, PMID:27122563, PMC4855389; page 4, Results (b), Test phase 1. Q and CAF denote cultured Physarum polycephalum plasmodia repeatedly exposed to quinine or caffeine bridges. Five daily exposures precede same/alternate-repellent tests; two plain-agar days precede retesting. Contact latency, crossing time and shape are different readouts. Caffeine does not show every quinine effect: initial crossing time was not slower than control, and recovery was incomplete. Residual aversiveness remains. Alternate-repellent responses support stimulus specificity, not universal exclusion of every confound. Main Methods, Results, Discussion and all five figures were inspected in a public publisher-formatted PDF bearing a 2016 download stamp, not verified as the current corrected VoR. Supplementary statistics and raw data were not assessed. The contiguous quote crosses PDF columns; direct text and visual checks agree. Native abstract lookup: NOT_IN_ABSTRACT.

  • DOI:10.1016/j.cub.2025.05.071
    the response to the low force stimuli shows extensive habituation even though the response to the alternating high force stimuli does not.
    -

    Rajan and Marshall 2025, PMID:40562036, PMC13499368; Figure 4F caption, concluding result clause in retained PMC author-manuscript HTML. Figure 4F is an experimental contraction response in cultured Stentor coeruleus, not the adjacent model panel. Preserved stronger-stimulus responses argue against general motor exhaustion. The caption describes identical control timing, while Methods describes one low-force control tap per minute versus alternating forces at one total tap per minute; exact cadence equivalence remains unresolved. Figure 4I uses intervening low-force stimulation, not a stimulus-free rest; Figure 5 separately tests recovery after training. Anchored healthy nondividing cells were selected from Ward's cultures; field-of-view denominators vary. Experimental Results, relevant Methods and actual Figures 4-7 were inspected. Receptor internalization is modeled, not an identified molecular mechanism. Supplements and simulations were not reanalyzed. Native abstract lookup: NOT_IN_ABSTRACT; the exact full-text caption match is a separate check.

    +

    Rajan and Marshall 2025, PMID:40562036, PMC13499368; Figure 4F caption, concluding result clause in retained PMC author-manuscript HTML. Figure 4F is an experimental contraction response in cultured Stentor coeruleus, not the adjacent model panel. Preserved stronger-stimulus responses argue against general motor exhaustion. The caption describes identical control timing, while Methods describes one low-force control tap per minute versus alternating forces at one total tap per minute; exact cadence equivalence remains unresolved. Figure 4I uses intervening low-force stimulation, not a stimulus-free rest; Figure 5 separately tests recovery after training. Anchored healthy nondividing cells were selected from Ward's cultures; field-of-view denominators vary. Experimental Results, relevant Methods and actual Figures 4-7 were inspected. Receptor internalization is modeled, not an identified molecular mechanism. Supplements and simulations were not reanalyzed. Native abstract lookup: NOT_IN_ABSTRACT; the exact full-text caption match is a separate check.

  • DOI:10.1016/j.cub.2026.03.080
    For cells treated with either cycloheximide or puromycin, the primary effect on learning was accelerating habituation (Figure 1C, 1E).
    -

    Rajan et al. 2026, PMID:42025171, PMC13192338; Results S3, retained PMC author manuscript. Stentor contraction assays compare drug-treated and vehicle cultures under repeated mechanical stimulation. Figure 1C uses puromycin with two-hour pretreatment; Figure 1E describes 12-hour cycloheximide pretreatment, unlike general short-term Methods prose. Dose, stimulus strength and cadence differ; conditions are not interchangeable. Drug effects do not prove universally protein-synthesis-independent learning. Relevant Results and Methods and actual Figures 1, 3, 4 and 6 were inspected, not all omics analyses or supplements. RNAi and pharmacology retain off-target, anchoring, feeding and subculture limitations. SteCoe_6763 recovery differences were not significant. Figure 6 follows division during continuing stimuli, not retention after withdrawal. Results and Methods point to different supplementary electrical-control panels. This follow-up shares a laboratory with the 2025 study, not an independent replication. Native abstract lookup: NOT_IN_ABSTRACT; directly matched Results quote.

    +

    Rajan et al. 2026, PMID:42025171, PMC13192338; Results S3, retained PMC author manuscript. Stentor contraction assays compare drug-treated and vehicle cultures under repeated mechanical stimulation. Figure 1C uses puromycin with two-hour pretreatment; Figure 1E describes 12-hour cycloheximide pretreatment, unlike general short-term Methods prose. Dose, stimulus strength and cadence differ; conditions are not interchangeable. Drug effects do not prove universally protein-synthesis-independent learning. Relevant Results and Methods and actual Figures 1, 3, 4 and 6 were inspected, not all omics analyses or supplements. RNAi and pharmacology retain off-target, anchoring, feeding and subculture limitations. SteCoe_6763 recovery differences were not significant. Figure 6 follows division during continuing stimuli, not retention after withdrawal. Results and Methods point to different supplementary electrical-control panels. This follow-up shares a laboratory with the 2025 study, not an independent replication. Native abstract lookup: NOT_IN_ABSTRACT; directly matched Results quote.

  • DOI:10.1016/j.nlm.2008.09.012
    Habituation is defined as a behavioral response decrement that results from repeated stimulation and that does not involve sensory adaptation/sensory fatigue or motor fatigue.
    -

    Rankin et al. 2009, PMID:18854219, PMC2754195; section 2, page 136 (PDF page 2), complete opening definition. This consensus review supports operational terminology, not a microbial experiment or independent replication. Its nervous-system framing is not imposed on non-neural microbes. The public institutional PDF was directly read and pages 2-4 visually inspected. PDF ligatures are expanded and whitespace folded for matching; no paraphrase is substituted. Partial recovery is allowed. Responding to a novel stimulus is not itself dishabituation, which restores the original response. The behavioral criteria are not a demonstrated common molecular mechanism. Source-qualified MED identity was checked; its absent commentCorrectionList is not exhaustive notice clearance.

    +

    Rankin et al. 2009, PMID:18854219, PMC2754195; section 2, page 136 (PDF page 2), complete opening definition. This consensus review supports operational terminology, not a microbial experiment or independent replication. Its nervous-system framing is not imposed on non-neural microbes. The public institutional PDF was directly read and pages 2-4 visually inspected. PDF ligatures are expanded and whitespace folded for matching; no paraphrase is substituted. Partial recovery is allowed. Responding to a novel stimulus is not itself dishabituation, which restores the original response. The behavioral criteria are not a demonstrated common molecular mechanism. Source-qualified MED identity was checked; its absent commentCorrectionList is not exhaustive notice clearance.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -345,7 +346,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -374,12 +384,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-13 04:48 UTC diff --git a/pages/traits/physiology/beta_galactosidase_activity.html b/pages/traits/physiology/beta_galactosidase_activity.html index f365d50a5f0..8f1d8b41c14 100644 --- a/pages/traits/physiology/beta_galactosidase_activity.html +++ b/pages/traits/physiology/beta_galactosidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -263,7 +264,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record pairs one EC 3.2.1.23 reaction snippet (DOI:10.3389/fmicb.2021.742300) with a diagnostic assay-panel list (DOI:10.1128/jcm.22.3.333-335.1985), leaving only one mechanistic quote.

    +

    The current record pairs one EC 3.2.1.23 reaction snippet (DOI:10.3389/fmicb.2021.742300) with a diagnostic assay-panel list (DOI:10.1128/jcm.22.3.333-335.1985), leaving only one mechanistic quote.

    @@ -345,7 +346,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -374,12 +384,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/beta_glucosidase_activity.html b/pages/traits/physiology/beta_glucosidase_activity.html index fb360f7bbef..ec9de6a6d74 100644 --- a/pages/traits/physiology/beta_glucosidase_activity.html +++ b/pages/traits/physiology/beta_glucosidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -269,7 +270,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record pairs one EC 3.2.1.21 definition snippet (DOI:10.1007/s13205-015-0328-z) with two API ZYM diagnostic survey snippets (DOI:10.2323/jgam.60.59, DOI:10.3390/microorganisms12040776), leaving only one mechanistic quote.

    +

    The current record pairs one EC 3.2.1.21 definition snippet (DOI:10.1007/s13205-015-0328-z) with two API ZYM diagnostic survey snippets (DOI:10.2323/jgam.60.59, DOI:10.3390/microorganisms12040776), leaving only one mechanistic quote.

    @@ -351,7 +352,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -380,12 +390,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/beta_glucuronidase_activity.html b/pages/traits/physiology/beta_glucuronidase_activity.html index af284d614e0..8b5cae0b6f2 100644 --- a/pages/traits/physiology/beta_glucuronidase_activity.html +++ b/pages/traits/physiology/beta_glucuronidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -82,7 +83,7 @@

    Trait evidence (3)

    Beta-glucuronidase hydrolysis of beta-D-glucuronosides to D-glucuronate

    Evidence-backed physiological mechanism sketch linking beta-glucuronidase catalytic activity and D-glucuronate release to the beta-glucuronidase activity phenotype.

    -

    MECHANISTIC · Mechanistic graph backed by EC 3.2.1.31, DOI:10.1128/aem.50.6.1383-1387.1985, and DOI:10.1073/pnas.83.22.8447; exemplified on beta_glucuronidase_uida with Escherichia coli K-12 (NCBITaxon:83333; UP000000625) beta-glucuronidase UidA (UniProtKB:P05804).

    +

    MECHANISTIC · Mechanistic graph backed by EC 3.2.1.31, DOI:10.1128/aem.50.6.1383-1387.1985, and DOI:10.1073/pnas.83.22.8447; exemplified on beta_glucuronidase_uida with Escherichia coli K-12 (NCBITaxon:83333; UP000000625) beta-glucuronidase UidA (UniProtKB:P05804).

    Loading graph…

    @@ -105,7 +106,7 @@

    Edge evidence

    GO:0004566 confers beta-glucuronidase activity - traitmech:000151 + traitmech:000151 METPO:2007700

    Cellular production of active beta-glucuronidase that cleaves beta-D-glucuronide substrates such as MUG confers the beta-glucuronidase activity phenotype.

      @@ -180,8 +181,8 @@

      Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -254,7 +255,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -419,7 +420,7 @@

    Discussions and Knowledge Gaps (3)

    -

    The current record pairs one IUBMB EC 3.2.1.31 reaction snippet with one fluorogenic MUG-assay snippet (DOI:10.1128/aem.50.6.1383-1387.1985) without physiological pathway or UniProtKB protein grounding.

    +

    The current record pairs one IUBMB EC 3.2.1.31 reaction snippet with one fluorogenic MUG-assay snippet (DOI:10.1128/aem.50.6.1383-1387.1985) without physiological pathway or UniProtKB protein grounding.

    @@ -462,7 +463,7 @@

    Evidence

    -

    The record's primary literature (EC 3.2.1.31, DOI:10.1128/aem.50.6.1383-1387.1985) establishes beta-D-glucuronoside hydrolysis to D-glucuronate and alcohol and MUG substrate cleavage in Escherichia coli (NCBITaxon:562), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    +

    The record's primary literature (EC 3.2.1.31, DOI:10.1128/aem.50.6.1383-1387.1985) establishes beta-D-glucuronoside hydrolysis to D-glucuronate and alcohol and MUG substrate cleavage in Escherichia coli (NCBITaxon:562), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    @@ -481,7 +482,7 @@

    Evidence

    -

    Resolution: Added canonical_examples entry Escherichia coli K-12 (NCBITaxon:83333; DOI:10.1073/pnas.83.22.8447) and promoted beta_glucuronidase_uida_sketch to MECHANISTIC by adding InterPro:IPR006101-grounded GENE_OR_PROTEIN node beta_glucuronidase_uida with reviewed Escherichia coli K-12 (NCBITaxon:83333; UP000000625) protein_examples UniProtKB:P05804 (UidA) backed by DOI:10.1073/pnas.83.22.8447.

    +

    Resolution: Added canonical_examples entry Escherichia coli K-12 (NCBITaxon:83333; DOI:10.1073/pnas.83.22.8447) and promoted beta_glucuronidase_uida_sketch to MECHANISTIC by adding InterPro:IPR006101-grounded GENE_OR_PROTEIN node beta_glucuronidase_uida with reviewed Escherichia coli K-12 (NCBITaxon:83333; UP000000625) protein_examples UniProtKB:P05804 (UidA) backed by DOI:10.1073/pnas.83.22.8447.

    @@ -504,7 +505,7 @@

    Curation history

  • · FIX_EVIDENCE_SNIPPET · codex -

    Corrected the IUBMB EC 3.2.1.31 water token from HTML-derived H_{2}O to source-visible H2O after Claude Code Review flagged the snippet as non-verbatim in https://github.com/CultureBotAI/TraitMech/issues/807.

    +

    Corrected the IUBMB EC 3.2.1.31 water token from HTML-derived H_{2}O to source-visible H2O after Claude Code Review flagged the snippet as non-verbatim in https://github.com/CultureBotAI/TraitMech/issues/807.

  • @@ -522,7 +523,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Added Escherichia coli K-12 (NCBITaxon:83333; DOI:10.1073/pnas.83.22.8447) canonical example; promoted beta_glucuronidase_uida_sketch to MECHANISTIC; added InterPro:IPR006101-grounded GENE_OR_PROTEIN node beta_glucuronidase_uida with reviewed Escherichia coli K-12 (NCBITaxon:83333) protein_examples UniProtKB:P05804 (UidA) backed by DOI:10.1073/pnas.83.22.8447; resolved beta-glucuronidase-activity-protein-example-gap.

    +

    Added Escherichia coli K-12 (NCBITaxon:83333; DOI:10.1073/pnas.83.22.8447) canonical example; promoted beta_glucuronidase_uida_sketch to MECHANISTIC; added InterPro:IPR006101-grounded GENE_OR_PROTEIN node beta_glucuronidase_uida with reviewed Escherichia coli K-12 (NCBITaxon:83333) protein_examples UniProtKB:P05804 (UidA) backed by DOI:10.1073/pnas.83.22.8447; resolved beta-glucuronidase-activity-protein-example-gap.

    • @@ -570,7 +571,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -934,12 +944,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 18:45 UTC diff --git a/pages/traits/physiology/beta_n_acetylhexosaminidase_activity.html b/pages/traits/physiology/beta_n_acetylhexosaminidase_activity.html index 4eca5a99c5f..ff0210c3f66 100644 --- a/pages/traits/physiology/beta_n_acetylhexosaminidase_activity.html +++ b/pages/traits/physiology/beta_n_acetylhexosaminidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -82,7 +83,7 @@

    Trait evidence (3)

    Beta-N-acetylhexosaminidase hydrolytic release of N-acetyl-D-hexosamine residues

    Evidence-backed physiological mechanism sketch linking beta-N-acetylhexosaminidase catalytic activity and N-acetyl-D-glucosamine release to the beta-N-acetylhexosaminidase activity phenotype.

    -

    MECHANISTIC · Mechanistic graph backed by EC 3.2.1.52, DOI:10.1021/jf020965x, and DOI:10.1016/0378-1119(95)00848-9; exemplified on beta_n_acetylhexosaminidase_chb with Serratia marcescens (NCBITaxon:615) chitobiase Chb (UniProtKB:Q54468).

    +

    MECHANISTIC · Mechanistic graph backed by EC 3.2.1.52, DOI:10.1021/jf020965x, and DOI:10.1016/0378-1119(95)00848-9; exemplified on beta_n_acetylhexosaminidase_chb with Serratia marcescens (NCBITaxon:615) chitobiase Chb (UniProtKB:Q54468).

    Loading graph…

    @@ -105,7 +106,7 @@

    Edge evidence

    GO:0004563 confers beta-N-acetylhexosaminidase activity - traitmech:000157 + traitmech:000157 METPO:2007700

    Production of active beta-N-acetylhexosaminidase by chitin-degrading bacteria confers the beta-N-acetylhexosaminidase activity phenotype.

      @@ -180,8 +181,8 @@

      Protein and taxon examples

    		 - Serratia marcescens -
    NCBITaxon:615 + Serratia marcescens +
    NCBITaxon:615         		REVIEWED
    @@ -247,13 +248,13 @@

    Parent traits (1)

    Synonyms (4)

      -
    • beta-N-acetyl-D-hexosaminide N-acetylhexosaminohydrolase activity EXACT_SYNONYM · https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/52.html
      • +
    • beta-N-acetyl-D-hexosaminide N-acetylhexosaminohydrolase activity EXACT_SYNONYM · https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/52.html
      • -
    • N-acetylhexosaminidase RELATED_SYNONYM · DOI:10.1021/jf020965x
      • +
    • N-acetylhexosaminidase RELATED_SYNONYM · DOI:10.1021/jf020965x
      • -
    • beta-N-acetylglucosaminidase RELATED_SYNONYM · https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/52.html
      • +
    • beta-N-acetylglucosaminidase RELATED_SYNONYM · https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/52.html
      • -
    • N-acetyl-beta-glucosaminidase RELATED_SYNONYM · TraitMech#453
      • +
    • N-acetyl-beta-glucosaminidase RELATED_SYNONYM · TraitMech#453
    @@ -269,7 +270,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -419,7 +420,7 @@

    Discussions and Knowledge Gaps (3)

    -

    The current record pairs one IUBMB EC 3.2.1.52 reaction snippet with a strain enzyme-production snippet (DOI:10.1021/jf020965x) that does not state a distinct second mechanistic step.

    +

    The current record pairs one IUBMB EC 3.2.1.52 reaction snippet with a strain enzyme-production snippet (DOI:10.1021/jf020965x) that does not state a distinct second mechanistic step.

    @@ -462,7 +463,7 @@

    Evidence

    -

    The record's primary literature (EC 3.2.1.52, DOI:10.1021/jf020965x) establishes hydrolytic release of terminal non-reducing N-acetyl-D-hexosamine residues and N-acetylhexosaminidase production in Serratia marcescens (NCBITaxon:615), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    +

    The record's primary literature (EC 3.2.1.52, DOI:10.1021/jf020965x) establishes hydrolytic release of terminal non-reducing N-acetyl-D-hexosamine residues and N-acetylhexosaminidase production in Serratia marcescens (NCBITaxon:615), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    @@ -481,7 +482,7 @@

    Evidence

    -

    Resolution: Promoted beta_n_acetylhexosaminidase_chb_sketch to MECHANISTIC by adding InterPro:IPR025705-grounded GENE_OR_PROTEIN node beta_n_acetylhexosaminidase_chb with reviewed Serratia marcescens (NCBITaxon:615) protein_examples UniProtKB:Q54468 (Chb) backed by DOI:10.1016/0378-1119(95)00848-9.

    +

    Resolution: Promoted beta_n_acetylhexosaminidase_chb_sketch to MECHANISTIC by adding InterPro:IPR025705-grounded GENE_OR_PROTEIN node beta_n_acetylhexosaminidase_chb with reviewed Serratia marcescens (NCBITaxon:615) protein_examples UniProtKB:Q54468 (Chb) backed by DOI:10.1016/0378-1119(95)00848-9.

    @@ -516,7 +517,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Promoted beta_n_acetylhexosaminidase_chb_sketch to MECHANISTIC; added InterPro:IPR025705-grounded GENE_OR_PROTEIN node beta_n_acetylhexosaminidase_chb with reviewed Serratia marcescens (NCBITaxon:615) protein_examples UniProtKB:Q54468 (Chb) backed by DOI:10.1016/0378-1119(95)00848-9; resolved beta-n-acetylhexosaminidase-activity-protein-example-gap.

    +

    Promoted beta_n_acetylhexosaminidase_chb_sketch to MECHANISTIC; added InterPro:IPR025705-grounded GENE_OR_PROTEIN node beta_n_acetylhexosaminidase_chb with reviewed Serratia marcescens (NCBITaxon:615) protein_examples UniProtKB:Q54468 (Chb) backed by DOI:10.1016/0378-1119(95)00848-9; resolved beta-n-acetylhexosaminidase-activity-protein-example-gap.

    • @@ -558,7 +559,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -922,12 +932,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 18:45 UTC diff --git a/pages/traits/physiology/bioluminescence.html b/pages/traits/physiology/bioluminescence.html index 8edb9da67cf..108d246ede2 100644 --- a/pages/traits/physiology/bioluminescence.html +++ b/pages/traits/physiology/bioluminescence.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -137,7 +138,7 @@

    Edge evidence

    GO:0008218 confers bioluminescence - traitmech:000085 + traitmech:000085 METPO:2007700

    The luciferase reaction realizes the bioluminescence trait.

      @@ -364,8 +365,8 @@

      Protein and taxon examples

    		 - Aliivibrio fischeri -
    NCBITaxon:668 + Aliivibrio fischeri +
    NCBITaxon:668         		REVIEWED
    @@ -431,7 +432,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -447,7 +448,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -723,7 +724,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1087,12 +1097,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/biomineralization.html b/pages/traits/physiology/biomineralization.html index 8218d30cf8a..aeaa239d728 100644 --- a/pages/traits/physiology/biomineralization.html +++ b/pages/traits/physiology/biomineralization.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -61,19 +62,19 @@

    Trait evidence (4)

    DOI:10.1128/AEM.07044-11
    All bacteria tested induce the precipitation of a significant amount of calcium carbonate when cultured in M-3P medium.
    -

    Rodriguez-Navarro et al. 2012, PMID:22447589, PMC3346411, Discussion, Bacterial carbonatogenesis. Publisher scientific Abstract, Introduction, Methods, Results and relevant Discussion directly read on 2026-10-10; actual Figures 1 and 6 inspected, other figures not visually audited. Inoculated assays produced carbonates whereas uninoculated substrate controls did not. Tested M. xanthus strain 422, B. diminuta SJ 63 and a stone bacterial community are assay labels, not verified canonical taxa here. Polymorph selection depends on the stated substrate/medium conditions, not a universal strain rule. The proposed amorphous precursor is not established by morphology alone. No universal urease requirement or functional protein mechanism is inferred.

    +

    Rodriguez-Navarro et al. 2012, PMID:22447589, PMC3346411, Discussion, Bacterial carbonatogenesis. Publisher scientific Abstract, Introduction, Methods, Results and relevant Discussion directly read on 2026-10-10; actual Figures 1 and 6 inspected, other figures not visually audited. Inoculated assays produced carbonates whereas uninoculated substrate controls did not. Tested M. xanthus strain 422, B. diminuta SJ 63 and a stone bacterial community are assay labels, not verified canonical taxa here. Polymorph selection depends on the stated substrate/medium conditions, not a universal strain rule. The proposed amorphous precursor is not established by morphology alone. No universal urease requirement or functional protein mechanism is inferred.

  • DOI:10.1038/ncomms11228
    Coccoliths are calcitic particles produced inside the cells of unicellular marine algae known as coccolithophores.
    -

    Sviben et al. 2016, PMID:27075521, PMC4834641. Scientific Abstract directly checked in Europe PMC full-text XML on 2026-10-10; Introduction, calcite-resupply Results and Discussion also inspected. This supports controlled mineral production and the coccolith child's placement. Historical E. huxleyi AWI1516 observations do not establish every strain's current phenotype. A separate calcium-rich compartment is not proven to be a necessary direct precursor or bulk-transfer route. No new figure or supplement audit is claimed for this parent; the child's more detailed provenance is retained.

    +

    Sviben et al. 2016, PMID:27075521, PMC4834641. Scientific Abstract directly checked in Europe PMC full-text XML on 2026-10-10; Introduction, calcite-resupply Results and Discussion also inspected. This supports controlled mineral production and the coccolith child's placement. Historical E. huxleyi AWI1516 observations do not establish every strain's current phenotype. A separate calcium-rich compartment is not proven to be a necessary direct precursor or bulk-transfer route. No new figure or supplement audit is claimed for this parent; the child's more detailed provenance is retained.

  • DOI:10.1016/j.protis.2016.05.002
    Scales were formed one by one in silica deposition vesicles (SDVs)
    -

    Nomura and Ishida 2016, PMID:27348459. Scientific abstract directly read on 2026-10-10 at https://rrc.nbrp.jp/references/56432?lang=en. Scale formation and silicon detection in immature-scale vesicles support mineral production beyond carbonates and the siliceous-scale child's placement. Historical Paulinella chromatophora naming does not establish current strain taxonomy. Full Methods and figures remain unread; proposed microtubule involvement is not molecular necessity. Scale production is distinct from subsequent shell assembly.

    +

    Nomura and Ishida 2016, PMID:27348459. Scientific abstract directly read on 2026-10-10 at https://rrc.nbrp.jp/references/56432?lang=en. Scale formation and silicon detection in immature-scale vesicles support mineral production beyond carbonates and the siliceous-scale child's placement. Historical Paulinella chromatophora naming does not establish current strain taxonomy. Full Methods and figures remain unread; proposed microtubule involvement is not molecular necessity. Scale production is distinct from subsequent shell assembly.

    • @@ -142,7 +143,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -238,7 +239,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    The definition includes controlled, induced and matrix-mediated formation when microbial mediation is demonstrated; it is not restricted to carbonate, intracellular deposition or a crystalline end product. Benzerara et al. DOI:10.1016/j.crte.2010.09.002 section 2 includes passive organic-matter effects under biologically influenced biomineralization. This broad terminology is retained, but precipitation near a cell, isolated nonliving-matrix activity, mineral adhesion, uptake of preformed particles or ion adsorption alone does not establish that organism's formation phenotype. Organic-substrate mineralization, mineral dissolution, metal tolerance and mineral use as an electron donor are not equivalent. Coccolith and siliceous-scale production are narrower endpoints. Magnetosome and ferrosome organelle records retain their structural parents; no automatic cross-axis reparenting or disjointness is asserted. The magnetosome graph's similarly named node has narrower scope and is not exactly grounded to this umbrella. No synonyms or xrefs are asserted pending authority-backed phenotype mapping.

    +

    The definition includes controlled, induced and matrix-mediated formation when microbial mediation is demonstrated; it is not restricted to carbonate, intracellular deposition or a crystalline end product. Benzerara et al. DOI:10.1016/j.crte.2010.09.002 section 2 includes passive organic-matter effects under biologically influenced biomineralization. This broad terminology is retained, but precipitation near a cell, isolated nonliving-matrix activity, mineral adhesion, uptake of preformed particles or ion adsorption alone does not establish that organism's formation phenotype. Organic-substrate mineralization, mineral dissolution, metal tolerance and mineral use as an electron donor are not equivalent. Coccolith and siliceous-scale production are narrower endpoints. Magnetosome and ferrosome organelle records retain their structural parents; no automatic cross-axis reparenting or disjointness is asserted. The magnetosome graph's similarly named node has narrower scope and is not exactly grounded to this umbrella. No synonyms or xrefs are asserted pending authority-backed phenotype mapping.

    @@ -332,7 +333,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -361,12 +371,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-10 08:07 UTC diff --git a/pages/traits/physiology/bipolar_mating_system.html b/pages/traits/physiology/bipolar_mating_system.html index 62c8681d2b9..c7a85797074 100644 --- a/pages/traits/physiology/bipolar_mating_system.html +++ b/pages/traits/physiology/bipolar_mating_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1073/pnas.91.15.7085
    A bipolar system is defined by a single genetic locus (MAT) that can have two or multiple alleles.
    -

    Bakkeren and Kronstad (1994), PMID:7913746, PMC44343. Exact scientific-abstract sentence directly retrieved from Europe PMC core metadata. The abstract reports cloning of Ustilago hordei a1 and physical linkage of a and b into a complex MAT region, contrasted with genetically unlinked loci in U. maydis. The compatibility factor is not necessarily one gene. This supports definition and a reported linkage architecture, not a fresh verification of native crossing assays. Full text, figures, methods, supplements and natural strain provenance remain uninspected; no canonical strain is inferred.

    +

    Bakkeren and Kronstad (1994), PMID:7913746, PMC44343. Exact scientific-abstract sentence directly retrieved from Europe PMC core metadata. The abstract reports cloning of Ustilago hordei a1 and physical linkage of a and b into a complex MAT region, contrasted with genetically unlinked loci in U. maydis. The compatibility factor is not necessarily one gene. This supports definition and a reported linkage architecture, not a fresh verification of native crossing assays. Full text, figures, methods, supplements and natural strain provenance remain uninspected; no canonical strain is inferred.

  • DOI:10.1534/genetics.105.051128
    All of the 24 collections displayed a bipolar mating system with only two mating types among all progeny of a collection.
    -

    James et al. (2006), PMID:16461425, PMC1456265. Exact sentence in the first Results subsection on p. 1881, visually checked in the published PDF at https://public.websites.umich.edu/~mycology/resources/Publications/james2006.genetics.pdf; not an abstract quote. Native Coprinellus disseminatus single-spore crosses support the compatibility phenotype. Two types per collection does not mean only two across the species. Methods score clamps and dikaryotization, not automatically completed fertile sex; poor-mating progeny were excluded when choosing population testers. Table 3 shows segregation in 13 TJ00/38 progeny: MIP tracks mating type, whereas CDSTE3.1-.3 do not. Its plus/minus states are PCR-RFLP genotypes, not gene presence or absence; CDSTE3.4 lacks segregation data. The abstract reports heterologous sexual responses, not loss of all pheromone-receptor function. PDF pp. 1877-1882 and actual Tables 1-3 were read; pp. 1883-1884 were text-extracted only. Actual figures, later Results/Discussion and supplements remain uninspected. Natural North Carolina fruit-body provenance is described in Methods, but active taxon authority and the intersterile Japanese group remain unresolved; no canonical taxon assertion is made.

    +

    James et al. (2006), PMID:16461425, PMC1456265. Exact sentence in the first Results subsection on p. 1881, visually checked in the published PDF at https://public.websites.umich.edu/~mycology/resources/Publications/james2006.genetics.pdf; not an abstract quote. Native Coprinellus disseminatus single-spore crosses support the compatibility phenotype. Two types per collection does not mean only two across the species. Methods score clamps and dikaryotization, not automatically completed fertile sex; poor-mating progeny were excluded when choosing population testers. Table 3 shows segregation in 13 TJ00/38 progeny: MIP tracks mating type, whereas CDSTE3.1-.3 do not. Its plus/minus states are PCR-RFLP genotypes, not gene presence or absence; CDSTE3.4 lacks segregation data. The abstract reports heterologous sexual responses, not loss of all pheromone-receptor function. PDF pp. 1877-1882 and actual Tables 1-3 were read; pp. 1883-1884 were text-extracted only. Actual figures, later Results/Discussion and supplements remain uninspected. Natural North Carolina fruit-body provenance is described in Methods, but active taxon authority and the intersterile Japanese group remain unresolved; no canonical taxon assertion is made.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -277,13 +278,13 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed bipolar mating system -

      Added traitmech:000616 as a PROPOSED PHYSIOLOGY class under released phenotype, with primary DOI:10.1073/pnas.91.15.7085 scientific-abstract definition and DOI:10.1534/genetics.105.051128 visually verified Results snippet. Distinguished single-factor compatibility from gene inventory, exactly two species-wide types, partner dependence and one molecular architecture. Reserved METPO:1057000 in v493 after ignored-and-hidden novelty and collision checks. Deferred canonical taxon assertions, native protein graphs and explicitly unread source sections in two discussions. Created via guarded write_validated_trait and record_curation_event; the seven writer tests and dry run passed before application.

    +

    Added traitmech:000616 as a PROPOSED PHYSIOLOGY class under released phenotype, with primary DOI:10.1073/pnas.91.15.7085 scientific-abstract definition and DOI:10.1534/genetics.105.051128 visually verified Results snippet. Distinguished single-factor compatibility from gene inventory, exactly two species-wide types, partner dependence and one molecular architecture. Reserved METPO:1057000 in v493 after ignored-and-hidden novelty and collision checks. Deferred canonical taxon assertions, native protein graphs and explicitly unread source sections in two discussions. Created via guarded write_validated_trait and record_curation_event; the seven writer tests and dry run passed before application.

    • Read this curation session
  • · codex
    • EDIT — Correct James Results locator -

      Issue #1706: corrected the James (2006) DOI:10.1534/genetics.105.051128 source locator from first Results sentence to a sentence in the first Results subsection, p. 1881. The exact quote, biology and references are unchanged. Applied through write_validated_trait against SHA256 9720398ee05729134dd310756258cf6cbcc40f4be815e301511bbb46044baa1a, preserving the original per-record event and adding a CORRECTED_EVIDENCE_LOCATOR event with record_curation_event. This follows history/records/bipolar_mating_system/2026-10-05T083627Z-codex-e4b16d.yaml without editing it. Updated writer, regression assertion and proposal to use the corrected locator.

    +

    Issue #1706: corrected the James (2006) DOI:10.1534/genetics.105.051128 source locator from first Results sentence to a sentence in the first Results subsection, p. 1881. The exact quote, biology and references are unchanged. Applied through write_validated_trait against SHA256 9720398ee05729134dd310756258cf6cbcc40f4be815e301511bbb46044baa1a, preserving the original per-record event and adding a CORRECTED_EVIDENCE_LOCATOR event with record_curation_event. This follows history/records/bipolar_mating_system/2026-10-05T083627Z-codex-e4b16d.yaml without editing it. Updated writer, regression assertion and proposal to use the corrected locator.

    • Read this curation session @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 08:39 UTC diff --git a/pages/traits/physiology/carbon_source_memory.html b/pages/traits/physiology/carbon_source_memory.html index fb85a509885..e521338aa3b 100644 --- a/pages/traits/physiology/carbon_source_memory.html +++ b/pages/traits/physiology/carbon_source_memory.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1371/journal.pgen.1004556
    Cells grown under cyclical glucose/lactose conditions thus displayed phenotypic memory of their previous metabolic adaptation.
    -

    Lambert and Kussell 2014, PMID:25255314, PMC4177670; Results / Phenotypic memory in response to sudden environmental changes, not the abstract. Primary text, actual Figure 2 and Text S1 were inspected. Repeated glucose/lactose switches demonstrate history-dependent growth; the paper distinguishes inherited protein persistence from continuing induction after stimulus removal. F3 is an engineered W3110 derivative, not an unmodified natural exemplar. Growth is a chamber-level relative elongation readout. DOI:10.1371/journal.pgen.1004793 corrects author-name typesetting, not the biological claims; the correction was read. Model predictions are not additional experimental replication. Other figures, raw data and equations were not independently reanalyzed.

    +

    Lambert and Kussell 2014, PMID:25255314, PMC4177670; Results / Phenotypic memory in response to sudden environmental changes, not the abstract. Primary text, actual Figure 2 and Text S1 were inspected. Repeated glucose/lactose switches demonstrate history-dependent growth; the paper distinguishes inherited protein persistence from continuing induction after stimulus removal. F3 is an engineered W3110 derivative, not an unmodified natural exemplar. Growth is a chamber-level relative elongation readout. DOI:10.1371/journal.pgen.1004793 corrects author-name typesetting, not the biological claims; the correction was read. Model predictions are not additional experimental replication. Other figures, raw data and equations were not independently reanalyzed.

  • DOI:10.7554/eLife.39234
    past exposure to an environmental condition can shorten the time needed to adapt when the condition re-occurs
    -

    Cerulus et al. 2018, PMID:30299256, PMC6211830; scientific abstract, confirmed against NCBI full-text XML. Relevant Results, Methods, Discussion, actual Figures 1, 2, 6 and Figure 1 supplement 4 were inspected. Carbon-shift assays separate population lag from single-cell growth resumption; cells not resuming within the observation window are not thereby proved dead. Cross-sugar effects and respiratory perturbations oppose an obligatory same-sugar or sugar-specific protein-inheritance mechanism. The main AN63 series is engineered; the separately reported non-laboratory strains have unreviewed primary provenance here. Publisher article access was challenged; public figure assets were accessible. Raw data and all other supplements were not reanalyzed.

    +

    Cerulus et al. 2018, PMID:30299256, PMC6211830; scientific abstract, confirmed against NCBI full-text XML. Relevant Results, Methods, Discussion, actual Figures 1, 2, 6 and Figure 1 supplement 4 were inspected. Carbon-shift assays separate population lag from single-cell growth resumption; cells not resuming within the observation window are not thereby proved dead. Cross-sugar effects and respiratory perturbations oppose an obligatory same-sugar or sugar-specific protein-inheritance mechanism. The main AN63 series is engineered; the separately reported non-laboratory strains have unreviewed primary provenance here. Publisher article access was challenged; public figure assets were accessible. Raw data and all other supplements were not reanalyzed.

  • DOI:10.1016/j.cub.2007.10.044
    This "galactose memory" persists for several generations
    -

    Zacharioudakis et al. 2007, PMID:17997309; directly retrieved, source-qualified MED scientific abstract only. The preceding sentence compares initial GAL activation with rapid reactivation in progeny after intervening glucose growth. This supports the induction endpoint, not a measured growth-rate benefit. Its Gal1 and cytoplasmic-factor interpretation remains assay-specific; the abstract's chromatin conclusion is not universalized. Full text, figures and strain provenance were not inspected. The index links a Comment in, not a correction or independent replication.

    +

    Zacharioudakis et al. 2007, PMID:17997309; directly retrieved, source-qualified MED scientific abstract only. The preceding sentence compares initial GAL activation with rapid reactivation in progeny after intervening glucose growth. This supports the induction endpoint, not a measured growth-rate benefit. Its Gal1 and cytoplasmic-factor interpretation remains assay-specific; the abstract's chromatin conclusion is not universalized. Full text, figures and strain provenance were not inspected. The index links a Comment in, not a correction or independent replication.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-12 03:35 UTC diff --git a/pages/traits/physiology/carboxydotrophic.html b/pages/traits/physiology/carboxydotrophic.html index 62b5aee4c03..b472692b02b 100644 --- a/pages/traits/physiology/carboxydotrophic.html +++ b/pages/traits/physiology/carboxydotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -402,8 +403,8 @@

    Protein and taxon examples

    		 - Rhodospirillum rubrum -
    NCBITaxon:1085 + Rhodospirillum rubrum +
    NCBITaxon:1085         		REVIEWED
    @@ -482,7 +483,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -818,7 +819,7 @@

    Curation history

  • · REVIEW_EVIDENCE_REFERENCE_CHURN · codex -

    Offline review for issue 520 retained 1 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1101/2023.01.17.524042 -> DOI:10.1128/aem.00185-23 (1 edge).

    +

    Offline review for issue 520 retained 1 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1101/2023.01.17.524042 -> DOI:10.1128/aem.00185-23 (1 edge).

  • @@ -878,7 +879,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1242,12 +1252,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/carboxylesterase_activity.html b/pages/traits/physiology/carboxylesterase_activity.html index e4acb94d84b..ae02ac25865 100644 --- a/pages/traits/physiology/carboxylesterase_activity.html +++ b/pages/traits/physiology/carboxylesterase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -354,7 +355,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -383,12 +393,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/caseinase_activity.html b/pages/traits/physiology/caseinase_activity.html index c851a3c25fb..ff6005923a8 100644 --- a/pages/traits/physiology/caseinase_activity.html +++ b/pages/traits/physiology/caseinase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -272,7 +273,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two general casein-hydrolysis screening snippets (DOI:10.3389/fmicb.2018.01148, DOI:10.2174/1874285801408010025) without specific protease gene/enzyme or multi-step mechanism quotes.

    +

    The current record carries two general casein-hydrolysis screening snippets (DOI:10.3389/fmicb.2018.01148, DOI:10.2174/1874285801408010025) without specific protease gene/enzyme or multi-step mechanism quotes.

    @@ -354,7 +355,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -383,12 +393,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/catalase_activity.html b/pages/traits/physiology/catalase_activity.html index 81ebcf6655d..189007bf4c4 100644 --- a/pages/traits/physiology/catalase_activity.html +++ b/pages/traits/physiology/catalase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -175,7 +176,7 @@

    Edge evidence

    InterPro:IPR018028 confers catalase activity - traitmech:000075 + traitmech:000075 METPO:2007700

    Production of catalase confers the catalase-activity phenotype.

      @@ -191,7 +192,7 @@

      Edge evidence

    • catalase activity - traitmech:000075 + traitmech:000075 decomposes hydrogen peroxide CHEBI:16240 @@ -232,7 +233,7 @@

      Edge evidence

      CHEBI:16240 favors scavenging by catalase activity - traitmech:000075 + traitmech:000075

      High hydrogen peroxide concentrations favor scavenging by catalases, which turn over much faster than alkyl hydroperoxide reductase.

        @@ -348,8 +349,8 @@

        Protein and taxon examples

    		•  - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) -
    NCBITaxon:559292 + Saccharomyces cerevisiae (strain ATCC 204508 / S288c) +
    NCBITaxon:559292         		REVIEWED
    @@ -378,8 +379,8 @@

    Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -408,8 +409,8 @@

    Protein and taxon examples

    		 - Staphylococcus aureus NCTC 8325 -
    NCBITaxon:93061 + Staphylococcus aureus NCTC 8325 +
    NCBITaxon:93061         		REVIEWED
    @@ -475,7 +476,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -491,7 +492,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -788,7 +789,7 @@

    Curation history

  • · REVIEW_EVIDENCE_REFERENCE_CHURN · codex -

    Offline review for issue 520 retained 7 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1007/s00018-003-3206-5 -> DOI:10.1021/ja9018572 (4 edges); DOI:10.1038/nrmicro3032 -> DOI:10.1021/ja9018572 (1 edge); DOI:10.1038/nrmicro3032 -> DOI:10.1073/pnas.96.11.6161 (1 edge); DOI:10.3390/biom14060697 -> DOI:10.1021/ja9018572 (1 edge).

    +

    Offline review for issue 520 retained 7 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1007/s00018-003-3206-5 -> DOI:10.1021/ja9018572 (4 edges); DOI:10.1038/nrmicro3032 -> DOI:10.1021/ja9018572 (1 edge); DOI:10.1038/nrmicro3032 -> DOI:10.1073/pnas.96.11.6161 (1 edge); DOI:10.3390/biom14060697 -> DOI:10.1021/ja9018572 (1 edge).

  • @@ -806,13 +807,13 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Added reviewed E. coli K-12 OxyR protein_example UniProtKB:P0ACQ4 (v144) on oxyr_regulator (DOI:10.1073/pnas.96.11.6161), updated scope_notes, and refreshed UniProtKB:Q2G282 entry_version 109 -> 110 on perr_regulator.

    +

    Added reviewed E. coli K-12 OxyR protein_example UniProtKB:P0ACQ4 (v144) on oxyr_regulator (DOI:10.1073/pnas.96.11.6161), updated scope_notes, and refreshed UniProtKB:Q2G282 entry_version 109 -> 110 on perr_regulator.

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.1007/s00018-003-3206-5 (already present on oxidative_stress_response.yaml evidence[1]) to record-level evidence[0] to match definition_source (Cycle 5 Stage 5 remediation of F-C5S4-DEF-SRC-007 in group G-C5S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.1007/s00018-003-3206-5 (already present on oxidative_stress_response.yaml evidence[1]) to record-level evidence[0] to match definition_source (Cycle 5 Stage 5 remediation of F-C5S4-DEF-SRC-007 in group G-C5S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -854,7 +855,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1218,12 +1228,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 21:40 UTC diff --git a/pages/traits/physiology/cell_body_contraction.html b/pages/traits/physiology/cell_body_contraction.html index 2c3dc0885a0..06cf7831348 100644 --- a/pages/traits/physiology/cell_body_contraction.html +++ b/pages/traits/physiology/cell_body_contraction.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1126/sciadv.add6550
    Ca2+ concentrations from 10−6 to 10−2 M in the culture medium could stimulate cell contraction while maintaining the viability of the cell.
    -

    Zhang et al. 2023, PMID:36812318, PMCID:PMC9946354, Results: functional analysis of giant backbone proteins, second paragraph. Direct JATS match; native NOT_IN_ABSTRACT retained. The study identified its East Lake, Wuhan isolate as Spirostomum minus using morphology, protargol staining and SSU rDNA, then established clonal cultures at 22 C. Actual Figure 1A shows extended and contracted cell bodies. The quoted treatment maintained viability; 38-to-16 seconds describes intervals between contractions, not contraction duration. Selected Results, Methods and Discussion, actual Figures 1, 6 and 9, and relevant supplement pages were inspected. Figure 9 is a mechanistic schematic. Supplementary Figure 7 shows shortening during death, which is insufficient for this trait. Abnormal-cell counts are in Supplementary Table 2, not Table S1 as cited in the RNAi Results. Rare twisted RNAi phenotypes do not establish contraction loss in every treated cell. The source's superscript exponents mean 10^(-6) to 10^(-2) M; the normalized plain-text quotation does not preserve superscript styling.

    +

    Zhang et al. 2023, PMID:36812318, PMCID:PMC9946354, Results: functional analysis of giant backbone proteins, second paragraph. Direct JATS match; native NOT_IN_ABSTRACT retained. The study identified its East Lake, Wuhan isolate as Spirostomum minus using morphology, protargol staining and SSU rDNA, then established clonal cultures at 22 C. Actual Figure 1A shows extended and contracted cell bodies. The quoted treatment maintained viability; 38-to-16 seconds describes intervals between contractions, not contraction duration. Selected Results, Methods and Discussion, actual Figures 1, 6 and 9, and relevant supplement pages were inspected. Figure 9 is a mechanistic schematic. Supplementary Figure 7 shows shortening during death, which is insufficient for this trait. Abnormal-cell counts are in Supplementary Table 2, not Table S1 as cited in the RNAi Results. Rare twisted RNAi phenotypes do not establish contraction loss in every treated cell. The source's superscript exponents mean 10^(-6) to 10^(-2) M; the normalized plain-text quotation does not preserve superscript styling.

  • DOI:10.1073/pnas.2217737120
    Asymmetric contraction can be observed as the top end begins contracting before the bottom end
    -

    Floyd et al. 2023, PMID:37307463, PMCID:PMC10288572, Figure 4 caption, contiguous observed-asymmetry clause. Direct JATS match; native NOT_IN_ABSTRACT retained. The quoted top and bottom ends are those of the imaged Spirostomum cell body in Figure 4A-C, not Vorticella's stalk or simulated springs. The actual panel A contours and panel B solid length trajectory show body shortening; panel C shows the staggered endpoint movements. Dashed model curves are separate from observations. The 15-word caption span replaces the data-presentation excerpt rejected in #1935; historical source receipts remain in the sidecar. Actual Figures 1A and 2A-B show Spirostomum body shortening and experimental trajectories separately from fitted curves. Methods used commercially sourced cultures and high-speed imaging without compressing cells; no species identity is inferred. Supplementary Figure S3 measures length along the central backbone curve, with increasing width. Supplementary Figure S6 states that repeated contractions of the same organism were not distinguished from contractions of different organisms: five traces are not five established biological replicates. Vorticella panels measure stalk contraction, not the body endpoint. Calcium-wave and energy models are not universal molecular proof. Selected experimental sections, actual Figures 1-2 and supplementary pages 3 and 5 were inspected; raw videos and the complete model were not reanalyzed.

    +

    Floyd et al. 2023, PMID:37307463, PMCID:PMC10288572, Figure 4 caption, contiguous observed-asymmetry clause. Direct JATS match; native NOT_IN_ABSTRACT retained. The quoted top and bottom ends are those of the imaged Spirostomum cell body in Figure 4A-C, not Vorticella's stalk or simulated springs. The actual panel A contours and panel B solid length trajectory show body shortening; panel C shows the staggered endpoint movements. Dashed model curves are separate from observations. The 15-word caption span replaces the data-presentation excerpt rejected in #1935; historical source receipts remain in the sidecar. Actual Figures 1A and 2A-B show Spirostomum body shortening and experimental trajectories separately from fitted curves. Methods used commercially sourced cultures and high-speed imaging without compressing cells; no species identity is inferred. Supplementary Figure S3 measures length along the central backbone curve, with increasing width. Supplementary Figure S6 states that repeated contractions of the same organism were not distinguished from contractions of different organisms: five traces are not five established biological replicates. Vorticella panels measure stalk contraction, not the body endpoint. Calcium-wave and energy models are not universal molecular proof. Selected experimental sections, actual Figures 1-2 and supplementary pages 3 and 5 were inspected; raw videos and the complete model were not reanalyzed.

  • DOI:10.1242/jeb.189.1.163
    Living Vorticella showed a graded shrinkage of the cell body when Ca2+ buffer was injected into the cell body
    -

    Katoh and Naitoh 1994, PMID:9317557, scientific Abstract item 3, first clause. Direct namespace-qualified Europe PMC MED abstract match and native VERIFIED. The same sentence contrasts graded cell-body shrinkage with all-or-nothing stalk coiling. Triton-extracted preparations in other abstract items are not the living-cell injection assay. Calcium-release causality is presented as an assumption, not direct molecular proof. Publisher HTML and PDF requests returned 403; full Methods, figures and strain provenance were not accessed. No species-wide example, quantitative threshold or universal trigger is inferred.

    +

    Katoh and Naitoh 1994, PMID:9317557, scientific Abstract item 3, first clause. Direct namespace-qualified Europe PMC MED abstract match and native VERIFIED. The same sentence contrasts graded cell-body shrinkage with all-or-nothing stalk coiling. Triton-extracted preparations in other abstract items are not the living-cell injection assay. Calcium-release causality is presented as an assumption, not direct molecular proof. Publisher HTML and PDF requests returned 403; full Methods, figures and strain provenance were not accessed. No species-wide example, quantitative threshold or universal trigger is inferred.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -389,7 +390,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -418,12 +428,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-14 22:39 UTC diff --git a/pages/traits/physiology/cellular_buoyancy.html b/pages/traits/physiology/cellular_buoyancy.html index 752c3054752..3ad715cadd0 100644 --- a/pages/traits/physiology/cellular_buoyancy.html +++ b/pages/traits/physiology/cellular_buoyancy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -124,7 +125,7 @@

    Edge evidence

    GO:0031411 confers cellular buoyancy - traitmech:000528 + traitmech:000528 METPO:2007700

    Gas-filled vesicles lower effective cellular density and provide buoyancy.

      @@ -190,7 +191,7 @@

      Parent traits (1)

      Synonyms (1)

    @@ -206,7 +207,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -391,7 +392,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -755,12 +765,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-01 22:50 UTC diff --git a/pages/traits/physiology/cellular_contraction.html b/pages/traits/physiology/cellular_contraction.html index 1c764d19bae..a24cc72900b 100644 --- a/pages/traits/physiology/cellular_contraction.html +++ b/pages/traits/physiology/cellular_contraction.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1242/jeb.189.1.163
    Living Vorticella showed a graded shrinkage of the cell body when Ca2+ buffer was injected into the cell body
    -

    Katoh and Naitoh 1994, PMID:9317557, scientific Abstract item 3, first clause. Direct namespace-qualified Europe PMC MED match; native VERIFIED. The same sentence contrasts graded cell-body shrinkage with all-or-nothing stalk coiling. This supports the curator-synthesized body/projection-shortening parent, not a universal calcium threshold. Other abstract items use Triton-extracted preparations, not the living-cell injection assay. Calcium-induced calcium release is an assumption, not direct molecular proof. Publisher requests returned 403; full Methods, figures and strain provenance were not accessed.

    +

    Katoh and Naitoh 1994, PMID:9317557, scientific Abstract item 3, first clause. Direct namespace-qualified Europe PMC MED match; native VERIFIED. The same sentence contrasts graded cell-body shrinkage with all-or-nothing stalk coiling. This supports the curator-synthesized body/projection-shortening parent, not a universal calcium threshold. Other abstract items use Triton-extracted preparations, not the living-cell injection assay. Calcium-induced calcium release is an assumption, not direct molecular proof. Publisher requests returned 403; full Methods, figures and strain provenance were not accessed.

  • DOI:10.2108/zsj.20.1367
    Axopodial contraction of the centrohelid heliozoon Raphidiophrys contractilis was induced by mechanical or electrical stimulation.
    -

    Khan et al. 2003, PMID:14624035, scientific Abstract opening sentence. Direct namespace-qualified Europe PMC MED match; native VERIFIED. This supports stimulated shortening of a cytoplasmic projection rather than whole-cell locomotion. Reported calcium dependence and speed apply to this assay, not every member of the parent class. Non-detection of other filaments after fixation is not proof of their absence. Full Methods and figures were not accessed; the publisher's HTTP 200 response was an access challenge, not readable article content. Current taxonomic and culture identities remain unresolved.

    +

    Khan et al. 2003, PMID:14624035, scientific Abstract opening sentence. Direct namespace-qualified Europe PMC MED match; native VERIFIED. This supports stimulated shortening of a cytoplasmic projection rather than whole-cell locomotion. Reported calcium dependence and speed apply to this assay, not every member of the parent class. Non-detection of other filaments after fixation is not proof of their absence. Full Methods and figures were not accessed; the publisher's HTTP 200 response was an access challenge, not readable article content. Current taxonomic and culture identities remain unresolved.

  • DOI:10.1083/jcb.118.3.585
    Both recording techniques showed that the rapid contraction involves 80% of the total cell length.
    -

    Febvre-Chevalier and Febvre 1992, PMID:1639845, PMCID:PMC2289557, Results, Kinetics of the Contraction, printed page 588, right column. Direct extracted-PDF match with the typeset passage visually checked; native NOT_IN_ABSTRACT retained. The primary PDF was retrieved from its Semantic Scholar mirror after official PDF attempts failed. Selected Methods/Results and actual Figures 1 and 3-6 were inspected. Length was measured from head top to stalk base, not isolated cell-body length; graph axes use stalk length. The percentage is study-specific. Natural-seawater responses differ from artificially slowed responses. The specimens were collected near Villefranche and cultured at 14-18 C; current taxonomic identity is not verified. The n=20 initial-length sample is not asserted as independent contraction replication. Microtubule disassembly accompanies shortening, but this study expressly does not establish force production. Its disassembly half-time is not automatically contraction duration. The accessible JATS contains an abstract and PDF pointer, not the complete experimental text.

    +

    Febvre-Chevalier and Febvre 1992, PMID:1639845, PMCID:PMC2289557, Results, Kinetics of the Contraction, printed page 588, right column. Direct extracted-PDF match with the typeset passage visually checked; native NOT_IN_ABSTRACT retained. The primary PDF was retrieved from its Semantic Scholar mirror after official PDF attempts failed. Selected Methods/Results and actual Figures 1 and 3-6 were inspected. Length was measured from head top to stalk base, not isolated cell-body length; graph axes use stalk length. The percentage is study-specific. Natural-seawater responses differ from artificially slowed responses. The specimens were collected near Villefranche and cultured at 14-18 C; current taxonomic identity is not verified. The n=20 initial-length sample is not asserted as independent contraction replication. Microtubule disassembly accompanies shortening, but this study expressly does not establish force production. Its disassembly half-time is not automatically contraction duration. The accessible JATS contains an abstract and PDF pointer, not the complete experimental text.

    • @@ -132,7 +133,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -376,7 +377,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -405,12 +415,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-15 03:55 UTC diff --git a/pages/traits/physiology/cellular_rejuvenation.html b/pages/traits/physiology/cellular_rejuvenation.html index 73cd295d591..91dfd2cbe40 100644 --- a/pages/traits/physiology/cellular_rejuvenation.html +++ b/pages/traits/physiology/cellular_rejuvenation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,31 +56,31 @@

    Trait evidence (5)

    DOI:10.1242/jcs.86.1.263
    This is the first description of the restoration of a senescent defect by microinjection of young cytoplasmic components into Paramecium.
    -

    Haga and Karino 1986, PMID:3654779; scientific abstract, directly read in the MED record. Young-cell cytoplasm restored sexual activity in senescent cells (about 700 fissions); recovery persisted for up to 20 fissions. Division rate and fertility after self-conjugation did not improve. This supports endpoint-specific recovery in treated old cells, not whole-cell or permanent rejuvenation. Full methods and figures were unavailable.

    +

    Haga and Karino 1986, PMID:3654779; scientific abstract, directly read in the MED record. Young-cell cytoplasm restored sexual activity in senescent cells (about 700 fissions); recovery persisted for up to 20 fissions. Division rate and fertility after self-conjugation did not improve. This supports endpoint-specific recovery in treated old cells, not whole-cell or permanent rejuvenation. Full methods and figures were unavailable.

  • DOI:10.1038/s41467-018-06154-9
    As this convergence was now downwards, doubling times decreased with each generation.
    -

    Proenca et al. 2018, PMID:30213942, PMC6137065; Results, Stable equilibria are connected by aging and rejuvenation (Sec6), directly checked in primary XML. Actual Figure 4d was visually inspected: new-daughter lineages from the old-cell equilibrium converge toward faster growth over successive generations. These doubling times are derived from elongation rates, not direct interdivision intervals. Recovery is in descendants, not the same old mother. The tested MG1655 conditions do not establish all-environment recovery or a universal damage mechanism.

    +

    Proenca et al. 2018, PMID:30213942, PMC6137065; Results, Stable equilibria are connected by aging and rejuvenation (Sec6), directly checked in primary XML. Actual Figure 4d was visually inspected: new-daughter lineages from the old-cell equilibrium converge toward faster growth over successive generations. These doubling times are derived from elongation rates, not direct interdivision intervals. Recovery is in descendants, not the same old mother. The tested MG1655 conditions do not establish all-environment recovery or a universal damage mechanism.

  • DOI:10.1126/science.1204349
    Gametes (spores) generated by aged cells show the same replicative potential as gametes generated by young cells.
    -

    Unal et al. 2011, PMID:21700873, PMC3923466; scientific abstract, directly checked in MED and an MIT-hosted author manuscript. Main text and Figure 1 support gamete replicative-potential reset. Figure 4 concerns the separate vegetative lifespan-extension experiment. Transient NDT80-dependent vegetative lifespan extension is a separate result and does not establish reversal of every aged-cell defect. Supplements and strain tables were not assessed. The retrieved PDF identifies the article but differs in size and checksum from MIT bitstream metadata; original deposited-byte identity remains unresolved.

    +

    Unal et al. 2011, PMID:21700873, PMC3923466; scientific abstract, directly checked in MED and an MIT-hosted author manuscript. Main text and Figure 1 support gamete replicative-potential reset. Figure 4 concerns the separate vegetative lifespan-extension experiment. Transient NDT80-dependent vegetative lifespan extension is a separate result and does not establish reversal of every aged-cell defect. Supplements and strain tables were not assessed. The retrieved PDF identifies the article but differs in size and checksum from MIT bitstream metadata; original deposited-byte identity remains unresolved.

  • DOI:10.3390/microorganisms11010082
    The cloned immaturin gene induces sexual rejuvenation in both mature and senescent cells by microinjection.
    -

    Haga 2023, PMID:36677375, PMC9865852; scientific abstract, directly checked in primary XML and PMC text. Results 3.1 uses rejuvenation for suppression of mating in mature cells: that maturation-state reset alone is outside this functional trait. Results 3.2 reports recovery of old-cell mating activity after transformation. Figure 6C measures total cell counts over four days, not direct division times, and lacks a young-cell growth comparator. Engineered treatment is not a natural canonical taxon example; inferred chemistry is not a proven mechanism.

    +

    Haga 2023, PMID:36677375, PMC9865852; scientific abstract, directly checked in primary XML and PMC text. Results 3.1 uses rejuvenation for suppression of mating in mature cells: that maturation-state reset alone is outside this functional trait. Results 3.2 reports recovery of old-cell mating activity after transformation. Figure 6C measures total cell counts over four days, not direct division times, and lacks a young-cell growth comparator. Engineered treatment is not a natural canonical taxon example; inferred chemistry is not a proven mechanism.

  • DOI:10.1016/j.isci.2022.103765
    Some cells rejuvenated immediately, even after extended starvation, but others only restarted growth after a delay or not at all.
    -

    Cesar et al. 2022, PMID:35243217, PMC8858994; scientific abstract, directly checked against MED and primary XML. Boundary evidence: culture duration during stationary phase is not individual replicative age. Immediate regrowth can reflect preserved function, not recovery from a demonstrated deficit. Regrowth classes use area-derived growth rates; nongrowth during the observation window is not proof of irreversible death. Results 2.1 and 2.3, Discussion, limitations and classification methods were read; figures and raw data were not independently assessed.

    +

    Cesar et al. 2022, PMID:35243217, PMC8858994; scientific abstract, directly checked against MED and primary XML. Boundary evidence: culture duration during stationary phase is not individual replicative age. Immediate regrowth can reflect preserved function, not recovery from a demonstrated deficit. Regrowth classes use area-derived growth rates; nongrowth during the observation window is not proof of irreversible death. Results 2.1 and 2.3, Discussion, limitations and classification methods were read; figures and raw data were not independently assessed.

    • @@ -131,7 +132,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -333,7 +334,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -362,12 +372,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-12 12:49 UTC diff --git a/pages/traits/physiology/chemoautolithotrophic.html b/pages/traits/physiology/chemoautolithotrophic.html index 5c1221aa249..f2030b258f2 100644 --- a/pages/traits/physiology/chemoautolithotrophic.html +++ b/pages/traits/physiology/chemoautolithotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -125,7 +126,7 @@

    Edge evidence

    example of inorganic electron donor METPO:1007502 - rdfs:subClassOf + rdfs:subClassOf

    Ammonia is an inorganic donor in chemolithoautotrophic nitrification.

      @@ -163,7 +164,7 @@

      Edge evidence

      example of inorganic electron donor METPO:1007502 - rdfs:subClassOf + rdfs:subClassOf

      Fe(II) is a representative inorganic electron donor.

        @@ -370,8 +371,8 @@

        Protein and taxon examples

    		 - Nitrosomonas europaea ATCC 19718 -
    NCBITaxon:228410 + Nitrosomonas europaea ATCC 19718 +
    NCBITaxon:228410         		REVIEWED
    @@ -437,7 +438,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • chemoautolithotroph RELATED_SYNONYM · metpo.owl
      • +
    • chemoautolithotroph RELATED_SYNONYM · metpo.owl
    @@ -453,7 +454,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -789,7 +790,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1153,12 +1163,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/chemoautotrophic.html b/pages/traits/physiology/chemoautotrophic.html index d83ebf72d1e..e428ce68c29 100644 --- a/pages/traits/physiology/chemoautotrophic.html +++ b/pages/traits/physiology/chemoautotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -440,8 +441,8 @@

    Protein and taxon examples

    		 - Nitrosomonas europaea ATCC 19718 -
    NCBITaxon:228410 + Nitrosomonas europaea ATCC 19718 +
    NCBITaxon:228410         		REVIEWED
    @@ -507,7 +508,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • chemoautotroph RELATED_SYNONYM · metpo.owl
      • +
    • chemoautotroph RELATED_SYNONYM · metpo.owl
    @@ -523,7 +524,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -868,7 +869,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1232,12 +1242,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/chemoheterotrophic.html b/pages/traits/physiology/chemoheterotrophic.html index 6138e843d92..716e3e7a849 100644 --- a/pages/traits/physiology/chemoheterotrophic.html +++ b/pages/traits/physiology/chemoheterotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -156,7 +157,7 @@

    Edge evidence

    GO:0009056 can proceed through respiration - METPO:1000800 + METPO:1000800

    Organic catabolism can conserve energy through respiration.

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -469,9 +470,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • aerobic_chemo_heterotrophy RELATED_SYNONYM · metpo.owl
      • +
    • aerobic_chemo_heterotrophy RELATED_SYNONYM · metpo.owl
      • -
    • chemoheterotroph RELATED_SYNONYM · metpo.owl
      • +
    • chemoheterotroph RELATED_SYNONYM · metpo.owl
    @@ -487,7 +488,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -820,7 +821,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1184,12 +1194,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 10:46 UTC diff --git a/pages/traits/physiology/chemokinesis.html b/pages/traits/physiology/chemokinesis.html index d5f353c3606..3d2625856d4 100644 --- a/pages/traits/physiology/chemokinesis.html +++ b/pages/traits/physiology/chemokinesis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.1038/ismej.2013.210
    chemokinesis is the ability to change swimming speed in response to a change in chemical concentration.
    -

    Discussion, page 1005, visually checked in the author-hosted published PDF at https://stockerlab.ethz.ch/wp-content/uploads/2015/03/49.-Garren_etal_ISME_2014.pdf. This bacterial usage defines chemokinesis by speed, in contrast to chemotactic directional bias. The two responses can coexist. This citation supports identity; no independent reanalysis of its supplementary assays is claimed.

    +

    Discussion, page 1005, visually checked in the author-hosted published PDF at https://stockerlab.ethz.ch/wp-content/uploads/2015/03/49.-Garren_etal_ISME_2014.pdf. This bacterial usage defines chemokinesis by speed, in contrast to chemotactic directional bias. The two responses can coexist. This citation supports identity; no independent reanalysis of its supplementary assays is claimed.

  • DOI:10.1073/pnas.1602307113
    Chemokinesis was also observed in the absence of a chemical gradient
    -

    SI Text, Chemokinesis, page 3 of 9; full article and SI inspected at https://pmc.ncbi.nlm.nih.gov/articles/PMC4978249/. Figure S5 and its caption were visually checked in the author PDF at https://stockerlab.ethz.ch/wp-content/uploads/2017/05/89._Son_atall.pdf (SI page 7 of 9). The uniform-serine assay supports a speed response without a gradient. Model block removals are in silico mutants, not biological gene deletions. YM4 cells were harvested in late exponential phase and resuspended in TMN motility medium, pH 7.5; Figure S5 uses uniform 5 micromolar serine at 600 mM sodium. YM4 is a laboratory mutant deficient in lateral flagella, as documented separately by DOI:10.7717/peerj.17126; it is retained as qualified experimental evidence, not a natural canonical example.

    +

    SI Text, Chemokinesis, page 3 of 9; full article and SI inspected at https://pmc.ncbi.nlm.nih.gov/articles/PMC4978249/. Figure S5 and its caption were visually checked in the author PDF at https://stockerlab.ethz.ch/wp-content/uploads/2017/05/89._Son_atall.pdf (SI page 7 of 9). The uniform-serine assay supports a speed response without a gradient. Model block removals are in silico mutants, not biological gene deletions. YM4 cells were harvested in late exponential phase and resuspended in TMN motility medium, pH 7.5; Figure S5 uses uniform 5 micromolar serine at 600 mM sodium. YM4 is a laboratory mutant deficient in lateral flagella, as documented separately by DOI:10.7717/peerj.17126; it is retained as qualified experimental evidence, not a natural canonical example.

  • DOI:10.1038/s41396-021-01024-7
    Thus, we hypothesize that the metabolism of mucus substrate stimulates Na+-NQR activity, which in turn enables sustained chemokinesis.
    -

    Discussion, page 3677, visually checked at https://stockerlab.ethz.ch/wp-content/uploads/2022/03/141.-Cherry-Gao_Coral-Muscus.pdf. The plus is superscript in the typeset sodium notation and plain text in extraction. The following sentence requires experimental testing of this hypothesis. Transcript associations do not establish a causal protein pathway; no supplementary gene-level result is curated here.

    +

    Discussion, page 3677, visually checked at https://stockerlab.ethz.ch/wp-content/uploads/2022/03/141.-Cherry-Gao_Coral-Muscus.pdf. The plus is superscript in the typeset sodium notation and plain text in extraction. The following sentence requires experimental testing of this hypothesis. Transcript associations do not establish a causal protein pathway; no supplementary gene-level result is curated here.

  • DOI:10.7717/peerj.17126
    two strains showing defects in the lateral flagellum (VIO5 and YM4)
    -

    Abstract, PMID:38515459. This primary genomic study identifies YM4 as a laboratory strain with defective lateral flagellation. It supplies strain provenance, not a chemokinesis measurement. The Son observation must not be generalized to unperturbed Vibrio alginolyticus. Canonical examples are deferred pending separate verification of a natural exemplar (issue #1653).

    +

    Abstract, PMID:38515459. This primary genomic study identifies YM4 as a laboratory strain with defective lateral flagellation. It supplies strain provenance, not a chemokinesis measurement. The Son observation must not be generalized to unperturbed Vibrio alginolyticus. Canonical examples are deferred pending separate verification of a natural exemplar (issue #1653).

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -321,7 +322,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -350,12 +360,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 04:09 UTC diff --git a/pages/traits/physiology/chemolithoautotrophic.html b/pages/traits/physiology/chemolithoautotrophic.html index 1505bbc7167..18d21ce9560 100644 --- a/pages/traits/physiology/chemolithoautotrophic.html +++ b/pages/traits/physiology/chemolithoautotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -383,8 +384,8 @@

    Protein and taxon examples

    		 - Acidithiobacillus ferrooxidans -
    NCBITaxon:920 + Acidithiobacillus ferrooxidans +
    NCBITaxon:920         		REVIEWED
    @@ -450,7 +451,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • chemolithoautotroph RELATED_SYNONYM · metpo.owl
      • +
    • chemolithoautotroph RELATED_SYNONYM · metpo.owl
    @@ -466,7 +467,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -793,7 +794,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Replaced elliptical record-level evidence[0].snippet on DOI:10.1146/annurev.micro.52.1.191 with contiguous verbatim snippet already present on causal_graphs[0].edges[5].evidence[0] and parent record chemoautotrophic.yaml evidence[0] (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-008 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Replaced elliptical record-level evidence[0].snippet on DOI:10.1146/annurev.micro.52.1.191 with contiguous verbatim snippet already present on causal_graphs[0].edges[5].evidence[0] and parent record chemoautotrophic.yaml evidence[0] (Cycle 4 Stage 5 remediation of F-C4S4-DEF-SRC-008 in group G-C4S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -826,7 +827,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1190,12 +1200,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 12:55 UTC diff --git a/pages/traits/physiology/chemolithoheterotrophic.html b/pages/traits/physiology/chemolithoheterotrophic.html index 07f6cf4e74b..ae36c428f6c 100644 --- a/pages/traits/physiology/chemolithoheterotrophic.html +++ b/pages/traits/physiology/chemolithoheterotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -119,7 +120,7 @@

    Edge evidence

    example of inorganic chemical donor - rdfs:subClassOf + rdfs:subClassOf

    Fe(II) is an experimentally supported inorganic donor for chemolithoheterotrophy.

      @@ -138,7 +139,7 @@

      Edge evidence

      example of inorganic chemical donor - rdfs:subClassOf + rdfs:subClassOf

      Reduced sulfur compounds can fuel chemolithoheterotrophic metabolism.

        @@ -157,7 +158,7 @@

        Edge evidence

        example of inorganic chemical donor - rdfs:subClassOf + rdfs:subClassOf

        H2 is a reduced inorganic donor that can supplement energy during organic-carbon-supported growth.

          @@ -385,7 +386,7 @@

          Edge evidence

          example of reduced sulfur compound - rdfs:subClassOf + rdfs:subClassOf

          Thiosulfate is a reduced sulfur electron donor oxidized during chemolithomixotrophic growth.

            @@ -440,8 +441,8 @@

            Protein and taxon examples

    		 - Sphingopyxis alaskensis RB2256 -
    NCBITaxon:317655 + Sphingopyxis alaskensis RB2256 +
    NCBITaxon:317655         		UNREVIEWED
    @@ -507,7 +508,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • chemolithoheterotroph RELATED_SYNONYM · metpo.owl
      • +
    • chemolithoheterotroph RELATED_SYNONYM · metpo.owl
    @@ -523,7 +524,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -862,7 +863,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1226,12 +1236,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 11:46 UTC diff --git a/pages/traits/physiology/chemolithotrophic.html b/pages/traits/physiology/chemolithotrophic.html index c3a888cb6b8..03e3d2cf1af 100644 --- a/pages/traits/physiology/chemolithotrophic.html +++ b/pages/traits/physiology/chemolithotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -296,7 +297,7 @@

    Edge evidence

    example of inorganic chemical electron donor - rdfs:subClassOf + rdfs:subClassOf

    Ammonia is the energy-yielding inorganic substrate for chemolithotrophic ammonia oxidizers.

      @@ -334,7 +335,7 @@

      Edge evidence

      example of inorganic chemical electron donor - rdfs:subClassOf + rdfs:subClassOf

      Thiosulfate can serve as the sole inorganic electron source for chemolithotrophic growth.

        @@ -389,8 +390,8 @@

        Protein and taxon examples

    		 - Nitrosomonas europaea ATCC 19718 -
    NCBITaxon:228410 + Nitrosomonas europaea ATCC 19718 +
    NCBITaxon:228410         		REVIEWED
    @@ -456,7 +457,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • chemolithotroph RELATED_SYNONYM · metpo.owl
      • +
    • chemolithotroph RELATED_SYNONYM · metpo.owl
    @@ -472,7 +473,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -853,7 +854,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1217,12 +1227,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/chemoorganoheterotrophic.html b/pages/traits/physiology/chemoorganoheterotrophic.html index dcd4bf97082..c8ff2a02119 100644 --- a/pages/traits/physiology/chemoorganoheterotrophic.html +++ b/pages/traits/physiology/chemoorganoheterotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -507,7 +508,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • chemoorganoheterotroph RELATED_SYNONYM · metpo.owl
      • +
    • chemoorganoheterotroph RELATED_SYNONYM · metpo.owl
    @@ -523,7 +524,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -877,7 +878,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1241,12 +1251,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/chemoorganotrophic.html b/pages/traits/physiology/chemoorganotrophic.html index a29d68efd13..3f07f2d72e8 100644 --- a/pages/traits/physiology/chemoorganotrophic.html +++ b/pages/traits/physiology/chemoorganotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -459,8 +460,8 @@

    Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -526,7 +527,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • chemoorganotroph RELATED_SYNONYM · metpo.owl
      • +
    • chemoorganotroph RELATED_SYNONYM · metpo.owl
    @@ -542,7 +543,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -911,7 +912,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1275,12 +1285,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/chemotaxis.html b/pages/traits/physiology/chemotaxis.html index 052af14cacd..131ac29e632 100644 --- a/pages/traits/physiology/chemotaxis.html +++ b/pages/traits/physiology/chemotaxis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    GO:0006935 confers chemotaxis - traitmech:000086 + traitmech:000086 METPO:2007700

    The chemotaxis signaling process realizes the trait.

      @@ -326,8 +327,8 @@

      Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -393,9 +394,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -418,7 +419,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -718,7 +719,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1082,12 +1092,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/chemotrophic.html b/pages/traits/physiology/chemotrophic.html index 5f5274a7bbe..acb2ec7fe88 100644 --- a/pages/traits/physiology/chemotrophic.html +++ b/pages/traits/physiology/chemotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -119,7 +120,7 @@

    Edge evidence

    example of reduced chemical substrate - rdfs:subClassOf + rdfs:subClassOf

    Inorganic substrates are chemical energy sources in lithotrophy.

      @@ -138,7 +139,7 @@

      Edge evidence

      example of reduced chemical substrate - rdfs:subClassOf + rdfs:subClassOf

      Organic substrates are chemical energy sources in organotrophy.

        @@ -383,8 +384,8 @@

        Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -450,9 +451,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • TT_chemotroph RELATED_SYNONYM · metpo.owl
      • +
    • TT_chemotroph RELATED_SYNONYM · metpo.owl
      • -
    • chemotroph RELATED_SYNONYM · metpo.owl
      • +
    • chemotroph RELATED_SYNONYM · metpo.owl
    @@ -468,7 +469,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -762,7 +763,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1126,12 +1136,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/chemotropism.html b/pages/traits/physiology/chemotropism.html index 98118656b48..d4fce1c9692 100644 --- a/pages/traits/physiology/chemotropism.html +++ b/pages/traits/physiology/chemotropism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1371/journal.pbio.3002726
    Notably, many hyphae changed direction near the boundary, opting to remain in the pH 6.5 layer (Fig 3B).
    -

    Results, Chemotropism to low pH; exact span in Europe PMC full text PMC11288418 (PMID:39078817), published 2024-07-30. The compared layers are pH 6.5 and 8. Figure 3 was visually inspected: tip trajectories support directional growth, not only greater biomass. Main Results and the primary abstract describe lower-pH preference in these comparisons; the separate summary abstract's acidic-pH avoidance wording conflicts with them. Growth inhibition at pH 3 and carbon-source growth differences confound those comparisons. The nitrogen Results separately report negative chemotropism. S1 Table (10.1371/journal.pbio.3002726.s002), inspected as PDF text and image, lists engineered backgrounds including TH122; no natural canonical strain is inferred. Other supplements and movies were not inspected.

    +

    Results, Chemotropism to low pH; exact span in Europe PMC full text PMC11288418 (PMID:39078817), published 2024-07-30. The compared layers are pH 6.5 and 8. Figure 3 was visually inspected: tip trajectories support directional growth, not only greater biomass. Main Results and the primary abstract describe lower-pH preference in these comparisons; the separate summary abstract's acidic-pH avoidance wording conflicts with them. Growth inhibition at pH 3 and carbon-source growth differences confound those comparisons. The nitrogen Results separately report negative chemotropism. S1 Table (10.1371/journal.pbio.3002726.s002), inspected as PDF text and image, lists engineered backgrounds including TH122; no natural canonical strain is inferred. Other supplements and movies were not inspected.

  • DOI:10.1038/s41598-020-67597-z
    They respond to changes in their environment by directing hyphal growth towards or away from a range of chemical stimuli.
    -

    Introduction, first paragraph; They refers to filamentous fungi. Exact span in Europe PMC full text PMC7329813 (PMID:32612109). This supports the polarity-neutral growth definition. The first Results subsection reports directional growth of Fusarium graminearum towards methionine, while rapid growth with other tested nitrogen compounds was not significantly directional. Table 1 identifies GZ-3639 as wild type, but natural provenance and an exact NCBI identity were not independently verified. Figures and supplements were not visually inspected. The paper's receptor and infection findings are not transferred into a universal chemotropism mechanism or canonical example.

    +

    Introduction, first paragraph; They refers to filamentous fungi. Exact span in Europe PMC full text PMC7329813 (PMID:32612109). This supports the polarity-neutral growth definition. The first Results subsection reports directional growth of Fusarium graminearum towards methionine, while rapid growth with other tested nitrogen compounds was not significantly directional. Table 1 identifies GZ-3639 as wild type, but natural provenance and an exact NCBI identity were not independently verified. Figures and supplements were not visually inspected. The paper's receptor and infection findings are not transferred into a universal chemotropism mechanism or canonical example.

    • @@ -124,7 +125,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -288,7 +289,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed chemotropism trait -

      Added traitmech:000597 as PROPOSED PHYSIOLOGY with DOI:10.1371/journal.pbio.3002726 and DOI:10.1038/s41598-020-67597-z, full-text snippets, and METPO v474 reservation METPO:1055100. Ignored-and-hidden searches and structured OWL review distinguish chemical-directed polarized growth from chemotaxis and other tropisms. Inspected Aspergillus Figure 3 and S1 strain table; retained contradictory summary wording and growth-rate confounds, deferring natural canonical taxa and protein-resolved mechanisms. Raw source matching caught a missing figure pointer in the uncommitted draft quote; the guarded writer restores it and preserves both curation events. Updated add-trait guidance on directional-growth evidence and conflicting summaries.

    +

    Added traitmech:000597 as PROPOSED PHYSIOLOGY with DOI:10.1371/journal.pbio.3002726 and DOI:10.1038/s41598-020-67597-z, full-text snippets, and METPO v474 reservation METPO:1055100. Ignored-and-hidden searches and structured OWL review distinguish chemical-directed polarized growth from chemotaxis and other tropisms. Inspected Aspergillus Figure 3 and S1 strain table; retained contradictory summary wording and growth-rate confounds, deferring natural canonical taxa and protein-resolved mechanisms. Raw source matching caught a missing figure pointer in the uncommitted draft quote; the guarded writer restores it and preserves both curation events. Updated add-trait guidance on directional-growth evidence and conflicting summaries.

    • Read this curation session @@ -320,7 +321,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -349,12 +359,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 13:44 UTC diff --git a/pages/traits/physiology/coagulase_activity.html b/pages/traits/physiology/coagulase_activity.html index 5c8e17ee9ee..1c8502601e0 100644 --- a/pages/traits/physiology/coagulase_activity.html +++ b/pages/traits/physiology/coagulase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -76,7 +77,7 @@

    Trait evidence (2)

    Staphylococcal coagulase prothrombin activation and fibrinogen cleavage

    Evidence-backed physiological mechanism linking secreted staphylocoagulases (Coa and vWbp) to non-proteolytic prothrombin activation and fibrinogen cleavage.

    -

    MECHANISTIC · Protein-anchored mechanism backed by DOI:10.1159/000333447 and DOI:10.1371/journal.ppat.1001036, with reviewed Staphylococcus aureus staphylocoagulase Coa (UniProtKB:P07767) curated on the InterPro:IPR019553 coagulase node.

    +

    MECHANISTIC · Protein-anchored mechanism backed by DOI:10.1159/000333447 and DOI:10.1371/journal.ppat.1001036, with reviewed Staphylococcus aureus staphylocoagulase Coa (UniProtKB:P07767) curated on the InterPro:IPR019553 coagulase node.

    Loading graph…

    @@ -155,8 +156,8 @@

    Protein and taxon examples

    		 - Staphylococcus aureus -
    NCBITaxon:1280 + Staphylococcus aureus +
    NCBITaxon:1280         		REVIEWED
    @@ -233,9 +234,9 @@

    Children (2)

    Synonyms (2)

      -
    • coagulase test EXACT_SYNONYM · metpo.owl
      • +
    • coagulase test EXACT_SYNONYM · metpo.owl
      • -
    • coagulase-positive RELATED_SYNONYM · DOI:10.1159/000333447
      • +
    • coagulase-positive RELATED_SYNONYM · DOI:10.1159/000333447
    @@ -251,7 +252,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -404,7 +405,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    SEEDED
    +
    SEEDED + + +
    + What this status means +

    Imported verbatim from metpo.owl; not yet curator-reviewed.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -768,12 +778,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 21:12 UTC diff --git a/pages/traits/physiology/coccolith_production.html b/pages/traits/physiology/coccolith_production.html index bbeebb3d581..baf39128817 100644 --- a/pages/traits/physiology/coccolith_production.html +++ b/pages/traits/physiology/coccolith_production.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1038/ncomms11228
    Coccoliths are calcitic particles produced inside the cells of unicellular marine algae known as coccolithophores.
    -

    Sviben et al. 2016, PMID:27075521, PMC4834641. Scientific Abstract and full article text directly read in Europe PMC XML on 2026-10-10; actual Figures 1 and 3 inspected. Calcium resupply to depleted AWI1516 cultures supports new calcite formation; imaging distinguishes forming coccoliths from a separate calcium-rich compartment. Its necessity, direct precursor identity and transfer route are not established. Figure 3's detector-panel caption repeats c in two pairs; no panel-specific detector assignment is imported. Other figures and supplements were not visually inspected. Historical Emiliania huxleyi is retained as the source name, not a current taxonomic or culture-collection phenotype assertion.

    +

    Sviben et al. 2016, PMID:27075521, PMC4834641. Scientific Abstract and full article text directly read in Europe PMC XML on 2026-10-10; actual Figures 1 and 3 inspected. Calcium resupply to depleted AWI1516 cultures supports new calcite formation; imaging distinguishes forming coccoliths from a separate calcium-rich compartment. Its necessity, direct precursor identity and transfer route are not established. Figure 3's detector-panel caption repeats c in two pairs; no panel-specific detector assignment is imported. Other figures and supplements were not visually inspected. Historical Emiliania huxleyi is retained as the source name, not a current taxonomic or culture-collection phenotype assertion.

  • DOI:10.1111/nph.15272
    The continued production of malformed coccoliths could be observed on successive days
    -

    Walker et al. 2018, PMID:29916209, PMC6175242, Results, time-lapse observations associated with Figure 8. Full article text and actual Figures 5 and 8 directly inspected on 2026-10-10; supplements and movies unread. This passage concerns Ge-treated Coccolithus braarudii PLY182g, not normal morphology. Production persists despite defective coccosphere integrity. Growth responses differ from the assayed E. huxleyi CCMP1516; neither growth dependence nor photosynthetic benefit is generalized. Preserve source discrepancies: Methods time-lapse stage 17 C versus Figure 5's 16 C; Methods/Results HEDP 50 micromolar versus Figure 1's 5 micromolar; Results low-Si threshold below 0.2 micromolar versus Discussion below 0.1. No unqualified quantitative claim depends on choosing between them.

    +

    Walker et al. 2018, PMID:29916209, PMC6175242, Results, time-lapse observations associated with Figure 8. Full article text and actual Figures 5 and 8 directly inspected on 2026-10-10; supplements and movies unread. This passage concerns Ge-treated Coccolithus braarudii PLY182g, not normal morphology. Production persists despite defective coccosphere integrity. Growth responses differ from the assayed E. huxleyi CCMP1516; neither growth dependence nor photosynthetic benefit is generalized. Preserve source discrepancies: Methods time-lapse stage 17 C versus Figure 5's 16 C; Methods/Results HEDP 50 micromolar versus Figure 1's 5 micromolar; Results low-Si threshold below 0.2 micromolar versus Discussion below 0.1. No unqualified quantitative claim depends on choosing between them.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    No canonical examples are assigned pending joint strain-provenance and current-taxonomy verification. Skeffington et al., DOI:10.1111/jpy.12942, p. 239, explicitly derives calcifying AWI1516 from CCMP1516; this does not make all descendants equivalent. The current collection https://ncma.bigelow.org/CCMP1516, read 2026-10-10, labels it Gephyrocapsa huxleyi and reports lost coccolith production. Keep historical assay observations separate from this current catalog state; loss alone does not establish engineering. PLY182g provenance remains unresolved here. No universal silicon requirement, ploidy restriction, growth dependence or protective function is inferred. Separate mineral deposition, transport, secretion and covering integrity before adding causal edges. A protein mechanism needs direct functional evidence and taxon-paired accessions; sequence features alone are insufficient. Mechanism is deferred, not claimed absent.

    +

    No canonical examples are assigned pending joint strain-provenance and current-taxonomy verification. Skeffington et al., DOI:10.1111/jpy.12942, p. 239, explicitly derives calcifying AWI1516 from CCMP1516; this does not make all descendants equivalent. The current collection https://ncma.bigelow.org/CCMP1516, read 2026-10-10, labels it Gephyrocapsa huxleyi and reports lost coccolith production. Keep historical assay observations separate from this current catalog state; loss alone does not establish engineering. PLY182g provenance remains unresolved here. No universal silicon requirement, ploidy restriction, growth dependence or protective function is inferred. Separate mineral deposition, transport, secretion and covering integrity before adding causal edges. A protein mechanism needs direct functional evidence and taxon-paired accessions; sequence features alone are insufficient. Mechanism is deferred, not claimed absent.

    @@ -279,7 +280,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed coccolith production phenotype -

      Added traitmech:000689 as PHYSIOLOGY/CLASS/PROPOSED under phenotype METPO:1000059 through the guarded add_coccolith_production_trait writer and record_curation_event. Two primary DOI citations (10.1038/ncomms11228 and 10.1111/nph.15272) and directly checked short scientific-abstract/Results snippets support production, including malformed elements, distinct from coccosphere integrity. Preserved source condition/caption discrepancies and historical strain limits. DOI:10.1111/jpy.12942 and the current CCMP1516 collection support qualified provenance context only. Left two explicit discussions for broader hierarchy, canonical exemplars and functional protein mechanism; no graph, xref or synonym inferred. Ignored-and-hidden searches across current main and 22 worktrees plus all five paginated open PR heads found no exact duplicate or competing allocation. Reserved full METPO block 1064200-1064299 in proposal v565, only 1064200 populated. Existing records, including protected spore germination, are unchanged. Validation and review results will be reported after execution, not presumed here.

    +

    Added traitmech:000689 as PHYSIOLOGY/CLASS/PROPOSED under phenotype METPO:1000059 through the guarded add_coccolith_production_trait writer and record_curation_event. Two primary DOI citations (10.1038/ncomms11228 and 10.1111/nph.15272) and directly checked short scientific-abstract/Results snippets support production, including malformed elements, distinct from coccosphere integrity. Preserved source condition/caption discrepancies and historical strain limits. DOI:10.1111/jpy.12942 and the current CCMP1516 collection support qualified provenance context only. Left two explicit discussions for broader hierarchy, canonical exemplars and functional protein mechanism; no graph, xref or synonym inferred. Ignored-and-hidden searches across current main and 22 worktrees plus all five paginated open PR heads found no exact duplicate or competing allocation. Reserved full METPO block 1064200-1064299 in proposal v565, only 1064200 populated. Existing records, including protected spore germination, are unchanged. Validation and review results will be reported after execution, not presumed here.

    • Read this curation session
  • @@ -317,7 +318,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -346,12 +356,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-10 08:07 UTC diff --git a/pages/traits/physiology/cold_shock_response.html b/pages/traits/physiology/cold_shock_response.html index dbe51406725..6ba655844b2 100644 --- a/pages/traits/physiology/cold_shock_response.html +++ b/pages/traits/physiology/cold_shock_response.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -187,7 +188,7 @@

    Edge evidence

    GO:0006412 confers cold shock response - traitmech:000206 + traitmech:000206 METPO:2007700

    Preservation of translation realizes the RNA-adaptation branch of the cold-shock-response trait.

      @@ -224,8 +225,8 @@

      Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -297,7 +298,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -313,7 +314,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -498,7 +499,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -862,12 +872,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 05:33 UTC diff --git a/pages/traits/physiology/contact_dependent_outer_membrane_exchange.html b/pages/traits/physiology/contact_dependent_outer_membrane_exchange.html index 1de80214915..d5a250e6fda 100644 --- a/pages/traits/physiology/contact_dependent_outer_membrane_exchange.html +++ b/pages/traits/physiology/contact_dependent_outer_membrane_exchange.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.7554/eLife.00868
    transient contacts between two cells are sufficient to transfer OM materials, proteins and lipids, at high efficiency.
    -

    PMID:23898400, PMC3721248. Scientific Abstract span directly read in Europe PMC XML, not the eLife digest. Selected Results s2-1 to s2-4 and Methods s4-1 to s4-4 were read; actual Figures 2 and 4 were visually inspected with their captions. Engineered Myxococcus xanthus DZ2 reporters and DiO assays distinguish OM material transfer from inner-membrane reporter exchange. Contact and traA controls support the observed endpoint. Dye continuity through some tubes does not establish significant protein transfer through them, which was not detected. Membrane fusion is the authors' mechanistic interpretation; not every contact transfers material. Videos and remaining supplementary panels were not inspected.

    +

    PMID:23898400, PMC3721248. Scientific Abstract span directly read in Europe PMC XML, not the eLife digest. Selected Results s2-1 to s2-4 and Methods s4-1 to s4-4 were read; actual Figures 2 and 4 were visually inspected with their captions. Engineered Myxococcus xanthus DZ2 reporters and DiO assays distinguish OM material transfer from inner-membrane reporter exchange. Contact and traA controls support the observed endpoint. Dye continuity through some tubes does not establish significant protein transfer through them, which was not detected. Membrane fusion is the authors' mechanistic interpretation; not every contact transfers material. Videos and remaining supplementary panels were not inspected.

  • DOI:10.1371/journal.pgen.1002626
    By use of a lipophilic fluorescent dye, we also discovered that OM lipids are exchanged.
    -

    PMID:22511878, PMC3325183. Scientific Abstract directly read in Europe PMC XML; Results s2c/s2d and Methods s4a/s4e/s4f also read. Reporter and DiD experiments in M. xanthus support TraA/TraB dependence in donors and recipients under the tested surface-growth conditions. Liquid and nonmotile-pair controls limit inference from dye labeling alone. Similar domain architecture in mxan_4924 did not yield an overt transfer defect when disrupted; sequence resemblance is not sufficient phenotype evidence. Proposed adhesion, fusion and social roles are not all directly established by this study. Actual panels and strain-table provenance remain uninspected.

    +

    PMID:22511878, PMC3325183. Scientific Abstract directly read in Europe PMC XML; Results s2c/s2d and Methods s4a/s4e/s4f also read. Reporter and DiD experiments in M. xanthus support TraA/TraB dependence in donors and recipients under the tested surface-growth conditions. Liquid and nonmotile-pair controls limit inference from dye labeling alone. Similar domain architecture in mxan_4924 did not yield an overt transfer defect when disrupted; sequence resemblance is not sufficient phenotype evidence. Proposed adhesion, fusion and social roles are not all directly established by this study. Actual panels and strain-table provenance remain uninspected.

  • DOI:10.1128/jb.00850-13
    Thus, genetic and environmental conditions that promote OMT production are incongruent with OM exchange.
    -

    PMID:24391054, PMC4011004. Scientific abstract directly retrieved through the Europe PMC core API. Full-text XML retrieval failed, so no full-text or panel verification is claimed. The abstract reports abundant OM tubes in traA/traB mutants and liquid conditions that do not permit transfer. Tube abundance alone is therefore insufficient for this trait; this does not negate the specific dye-conducting connections imaged in 2013. This paper shares investigators with the 2012 study and is not independent-laboratory replication.

    +

    PMID:24391054, PMC4011004. Scientific abstract directly retrieved through the Europe PMC core API. Full-text XML retrieval failed, so no full-text or panel verification is claimed. The abstract reports abundant OM tubes in traA/traB mutants and liquid conditions that do not permit transfer. Tube abundance alone is therefore insufficient for this trait; this does not negate the specific dye-conducting connections imaged in 2013. This paper shares investigators with the 2012 study and is not independent-laboratory replication.

  • DOI:10.1371/journal.pone.0224817
    Collectively, our results suggest that most mechanisms of interference competition and inter-colony kin discrimination in natural populations of myxobacteria do not require OME.
    -

    PMID:31774841, PMC6880969. Scientific Abstract and Results sec012/sec014 directly read in Europe PMC XML. In the tested natural-isolate pairs, traA disruption or the A60 deletion did not remove colony-merger incompatibility. This is a boundary on ecological-function claims, not evidence that membrane exchange never occurs. The GJV1 control uses swarm inhibition as an inferred OME-dependent toxin readout, not direct fluorescent membrane transfer in every isolate. The directly read correction DOI:10.1371/journal.pone.0228697 (PMID:31999808, PMC6991971) concerns Table 3 typesetting; no Table 3 numerical claim is used here. Actual panels were not visually inspected.

    +

    PMID:31774841, PMC6880969. Scientific Abstract and Results sec012/sec014 directly read in Europe PMC XML. In the tested natural-isolate pairs, traA disruption or the A60 deletion did not remove colony-merger incompatibility. This is a boundary on ecological-function claims, not evidence that membrane exchange never occurs. The GJV1 control uses swarm inhibition as an inferred OME-dependent toxin readout, not direct fluorescent membrane transfer in every isolate. The directly read correction DOI:10.1371/journal.pone.0228697 (PMID:31999808, PMC6991971) concerns Table 3 typesetting; no Table 3 numerical claim is used here. Actual panels were not visually inspected.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 21:02 UTC diff --git a/pages/traits/physiology/copiotrophic.html b/pages/traits/physiology/copiotrophic.html index 5db99214b1c..d6d00ef814b 100644 --- a/pages/traits/physiology/copiotrophic.html +++ b/pages/traits/physiology/copiotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -374,7 +375,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • copiotroph RELATED_SYNONYM · metpo.owl
      • +
    • copiotroph RELATED_SYNONYM · metpo.owl
    @@ -390,7 +391,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -675,7 +676,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1039,12 +1049,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-24 21:00 UTC diff --git a/pages/traits/physiology/cue_triggered_environmental_anticipation.html b/pages/traits/physiology/cue_triggered_environmental_anticipation.html index 2b368a2982d..46479d19512 100644 --- a/pages/traits/physiology/cue_triggered_environmental_anticipation.html +++ b/pages/traits/physiology/cue_triggered_environmental_anticipation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1038/nature08112
    early stimuli pre-induce genes that would be needed for later ones, yet later stimuli only induce genes needed to cope with them.
    -

    Mitchell et al. 2009, PMID:19536156; scientific abstract, checked against publisher and source-qualified MED text. Main Figures 2-3 and supplementary Figures 3 and 6 were visually inspected, with their relevant Methods and control explanations. MG1655 sugar-switch assays distinguish early induction from subsequent growth; glycerol normalization and residual-sugar controls matter. Loss of the association in laboratory-evolved strains concerns selection across generations, not cognitive learning. Ecological explanations remain author interpretations. Not all raw data were reanalyzed.

    +

    Mitchell et al. 2009, PMID:19536156; scientific abstract, checked against publisher and source-qualified MED text. Main Figures 2-3 and supplementary Figures 3 and 6 were visually inspected, with their relevant Methods and control explanations. MG1655 sugar-switch assays distinguish early induction from subsequent growth; glycerol normalization and residual-sugar controls matter. Loss of the association in laboratory-evolved strains concerns selection across generations, not cognitive learning. Ecological explanations remain author interpretations. Not all raw data were reanalyzed.

  • DOI:10.1038/nmicrobiol.2017.84
    Here, we identify a metabolic adaptation that is triggered upon entry into hypoxia-induced quiescence but facilitates subsequent cell cycle re-entry.
    -

    Eoh et al. 2017, PMID:28530656, PMC5540153; scientific abstract, checked against publisher and source-qualified MED text. The abstract and qualitative main-text framing support metabolically encoded preparation, with hypoxia preceding re-aeration in the studied Mycobacterium tuberculosis system. This is not evidence for a universal transcriptional mechanism or an in-vivo demonstration of anticipation. Figures, supplements and raw data were not independently assessed; no molecular causal edges are asserted.

    +

    Eoh et al. 2017, PMID:28530656, PMC5540153; scientific abstract, checked against publisher and source-qualified MED text. The abstract and qualitative main-text framing support metabolically encoded preparation, with hypoxia preceding re-aeration in the studied Mycobacterium tuberculosis system. This is not evidence for a universal transcriptional mechanism or an in-vivo demonstration of anticipation. Figures, supplements and raw data were not independently assessed; no molecular causal edges are asserted.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -239,7 +240,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    No canonical_examples, causal_graphs, exact synonyms or xrefs are asserted. The studies do not establish a uniform species-wide phenotype or a common protein mechanism; strain provenance and authority-resolved taxa require further review. Source-qualified MED, Crossref and visible publisher notice links were checked on 2026-10-12; their commentary/review links are not corrections or independent experiments. No correction or retraction was exposed for the two retained papers in these bounded checks. The separate Tagkopoulos 2008 lead (DOI:10.1126/science.1154456) is not counted evidence: its main PMC text was readable, but the indexed 9 June 2008 supplement correction could not be directly inspected. Broad environmental anticipation and adaptive prediction are not assumed exactly equivalent to this qualified class. No exact candidate was found in the pinned/current METPO RDF and ignored/hidden novelty searches; the pinned ontology remains unchanged.

    +

    No canonical_examples, causal_graphs, exact synonyms or xrefs are asserted. The studies do not establish a uniform species-wide phenotype or a common protein mechanism; strain provenance and authority-resolved taxa require further review. Source-qualified MED, Crossref and visible publisher notice links were checked on 2026-10-12; their commentary/review links are not corrections or independent experiments. No correction or retraction was exposed for the two retained papers in these bounded checks. The separate Tagkopoulos 2008 lead (DOI:10.1126/science.1154456) is not counted evidence: its main PMC text was readable, but the indexed 9 June 2008 supplement correction could not be directly inspected. Broad environmental anticipation and adaptive prediction are not assumed exactly equivalent to this qualified class. No exact candidate was found in the pinned/current METPO RDF and ignored/hidden novelty searches; the pinned ontology remains unchanged.

    @@ -271,7 +272,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add cue-triggered environmental anticipation -

      Added traitmech:000707 as a PROPOSED physiological phenotype under METPO:1000059 with primary DOI:10.1038/nature08112 and DOI:10.1038/nmicrobiol.2017.84 evidence and directly checked scientific-abstract snippets. Preserved cue-specific scope and explicit hierarchy, strain-provenance, mechanism and source-access limits in two OPEN discussions. Added guarded writer, tests and companion v583 METPO proposal after ignored/hidden worktree, current ontology and pending-PR reservation checks. No existing TraitRecord was changed; canonical examples, causal graphs and exact mappings are unasserted. Validation outcomes are recorded in the subsequent structured review and PR.

    +

    Added traitmech:000707 as a PROPOSED physiological phenotype under METPO:1000059 with primary DOI:10.1038/nature08112 and DOI:10.1038/nmicrobiol.2017.84 evidence and directly checked scientific-abstract snippets. Preserved cue-specific scope and explicit hierarchy, strain-provenance, mechanism and source-access limits in two OPEN discussions. Added guarded writer, tests and companion v583 METPO proposal after ignored/hidden worktree, current ontology and pending-PR reservation checks. No existing TraitRecord was changed; canonical examples, causal graphs and exact mappings are unasserted. Validation outcomes are recorded in the subsequent structured review and PR.

    • Read this curation session @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-12 05:09 UTC diff --git a/pages/traits/physiology/cystine_arylamidase_activity.html b/pages/traits/physiology/cystine_arylamidase_activity.html index 9d79b9c2e98..1ccb4ca2df8 100644 --- a/pages/traits/physiology/cystine_arylamidase_activity.html +++ b/pages/traits/physiology/cystine_arylamidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -351,7 +352,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -380,12 +390,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/cytogamy.html b/pages/traits/physiology/cytogamy.html index 7fe16a26b64..74c2d5b1dad 100644 --- a/pages/traits/physiology/cytogamy.html +++ b/pages/traits/physiology/cytogamy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (3)

    DOI:10.1017/S0016672300010740
    Cytogamy is a process of internal self-fertilization in animals which appear to conjugate, but which in fact do not exchange nuclei
    -

    Nobili and Luporini (1967), PMID:4964874, p.39 parenthetical before the Wichterman citation, checked in the typeset PDF. This directly read definition supports paired-cell internal self-fertilization without nuclear exchange. The surrounding Results and Table 2 offer cytogamy as an explanation for three mating-type outlier clones; they do not directly demonstrate cytogamy in those clones. The paper's primary experiments concern autogamy in Euplotes minuta. Do not count this terminology passage as independent experimental replication or turn its proposed explanation into a canonical taxon example. The cited 1940 original was not read beyond bibliographic metadata.

    +

    Nobili and Luporini (1967), PMID:4964874, p.39 parenthetical before the Wichterman citation, checked in the typeset PDF. This directly read definition supports paired-cell internal self-fertilization without nuclear exchange. The surrounding Results and Table 2 offer cytogamy as an explanation for three mating-type outlier clones; they do not directly demonstrate cytogamy in those clones. The paper's primary experiments concern autogamy in Euplotes minuta. Do not count this terminology passage as independent experimental replication or turn its proposed explanation into a canonical taxon example. The cited 1940 original was not read beyond bibliographic metadata.

  • @@ -67,7 +68,7 @@

    Trait evidence (3)

    DOI:10.1093/genetics/91.4.657
    cytogamy generates exconjugant clones that derive their entire genetic information from a single meiotic product of their cytoplasmic parent.
    -

    Orias and Hamilton (1979), PMID:17248904, PMC1216858, scientific abstract clause after By analogy to Paramecium, directly checked in Europe PMC core metadata and NCBI PMC EFetch front-matter XML. The abstract reports hyperosmotic-shock-induced cytogamy in tested Tetrahymena thermophila strains and high fertility in most progeny. Its whole-genome-homozygote interpretation is source-specific, not a universal definition requirement or a genome-sequencing result established here. Other rare transmission abnormalities were not characterized in that abstract. The full text, Methods, actual figures and tables remain unread: PMC EFetch withholds body XML, and attempted public PDF retrieval did not yield a readable PDF. Strain provenance is unresolved; no natural canonical example or protein-level causal mechanism is inferred from this abstract.

    +

    Orias and Hamilton (1979), PMID:17248904, PMC1216858, scientific abstract clause after By analogy to Paramecium, directly checked in Europe PMC core metadata and NCBI PMC EFetch front-matter XML. The abstract reports hyperosmotic-shock-induced cytogamy in tested Tetrahymena thermophila strains and high fertility in most progeny. Its whole-genome-homozygote interpretation is source-specific, not a universal definition requirement or a genome-sequencing result established here. Other rare transmission abnormalities were not characterized in that abstract. The full text, Methods, actual figures and tables remain unread: PMC EFetch withholds body XML, and attempted public PDF retrieval did not yield a readable PDF. Strain provenance is unresolved; no natural canonical example or protein-level causal mechanism is inferred from this abstract.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -245,7 +246,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    The 1967 definitional passage is not a direct cytogamy experiment, the 1958 observation is tentative, and the 1979 evidence here is limited to its scientific abstract. Retrieve the original primary study DOI:10.1002/jmor.1050660303 (Wichterman, 1940) and the remaining experimental material before stronger cytological or natural-strain claims. That 1940 DOI is a metadata-verified research lead, not counted trait evidence. No canonical example is assigned from unresolved provenance or tentative marker explanations. Induced transmission outcomes do not identify a molecular causal pathway; graphs and protein accessions remain deferred. Retain actual snippet-resolver outcomes separately from direct source checks.

    +

    The 1967 definitional passage is not a direct cytogamy experiment, the 1958 observation is tentative, and the 1979 evidence here is limited to its scientific abstract. Retrieve the original primary study DOI:10.1002/jmor.1050660303 (Wichterman, 1940) and the remaining experimental material before stronger cytological or natural-strain claims. That 1940 DOI is a metadata-verified research lead, not counted trait evidence. No canonical example is assigned from unresolved provenance or tentative marker explanations. Induced transmission outcomes do not identify a molecular causal pathway; graphs and protein accessions remain deferred. Retain actual snippet-resolver outcomes separately from direct source checks.

    @@ -289,7 +290,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add paired-cell cytogamy with qualified primary-source evidence -

      Added traitmech:000623 with definition authority DOI:10.1017/S0016672300010740 and scientific-abstract evidence DOI:10.1111/j.1550-7408.1958.tb02567.x and DOI:10.1093/genetics/91.4.657. Three contiguous snippets distinguish terminology, tentative cytology and hyperosmotic-induced outcomes. Whole-repository ignored-and-hidden and concurrent proposal checks preceded reservation of METPO:1057600 in v499. Kept phenotype parent, explicit broader double-autogamy usage, source access limits, and deferred canonical examples, mappings and molecular graphs. Writer dry run and 21 focused new/neighbor tests passed before application; broader validation follows.

    +

    Added traitmech:000623 with definition authority DOI:10.1017/S0016672300010740 and scientific-abstract evidence DOI:10.1111/j.1550-7408.1958.tb02567.x and DOI:10.1093/genetics/91.4.657. Three contiguous snippets distinguish terminology, tentative cytology and hyperosmotic-induced outcomes. Whole-repository ignored-and-hidden and concurrent proposal checks preceded reservation of METPO:1057600 in v499. Kept phenotype parent, explicit broader double-autogamy usage, source access limits, and deferred canonical examples, mappings and molecular graphs. Writer dry run and 21 focused new/neighbor tests passed before application; broader validation follows.

    • Read this curation session
  • @@ -333,7 +334,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -362,12 +372,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 18:22 UTC diff --git a/pages/traits/physiology/diatom_frustule_production.html b/pages/traits/physiology/diatom_frustule_production.html index 3c057c3d668..d41414f480f 100644 --- a/pages/traits/physiology/diatom_frustule_production.html +++ b/pages/traits/physiology/diatom_frustule_production.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1007/s00709-017-1199-4
    The basic stages of frustule morphogenesis characteristic of raphid pennate diatoms have been traced
    -

    Bedoshvili et al., journal issue May 2018, online 2017-12-21, PMID:29270874. Scientific Abstract directly read at https://pubmed.ncbi.nlm.nih.gov/29270874/ and in Europe PMC CORE on 2026-10-10 using EXT_ID:29270874 AND SRC:MED; exact ID, source, title and DOI checked together. The abstract defines frustule components as silica valves and girdle bands and reports microscopy of morphogenesis in Encyonema ventricosum under the source name. This supports formation, not just an isolated shell's presence. Cytoskeletal proximity is not functional necessity. Full text, Methods, actual figures and supplements were not inspected; no canonical taxon or universal membrane-release mechanism is inferred.

    +

    Bedoshvili et al., journal issue May 2018, online 2017-12-21, PMID:29270874. Scientific Abstract directly read at https://pubmed.ncbi.nlm.nih.gov/29270874/ and in Europe PMC CORE on 2026-10-10 using EXT_ID:29270874 AND SRC:MED; exact ID, source, title and DOI checked together. The abstract defines frustule components as silica valves and girdle bands and reports microscopy of morphogenesis in Encyonema ventricosum under the source name. This supports formation, not just an isolated shell's presence. Cytoskeletal proximity is not functional necessity. Full text, Methods, actual figures and supplements were not inspected; no canonical taxon or universal membrane-release mechanism is inferred.

  • DOI:10.1038/s41467-024-52211-x
    A diatom cell wall consists of two types of building blocks: two plate-shaped valves and several ring-shaped girdle bands.
    -

    Aram et al. 2024, PMID:39251596, PMC11385223, Introduction. Scientific Abstract, Introduction, Results, Discussion and Methods directly read in official Europe PMC full-text XML on 2026-10-10; actual Figure 2 inspected, other actual figures and supplements unread. Source-qualified CORE lookup EXT_ID:39251596 AND SRC:MED confirmed ID, source, title and DOI. Silicon-starved CCMP1335 cultures were resupplied and imaged during valve formation. Figure 2 orders different cells by inferred maturation, not a live-cell time series. The paper retains historical Thalassiosira pseudonana naming while noting Cyclotella nana; this is not a current taxonomy assignment. Structural correlations support a membrane-mold hypothesis, not proven contact-site function or a universal molecular mechanism. The quote defines wall elements; the Results provide the production observations.

    +

    Aram et al. 2024, PMID:39251596, PMC11385223, Introduction. Scientific Abstract, Introduction, Results, Discussion and Methods directly read in official Europe PMC full-text XML on 2026-10-10; actual Figure 2 inspected, other actual figures and supplements unread. Source-qualified CORE lookup EXT_ID:39251596 AND SRC:MED confirmed ID, source, title and DOI. Silicon-starved CCMP1335 cultures were resupplied and imaged during valve formation. Figure 2 orders different cells by inferred maturation, not a live-cell time series. The paper retains historical Thalassiosira pseudonana naming while noting Cyclotella nana; this is not a current taxonomy assignment. Structural correlations support a membrane-mold hypothesis, not proven contact-site function or a universal molecular mechanism. The quote defines wall elements; the Results provide the production observations.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -271,7 +272,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add source-bounded diatom frustule production -

      Added traitmech:000691 as a PROPOSED PHYSIOLOGY class beneath biomineralization traitmech:000690. Bedoshvili et al. DOI:10.1007/s00709-017-1199-4 scientific abstract defines frustule components and describes morphogenesis; Aram et al. DOI:10.1038/s41467-024-52211-x Introduction supplies the valve/girdle definition and its Results/Methods support valve formation. Short contiguous snippets checked directly. Aram main scientific sections and actual Figure 2 were inspected; other actual figures/supplements and the Bedoshvili full text remain unread. Reserved local 000691, cohort v567 and METPO block 1064400-1064499 after ignored-and-hidden main/all-worktree/current open-PR checks. Proposal uses released phenotype as ancestor and explicitly requests the biomineralization refinement with v566. No canonical taxa, xrefs, synonyms, protein accessions or causal graph added; two open discussions retain scope, provenance and mechanism questions. Existing trait YAMLs are unchanged. Written using the guarded dry-run-default validated writer; focused writer tests and dry run passed before application. Full corpus validation and review outcomes are recorded separately when completed.

    +

    Added traitmech:000691 as a PROPOSED PHYSIOLOGY class beneath biomineralization traitmech:000690. Bedoshvili et al. DOI:10.1007/s00709-017-1199-4 scientific abstract defines frustule components and describes morphogenesis; Aram et al. DOI:10.1038/s41467-024-52211-x Introduction supplies the valve/girdle definition and its Results/Methods support valve formation. Short contiguous snippets checked directly. Aram main scientific sections and actual Figure 2 were inspected; other actual figures/supplements and the Bedoshvili full text remain unread. Reserved local 000691, cohort v567 and METPO block 1064400-1064499 after ignored-and-hidden main/all-worktree/current open-PR checks. Proposal uses released phenotype as ancestor and explicitly requests the biomineralization refinement with v566. No canonical taxa, xrefs, synonyms, protein accessions or causal graph added; two open discussions retain scope, provenance and mechanism questions. Existing trait YAMLs are unchanged. Written using the guarded dry-run-default validated writer; focused writer tests and dry run passed before application. Full corpus validation and review outcomes are recorded separately when completed.

    • Read this curation session @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-10 20:18 UTC diff --git a/pages/traits/physiology/diatom_perizonium_production.html b/pages/traits/physiology/diatom_perizonium_production.html index a786dc329bc..69aff7522b7 100644 --- a/pages/traits/physiology/diatom_perizonium_production.html +++ b/pages/traits/physiology/diatom_perizonium_production.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1371/journal.pone.0272778
    The deposition of the primary TP band became evident when the auxospore center attained a slim and rigid appearance.
    -

    Kaczmarska et al. 2022, PMID:36067191, PMC9447881, Results: Epizonium and perizonium. TP means transverse perizonium. Scientific Abstract, Introduction, Methods, early Results, this subsection and Discussion: Auxospore structure and development read in official Europe PMC XML on 2026-10-10; actual Figure 11 inspected. Other actual figures and S1 Appendix unread. EXT_ID:36067191 AND SRC:MED confirmed ID, title, DOI and scientific abstract. Clone HK328 (= ECT3902) originated from Florida Bay material in 2011; atypical morphology and prolonged cultivation limit canonical assignment. PDMPO labels silica deposited after addition. SEM resolves inner TP/LP bands apart from initial valves; fixed images do not establish live kinetics. Authors leave some epizonium/perizonium layer boundaries uncertain. Scaly-band architecture and proposed shape control are not universal or demonstrated necessities.

    +

    Kaczmarska et al. 2022, PMID:36067191, PMC9447881, Results: Epizonium and perizonium. TP means transverse perizonium. Scientific Abstract, Introduction, Methods, early Results, this subsection and Discussion: Auxospore structure and development read in official Europe PMC XML on 2026-10-10; actual Figure 11 inspected. Other actual figures and S1 Appendix unread. EXT_ID:36067191 AND SRC:MED confirmed ID, title, DOI and scientific abstract. Clone HK328 (= ECT3902) originated from Florida Bay material in 2011; atypical morphology and prolonged cultivation limit canonical assignment. PDMPO labels silica deposited after addition. SEM resolves inner TP/LP bands apart from initial valves; fixed images do not establish live kinetics. Authors leave some epizonium/perizonium layer boundaries uncertain. Scaly-band architecture and proposed shape control are not universal or demonstrated necessities.

  • DOI:10.1371/journal.pone.0181413
    transverse perizonial bands produced all together or in quick succession rather than being added to the auxospore apex one at a time
    -

    Kaczmarska et al. 2017, PMID:28813426, PMC5558960, scientific Abstract; EXT_ID:28813426 AND SRC:MED confirmed identity. Abstract, Methods prose, Results: Auxospore wall fine structure, related Discussion paragraphs and actual Figure 5 read on 2026-10-10. Table 1/2 headers, footnotes and StA:7/8 and Van5:5/6 rows inspected; other rows not fully interpreted. Other actual figures and supplements unread. Fixed stages support the authors' inferred collapsible-cup sequence, not a live secretion time course. No longitudinal perizonia found under their structural criterion; initial epivalves must be distinguished. Discussion retains the Tabularia fasciculata study (reference 100); reinterpretation targets other papers. Aged small cultures, original isolates and progeny are distinct; culture abnormalities do not define canonical morphology.

    +

    Kaczmarska et al. 2017, PMID:28813426, PMC5558960, scientific Abstract; EXT_ID:28813426 AND SRC:MED confirmed identity. Abstract, Methods prose, Results: Auxospore wall fine structure, related Discussion paragraphs and actual Figure 5 read on 2026-10-10. Table 1/2 headers, footnotes and StA:7/8 and Van5:5/6 rows inspected; other rows not fully interpreted. Other actual figures and supplements unread. Fixed stages support the authors' inferred collapsible-cup sequence, not a live secretion time course. No longitudinal perizonia found under their structural criterion; initial epivalves must be distinguished. Discussion retains the Tabularia fasciculata study (reference 100); reinterpretation targets other papers. Aged small cultures, original isolates and progeny are distinct; culture abnormalities do not define canonical morphology.

  • DOI:10.1016/j.ejop.2013.06.002
    Silica precipitation began throughout the auxospore at or near maximal length, but initially was detectable in isolated regions throughout the structure.
    -

    Mather et al., online 2013-08-22, 2014 issue, PMID:23972513. Complete scientific Abstract directly read in official Europe PMC CORE on 2026-10-10 using EXT_ID:23972513 AND SRC:MED; one exact MED result with matching ID, title and DOI. Tabularia fasciculata under the source name lacked transverse perizonium; longitudinal deposition preceded initial valves near maximal auxospore length. Undetectable silicon by EDS is not absolute absence. Publisher full text unavailable; Methods, actual figures and supplements unread. These three primary studies have overlapping authors, not independent-laboratory replication.

    +

    Mather et al., online 2013-08-22, 2014 issue, PMID:23972513. Complete scientific Abstract directly read in official Europe PMC CORE on 2026-10-10 using EXT_ID:23972513 AND SRC:MED; one exact MED result with matching ID, title and DOI. Tabularia fasciculata under the source name lacked transverse perizonium; longitudinal deposition preceded initial valves near maximal auxospore length. Undetectable silicon by EDS is not absolute absence. Publisher full text unavailable; Methods, actual figures and supplements unread. These three primary studies have overlapping authors, not independent-laboratory replication.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-10 23:19 UTC diff --git a/pages/traits/physiology/diatom_seta_production.html b/pages/traits/physiology/diatom_seta_production.html index 89920f5d68b..02132b62f6b 100644 --- a/pages/traits/physiology/diatom_seta_production.html +++ b/pages/traits/physiology/diatom_seta_production.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1038/s41467-021-24944-6
    A striking example for such long elements are whisker-like extensions, called setae, which characterize the genus Chaetoceros
    -

    Mayzel et al. 2021, PMID:34330922, PMC8324917, Introduction. Scientific Abstract, Introduction, Results, Discussion, Methods, main figure captions and Table 1 read in official Europe PMC full-text XML on 2026-10-10; actual Figures 2, 3 and 5 inspected. Other actual figures, supplements and movies remain unread. EXT_ID:34330922 AND SRC:MED confirmed the scientific abstract, ID, source, title and DOI. The quote identifies the structures; Results report seta formation in Chaetoceros tenuissimus under the source name. Figure 2 PDMPO labeling at growing tips supports new silica deposition, not only inherited appendage possession. Figure 3 resolves membrane, silica and an external organic layer; this supports a proposed extracellular route, not universal absence of a silica deposition vesicle. Figure 5 scores silicon limitation per cell, but germanium/PDMPO inhibition per valve; these denominators are not interchangeable. New valves still form under the germanium treatment, with altered texture, so valves are not claimed unaffected. No universal concentration threshold, growth rate or molecular necessity is inferred.

    +

    Mayzel et al. 2021, PMID:34330922, PMC8324917, Introduction. Scientific Abstract, Introduction, Results, Discussion, Methods, main figure captions and Table 1 read in official Europe PMC full-text XML on 2026-10-10; actual Figures 2, 3 and 5 inspected. Other actual figures, supplements and movies remain unread. EXT_ID:34330922 AND SRC:MED confirmed the scientific abstract, ID, source, title and DOI. The quote identifies the structures; Results report seta formation in Chaetoceros tenuissimus under the source name. Figure 2 PDMPO labeling at growing tips supports new silica deposition, not only inherited appendage possession. Figure 3 resolves membrane, silica and an external organic layer; this supports a proposed extracellular route, not universal absence of a silica deposition vesicle. Figure 5 scores silicon limitation per cell, but germanium/PDMPO inhibition per valve; these denominators are not interchangeable. New valves still form under the germanium treatment, with altered texture, so valves are not claimed unaffected. No universal concentration threshold, growth rate or molecular necessity is inferred.

  • DOI:10.1016/j.jsb.2025.108205
    Here, we study a relatively large species, Chaetoceros rostratus, that forms long and intricate setae.
    -

    Safadi et al. 2025, PMID:40294667, online 2025-04-26, June issue. Complete scientific Abstract directly read in source-qualified Europe PMC CORE on 2026-10-10 using EXT_ID:40294667 AND SRC:MED; one exact MED result with matching ID, title and DOI. The abstract reports in-cell cryo-electron tomography during seta formation in Chaetoceros rostratus under the source name and describes an organic sheath covering newly formed silica outside the plasma membrane. Structural macromolecules might regulate architecture; their necessity is not demonstrated by this abstract. Full Methods, actual figures and supplements were not inspected. This is a distinct primary study with overlapping authors, not independent-laboratory replication. No current taxon or strain provenance is assigned from the abstract alone.

    +

    Safadi et al. 2025, PMID:40294667, online 2025-04-26, June issue. Complete scientific Abstract directly read in source-qualified Europe PMC CORE on 2026-10-10 using EXT_ID:40294667 AND SRC:MED; one exact MED result with matching ID, title and DOI. The abstract reports in-cell cryo-electron tomography during seta formation in Chaetoceros rostratus under the source name and describes an organic sheath covering newly formed silica outside the plasma membrane. Structural macromolecules might regulate architecture; their necessity is not demonstrated by this abstract. Full Methods, actual figures and supplements were not inspected. This is a distinct primary study with overlapping authors, not independent-laboratory replication. No current taxon or strain provenance is assigned from the abstract alone.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-10 21:57 UTC diff --git a/pages/traits/physiology/diauxic_growth.html b/pages/traits/physiology/diauxic_growth.html index f7804c3bbdc..d4ab2f1d19c 100644 --- a/pages/traits/physiology/diauxic_growth.html +++ b/pages/traits/physiology/diauxic_growth.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,31 +56,31 @@

    Trait evidence (5)

    DOI:10.1371/journal.pone.0061686
    However, a significant fraction of cells maintains a high rate of elongation and displays no detectable growth lag during the shift.
    -

    Boulineau et al. 2013, PMID:23637881, PMC3640066; scientific abstract. Introduction defines diauxic growth by sequential carbon-source use, supporting the definition's nutrient-switching differentia. Relevant Results, Discussion, Methods, actual Figure 2 and Text S1 prose were inspected. AB460 is an engineered MG1655 derivative; single-cell medium exchange is not the same assay as mixed-substrate batch growth. Population lag does not imply arrest of every cell. Contaminant-supported growth and model assumptions remain relevant. Text S1 DOC extraction loses embedded equations; no equation was visually verified or used as a curated mechanistic claim.

    +

    Boulineau et al. 2013, PMID:23637881, PMC3640066; scientific abstract. Introduction defines diauxic growth by sequential carbon-source use, supporting the definition's nutrient-switching differentia. Relevant Results, Discussion, Methods, actual Figure 2 and Text S1 prose were inspected. AB460 is an engineered MG1655 derivative; single-cell medium exchange is not the same assay as mixed-substrate batch growth. Population lag does not imply arrest of every cell. Contaminant-supported growth and model assumptions remain relevant. Text S1 DOC extraction loses embedded equations; no equation was visually verified or used as a curated mechanistic claim.

  • DOI:10.1128/jb.164.2.866-871.1985
    Azotobacter vinelandii exhibited diauxie when grown in a medium containing both acetate and glucose as carbon sources.
    -

    George et al. 1985, PMID:3863813, PMC214331; directly retrieved source-qualified MED abstract only. Acetate preference in this experiment contradicts a universal glucose-first requirement and supports the lexical name diauxie. Full paper and figures were not inspected; a full-text XML endpoint returned HTTP 500. This access failure is not evidence that full text does not exist.

    +

    George et al. 1985, PMID:3863813, PMC214331; directly retrieved source-qualified MED abstract only. Acetate preference in this experiment contradicts a universal glucose-first requirement and supports the lexical name diauxie. Full paper and figures were not inspected; a full-text XML endpoint returned HTTP 500. This access failure is not evidence that full text does not exist.

  • DOI:10.1128/jb.01571-06
    Following recovery of growth on the alternative carbon or nitrogen source, RpoS protein concentrations declined rapidly to a basal level.
    -

    Sandercock and Page 2008, PMID:18055600, PMC2223558; scientific abstract. Relevant Methods/Results and actual Figure 3 support UW batch-culture acetate/glucose and ammonium/N2 transitions. This supports nutrient-source scope rather than sugars or carbon alone. Ammonium augmentation addresses an oxygen-limitation alternative for the stress response. RpoS dynamics are not a universal causal mechanism of diauxie; later PHB consumption was explicitly unmeasured. Publisher text and Figure 3 were accessible despite requests HTML 403 and Europe PMC XML 500 responses.

    +

    Sandercock and Page 2008, PMID:18055600, PMC2223558; scientific abstract. Relevant Methods/Results and actual Figure 3 support UW batch-culture acetate/glucose and ammonium/N2 transitions. This supports nutrient-source scope rather than sugars or carbon alone. Ammonium augmentation addresses an oxygen-limitation alternative for the stress response. RpoS dynamics are not a universal causal mechanism of diauxie; later PHB consumption was explicitly unmeasured. Publisher text and Figure 3 were accessible despite requests HTML 403 and Europe PMC XML 500 responses.

  • DOI:10.1371/journal.pbio.1002041
    many natural isolates of Saccharomyces cerevisiae display short or nonexistent diauxic lags when grown in mixtures of glucose (preferred) and galactose.
    -

    Wang et al. 2015, PMID:25626068, PMC4308108; scientific abstract, not the XML's preceding TOC teaser or separate Author Summary. Relevant Results, growth-curve Methods, actual Figure 1 and S1 EPS were inspected. Operational zero lag means the smoothed growth-rate curve has no local minimum, not simultaneous equal use of both substrates. Natural-origin growth panels and engineered reporter derivatives require separate provenance. Figure 1 caption says eleven strains but the image has twelve labels; no strain count is inferred here. The observations oppose mandatory positive lag.

    +

    Wang et al. 2015, PMID:25626068, PMC4308108; scientific abstract, not the XML's preceding TOC teaser or separate Author Summary. Relevant Results, growth-curve Methods, actual Figure 1 and S1 EPS were inspected. Operational zero lag means the smoothed growth-rate curve has no local minimum, not simultaneous equal use of both substrates. Natural-origin growth panels and engineered reporter derivatives require separate provenance. Figure 1 caption says eleven strains but the image has twelve labels; no strain count is inferred here. The observations oppose mandatory positive lag.

  • DOI:10.1038/msb.2013.11
    Once glucose is depleted, the cells consume the earlier produced ethanol
    -

    Zampar et al. 2013, PMID:23549479, PMC3693829; Introduction, second paragraph, not an abstract quote. Relevant Results, culture and measurement Methods and actual Figure 1 were inspected. FY4 was initially supplied glucose and later consumed produced ethanol; the definition therefore does not require both nutrients to be supplied initially. Figure 1 distinguishes concentration observations from fitted rates. Intracellular flux ranges are model-constrained, not direct flux measurements; raw supplemental data and the full mechanistic analysis were not reanalyzed.

    +

    Zampar et al. 2013, PMID:23549479, PMC3693829; Introduction, second paragraph, not an abstract quote. Relevant Results, culture and measurement Methods and actual Figure 1 were inspected. FY4 was initially supplied glucose and later consumed produced ethanol; the definition therefore does not require both nutrients to be supplied initially. Figure 1 distinguishes concentration observations from fitted rates. Intracellular flux ranges are model-constrained, not direct flux measurements; raw supplemental data and the full mechanistic analysis were not reanalyzed.

    • @@ -124,7 +125,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -140,7 +141,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -330,7 +331,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -359,12 +369,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-11 23:44 UTC diff --git a/pages/traits/physiology/diversifying_bet_hedging.html b/pages/traits/physiology/diversifying_bet_hedging.html index ee649fcad22..49e27e3ab71 100644 --- a/pages/traits/physiology/diversifying_bet_hedging.html +++ b/pages/traits/physiology/diversifying_bet_hedging.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1038/nature08504
    Here we report the de novo evolution of bet hedging in experimental bacterial populations.
    -

    Beaumont et al. 2009, PMID:19890329; scientific abstract, directly checked against publisher and source-qualified MED text, not the publisher's Editorial Summary. Supports experimentally evolved risk spreading by rapid phenotype switching under a changing selection regime. Mutational evolution of a switching genotype is not the same claim as mutations generating each alternative cell state. Main figures, supplements and raw data were not independently assessed; no gene-level mechanism or natural canonical exemplar is asserted.

    +

    Beaumont et al. 2009, PMID:19890329; scientific abstract, directly checked against publisher and source-qualified MED text, not the publisher's Editorial Summary. Supports experimentally evolved risk spreading by rapid phenotype switching under a changing selection regime. Mutational evolution of a switching genotype is not the same claim as mutations generating each alternative cell state. Main figures, supplements and raw data were not independently assessed; no gene-level mechanism or natural canonical exemplar is asserted.

  • DOI:10.1371/journal.pbio.1001325
    Our results suggest that yeast bet hedging results from multiple epigenetic growth states determined by a combination of stochastic and deterministic factors.
    -

    Levy, Ziv and Siegal 2012, PMID:22589700, PMC3348152; scientific abstract, directly checked against publisher, MED and full-text XML, separately from the Author Summary. Box 1 supplies the definition framework and explicitly leaves adaptive origin untested in this yeast study. The record preserves that limit: reversible state variation and differential stress survival do not alone establish evolutionary optimization. Binary states and a purely stochastic mechanism are not required.

    +

    Levy, Ziv and Siegal 2012, PMID:22589700, PMC3348152; scientific abstract, directly checked against publisher, MED and full-text XML, separately from the Author Summary. Box 1 supplies the definition framework and explicitly leaves adaptive origin untested in this yeast study. The record preserves that limit: reversible state variation and differential stress survival do not alone establish evolutionary optimization. Binary states and a purely stochastic mechanism are not required.

  • DOI:10.1038/s41467-024-46297-6
    Mobile cells grow faster but are stress-sensitive, while non-mobile cells prioritise stress resistance over growth.
    -

    Tang et al. 2024, PMID:38453919; scientific abstract, directly checked against publisher and source-qualified MED text. The Introduction and Discussion distinguish early diversification of Haematococcus pluvialis cultures from later stress-induced conversion. Growth and survival are fitness proxies, not a demonstration of optimized long-term geometric mean fitness. Figures, supplements and raw data were not independently assessed; proposed transcriptional explanations are not encoded as causal edges.

    +

    Tang et al. 2024, PMID:38453919; scientific abstract, directly checked against publisher and source-qualified MED text. The Introduction and Discussion distinguish early diversification of Haematococcus pluvialis cultures from later stress-induced conversion. Growth and survival are fitness proxies, not a demonstration of optimized long-term geometric mean fitness. Figures, supplements and raw data were not independently assessed; proposed transcriptional explanations are not encoded as causal edges.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -333,7 +334,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -362,12 +372,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-12 08:11 UTC diff --git a/pages/traits/physiology/dnase_activity.html b/pages/traits/physiology/dnase_activity.html index 52c26dbeb33..cccd2ac75bc 100644 --- a/pages/traits/physiology/dnase_activity.html +++ b/pages/traits/physiology/dnase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • DNase production RELATED_SYNONYM · DOI:10.22207/JPAM.14.1.44
      • +
    • DNase production RELATED_SYNONYM · DOI:10.22207/JPAM.14.1.44
    @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -272,7 +273,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two general DNase agar-screening snippets (DOI:10.3389/fmicb.2019.00969, DOI:10.22207/JPAM.14.1.44) without specific nuclease enzyme or catalytic product quotes.

    +

    The current record carries two general DNase agar-screening snippets (DOI:10.3389/fmicb.2019.00969, DOI:10.22207/JPAM.14.1.44) without specific nuclease enzyme or catalytic product quotes.

    @@ -354,7 +355,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -383,12 +393,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/dormancy.html b/pages/traits/physiology/dormancy.html index 7c89f7ccb35..5d07c0eacfb 100644 --- a/pages/traits/physiology/dormancy.html +++ b/pages/traits/physiology/dormancy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    GO:0022611 confers dormancy - traitmech:000080 + traitmech:000080 METPO:2007700

    The dormancy process realizes the dormancy trait.

      @@ -288,8 +289,8 @@

      Protein and taxon examples

    		 - Mycobacterium tuberculosis H37Rv -
    NCBITaxon:83332 + Mycobacterium tuberculosis H37Rv +
    NCBITaxon:83332         		REVIEWED
    @@ -366,7 +367,7 @@

    Children (2)

    Synonyms (1)

      -
    • dormant state RELATED_SYNONYM · DOI:10.1038/nrmicro2504
      • +
    • dormant state RELATED_SYNONYM · DOI:10.1038/nrmicro2504
    @@ -382,7 +383,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -670,7 +671,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1034,12 +1044,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/durotaxis.html b/pages/traits/physiology/durotaxis.html index c92ddc3111a..7ee069ef3f6 100644 --- a/pages/traits/physiology/durotaxis.html +++ b/pages/traits/physiology/durotaxis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.7554/eLife.96821
    Dictyostelium also displayed stiff-side directed motility when seeded on the gradient gel
    -

    Kang et al., Version of Record (v4), 2024-12-13, https://doi.org/10.7554/eLife.96821.4; full text https://pmc.ncbi.nlm.nih.gov/articles/PMC11643633/ (PMID:39671466). Exact Results paragraph span in Amoeboid durotaxis is evolutionarily conserved, not an abstract quote. Figure 4 was visually inspected: confined Dictyostelium cells on polyacrylamide stiffness gradients had greater directional migration than uniform-gel controls, without a significant velocity difference. Blebbistatin reduced directionality and speed; Rho activator II increased them. These pharmacological results do not isolate a dedicated stiffness sensor. Supplementary file 1 contains simulation parameters; the MDAR checklist refers to cell-culture methods but does not resolve the assayed Dictyostelium strain. Mammalian NMIIA localization and knockdown results are not direct microbial protein evidence.

    +

    Kang et al., Version of Record (v4), 2024-12-13, https://doi.org/10.7554/eLife.96821.4; full text https://pmc.ncbi.nlm.nih.gov/articles/PMC11643633/ (PMID:39671466). Exact Results paragraph span in Amoeboid durotaxis is evolutionarily conserved, not an abstract quote. Figure 4 was visually inspected: confined Dictyostelium cells on polyacrylamide stiffness gradients had greater directional migration than uniform-gel controls, without a significant velocity difference. Blebbistatin reduced directionality and speed; Rho activator II increased them. These pharmacological results do not isolate a dedicated stiffness sensor. Supplementary file 1 contains simulation parameters; the MDAR checklist refers to cell-culture methods but does not resolve the assayed Dictyostelium strain. Mammalian NMIIA localization and knockdown results are not direct microbial protein evidence.

  • DOI:10.1088/1361-6463/adb6b8
    Our findings reveal directional persistence and strong polarization of the plasmodia towards regions of stiffer substrates, indicating a guided migration response.
    -

    Filipinas and Confesor, published online 2025-02-27. Exact abstract span in the publisher-deposited Crossref record, https://api.crossref.org/works/10.1088/1361-6463/adb6b8. The authors report tracking Physarum polycephalum plasmodial nodes on agar stiffness gradients. This is independent microbial support for stiffness-directed migration, not merely a simulation prediction. Full methods, figures and supplements were not inspected; strain provenance, gradient controls and the distinction between node migration and growth remain to be assessed before adding a canonical example or mechanistic graph. The abstract's simulation-supported gradient-independence claim is not generalized to all microbes.

    +

    Filipinas and Confesor, published online 2025-02-27. Exact abstract span in the publisher-deposited Crossref record, https://api.crossref.org/works/10.1088/1361-6463/adb6b8. The authors report tracking Physarum polycephalum plasmodial nodes on agar stiffness gradients. This is independent microbial support for stiffness-directed migration, not merely a simulation prediction. Full methods, figures and supplements were not inspected; strain provenance, gradient controls and the distinction between node migration and growth remain to be assessed before adding a canonical example or mechanistic graph. The abstract's simulation-supported gradient-independence claim is not generalized to all microbes.

  • DOI:10.1038/s41563-022-01294-2
    Our results identify the molecular mechanism driving context-dependent positive or negative durotaxis, determined by a cell's contractile and adhesive machinery.
    -

    Isomursu et al., published 2022-07-11, PMID:35817964. Exact final abstract sentence in the Europe PMC MED record, https://europepmc.org/article/MED/35817964; the publisher's abstract corroborates positive and negative durotaxis usage. This mammalian cell study supports polarity-neutral terminology only, not an additional microbial observation. Its mechanism claim is not transferred to microbes. Full methods, figures and supplements were not inspected for this terminology check. The two microbial studies above report stiff-side migration; negative microbial durotaxis is not established by these sources.

    +

    Isomursu et al., published 2022-07-11, PMID:35817964. Exact final abstract sentence in the Europe PMC MED record, https://europepmc.org/article/MED/35817964; the publisher's abstract corroborates positive and negative durotaxis usage. This mammalian cell study supports polarity-neutral terminology only, not an additional microbial observation. Its mechanism claim is not transferred to microbes. Full methods, figures and supplements were not inspected for this terminology check. The two microbial studies above report stiff-side migration; negative microbial durotaxis is not established by these sources.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -215,7 +216,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    The class is polarity-neutral: positive and negative responses are directions along the stiffness gradient, not different stimuli. Isomursu et al. (DOI:10.1038/s41563-022-01294-2) support this terminology in mammalian cells, not negative microbial durotaxis. Both microbial studies here report stiff-side migration; no opposite microbial response is inferred. Speed changes on uniform substrates, passive displacement and differential growth alone are insufficient. Contact-guided polarized growth in thigmotropism (traitmech:000594) is a different response. Do not infer durotaxis from a friction gradient, surface topography or remote substrate deformation without direct evidence for stiffness-directed migration. Mechanotaxis is broader, not an exact synonym. QuickGO returned zero durotaxis hits on 2026-10-04; other external equivalences remain unverified. No xref or synonym is inferred.

    +

    The class is polarity-neutral: positive and negative responses are directions along the stiffness gradient, not different stimuli. Isomursu et al. (DOI:10.1038/s41563-022-01294-2) support this terminology in mammalian cells, not negative microbial durotaxis. Both microbial studies here report stiff-side migration; no opposite microbial response is inferred. Speed changes on uniform substrates, passive displacement and differential growth alone are insufficient. Contact-guided polarized growth in thigmotropism (traitmech:000594) is a different response. Do not infer durotaxis from a friction gradient, surface topography or remote substrate deformation without direct evidence for stiffness-directed migration. Mechanotaxis is broader, not an exact synonym. QuickGO returned zero durotaxis hits on 2026-10-04; other external equivalences remain unverified. No xref or synonym is inferred.

    @@ -245,7 +246,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Kang's methods cite Li et al. (DOI:10.3389/fcell.2022.835185), whose cell-culture methods describe Ax2-derived cells and expression constructs. That citation does not uniquely identify the cells used for Kang's Figure 4 or establish natural-strain provenance. Resolve that identity and inspect the Physarum full methods before adding NCBI-grounded canonical examples. Dictyostelium inhibitor/activator responses support a contractility-related interpretation, not a resolved protein-level sensing pathway. Do not transfer mammalian NMIIA polarization or knockdown effects to an unverified microbial accession, or treat the active gel model as a biological perturbation. Mechanistic graphs are deferred pending taxon-paired proteins and bounded causal evidence; NONMECHANISTIC is not a workaround.

    +

    Kang's methods cite Li et al. (DOI:10.3389/fcell.2022.835185), whose cell-culture methods describe Ax2-derived cells and expression constructs. That citation does not uniquely identify the cells used for Kang's Figure 4 or establish natural-strain provenance. Resolve that identity and inspect the Physarum full methods before adding NCBI-grounded canonical examples. Dictyostelium inhibitor/activator responses support a contractility-related interpretation, not a resolved protein-level sensing pathway. Do not transfer mammalian NMIIA polarization or knockdown effects to an unverified microbial accession, or treat the active gel model as a biological perturbation. Mechanistic graphs are deferred pending taxon-paired proteins and bounded causal evidence; NONMECHANISTIC is not a workaround.

    @@ -289,7 +290,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Correct durotaxis polarity scope after independent review -

      Addresses issue #1669 and corrects history/records/durotaxis/2026-10-04T120347Z-codex-3de17e.yaml without editing it. Changed the unqualified class and proposal to directional active migration in a spatial substrate stiffness gradient. Retained both stiff-side microbial observations and added DOI:10.1038/s41563-022-01294-2 only for positive/negative terminology, with exact Europe PMC MED abstract wording and explicit nonmicrobial scope. Did not infer negative microbial durotaxis or transfer mammalian mechanisms. Preserved the original per-record event and appended CORRECTED_DEFINITION_SCOPE through record_curation_event. The validated writer accepts exact reviewed SHA-256 preimages, rejects drift and defaults to dry run; eight focused tests and Ruff pass. Added polarity-scope guidance to add-trait. Derived-artifact regeneration, broader validation and independent re-review follow this history entry.

    +

    Addresses issue #1669 and corrects history/records/durotaxis/2026-10-04T120347Z-codex-3de17e.yaml without editing it. Changed the unqualified class and proposal to directional active migration in a spatial substrate stiffness gradient. Retained both stiff-side microbial observations and added DOI:10.1038/s41563-022-01294-2 only for positive/negative terminology, with exact Europe PMC MED abstract wording and explicit nonmicrobial scope. Did not infer negative microbial durotaxis or transfer mammalian mechanisms. Preserved the original per-record event and appended CORRECTED_DEFINITION_SCOPE through record_curation_event. The validated writer accepts exact reviewed SHA-256 preimages, rejects drift and defaults to dry run; eight focused tests and Ruff pass. Added polarity-scope guidance to add-trait. Derived-artifact regeneration, broader validation and independent re-review follow this history entry.

    • Read this curation session @@ -321,7 +322,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -350,12 +360,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 12:39 UTC diff --git a/pages/traits/physiology/endocytosis.html b/pages/traits/physiology/endocytosis.html index 57597e4ed34..be5c748cf68 100644 --- a/pages/traits/physiology/endocytosis.html +++ b/pages/traits/physiology/endocytosis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1083/jcb.128.5.779
    After an additional 20-40 min, the PM and cytoplasmic punctate staining disappeared concomitant with staining of the vacuolar membrane.
    -

    PMID:7533169, PMC2120394. Scientific Abstract quote verified in Europe PMC XML; full-text OCR, including Introduction, Methods, Results and Discussion, was read at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC2120394/fullTextXML. FM 4-64 tracks plasma-membrane-to-vacuole transport in Saccharomyces cerevisiae. Early experiments used BHY10.5, a CPY-invertase reporter background, not the SEY6210 control in later mutant comparisons. Endosome identity is qualified as likely. Mutant effects on vacuolar delivery are not necessarily initial-internalization defects; in vitro ATP/cytosol dependence concerns later transport. Marker-specific results do not establish a universal route. PDF/figures were unavailable and were not visually audited.

    +

    PMID:7533169, PMC2120394. Scientific Abstract quote verified in Europe PMC XML; full-text OCR, including Introduction, Methods, Results and Discussion, was read at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC2120394/fullTextXML. FM 4-64 tracks plasma-membrane-to-vacuole transport in Saccharomyces cerevisiae. Early experiments used BHY10.5, a CPY-invertase reporter background, not the SEY6210 control in later mutant comparisons. Endosome identity is qualified as likely. Mutant effects on vacuolar delivery are not necessarily initial-internalization defects; in vitro ATP/cytosol dependence concerns later transport. Marker-specific results do not establish a universal route. PDF/figures were unavailable and were not visually audited.

  • DOI:10.1128/mcb.14.11.7245-7255.1994
    This report presents direct evidence for alpha-factor-induced internalization of cell surface receptors.
    -

    PMID:7935439, PMC359259. Scientific Abstract directly read in NCBI PubMed XML and Europe PMC metadata, which agree on this DOI. Density fractionation and extracellular-protease protection support receptor internalization in Saccharomyces cerevisiae. The abstract distinguishes receptor signaling, internalization and subsequent vacuolar degradation. No fixed transit time or universal receptor requirement is imposed. Full text and figures were unavailable: the Europe PMC full-text endpoint returned HTTP 500 and the indexed PDF mirror returned 404. Strain provenance and unread assay details are not inferred.

    +

    PMID:7935439, PMC359259. Scientific Abstract directly read in NCBI PubMed XML and Europe PMC metadata, which agree on this DOI. Density fractionation and extracellular-protease protection support receptor internalization in Saccharomyces cerevisiae. The abstract distinguishes receptor signaling, internalization and subsequent vacuolar degradation. No fixed transit time or universal receptor requirement is imposed. Full text and figures were unavailable: the Europe PMC full-text endpoint returned HTTP 500 and the indexed PDF mirror returned 404. Strain provenance and unread assay details are not inferred.

    • @@ -124,7 +125,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -220,7 +221,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    This is the microbial cell's uptake phenotype, not a host response, a sequence feature or intracellular trafficking alone. Surface adsorption, passive diffusion, transporter entry, open membrane invaginations and autophagy alone are insufficient. Pinocytosis traitmech:000635 and phagocytosis traitmech:000627 entail this scope; macropinocytosis traitmech:000634 remains below pinocytosis. No fixed size, clathrin/actin dependence, nutritional assimilation or degradation is required. Trogocytosis traitmech:000633 describes removal and uptake of living-cell portions without universally specifying membrane-bound enclosure. Myzocytosis traitmech:000631 describes prey-content aspiration. Its cited 2023 Discussion (DOI:10.3390/microorganisms11081945) calls myzocytosis a form of endocytosis in the studied Colpodella system; that source-attributed umbrella usage is retained, not treated as proof that every aspiration phenotype meets this operational membrane-bound scope. Their broader parent decisions remain unresolved, not exclusions or disjointness claims. Nutritional phagotrophy is not an equivalent. Review process-level ontology mappings separately; no unverified synonyms or xrefs are asserted.

    +

    This is the microbial cell's uptake phenotype, not a host response, a sequence feature or intracellular trafficking alone. Surface adsorption, passive diffusion, transporter entry, open membrane invaginations and autophagy alone are insufficient. Pinocytosis traitmech:000635 and phagocytosis traitmech:000627 entail this scope; macropinocytosis traitmech:000634 remains below pinocytosis. No fixed size, clathrin/actin dependence, nutritional assimilation or degradation is required. Trogocytosis traitmech:000633 describes removal and uptake of living-cell portions without universally specifying membrane-bound enclosure. Myzocytosis traitmech:000631 describes prey-content aspiration. Its cited 2023 Discussion (DOI:10.3390/microorganisms11081945) calls myzocytosis a form of endocytosis in the studied Colpodella system; that source-attributed umbrella usage is retained, not treated as proof that every aspiration phenotype meets this operational membrane-bound scope. Their broader parent decisions remain unresolved, not exclusions or disjointness claims. Nutritional phagotrophy is not an equivalent. Review process-level ontology mappings separately; no unverified synonyms or xrefs are asserted.

    @@ -314,7 +315,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -343,12 +353,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 06:50 UTC diff --git a/pages/traits/physiology/energy_taxis.html b/pages/traits/physiology/energy_taxis.html index 7c017c5e01b..6028fd1f233 100644 --- a/pages/traits/physiology/energy_taxis.html +++ b/pages/traits/physiology/energy_taxis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1128/jb.182.21.6042-6048.2000
    behavioral responses to most stimuli in A. brasilense are triggered by changes in the electron transport system.
    -

    Abstract exact-matched at Europe PMC (PMID:11029423). Publisher Methods, Results and Discussion also inspected. Sp7 (ATCC 29145), wild type for chemotaxis, is distinguished from the cytN mutant FAJ851. Spatial and temporal assays, metabolic inhibition and electron-donor bypass support the sensing interpretation beyond growth correlation. Nitrate and DMSO taxis are reported under anaerobic conditions. The study does not decide whether redox state or ion motive force is the sensed signal; capillary aerotaxis can confound apparent substrate chemotaxis. No universal substrate range is inferred.

    +

    Abstract exact-matched at Europe PMC (PMID:11029423). Publisher Methods, Results and Discussion also inspected. Sp7 (ATCC 29145), wild type for chemotaxis, is distinguished from the cytN mutant FAJ851. Spatial and temporal assays, metabolic inhibition and electron-donor bypass support the sensing interpretation beyond growth correlation. Nitrate and DMSO taxis are reported under anaerobic conditions. The study does not decide whether redox state or ion motive force is the sensed signal; capillary aerotaxis can confound apparent substrate chemotaxis. No universal substrate range is inferred.

  • DOI:10.1128/jb.186.19.6595-6604.2004
    Motility responses triggered by changes in the electron transport system are collectively known as energy taxis.
    -

    Abstract exact-matched at Europe PMC (PMID:15375141); full text not fully inspected. The tlp1 mutant is deficient in responses to oxidizable substrates, terminal electron acceptors and redox conditions. The proposed sensory domain's function remains unknown in this source. Root-colonization impairment supports an ecological hypothesis, not universal host specificity or an identified direct ligand. No complete protein-resolved pathway is inferred from the abstract.

    +

    Abstract exact-matched at Europe PMC (PMID:15375141); full text not fully inspected. The tlp1 mutant is deficient in responses to oxidizable substrates, terminal electron acceptors and redox conditions. The proposed sensory domain's function remains unknown in this source. Root-colonization impairment supports an ecological hypothesis, not universal host specificity or an identified direct ligand. No complete protein-resolved pathway is inferred from the abstract.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Canonical examples DOI:10.1128/jb.182.21.6042-6048.2000 - Sp7 (ATCC 29145), the study's wild type for chemotaxis, not the cytN mutant FAJ851. Observed substrate, electron-acceptor and repellent responses support energy taxis under the reported conditions. Environmental provenance is independently documented at https://www.atcc.org/products/29145. NCBI resolved 192 on 2026-10-04 at species rank; it is not an exact strain accession or a claim about all strains. + Sp7 (ATCC 29145), the study's wild type for chemotaxis, not the cytN mutant FAJ851. Observed substrate, electron-acceptor and repellent responses support energy taxis under the reported conditions. Environmental provenance is independently documented at https://www.atcc.org/products/29145. NCBI resolved 192 on 2026-10-04 at species rank; it is not an exact strain accession or a claim about all strains. @@ -302,7 +303,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add source-bounded energy taxis phenotype -

      Created traitmech:000590 as PROPOSED under METPO:1000702 using DOI:10.1128/jb.182.21.6042-6048.2000 and DOI:10.1128/jb.186.19.6595-6604.2004; exact abstract snippets and ATCC 29145 provenance fields independently checked. NCBITaxon:192 is species-ranked and the exemplar is qualified to Sp7, not cytN mutant FAJ851. Whole-repository novelty and identifier searches included ignored and hidden files. Reserved METPO:1054400 in proposal v467; kept stimulus-defined taxis classes and metabolic power supply distinct from energy sensing. Deferred unresolved molecular grounding and external mappings in two discussions. Writer dry run and nine regression tests passed before application; broad gates and reviewed PR workflow follow.

    +

    Created traitmech:000590 as PROPOSED under METPO:1000702 using DOI:10.1128/jb.182.21.6042-6048.2000 and DOI:10.1128/jb.186.19.6595-6604.2004; exact abstract snippets and ATCC 29145 provenance fields independently checked. NCBITaxon:192 is species-ranked and the exemplar is qualified to Sp7, not cytN mutant FAJ851. Whole-repository novelty and identifier searches included ignored and hidden files. Reserved METPO:1054400 in proposal v467; kept stimulus-defined taxis classes and metabolic power supply distinct from energy sensing. Deferred unresolved molecular grounding and external mappings in two discussions. Writer dry run and nine regression tests passed before application; broad gates and reviewed PR workflow follow.

    • Read this curation session
  • @@ -340,7 +341,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -369,12 +379,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 07:28 UTC diff --git a/pages/traits/physiology/enhanced_transcriptional_reactivation_memory.html b/pages/traits/physiology/enhanced_transcriptional_reactivation_memory.html index 51a674d92ab..1bb3e3ff0b4 100644 --- a/pages/traits/physiology/enhanced_transcriptional_reactivation_memory.html +++ b/pages/traits/physiology/enhanced_transcriptional_reactivation_memory.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.7554/eLife.77646
    Upon Anchor Away of Opi1, reactivation was faster than activation
    -

    Sump et al. 2022, PMID:35579426, PMC9129879; Results s2-1, paragraph 2, contiguous in primary XML and publisher Version of Record HTML. Figure 1D uses synthetic Opi1 Anchor Away to bypass upstream induction control; enhancement is lost in mrs and nup100 mutants. Ordinary-starvation INO1 reactivation in Figure 1B is not clearly faster than activation. Figure 1 supplement 1C separately measures CHO1/ACT1 after three-hour repression; its generic statistical-comparator caption is ambiguous. Figure 1 supplement 2E measures 18-hour peripheral localization, not that duration of enhanced transcription; the main Results mispoints to supplement 1. Figure 1G competitive fitness is a different endpoint, not proof of transcriptional causality. Selected Results, Methods, scientific abstract, actual figures and strain-table rows were inspected. RT-qPCR mRNA kinetics are not direct measurements of initiation rate. Native abstract lookup returns NOT_IN_ABSTRACT; direct full-text matching supports the quotation, not a native VERIFIED verdict.

    +

    Sump et al. 2022, PMID:35579426, PMC9129879; Results s2-1, paragraph 2, contiguous in primary XML and publisher Version of Record HTML. Figure 1D uses synthetic Opi1 Anchor Away to bypass upstream induction control; enhancement is lost in mrs and nup100 mutants. Ordinary-starvation INO1 reactivation in Figure 1B is not clearly faster than activation. Figure 1 supplement 1C separately measures CHO1/ACT1 after three-hour repression; its generic statistical-comparator caption is ambiguous. Figure 1 supplement 2E measures 18-hour peripheral localization, not that duration of enhanced transcription; the main Results mispoints to supplement 1. Figure 1G competitive fitness is a different endpoint, not proof of transcriptional causality. Selected Results, Methods, scientific abstract, actual figures and strain-table rows were inspected. RT-qPCR mRNA kinetics are not direct measurements of initiation rate. Native abstract lookup returns NOT_IN_ABSTRACT; direct full-text matching supports the quotation, not a native VERIFIED verdict.

  • DOI:10.1534/genetics.112.143016
    Cells with prior NaCl exposure have a faster gene-expression response to H2O2.
    -

    Guan et al. 2012, PMID:22851651, PMC3454879; complete opening sentence of the Figure 4 caption, contiguous in publisher HTML with chemical subscripts retained as text. BY4741-background laboratory yeast received 0.7 M NaCl for 60 minutes, washing and 240 minutes of stress-free YPD recovery (two generations in Results), then 0.5 mM H2O2, compared with mock-treated cells. No significant pre-challenge expression difference at FDR 0.05 does not prove identical baselines. Figure 4 includes induced and repressed genes; only the enhanced-induction subset supports this activation phenotype. The 449-gene count is not a count of induced genes. Methods and Figure 4A sample through 40 minutes, whereas Results describes a 60-minute response. Figure 5 shows TSA2 mRNA kinetics by qPCR; nup42 deletion reduces the priming benefit, while nup100 naive and primed responses are both fast, not simple evidence of a universal mechanism. Four-to-five generation resistance persistence is a different endpoint. Relevant Results, Methods, scientific abstract and actual Figures 4 and 5 were inspected; raw data were not reanalyzed. Native abstract-verifier results are retained separately in the source sidecar; exact publisher full-text matching supports this caption quotation.

    +

    Guan et al. 2012, PMID:22851651, PMC3454879; complete opening sentence of the Figure 4 caption, contiguous in publisher HTML with chemical subscripts retained as text. BY4741-background laboratory yeast received 0.7 M NaCl for 60 minutes, washing and 240 minutes of stress-free YPD recovery (two generations in Results), then 0.5 mM H2O2, compared with mock-treated cells. No significant pre-challenge expression difference at FDR 0.05 does not prove identical baselines. Figure 4 includes induced and repressed genes; only the enhanced-induction subset supports this activation phenotype. The 449-gene count is not a count of induced genes. Methods and Figure 4A sample through 40 minutes, whereas Results describes a 60-minute response. Figure 5 shows TSA2 mRNA kinetics by qPCR; nup42 deletion reduces the priming benefit, while nup100 naive and primed responses are both fast, not simple evidence of a universal mechanism. Four-to-five generation resistance persistence is a different endpoint. Relevant Results, Methods, scientific abstract and actual Figures 4 and 5 were inspected; raw data were not reanalyzed. Native abstract-verifier results are retained separately in the source sidecar; exact publisher full-text matching supports this caption quotation.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -313,7 +314,7 @@

    Recorded curation sessions

  • · claude-code
    • CREATE — Add enhanced transcriptional reactivation memory as a qualified proposed phenotype -

      Created traitmech:000713 with primary DOI:10.7554/eLife.77646 and DOI:10.7554/eLife.16691, contiguous full-text Results snippets, qualified synthetic induction and transcript endpoints, historical identity TODO, and v589 proposal reserving 1066600-1066699. Bounded ignored/hidden and retained-tree novelty plus current pending/upstream reservation checks are retained in the source-verification sidecar. Canonical examples, exact synonyms, equivalence xrefs and causal graphs are omitted. Existing records, protected spore germination, pinned ontology and snippet baseline are unchanged. Native validation, artifact generation and immutable scientific review are separate required gates; no claim of discovery exhaustion.

    +

    Created traitmech:000713 with primary DOI:10.7554/eLife.77646 and DOI:10.7554/eLife.16691, contiguous full-text Results snippets, qualified synthetic induction and transcript endpoints, historical identity TODO, and v589 proposal reserving 1066600-1066699. Bounded ignored/hidden and retained-tree novelty plus current pending/upstream reservation checks are retained in the source-verification sidecar. Canonical examples, exact synonyms, equivalence xrefs and causal graphs are omitted. Existing records, protected spore germination, pinned ontology and snippet baseline are unchanged. Native validation, artifact generation and immutable scientific review are separate required gates; no claim of discovery exhaustion.

    • Read this curation session
  • @@ -331,7 +332,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Replace anaphoric confirmation with a self-contained primary result -

      For PR 1903 issue 1905, replaced the D Urso 2016 snippet with Guan 2012 DOI 10.1534/genetics.112.143016 Figure 4 caption opening. Exact publisher text and source identity were checked and actual Figures 4 and 5 inspected. Qualified four-hour recovery, mixed induced/repressed genes and Results versus Methods timing discrepancy. Prior source checks and curation history are retained; definition, identifiers and PROPOSED status unchanged. Native checks and regenerated artifact gates are recorded separately.

    +

    For PR 1903 issue 1905, replaced the D Urso 2016 snippet with Guan 2012 DOI 10.1534/genetics.112.143016 Figure 4 caption opening. Exact publisher text and source identity were checked and actual Figures 4 and 5 inspected. Qualified four-hour recovery, mixed induced/repressed genes and Results versus Methods timing discrepancy. Prior source checks and curation history are retained; definition, identifiers and PROPOSED status unchanged. Native checks and regenerated artifact gates are recorded separately.

    • Read this curation session @@ -363,7 +364,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -392,12 +402,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-13 01:59 UTC diff --git a/pages/traits/physiology/er_phagy.html b/pages/traits/physiology/er_phagy.html index 2ce03b56635..d784cc5cb77 100644 --- a/pages/traits/physiology/er_phagy.html +++ b/pages/traits/physiology/er_phagy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1242/jcs.154716
    Finally, we provide evidence that ER-phagy degrades excess ER membrane, suggesting that it contributes to cell homeostasis by controlling organelle size.
    -

    PMID:25052096, PMC4163648. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. XML Results s2c/s2e and Methods s4b/s4f were read. In Saccharomyces cerevisiae, ER-targeted Pho8 reporters distinguish selective turnover from cytosolic and mitochondrial cargo; Atg7 and vacuolar-protease controls distinguish routes and reporter activation. ER whorls enter the vacuole by microautophagy. DTT and tunicamycin interfere with vacuolar proteolysis, so stress-induced whorl accumulation alone is not completed degradation. Untreated opi1 mutants show partly disintegrated vacuolar whorls, unlike opi1 pep4 prb1 mutants; membrane expansion can elicit this response without misfolded-protein stress. The strains derive from W303, but independent natural provenance was not verified. Figure 5/7 captions were read; actual figures, supplements and complete Methods were not inspected.

    +

    PMID:25052096, PMC4163648. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. XML Results s2c/s2e and Methods s4b/s4f were read. In Saccharomyces cerevisiae, ER-targeted Pho8 reporters distinguish selective turnover from cytosolic and mitochondrial cargo; Atg7 and vacuolar-protease controls distinguish routes and reporter activation. ER whorls enter the vacuole by microautophagy. DTT and tunicamycin interfere with vacuolar proteolysis, so stress-induced whorl accumulation alone is not completed degradation. Untreated opi1 mutants show partly disintegrated vacuolar whorls, unlike opi1 pep4 prb1 mutants; membrane expansion can elicit this response without misfolded-protein stress. The strains derive from W303, but independent natural provenance was not verified. Figure 5/7 captions were read; actual figures, supplements and complete Methods were not inspected.

  • DOI:10.1038/nature14506
    Atg40 is enriched in the cortical and cytoplasmic ER, and loads these ER subdomains into autophagosomes.
    -

    PMID:26040717. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. This Saccharomyces cerevisiae study explicitly restricts its use of autophagy to macroautophagy. Atg40 targets cortical/cytoplasmic ER, whereas Atg39 targets perinuclear ER and nuclear material. These source-specific subdomain assignments do not make ER-phagy and nucleophagy synonyms or restrict all ER-phagy to the macro route. The proposed mammalian FAM134B functional counterpart is qualified as probable, not experimentally universal. Full text, actual figures, supplements and strain provenance were not inspected.

    +

    PMID:26040717. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. This Saccharomyces cerevisiae study explicitly restricts its use of autophagy to macroautophagy. Atg40 targets cortical/cytoplasmic ER, whereas Atg39 targets perinuclear ER and nuclear material. These source-specific subdomain assignments do not make ER-phagy and nucleophagy synonyms or restrict all ER-phagy to the macro route. The proposed mammalian FAM134B functional counterpart is qualified as probable, not experimentally universal. Full text, actual figures, supplements and strain provenance were not inspected.

  • DOI:10.15252/embj.2019102586
    Third, we demonstrate that macro- and micro-ER-phagy are parallel pathways with distinct molecular requirements.
    -

    PMID:31802527, PMC6960443. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. XML Results embj2019102586-sec-0005 and Methods sec-0011/sec-0018/sec-0019 were read. This yeast study explicitly includes macro- and microautophagic ER turnover. Their contributions depend on the trigger; do not universalize measured proportions. Nem1-Spo7 and ESCRTs contribute to micro-ER-phagy, but ESCRT mutants also impair nonselective autophagy and vacuolar function, so their defects are not micro-ER-phagy-specific absence tests. Atg40 is dispensable for the Atg7-independent micro route. Pho8 assays require background correction; the Sec63-GFP assay quantifies Pep4-dependent, Atg7-independent cleavage products using unsaturated exposures. Uptake or membrane scission alone does not prove complete degradation. Actual figures, supplements, complete Methods and independent strain provenance were not inspected.

    +

    PMID:31802527, PMC6960443. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. XML Results embj2019102586-sec-0005 and Methods sec-0011/sec-0018/sec-0019 were read. This yeast study explicitly includes macro- and microautophagic ER turnover. Their contributions depend on the trigger; do not universalize measured proportions. Nem1-Spo7 and ESCRTs contribute to micro-ER-phagy, but ESCRT mutants also impair nonselective autophagy and vacuolar function, so their defects are not micro-ER-phagy-specific absence tests. Atg40 is dispensable for the Atg7-independent micro route. Pho8 assays require background correction; the Sec63-GFP assay quantifies Pep4-dependent, Atg7-independent cleavage products using unsaturated exposures. Uptake or membrane scission alone does not prove complete degradation. Actual figures, supplements, complete Methods and independent strain provenance were not inspected.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -215,7 +216,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Use autophagy traitmech:000638 as parent. The 2014 microautophagy study and the 2019 online/2020 issue ESCRT paper support a route-inclusive phenotype, whereas Mochida et al. 2015 use autophagy specifically for macroautophagy. GO:0061709 reticulophagy, resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0061709, is a nonobsolete biological process whose definition specifies autophagosomes and whose exact synonyms include ER-phagy. That route restriction and the process-to-phenotype shift prevent an exact xref here; retain the source-attributed difference for human review without silently narrowing the microbial phenotype. No synonyms or SSSOM mapping are asserted. ER stress, unfolded-protein responses, ER-associated protein degradation outside the lysosome/vacuole, bulk cytoplasmic turnover, gene presence, puncta or accumulated whorls alone are insufficient. Nuclear-envelope cargo can overlap nucleophagy without making the two traits equivalent.

    +

    Use autophagy traitmech:000638 as parent. The 2014 microautophagy study and the 2019 online/2020 issue ESCRT paper support a route-inclusive phenotype, whereas Mochida et al. 2015 use autophagy specifically for macroautophagy. GO:0061709 reticulophagy, resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0061709, is a nonobsolete biological process whose definition specifies autophagosomes and whose exact synonyms include ER-phagy. That route restriction and the process-to-phenotype shift prevent an exact xref here; retain the source-attributed difference for human review without silently narrowing the microbial phenotype. No synonyms or SSSOM mapping are asserted. ER stress, unfolded-protein responses, ER-associated protein degradation outside the lysosome/vacuole, bulk cytoplasmic turnover, gene presence, puncta or accumulated whorls alone are insufficient. Nuclear-envelope cargo can overlap nucleophagy without making the two traits equivalent.

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 12:50 UTC diff --git a/pages/traits/physiology/eukaryotic_flagellar_autotomy.html b/pages/traits/physiology/eukaryotic_flagellar_autotomy.html index 5b2e4969dd3..39e36388a80 100644 --- a/pages/traits/physiology/eukaryotic_flagellar_autotomy.html +++ b/pages/traits/physiology/eukaryotic_flagellar_autotomy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1186/1471-2121-4-11
    fla10 cells lose flagella by deflagellation at 33 degrees C.
    -

    Parker and Quarmby 2003, PMID:12930563, PMCID:PMC194436, scientific abstract Results, second sentence. Direct MED text match; native VERIFIED applies to that text, not the PDF degree-symbol typography. Background distinguishes basal axonemal severing from resorption. The quoted response concerns source-named Chlamydomonas fla10 in calcium-containing medium, not reference strain WTB214. Released flagella were counted per 100 cells, with the initial count subtracted; lengths are a separate endpoint. Low calcium is not calcium-free, and buffer exchange is a confound. All twelve main PDF pages and eight figures were inspected. No universal IFT or calcium requirement follows.

    +

    Parker and Quarmby 2003, PMID:12930563, PMCID:PMC194436, scientific abstract Results, second sentence. Direct MED text match; native VERIFIED applies to that text, not the PDF degree-symbol typography. Background distinguishes basal axonemal severing from resorption. The quoted response concerns source-named Chlamydomonas fla10 in calcium-containing medium, not reference strain WTB214. Released flagella were counted per 100 cells, with the initial count subtracted; lengths are a separate endpoint. Low calcium is not calcium-free, and buffer exchange is a confound. All twelve main PDF pages and eight figures were inspected. No universal IFT or calcium requirement follows.

  • DOI:10.1534/g3.116.034264
    Wild-type cells deflagellate completely in response to pH shock or dibucaine, regardless of the temperature
    -

    Hilton et al. 2016, PMID:27520959, PMCID:PMC5068960.1, page 3416, Results and Discussion subsection ADF2 and ADF4 remain unassigned, first paragraph and Figure 4A. Contiguous JATS and typeset match; native NOT_IN_ABSTRACT retained. The comparison is 21 versus 33 degrees C after six hours, not every temperature. The assay scores the control-normalized decrease in biflagellate cells per 100 cells, not a direct count of released flagella or proof that every responding cell loses both. Figure 4A reports three independent experiments with SD. All ten main pages, four figures and three tables were inspected; supplements remain unread. Phototaxis screening alone is not the shedding endpoint.

    +

    Hilton et al. 2016, PMID:27520959, PMCID:PMC5068960.1, page 3416, Results and Discussion subsection ADF2 and ADF4 remain unassigned, first paragraph and Figure 4A. Contiguous JATS and typeset match; native NOT_IN_ABSTRACT retained. The comparison is 21 versus 33 degrees C after six hours, not every temperature. The assay scores the control-normalized decrease in biflagellate cells per 100 cells, not a direct count of released flagella or proof that every responding cell loses both. Figure 4A reports three independent experiments with SD. All ten main pages, four figures and three tables were inspected; supplements remain unread. Phototaxis screening alone is not the shedding endpoint.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -239,7 +240,7 @@

    Discussions and Knowledge Gaps (4)

    mechanism it concerns.

    -

    The inspected pinned and current METPO release/editor/template scope has no active exact shedding class. Historical METPO:0000089 and METPO:000090 are deprecated with OMO:0001000; METPO:1000381 is deprecated with IAO:0000226. All point to METPO:1000704, which denotes locomotory flagellar possession, not autotomy. Deprecated ciliated METPO:0000093 and METPO:000094 carry OMO:0001000, while METPO:1000385 carries IAO:0000226; no replacement or consider annotation was observed for these or deprecated flagellum METPO:1000123, whose recorded reason is OMO:0001000. Those historical morphology terms are not exact xrefs and are not reactivated. METPO issue https://github.com/berkeleybop/metpo/issues/521 records unresolved reason-code interpretation. Current upstream describes a bacterial/archaeal focus, so adoption of this microbial-eukaryote proposal requires maintainer review. The ontology pin stays unchanged. Proposal v607 reserves METPO:1068400 within 1068400-1068499; no upstream release or human sign-off is implied.

    +

    The inspected pinned and current METPO release/editor/template scope has no active exact shedding class. Historical METPO:0000089 and METPO:000090 are deprecated with OMO:0001000; METPO:1000381 is deprecated with IAO:0000226. All point to METPO:1000704, which denotes locomotory flagellar possession, not autotomy. Deprecated ciliated METPO:0000093 and METPO:000094 carry OMO:0001000, while METPO:1000385 carries IAO:0000226; no replacement or consider annotation was observed for these or deprecated flagellum METPO:1000123, whose recorded reason is OMO:0001000. Those historical morphology terms are not exact xrefs and are not reactivated. METPO issue https://github.com/berkeleybop/metpo/issues/521 records unresolved reason-code interpretation. Current upstream describes a bacterial/archaeal focus, so adoption of this microbial-eukaryote proposal requires maintainer review. The ontology pin stays unchanged. Proposal v607 reserves METPO:1068400 within 1068400-1068499; no upstream release or human sign-off is implied.

    @@ -375,7 +376,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -404,12 +414,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-15 08:01 UTC diff --git a/pages/traits/physiology/eukaryotic_flagellar_axoneme_internalization.html b/pages/traits/physiology/eukaryotic_flagellar_axoneme_internalization.html index 2f3a44af732..d979fe4d26b 100644 --- a/pages/traits/physiology/eukaryotic_flagellar_axoneme_internalization.html +++ b/pages/traits/physiology/eukaryotic_flagellar_axoneme_internalization.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1002/cm.21637
    axonemes remain intact during internalization
    -

    Venard et al. 2020, PMID:33103844, PMCID:PMC7944584, Results 2.2, TEM interpretation paragraph following Figure 2. Contiguous span checked in direct PMC HTML; native NOT_IN_ABSTRACT retained. Live phase microscopy, fixed immunofluorescence and TEM concern Rhizoclosmatium globosum JEL800 and Spizellomyces punctatus DAOM BR117. Internalized cross-sections retain 9+2 architecture without a surrounding ciliary membrane; fixed TEM is not continuous same-cell tracking. Figure 1's 23 and 32 cells are selected retraction events, not biological-culture counts. Methods time zero is plating, whereas Figure 2's TEM caption says post-retraction; retain that timing discrepancy. Table 1 labels length/diameter with rate units unlike Table 2; no numerical conversion or rate is asserted here. Main text and all five actual main figures were inspected. The main PDF and actual supplemental PDFs/videos remain unread. Subsequent degradation is a separate phase, not a requirement for this internalization phenotype.

    +

    Venard et al. 2020, PMID:33103844, PMCID:PMC7944584, Results 2.2, TEM interpretation paragraph following Figure 2. Contiguous span checked in direct PMC HTML; native NOT_IN_ABSTRACT retained. Live phase microscopy, fixed immunofluorescence and TEM concern Rhizoclosmatium globosum JEL800 and Spizellomyces punctatus DAOM BR117. Internalized cross-sections retain 9+2 architecture without a surrounding ciliary membrane; fixed TEM is not continuous same-cell tracking. Figure 1's 23 and 32 cells are selected retraction events, not biological-culture counts. Methods time zero is plating, whereas Figure 2's TEM caption says post-retraction; retain that timing discrepancy. Table 1 labels length/diameter with rate units unlike Table 2; no numerical conversion or rate is asserted here. Main text and all five actual main figures were inspected. The main PDF and actual supplemental PDFs/videos remain unread. Subsequent degradation is a separate phase, not a requirement for this internalization phenotype.

  • DOI:10.1083/jcb.201701074
    Bd zoospores retracting their flagella by coiling the entire axoneme into the cell body
    -

    Fritz-Laylin et al. 2017, PMID:28473602, PMCID:PMC5461030.1, Discussion JATS s11, printed page 1681, PDF page 9. Direct normalized JATS and typeset passage checked; native NOT_IN_ABSTRACT retained. Bd denotes Batrachochytrium dendrobatidis, source strain JEL423, with synchronized zoospores observed under the described confinement preparation. Results s10, Discussion s11 and Methods s20 were read, along with selected PDF pages. Video 5 was inspected through 16 sampled frames and one enlarged frame, not continuous playback or every-frame analysis. File metadata reports 10.1 seconds at nominal 10 fps, burned-in labels span 0-20 seconds, and the caption states 0.1-second acquisition with 20-fps playback. These are not silently reconciled; no retraction rate or replicate count is inferred. The paper's WASP/SCAR pseudopod experiments do not establish an axoneme-internalization mechanism.

    +

    Fritz-Laylin et al. 2017, PMID:28473602, PMCID:PMC5461030.1, Discussion JATS s11, printed page 1681, PDF page 9. Direct normalized JATS and typeset passage checked; native NOT_IN_ABSTRACT retained. Bd denotes Batrachochytrium dendrobatidis, source strain JEL423, with synchronized zoospores observed under the described confinement preparation. Results s10, Discussion s11 and Methods s20 were read, along with selected PDF pages. Video 5 was inspected through 16 sampled frames and one enlarged frame, not continuous playback or every-frame analysis. File metadata reports 10.1 seconds at nominal 10 fps, burned-in labels span 0-20 seconds, and the caption states 0.1-second acquisition with 20-fps playback. These are not silently reconciled; no retraction rate or replicate count is inferred. The paper's WASP/SCAR pseudopod experiments do not establish an axoneme-internalization mechanism.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -251,7 +252,7 @@

    Evidence

    mechanism it concerns.

    -

    No active exact term was identified in the inspected pinned/current METPO release, editor and templates. Deprecated METPO:0000089 and METPO:000090 carry OMO:0001000; METPO:1000381 carries IAO:0000226. Their active replacement METPO:1000704 denotes locomotory flagellar possession, not internalization. Deprecated ciliated METPO:0000093 and METPO:000094 carry OMO:0001000, while METPO:1000385 carries IAO:0000226; no replacement or consider annotation was observed for those or deprecated flagellum METPO:1000123 with OMO:0001000. Historical identifiers are not exact xrefs and are not reactivated. https://github.com/berkeleybop/metpo/issues/521 leaves reason-code interpretation unresolved. Upstream's bacterial/archaeal focus requires maintainer review of microbial-eukaryote inclusion. Proposal v610 reserves METPO:1068700 in 1068700-1068799, not a released identifier or human-approved mapping. The ontology pin is unchanged.

    +

    No active exact term was identified in the inspected pinned/current METPO release, editor and templates. Deprecated METPO:0000089 and METPO:000090 carry OMO:0001000; METPO:1000381 carries IAO:0000226. Their active replacement METPO:1000704 denotes locomotory flagellar possession, not internalization. Deprecated ciliated METPO:0000093 and METPO:000094 carry OMO:0001000, while METPO:1000385 carries IAO:0000226; no replacement or consider annotation was observed for those or deprecated flagellum METPO:1000123 with OMO:0001000. Historical identifiers are not exact xrefs and are not reactivated. https://github.com/berkeleybop/metpo/issues/521 leaves reason-code interpretation unresolved. Upstream's bacterial/archaeal focus requires maintainer review of microbial-eukaryote inclusion. Proposal v610 reserves METPO:1068700 in 1068700-1068799, not a released identifier or human-approved mapping. The ontology pin is unchanged.

    @@ -311,7 +312,7 @@

    Evidence

    mechanism it concerns.

    -

    The named laboratory strains remain qualified life-stage observations, not authority-verified canonical taxa or proof of natural provenance. Two distinct supporting publications are not a claim of independent-lab replication. The 2025 follow-up shares authors with earlier work and is scope context, not a third definition citation. Qualified MED/Crossref identities and available notice fields were checked, not comprehensive correction/retraction clearance. The linked 2017 Comment/Editorial, DOI:10.1080/15384101.2017.1360655, PMID:28820330, PMC5628642, has no returned abstract and its content remains unread; it is not counted evidence. Publisher/PMC access failures remain failures. The 2020 supplement endpoint returned an API error with HTTP 200, not a ZIP; no actual supplement contents are inferred. No raw-data reanalysis, paid research or human scientific sign-off is implied.

    +

    The named laboratory strains remain qualified life-stage observations, not authority-verified canonical taxa or proof of natural provenance. Two distinct supporting publications are not a claim of independent-lab replication. The 2025 follow-up shares authors with earlier work and is scope context, not a third definition citation. Qualified MED/Crossref identities and available notice fields were checked, not comprehensive correction/retraction clearance. The linked 2017 Comment/Editorial, DOI:10.1080/15384101.2017.1360655, PMID:28820330, PMC5628642, has no returned abstract and its content remains unread; it is not counted evidence. Publisher/PMC access failures remain failures. The 2020 supplement endpoint returned an API error with HTTP 200, not a ZIP; no actual supplement contents are inferred. No raw-data reanalysis, paid research or human scientific sign-off is implied.

    @@ -387,7 +388,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -416,12 +426,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-15 21:06 UTC diff --git a/pages/traits/physiology/eukaryotic_flagellar_resorption.html b/pages/traits/physiology/eukaryotic_flagellar_resorption.html index a8a2b035890..d237f67191f 100644 --- a/pages/traits/physiology/eukaryotic_flagellar_resorption.html +++ b/pages/traits/physiology/eukaryotic_flagellar_resorption.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1083/jcb.100.2.457
    Cells under resorption-inducing conditions rapidly shortened their flagella
    -

    L'Hernault and Rosenbaum 1985, PMID:3968171, PMCID:PMC2113451.1, printed page 458, Results, Monitoring of Flagellar Length during In Vivo Labeling, sole paragraph; Figure 2 on page 459. Contiguous typeset and whitespace-normalized OCR match; native NOT_IN_ABSTRACT retained. The XML body is a single OCR preformat block, not a section-structured JATS paragraph. Source-designated wild-type Chlamydomonas reinhardtii 21gr was mechanically deflagellated and pulse-chase labelled during regeneration before resorption was induced with 15 mM sodium pyrophosphate at pH 7.5 plus cycloheximide; HEPES was the control. The shortening concerns regenerated flagella, not failed assembly. Apparent flagellalessness after 90 minutes still permits the reported short stubs. Protein fractionation supports transfer to the cell body, not complete recycling. All six main PDF pages, three figures and Table I were inspected; raw data were not reanalyzed. Figure 1's two determinations and Table I's two gels per sample are not established biological-replicate counts.

    +

    L'Hernault and Rosenbaum 1985, PMID:3968171, PMCID:PMC2113451.1, printed page 458, Results, Monitoring of Flagellar Length during In Vivo Labeling, sole paragraph; Figure 2 on page 459. Contiguous typeset and whitespace-normalized OCR match; native NOT_IN_ABSTRACT retained. The XML body is a single OCR preformat block, not a section-structured JATS paragraph. Source-designated wild-type Chlamydomonas reinhardtii 21gr was mechanically deflagellated and pulse-chase labelled during regeneration before resorption was induced with 15 mM sodium pyrophosphate at pH 7.5 plus cycloheximide; HEPES was the control. The shortening concerns regenerated flagella, not failed assembly. Apparent flagellalessness after 90 minutes still permits the reported short stubs. Protein fractionation supports transfer to the cell body, not complete recycling. All six main PDF pages, three figures and Table I were inspected; raw data were not reanalyzed. Figure 1's two determinations and Table I's two gels per sample are not established biological-replicate counts.

  • DOI:10.1186/1471-2121-4-11
    Acid shock causes resorption of mutants unable to deflagellate.
    -

    Parker and Quarmby 2003, PMID:12930563, PMCID:PMC194436, Figure 7 caption, first sentence, page 9 of 12; JATS F7 under sec9/sec5. Direct caption and typeset match; native NOT_IN_ABSTRACT retained. The acid-shock experiments concern Chlamydomonas fa1, fa2 and adf1 mutants, with coiling and incomplete resorption described; wild-type cells instead shed and regrow their flagella in this comparison. Figure 7 scores the fraction of cells with flagella longer than 7 micrometers, not a resorption rate or count of released organelles. The separate fla10 temperature experiments must not be merged with this assay. Low-calcium HEPES is not calcium-free: Methods retain trace calcium and do not add chelators. The main length measurements count at least 70 cells per time point and use at least three independent cultures. All twelve main PDF pages and eight figures were inspected. Proposed basal disassembly and shared severing machinery are not universal requirements of this class.

    +

    Parker and Quarmby 2003, PMID:12930563, PMCID:PMC194436, Figure 7 caption, first sentence, page 9 of 12; JATS F7 under sec9/sec5. Direct caption and typeset match; native NOT_IN_ABSTRACT retained. The acid-shock experiments concern Chlamydomonas fa1, fa2 and adf1 mutants, with coiling and incomplete resorption described; wild-type cells instead shed and regrow their flagella in this comparison. Figure 7 scores the fraction of cells with flagella longer than 7 micrometers, not a resorption rate or count of released organelles. The separate fla10 temperature experiments must not be merged with this assay. Low-calcium HEPES is not calcium-free: Methods retain trace calcium and do not add chelators. The main length measurements count at least 70 cells per time point and use at least three independent cultures. All twelve main PDF pages and eight figures were inspected. Proposed basal disassembly and shared severing machinery are not universal requirements of this class.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -251,7 +252,7 @@

    Evidence

    mechanism it concerns.

    -

    The inspected pinned/current METPO releases, editor and templates have no active exact resorption class. Historical METPO:0000089 and METPO:000090 carry OMO:0001000; METPO:1000381 carries IAO:0000226. All are deprecated and point to active METPO:1000704, which denotes locomotory flagellar possession, not resorption. Deprecated ciliated METPO:0000093 and METPO:000094 carry OMO:0001000, while METPO:1000385 carries IAO:0000226; no replacement or consider annotation was observed for those or deprecated flagellum METPO:1000123, whose reason is OMO:0001000. Historical terms are not exact xrefs and are not reactivated. https://github.com/berkeleybop/metpo/issues/521 records unresolved reason-code interpretation. Upstream's bacterial/archaeal focus requires maintainer review of this microbial-eukaryote proposal. The ontology pin stays unchanged. Proposal v609 reserves METPO:1068600 in 1068600-1068699; neither upstream release nor human sign-off is implied.

    +

    The inspected pinned/current METPO releases, editor and templates have no active exact resorption class. Historical METPO:0000089 and METPO:000090 carry OMO:0001000; METPO:1000381 carries IAO:0000226. All are deprecated and point to active METPO:1000704, which denotes locomotory flagellar possession, not resorption. Deprecated ciliated METPO:0000093 and METPO:000094 carry OMO:0001000, while METPO:1000385 carries IAO:0000226; no replacement or consider annotation was observed for those or deprecated flagellum METPO:1000123, whose reason is OMO:0001000. Historical terms are not exact xrefs and are not reactivated. https://github.com/berkeleybop/metpo/issues/521 records unresolved reason-code interpretation. Upstream's bacterial/archaeal focus requires maintainer review of this microbial-eukaryote proposal. The ontology pin stays unchanged. Proposal v609 reserves METPO:1068600 in 1068600-1068699; neither upstream release nor human sign-off is implied.

    @@ -387,7 +388,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -416,12 +426,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-15 17:06 UTC diff --git a/pages/traits/physiology/exocytosis.html b/pages/traits/physiology/exocytosis.html index 02888ae62a2..effd50c88de 100644 --- a/pages/traits/physiology/exocytosis.html +++ b/pages/traits/physiology/exocytosis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1083/jcb.56.1.153
    The cytoplasm between the two matching membrane sites is squeezed away and the membranes fuse
    -

    PMID:4629881, PMC2108847. Scientific Abstract directly read in Europe PMC XML and PubMed. The quote retains the source's missing terminal punctuation. Freeze-fracture/etch observations in the historically named Tetrahymena pyriformis system connect mucocyst-plasma-membrane fusion, opening enlargement and contents release. Fixation triggers some discharge. Abstract-level evidence does not establish a universal pore size or fusion machinery. The XML has sparse body content and the PDF endpoint returned HTML; full methods, figures and strain provenance were not inspected.

    +

    PMID:4629881, PMC2108847. Scientific Abstract directly read in Europe PMC XML and PubMed. The quote retains the source's missing terminal punctuation. Freeze-fracture/etch observations in the historically named Tetrahymena pyriformis system connect mucocyst-plasma-membrane fusion, opening enlargement and contents release. Fixation triggers some discharge. Abstract-level evidence does not establish a universal pore size or fusion machinery. The XML has sparse body content and the PDF endpoint returned HTML; full methods, figures and strain provenance were not inspected.

  • DOI:10.1007/BF01870409
    Upon returning the cells to the permissive temperature the contents of the accumulated vesicles were secreted.
    -

    PMID:1744905. Scientific Abstract directly read in NCBI PubMed XML and Europe PMC metadata, which agree on the DOI. Constitutive secretion in Saccharomyces cerevisiae is examined using temperature-sensitive sec mutants, accumulated vesicles and blocked protein synthesis. Calcium perturbations did not affect the measured release under these conditions; this does not establish calcium irrelevance in every yeast context. No universal rate or requirement for extracellular stimulation is inferred. Full methods, figures and strain provenance remain unread.

    +

    PMID:1744905. Scientific Abstract directly read in NCBI PubMed XML and Europe PMC metadata, which agree on the DOI. Constitutive secretion in Saccharomyces cerevisiae is examined using temperature-sensitive sec mutants, accumulated vesicles and blocked protein synthesis. Calcium perturbations did not affect the measured release under these conditions; this does not establish calcium irrelevance in every yeast context. No universal rate or requirement for extracellular stimulation is inferred. Full methods, figures and strain provenance remain unread.

  • DOI:10.1016/s0143-4160(98)90030-6
    This is a detailed characterization of a secretory mutant incapable of releasing secretory contents despite normal exocytotic membrane fusion performance.
    -

    PMID:9681197. Scientific Abstract verified in PubMed XML and Europe PMC metadata. Relevant Methods, Results and Discussion were read in the primary PDF at https://d-nb.info/1107191386/34; pages 349-350 and 354-356, including Figures 6-9, were visually inspected. Paramecium caudatum tnd1 retains condensed cargo despite fusion and extracellular fluorochrome access. Figure 9 shows untriggered mutant cells, not a wildtype experiment. This supports separation of fusion and discharge, not tnd1 as a positive example of completed secretion. Reduced calcium binding is a proposed explanation, not a proven molecular lesion. Other figures and tables were not visually audited.

    +

    PMID:9681197. Scientific Abstract verified in PubMed XML and Europe PMC metadata. Relevant Methods, Results and Discussion were read in the primary PDF at https://d-nb.info/1107191386/34; pages 349-350 and 354-356, including Figures 6-9, were visually inspected. Paramecium caudatum tnd1 retains condensed cargo despite fusion and extracellular fluorochrome access. Figure 9 shows untriggered mutant cells, not a wildtype experiment. This supports separation of fusion and discharge, not tnd1 as a positive example of completed secretion. Reduced calcium binding is a proposed explanation, not a proven molecular lesion. Other figures and tables were not visually audited.

    • @@ -130,7 +131,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    This concerns secretion by the microbe, not a host-cell response. Docking, intracellular trafficking or fusion alone does not demonstrate cargo release. Transporter-mediated export, membrane budding, lysis, cell-cell fusion and endocytosis are not equivalents. Constitutive and stimulus-regulated secretion are included; total emptying, permanent vesicle collapse and a shared calcium response are not required. GO:0006887 was resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0006887 and includes partial secretion through transient pores, but denotes a biological process rather than an equivalent organismal phenotype. No xref or synonym is inferred. The obsolete METPO secretion classes are broader, not exact replacements or usable parents. Retain phenotype METPO:1000059 pending human mapping review.

    +

    This concerns secretion by the microbe, not a host-cell response. Docking, intracellular trafficking or fusion alone does not demonstrate cargo release. Transporter-mediated export, membrane budding, lysis, cell-cell fusion and endocytosis are not equivalents. Constitutive and stimulus-regulated secretion are included; total emptying, permanent vesicle collapse and a shared calcium response are not required. GO:0006887 was resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0006887 and includes partial secretion through transient pores, but denotes a biological process rather than an equivalent organismal phenotype. No xref or synonym is inferred. The obsolete METPO secretion classes are broader, not exact replacements or usable parents. Retain phenotype METPO:1000059 pending human mapping review.

    @@ -320,7 +321,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -349,12 +359,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 08:10 UTC diff --git a/pages/traits/physiology/extracellular_membrane_vesicle_production.html b/pages/traits/physiology/extracellular_membrane_vesicle_production.html index 0d2c426d008..24a8479fecc 100644 --- a/pages/traits/physiology/extracellular_membrane_vesicle_production.html +++ b/pages/traits/physiology/extracellular_membrane_vesicle_production.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.1038/ncomms11220
    Super-resolution microscopy reveals that explosive cell lysis also produces shattered membrane fragments that rapidly form MVs.
    -

    PMID:27075392, PMC4834629. Scientific Abstract, not the editorial teaser, directly read in Europe PMC XML; selected Results and strain/isolation Methods also read. Live super-resolution imaging in Pseudomonas aeruginosa distinguishes vesicles from fragments and supports membrane reassembly after lysis. Lys dependence in biofilms/stress does not extend to ordinary oxic planktonic cultures, where the lys mutant retains comparable MV levels. Reporter/deletion/rescue experiments are qualified observations, not proof of one universal route. Actual panels and supplements were not visually inspected.

    +

    PMID:27075392, PMC4834629. Scientific Abstract, not the editorial teaser, directly read in Europe PMC XML; selected Results and strain/isolation Methods also read. Live super-resolution imaging in Pseudomonas aeruginosa distinguishes vesicles from fragments and supports membrane reassembly after lysis. Lys dependence in biofilms/stress does not extend to ordinary oxic planktonic cultures, where the lys mutant retains comparable MV levels. Reporter/deletion/rescue experiments are qualified observations, not proof of one universal route. Actual panels and supplements were not visually inspected.

  • DOI:10.1038/s41467-017-00492-w
    Through these openings, cytoplasmic membrane material protrudes into the extracellular space and is released as MVs.
    -

    PMID:28883390, PMC5589764. Scientific Abstract, separate from the appended teaser, and selected Results/Methods directly read in Europe PMC XML. The openings are endolysin-associated peptidoglycan holes in Bacillus subtilis. Live imaging and induced strains support extrusion from cells that ultimately die; tomography uses an engineered skinny ponA deletion, not wild-type cells. Static tomographic stages are not a measured time sequence. This route differs from explosive-fragment reassembly. This study and the 2016 paper share investigators; they are not independent-laboratory replications. Actual panels were not visually inspected.

    +

    PMID:28883390, PMC5589764. Scientific Abstract, separate from the appended teaser, and selected Results/Methods directly read in Europe PMC XML. The openings are endolysin-associated peptidoglycan holes in Bacillus subtilis. Live imaging and induced strains support extrusion from cells that ultimately die; tomography uses an engineered skinny ponA deletion, not wild-type cells. Static tomographic stages are not a measured time sequence. This route differs from explosive-fragment reassembly. This study and the 2016 paper share investigators; they are not independent-laboratory replications. Actual panels were not visually inspected.

  • DOI:10.1371/journal.pone.0011113
    Bilayered vesicles with diameters at the 100–300 nm range were found in extracellular fractions from yeast cultures.
    -

    PMID:20559436, PMC2885426. Scientific Abstract and Methods s2a-s2c, Results s3a/s3d directly read in Europe PMC XML. Saccharomyces cerevisiae WT and trafficking mutants yield vesicles after supernatant fractionation and TEM. Heat-killed controls yielded no vesicle-like structures; viability controls were reported without displayed data. SEC/MVB perturbations alter composition and sterol-based release proxies without abolishing production. The abstract's concluding requirement language is not taken as a universal necessity claim. Size is assay-specific; WT denotes laboratory comparators, not verified natural isolates. Actual panels were not visually inspected.

    +

    PMID:20559436, PMC2885426. Scientific Abstract and Methods s2a-s2c, Results s3a/s3d directly read in Europe PMC XML. Saccharomyces cerevisiae WT and trafficking mutants yield vesicles after supernatant fractionation and TEM. Heat-killed controls yielded no vesicle-like structures; viability controls were reported without displayed data. SEC/MVB perturbations alter composition and sterol-based release proxies without abolishing production. The abstract's concluding requirement language is not taken as a universal necessity claim. Size is assay-specific; WT denotes laboratory comparators, not verified natural isolates. Actual panels were not visually inspected.

  • DOI:10.1038/s41467-025-60272-9
    The EVs were isolated from exponentially growing M. smithii cultures to limit the contamination of the EV preparations with cell debris.
    -

    PMID:40461479, PMC12134362. Full-text Results Sec3 quote, not an abstract quote, checked in Europe PMC XML. Sec3/Sec7 and Methods Sec10-Sec12 describe PS cultures, density-gradient purification, TEM and particle assays. Instrument detection limits yield different size distributions. Cryo-ET suggests budding and wall passage; the large-vesicle lysis route is hypothesized, not directly demonstrated. DNA/protein cargo annotations do not demonstrate increased methane production. Actual panels and supplements were not visually inspected.

    +

    PMID:40461479, PMC12134362. Full-text Results Sec3 quote, not an abstract quote, checked in Europe PMC XML. Sec3/Sec7 and Methods Sec10-Sec12 describe PS cultures, density-gradient purification, TEM and particle assays. Instrument detection limits yield different size distributions. Cryo-ET suggests budding and wall passage; the large-vesicle lysis route is hypothesized, not directly demonstrated. DNA/protein cargo annotations do not demonstrate increased methane production. Actual panels and supplements were not visually inspected.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Canonical examples DOI:10.1038/s41467-025-60272-9 - Type strain PS (= ATCC 35061 = DSM 861). Vesicles were purified from exponentially growing cultures at 37 C in modified DSM 119 medium under H2/CO2 and examined by TEM. The collection record https://www.dsmz.de/collection/catalogue/details/culture/DSM-861 traces PS to a primary sewage digester in Gainesville, not to a human donor; it supplies provenance, not independent vesicle evidence. NCBI Taxonomy resolves this strain to species 2173. This is a culture observation, not direct in-gut vesicle production. + Type strain PS (= ATCC 35061 = DSM 861). Vesicles were purified from exponentially growing cultures at 37 C in modified DSM 119 medium under H2/CO2 and examined by TEM. The collection record https://www.dsmz.de/collection/catalogue/details/culture/DSM-861 traces PS to a primary sewage digester in Gainesville, not to a human donor; it supplies provenance, not independent vesicle evidence. NCBI Taxonomy resolves this strain to species 2173. This is a culture observation, not direct in-gut vesicle production. @@ -340,7 +341,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -369,12 +379,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 19:56 UTC diff --git a/pages/traits/physiology/extracellular_trail_based_spatial_memory.html b/pages/traits/physiology/extracellular_trail_based_spatial_memory.html index 1acfbe02bc0..ca986524593 100644 --- a/pages/traits/physiology/extracellular_trail_based_spatial_memory.html +++ b/pages/traits/physiology/extracellular_trail_based_spatial_memory.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (3)

    DOI:10.1073/pnas.1215037109
    When one arm contained extracellular slime, 39 of 40 plasmodia chose the blank agar arm
    -

    Reid et al. 2012, PMID:23045640, PMC3491460; Results opening paragraph, printed page 17490 / PDF page 1. Cultured Physarum polycephalum avoided previously deposited slime in a Y maze. Same-stock coatings do not demonstrate individual recognition of one's own trace. In the separate U-trap experiment, 23/24 plasmodia on blank agar versus 8/24 on slime-coated agar reached the target within 120 hours. Coating masks newly informative trails; it does not abolish secretion or lesion internal memory. Success, completion time among successful trials, speed, path length and revisitation are distinct endpoints. No-trap and speed controls do not exclude every environmental confound. Main Methods, Results, Discussion and all four figures were inspected in an author-hosted publisher-formatted PDF bearing a 2012 download stamp, not verified as the current corrected VoR. Supplements and raw data were not assessed. Southern Biological Supplies culture provenance remains unresolved. The contiguous result span was text-matched and visually checked.

    +

    Reid et al. 2012, PMID:23045640, PMC3491460; Results opening paragraph, printed page 17490 / PDF page 1. Cultured Physarum polycephalum avoided previously deposited slime in a Y maze. Same-stock coatings do not demonstrate individual recognition of one's own trace. In the separate U-trap experiment, 23/24 plasmodia on blank agar versus 8/24 on slime-coated agar reached the target within 120 hours. Coating masks newly informative trails; it does not abolish secretion or lesion internal memory. Success, completion time among successful trials, speed, path length and revisitation are distinct endpoints. No-trap and speed controls do not exclude every environmental confound. Main Methods, Results, Discussion and all four figures were inspected in an author-hosted publisher-formatted PDF bearing a 2012 download stamp, not verified as the current corrected VoR. Supplements and raw data were not assessed. Southern Biological Supplies culture provenance remains unresolved. The contiguous result span was text-matched and visually checked.

  • @@ -67,7 +68,7 @@

    Trait evidence (3)

    DOI:10.1073/pnas.2312611121
    In accordance with the literature, we observe that plasmodia generally avoid previously visited areas marked by their slime trail
    -

    Troger et al. 2024, PMID:38517977, PMC10990088; Results, Quantifying Run-and-Tumble and Self-Avoiding Behavior, page 3. The authors report their own Physarum observations, not only a background citation. Actual trajectories, including Figure 2A, are distinct from simulated-model panels. Page 5 describes 14 trajectories divided into groups of nine each; Figure 4 instead gives seven small and seven large. The discrepancy remains unresolved. The 0.65 square-millimeter median is a cohort split, not a universal threshold. Small plasmodia can cross trails; a modeled three-hour forgetting time is not a measured chemical half-life or internal-memory duration. Main text, Methods and all four main figures were inspected in the author-hosted publisher-formatted PDF with a March 2024 download stamp, not verified current corrected VoR equivalence. Publisher supplements and raw data were not reanalyzed. This different laboratory's assay is not a replication of the earlier maze experiments; no universal molecular receptor is established.

    +

    Troger et al. 2024, PMID:38517977, PMC10990088; Results, Quantifying Run-and-Tumble and Self-Avoiding Behavior, page 3. The authors report their own Physarum observations, not only a background citation. Actual trajectories, including Figure 2A, are distinct from simulated-model panels. Page 5 describes 14 trajectories divided into groups of nine each; Figure 4 instead gives seven small and seven large. The discrepancy remains unresolved. The 0.65 square-millimeter median is a cohort split, not a universal threshold. Small plasmodia can cross trails; a modeled three-hour forgetting time is not a measured chemical half-life or internal-memory duration. Main text, Methods and all four main figures were inspected in the author-hosted publisher-formatted PDF with a March 2024 download stamp, not verified current corrected VoR equivalence. Publisher supplements and raw data were not reanalyzed. This different laboratory's assay is not a replication of the earlier maze experiments; no universal molecular receptor is established.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -339,7 +340,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -368,12 +378,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-13 06:45 UTC diff --git a/pages/traits/physiology/galvanotaxis.html b/pages/traits/physiology/galvanotaxis.html index 84edfbbf0ff..8f7a2d2bb9e 100644 --- a/pages/traits/physiology/galvanotaxis.html +++ b/pages/traits/physiology/galvanotaxis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1101/sqb.1988.053.01.006
    movement of a motile organism or cell in direct response to an electric current
    -

    Adler and Shi, publisher's freely accessible Excerpt, https://symposium.cshlp.org/content/53/23.short. The full paywalled paper was not accessed. The disposition requires active motility; passive electrophoretic displacement alone is insufficient.

    +

    Adler and Shi, publisher's freely accessible Excerpt, https://symposium.cshlp.org/content/53/23.short. The full paywalled paper was not accessed. The disposition requires active motility; passive electrophoretic displacement alone is insufficient.

  • DOI:10.1128/jb.178.4.1113-1119.1996
    motile Escherichia coli K-12 placed in an electric field swims toward the anode
    -

    Shi, Stocker and Adler, primary abstract (PMID:8576046), verified through Europe PMC. Rough K-12 and smooth Salmonella differ in direction; surface composition and capsules qualify the response. Only the abstract was accessed, not the full paper.

    +

    Shi, Stocker and Adler, primary abstract (PMID:8576046), verified through Europe PMC. Rough K-12 and smooth Salmonella differ in direction; surface composition and capsules qualify the response. Only the abstract was accessed, not the full paper.

    • @@ -126,7 +127,7 @@

    Edge evidence

  • https://www.ebi.ac.uk/interpro/entry/InterPro/IPR001492/ Flagellin is the subunit protein that polymerises to form the flagella - InterPro IPR001492 family description, verified through https://www.ebi.ac.uk/interpro/api/entry/interpro/IPR001492/ on 2026-10-03. This is a family, not merely an N- or C-terminal domain. Filament assembly and the motor are also required; flagellin alone is not sufficient for movement. + InterPro IPR001492 family description, verified through https://www.ebi.ac.uk/interpro/api/entry/interpro/IPR001492/ on 2026-10-03. This is a family, not merely an N- or C-terminal domain. Filament assembly and the motor are also required; flagellin alone is not sufficient for movement.
    • @@ -156,7 +157,7 @@

    Edge evidence

    confers galvanotaxis - traitmech:000581 + traitmech:000581 METPO:2007700

    Electric-field-guided active movement realizes the galvanotaxis phenotype.

      @@ -193,8 +194,8 @@

      Protein and taxon examples

    		 - Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S -
    NCBITaxon:588858 + Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S +
    NCBITaxon:588858         		UNREVIEWED
    @@ -207,7 +208,7 @@

    Protein and taxon examples

  • DOI:10.1038/s41564-024-01778-8 Most of these mutants were non-motile - Results, flagellar-mutant paragraph and Supplementary Table 1: SW473 is an IR715 fliC/fljB double mutant. The exact 14028S FliC identity, taxon and versions were resolved at https://www.ebi.ac.uk/proteins/api/proteins/A0A0F6B2U2; https://rest.uniprot.org/proteomes/UP000002695.json confirms reference-proteome membership. UniProtKB REST protein requests failed during retrieval; the EBI Proteins API supplied the metadata. This accession anchors the strain background, not an experimentally sequenced SW473 protein. + Results, flagellar-mutant paragraph and Supplementary Table 1: SW473 is an IR715 fliC/fljB double mutant. The exact 14028S FliC identity, taxon and versions were resolved at https://www.ebi.ac.uk/proteins/api/proteins/A0A0F6B2U2; https://rest.uniprot.org/proteomes/UP000002695.json confirms reference-proteome membership. UniProtKB REST protein requests failed during retrieval; the EBI Proteins API supplied the metadata. This accession anchors the strain background, not an experimentally sequenced SW473 protein.
    • @@ -267,7 +268,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -403,7 +404,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    DOI:10.1128/jb.178.4.1113-1119.1996 proposes differential electrophoretic mobility of the body and flagellar filaments as an orientation model. DOI:10.1038/s41564-024-01778-8 observes flagellar redistribution and a largely non-motile double mutant; it does not establish a universal receptor circuit or separate the individual flagellin contributions. A cheB mutant retains the electrical response. The source's weakly biased B. subtilis assay is not a robust canonical example. Physical orientation can guide powered locomotion, but fixed-cell drift alone is not this phenotype. QuickGO searches for galvanotaxis and electrotaxis found no exact term on 2026-10-03; MeSH Taxis Response is broader and excluded from xrefs. GO:0071973 grounds only the flagellar process.

    +

    DOI:10.1128/jb.178.4.1113-1119.1996 proposes differential electrophoretic mobility of the body and flagellar filaments as an orientation model. DOI:10.1038/s41564-024-01778-8 observes flagellar redistribution and a largely non-motile double mutant; it does not establish a universal receptor circuit or separate the individual flagellin contributions. A cheB mutant retains the electrical response. The source's weakly biased B. subtilis assay is not a robust canonical example. Physical orientation can guide powered locomotion, but fixed-cell drift alone is not this phenotype. QuickGO searches for galvanotaxis and electrotaxis found no exact term on 2026-10-03; MeSH Taxis Response is broader and excluded from xrefs. GO:0071973 grounds only the flagellar process.

    @@ -433,7 +434,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Sun et al., Figure 5d and Results report negative directedness for E. coli and positive for Salmonella. The source workbook's Fig. 5d,e sheet labels Red to anode and Green to cathode but contains opposite-signed cosine values. Direction labels agree with Figure 5c and the 1996 primary abstract; the coordinate conventions need reconciliation. No numerical directedness values are imported and no correction is inferred. Source: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-024-01778-8/MediaObjects/41564_2024_1778_MOESM10_ESM.xlsx

    +

    Sun et al., Figure 5d and Results report negative directedness for E. coli and positive for Salmonella. The source workbook's Fig. 5d,e sheet labels Red to anode and Green to cathode but contains opposite-signed cosine values. Direction labels agree with Figure 5c and the 1996 primary abstract; the coordinate conventions need reconciliation. No numerical directedness values are imported and no correction is inferred. Source: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-024-01778-8/MediaObjects/41564_2024_1778_MOESM10_ESM.xlsx

    @@ -497,7 +498,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -861,12 +871,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 23:24 UTC diff --git a/pages/traits/physiology/galvanotropism.html b/pages/traits/physiology/galvanotropism.html index 5da090ece07..69be1b986d0 100644 --- a/pages/traits/physiology/galvanotropism.html +++ b/pages/traits/physiology/galvanotropism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1128/jb.176.3.702-713.1994
    Field-treated (but not control) Enterobacter cloacae and Escherichia coli cells curved rapidly toward the anode.
    -

    Abstract, exact-matched at Europe PMC (PMID:8300526; PMCID:PMC205108); full text not inspected. Curvature depended on field strength and pH and reversed with field polarity. The authors report controls excluding passive bending and field-induced gradients of tropic substances in their assay. Bacillus subtilis required a higher field threshold. Spatial wall-growth measurements support growth asymmetry, not a resolved universal electrical sensor. The historical actin-absence premise is not adopted as current biology.

    +

    Abstract, exact-matched at Europe PMC (PMID:8300526; PMCID:PMC205108); full text not inspected. Curvature depended on field strength and pH and reversed with field polarity. The authors report controls excluding passive bending and field-induced gradients of tropic substances in their assay. Bacillus subtilis required a higher field threshold. Spatial wall-growth measurements support growth asymmetry, not a resolved universal electrical sensor. The historical actin-absence premise is not adopted as current biology.

  • DOI:10.1099/00221287-136-2-311
    germ tubes grew unidirectionally towards the cathode for extended periods and did not deviate to a perpendicular orientation.
    -

    Abstract, exact-matched at Europe PMC (PMID:2182770); full text not inspected. Candida albicans cells were attached to polylysine-coated slides. Budding and germ-tube emergence sites, as well as subsequent growth, were biased toward the cathode. Higher fields delayed emergence and reduced extension rate; those effects are not themselves directional growth. Cathodal growth here does not imply one electrode preference for all microbial galvanotropism.

    +

    Abstract, exact-matched at Europe PMC (PMID:2182770); full text not inspected. Candida albicans cells were attached to polylysine-coated slides. Budding and germ-tube emergence sites, as well as subsequent growth, were biased toward the cathode. Higher fields delayed emergence and reduced extension rate; those effects are not themselves directional growth. Cathodal growth here does not imply one electrode preference for all microbial galvanotropism.

  • DOI:10.1016/j.cub.2006.12.043
    extending hyphae grew toward the cathode and reoriented their direction of growth when the field polarity was reversed
    -

    Full-text Results, Calcium Ions and CaCch1p Mediate Cathodal Germ-Tube Emergence (PMID:17275302; PMCID:PMC1885950), https://pmc.ncbi.nlm.nih.gov/articles/PMC1885950/. Exact contiguous JATS paragraph span, not an abstract quote. Main Figs. 1 and 2 and supplemental Table S1 were inspected. The quoted response occurred even in low-calcium medium. Calcium depletion, channel blockers and CCH1 deletion primarily reduced cathodal emergence; after six hours, tip orientation could recover. Calcineurin perturbations affected cathodal emergence, not thigmotropism. Localized channel activation is a proposed model, not direct proof of a universal sensor. The supplement identifies CAI4/CIp10 as the isogenic control (NGY152) and lists engineered derivatives. These are qualified experimental backgrounds, not verified natural canonical exemplars.

    +

    Full-text Results, Calcium Ions and CaCch1p Mediate Cathodal Germ-Tube Emergence (PMID:17275302; PMCID:PMC1885950), https://pmc.ncbi.nlm.nih.gov/articles/PMC1885950/. Exact contiguous JATS paragraph span, not an abstract quote. Main Figs. 1 and 2 and supplemental Table S1 were inspected. The quoted response occurred even in low-calcium medium. Calcium depletion, channel blockers and CCH1 deletion primarily reduced cathodal emergence; after six hours, tip orientation could recover. Calcineurin perturbations affected cathodal emergence, not thigmotropism. Localized channel activation is a proposed model, not direct proof of a universal sensor. The supplement identifies CAI4/CIp10 as the isogenic control (NGY152) and lists engineered derivatives. These are qualified experimental backgrounds, not verified natural canonical exemplars.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -277,7 +278,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add electric-field-directed growth with stage-specific evidence limits -

      Minted traitmech:000595 under phenotype with three primary DOI sources: 10.1128/jb.176.3.702-713.1994, 10.1099/00221287-136-2-311 and 10.1016/j.cub.2006.12.043. The first two snippets are abstract spans; the third was inspected directly in PMC1885950 full text. Brand Figs. 1 and 2 and supplemental Table S1 distinguish emergence from later tip orientation and identify engineered CAI4/CIp10 control NGY152. No natural canonical example, protein accession or mechanism graph is inferred. Ignored-and-hidden novelty searches and structured OWL review distinguish galvanotaxis and thigmotropism. Reserved METPO:1054900 in proposal v472. The guarded writer passed seven focused tests; skill guidance now separates establishment and maintenance readouts. README counts and maintained derived artifacts are updated in this change; full validation outcomes belong in the PR receipt.

    +

    Minted traitmech:000595 under phenotype with three primary DOI sources: 10.1128/jb.176.3.702-713.1994, 10.1099/00221287-136-2-311 and 10.1016/j.cub.2006.12.043. The first two snippets are abstract spans; the third was inspected directly in PMC1885950 full text. Brand Figs. 1 and 2 and supplemental Table S1 distinguish emergence from later tip orientation and identify engineered CAI4/CIp10 control NGY152. No natural canonical example, protein accession or mechanism graph is inferred. Ignored-and-hidden novelty searches and structured OWL review distinguish galvanotaxis and thigmotropism. Reserved METPO:1054900 in proposal v472. The guarded writer passed seven focused tests; skill guidance now separates establishment and maintenance readouts. README counts and maintained derived artifacts are updated in this change; full validation outcomes belong in the PR receipt.

    • Read this curation session @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 11:12 UTC diff --git a/pages/traits/physiology/gamma_glutamyltransferase_activity.html b/pages/traits/physiology/gamma_glutamyltransferase_activity.html index 01864012ee6..9fdfe21fb6a 100644 --- a/pages/traits/physiology/gamma_glutamyltransferase_activity.html +++ b/pages/traits/physiology/gamma_glutamyltransferase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -112,11 +113,11 @@

    Parent traits (1)

    Synonyms (3)

    @@ -132,7 +133,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -282,7 +283,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record pairs one IUBMB EC 3.4.19.13 reaction snippet with two diagnostic strain-phenotyping snippets (DOI:10.3389/fgene.2023.1240581), leaving only one catalytic reaction quote.

    +

    The current record pairs one IUBMB EC 3.4.19.13 reaction snippet with two diagnostic strain-phenotyping snippets (DOI:10.3389/fgene.2023.1240581), leaving only one catalytic reaction quote.

    @@ -364,7 +365,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -393,12 +403,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/gelatinase_activity.html b/pages/traits/physiology/gelatinase_activity.html index 9b5f24009d9..9946a37ba1d 100644 --- a/pages/traits/physiology/gelatinase_activity.html +++ b/pages/traits/physiology/gelatinase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,9 +107,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -124,7 +125,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -356,7 +357,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -385,12 +395,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/glutamyl_glutamic_acid_arylamidase_activity.html b/pages/traits/physiology/glutamyl_glutamic_acid_arylamidase_activity.html index b587e03419f..00a15ee6ec9 100644 --- a/pages/traits/physiology/glutamyl_glutamic_acid_arylamidase_activity.html +++ b/pages/traits/physiology/glutamyl_glutamic_acid_arylamidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • glutamyl glutamic acid arylamidase RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
      • +
    • glutamyl glutamic acid arylamidase RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
    @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -272,7 +273,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two diagnostic enzyme-panel survey snippets (DOI:10.1099/ijsem.0.006017, DOI:10.1099/ijs.0.63642-0) without verbatim catalytic reaction or enzyme-mechanism quotes.

    +

    The current record carries two diagnostic enzyme-panel survey snippets (DOI:10.1099/ijsem.0.006017, DOI:10.1099/ijs.0.63642-0) without verbatim catalytic reaction or enzyme-mechanism quotes.

    @@ -354,7 +355,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -383,12 +393,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/glycine_arylamidase_activity.html b/pages/traits/physiology/glycine_arylamidase_activity.html index 42ef640d54e..abde110564b 100644 --- a/pages/traits/physiology/glycine_arylamidase_activity.html +++ b/pages/traits/physiology/glycine_arylamidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • glycine arylamidase RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
      • +
    • glycine arylamidase RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
    @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -354,7 +355,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -383,12 +393,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/gravikinesis.html b/pages/traits/physiology/gravikinesis.html index a1462097f99..c051d347880 100644 --- a/pages/traits/physiology/gravikinesis.html +++ b/pages/traits/physiology/gravikinesis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.2187/bss.20.44
    We confirmed the gravikinesis from the analysis on the swimming of single cells.
    -

    Abstract; full publisher PDF inspected at https://www.jstage.jst.go.jp/article/bss/20/2/20_2_44/_pdf. Methods and Results (pages 45-46, Table 1) distinguish active propulsion from passive drift using subsequent 10-18 mM NiCl2 immobilization of the same cell. The drift controls retained contractile-vacuole activity and lacked visible deformation. Curved-swimmer responses reverse in 72% Percoll; straight-swimmer responses were not significant. Results N=55 and Table 1 straight-swimmer N=57 are unreconciled; no aggregate sample count is asserted. Table and method pages were visually checked.

    +

    Abstract; full publisher PDF inspected at https://www.jstage.jst.go.jp/article/bss/20/2/20_2_44/_pdf. Methods and Results (pages 45-46, Table 1) distinguish active propulsion from passive drift using subsequent 10-18 mM NiCl2 immobilization of the same cell. The drift controls retained contractile-vacuole activity and lacked visible deformation. Curved-swimmer responses reverse in 72% Percoll; straight-swimmer responses were not significant. Results N=55 and Table 1 straight-swimmer N=57 are unreconciled; no aggregate sample count is asserted. Table and method pages were visually checked.

  • DOI:10.1007/s001140050634
    The resulting potential-induced modulation of the speed of propulsion is called gravikinesis because it acts to neutralize, fully or in part, sedimentation.
    -

    Publisher abstract and Europe PMC PMID:11536922 checked. Orientation-dependent membrane-potential changes support a physiological component of propulsion control in Paramecium. The sedimentation-opposing response described here is not a universal sign convention or proof of one receptor in all taxa. The subscription full text was not inspected; no strain, channel accession or full-text-only measurement is inferred.

    +

    Publisher abstract and Europe PMC PMID:11536922 checked. Orientation-dependent membrane-potential changes support a physiological component of propulsion control in Paramecium. The sedimentation-opposing response described here is not a universal sign convention or proof of one receptor in all taxa. The subscription full text was not inspected; no strain, channel accession or full-text-only measurement is inferred.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -296,7 +297,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add gravity-relative active-propulsion phenotype -

      Created traitmech:000585 gravikinesis under motile (METPO:1000702) from DOI:10.2187/bss.20.44 and DOI:10.1007/s001140050634 with contiguous abstract snippets. Takeda full text and method/table images were inspected; Gebauer publisher and Europe PMC abstracts were checked without subscription full text. Qualified NCBITaxon:5885 Paramecium caudatum by culture, surface selection, curved swimming and control medium; nickel immobilization was a subsequent passive-drift control. Preserved unresolved Results/Table 1 counts without an aggregate count. Ignored-and-hidden novelty searches and temporary seeding preceded minting; added proposal v462 with placeholder METPO:1053900. Deferred exact protein-grounded mechanism and kept propulsion, passive drift and orientation distinct in two discussions.

    +

    Created traitmech:000585 gravikinesis under motile (METPO:1000702) from DOI:10.2187/bss.20.44 and DOI:10.1007/s001140050634 with contiguous abstract snippets. Takeda full text and method/table images were inspected; Gebauer publisher and Europe PMC abstracts were checked without subscription full text. Qualified NCBITaxon:5885 Paramecium caudatum by culture, surface selection, curved swimming and control medium; nickel immobilization was a subsequent passive-drift control. Preserved unresolved Results/Table 1 counts without an aggregate count. Ignored-and-hidden novelty searches and temporary seeding preceded minting; added proposal v462 with placeholder METPO:1053900. Deferred exact protein-grounded mechanism and kept propulsion, passive drift and orientation distinct in two discussions.

    • Read this curation session @@ -328,7 +329,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -357,12 +367,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 03:24 UTC diff --git a/pages/traits/physiology/gravitaxis.html b/pages/traits/physiology/gravitaxis.html index 3433b39619d..b3a68730df5 100644 --- a/pages/traits/physiology/gravitaxis.html +++ b/pages/traits/physiology/gravitaxis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1038/s41598-018-26046-8
    Predominantly, E. gracilis shows a negative gravitaxis behavior.
    -

    Introduction, page 1, visually verified at https://d-nb.info/1186379677/34 (PMID:29765103; PMC5954063). Direction varies with culture age. Results, Figure 4 and Supplementary Figure 6e-g distinguish upward-biased controls from EgPCDUF4201/CaM2 knockdowns. Full main text and supplement 41598_2018_26046_MOESM1_ESM.pdf inspected via Europe PMC. Supplementary Figure 5e, not the main text's 5c, measures flagellar length; Supplementary Table 1 reports comparable, not identical, speeds. These controls do not exclude every flagellar defect. PKA phosphorylation and a direct dynein link remain hypotheses.

    +

    Introduction, page 1, visually verified at https://d-nb.info/1186379677/34 (PMID:29765103; PMC5954063). Direction varies with culture age. Results, Figure 4 and Supplementary Figure 6e-g distinguish upward-biased controls from EgPCDUF4201/CaM2 knockdowns. Full main text and supplement 41598_2018_26046_MOESM1_ESM.pdf inspected via Europe PMC. Supplementary Figure 5e, not the main text's 5c, measures flagellar length; Supplementary Table 1 reports comparable, not identical, speeds. These controls do not exclude every flagellar defect. PKA phosphorylation and a direct dynein link remain hypotheses.

  • DOI:10.1242/jeb.050666
    the ability to swim preferentially upwards (negative gravitaxis) is primarily the result of upwardly curving trajectories
    -

    Summary (PMID:21112996); publisher main-text Methods, Results and Discussion inspected. Curved trajectories agree with a physical shape-orientation model, but shape and orientation rate were not measured simultaneously in the same individual. This is not proof that all protists lack gravity receptors. Gravikinesis concerns orientation-dependent swimming speed, not the directional phenotype. Equation images and supplementary material were not inspected; no equation-derived or supplement-only claim is asserted.

    +

    Summary (PMID:21112996); publisher main-text Methods, Results and Discussion inspected. Curved trajectories agree with a physical shape-orientation model, but shape and orientation rate were not measured simultaneously in the same individual. This is not proof that all protists lack gravity receptors. Gravikinesis concerns orientation-dependent swimming speed, not the directional phenotype. Equation images and supplementary material were not inspected; no equation-derived or supplement-only claim is asserted.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -311,7 +312,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add gravity-relative swimming trait -

      Added traitmech:000584 gravitaxis under motile with DOI:10.1038/s41598-018-26046-8 and DOI:10.1242/jeb.050666, contiguous snippets, species-qualified Euglena gracilis and Paramecium caudatum examples, and companion METPO proposal v461 reserving METPO:1053800. Ignored-and-hidden searches found no exact existing record. Read primary text and Nasir supplement; verified the flagellar-length panel is Supplementary Figure 5e despite the main-text 5c pointer. Kept GO process equivalence and exact protein/physical-graph representation gaps explicit. Wrote through write_validated_trait and record_curation_event.

    +

    Added traitmech:000584 gravitaxis under motile with DOI:10.1038/s41598-018-26046-8 and DOI:10.1242/jeb.050666, contiguous snippets, species-qualified Euglena gracilis and Paramecium caudatum examples, and companion METPO proposal v461 reserving METPO:1053800. Ignored-and-hidden searches found no exact existing record. Read primary text and Nasir supplement; verified the flagellar-length panel is Supplementary Figure 5e despite the main-text 5c pointer. Kept GO process equivalence and exact protein/physical-graph representation gaps explicit. Wrote through write_validated_trait and record_curation_event.

    • Read this curation session @@ -343,7 +344,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -372,12 +382,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 02:22 UTC diff --git a/pages/traits/physiology/gravitropism.html b/pages/traits/physiology/gravitropism.html index 93b2a508c45..6661003e2f9 100644 --- a/pages/traits/physiology/gravitropism.html +++ b/pages/traits/physiology/gravitropism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.4161/cib.22291
    Phycomyces sporangiophores grow in the air and display negative gravitropic bending upon displacement from vertical position.
    -

    Intracellular Reorganization upon Gravistimulation; exact contiguous Europe PMC full-text XML (PMID:23650568; PMC3642927). The full article and all three figure images were inspected. Figure 1 shows bending growth of an intact wild-type stage I sporangiophore after a 45-degree tilt; no strain identifier is given. Figure 2 concerns intracellular reorganization, and Figure 3 measures touch-induced ion fluxes, not a gravity assay. The author explicitly leaves open whether vacuolization reflects gravity signaling or coincident development. The article declares no supplement; the Europe PMC supplementaryFiles download contained ordinary figure assets.

    +

    Intracellular Reorganization upon Gravistimulation; exact contiguous Europe PMC full-text XML (PMID:23650568; PMC3642927). The full article and all three figure images were inspected. Figure 1 shows bending growth of an intact wild-type stage I sporangiophore after a 45-degree tilt; no strain identifier is given. Figure 2 concerns intracellular reorganization, and Figure 3 measures touch-induced ion fluxes, not a gravity assay. The author explicitly leaves open whether vacuolization reflects gravity signaling or coincident development. The article declares no supplement; the Europe PMC supplementaryFiles download contained ordinary figure assets.

  • DOI:10.1078/0176-1617-01082
    The threshold for the polar angle of the wild type NRRL 1555 (with crystals) is near 8 x 10(-2) x g.
    -

    Abstract, exact-matched at Europe PMC (PMID:15266721). A clinostat centrifuge measures negative gravitropic bending of Phycomyces blakesleeanus sporangiophores. Polar angle and aiming-error angle are distinct readouts; the quoted value belongs to the wild-type polar angle, not the mutant strains or aiming error. It is assay-specific, not a universal threshold. Subscription full text and figures were not inspected.

    +

    Abstract, exact-matched at Europe PMC (PMID:15266721). A clinostat centrifuge measures negative gravitropic bending of Phycomyces blakesleeanus sporangiophores. Polar angle and aiming-error angle are distinct readouts; the quoted value belongs to the wild-type polar angle, not the mutant strains or aiming error. It is assay-specific, not a universal threshold. Subscription full text and figures were not inspected.

  • DOI:10.1007/s004250050744
    In rhizoids, positive gravitropic curvature is caused by differential growth limited to the opposite subapical flanks of the apical dome
    -

    Abstract, exact-matched at Europe PMC (PMID:10550622). The primary Chara study describes downward-positive rhizoid growth and upward-negative protonematal growth. This supports polarity-neutral terminology, not positive gravitropism in Phycomyces. The remainder of the quoted sentence excludes displacement of the rhizoid growth centre, calcium gradient or channels. No Chara mechanism or canonical taxon is transferred to the fungus; full text and figures were not inspected.

    +

    Abstract, exact-matched at Europe PMC (PMID:10550622). The primary Chara study describes downward-positive rhizoid growth and upward-negative protonematal growth. This supports polarity-neutral terminology, not positive gravitropism in Phycomyces. The remainder of the quoted sentence excludes displacement of the rhizoid growth centre, calcium gradient or channels. No Chara mechanism or canonical taxon is transferred to the fungus; full text and figures were not inspected.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1078/0176-1617-01082 - Wild-type sporangiophore negative gravitropic bending in the clinostat-centrifuge study, with a source-qualified polar-angle threshold. This is not a mutant example and is not assigned the unnamed 2013 study's stage I observations. Natural-isolate provenance: DOI:10.1128/EC.00203-13, Materials and Methods, Strains and growth conditions (https://pmc.ncbi.nlm.nih.gov/articles/PMC3910969/); NRRL1555 is distinguished from backcrossed A56. Exact strain name and rank resolved directly at NCBI Taxonomy on 2026-10-04. + Wild-type sporangiophore negative gravitropic bending in the clinostat-centrifuge study, with a source-qualified polar-angle threshold. This is not a mutant example and is not assigned the unnamed 2013 study's stage I observations. Natural-isolate provenance: DOI:10.1128/EC.00203-13, Materials and Methods, Strains and growth conditions (https://pmc.ncbi.nlm.nih.gov/articles/PMC3910969/); NRRL1555 is distinguished from backcrossed A56. Exact strain name and rank resolved directly at NCBI Taxonomy on 2026-10-04. @@ -308,7 +309,7 @@

    Recorded curation sessions

  • · codex
    • AUDIT — Correct gravitropism creation-history section attribution -

      Addresses issue #1674. This record supersedes only the events[0].sections claim in history/records/gravitropism/2026-10-04T153928Z-codex-c87cd2.yaml, which is preserved byte-for-byte under the append-only policy. The correct CREATE sections are identity, evidence, canonical_examples, and discussions: two discussions were added and no causal_graphs slot was written. The TraitRecord and its per-record curation_history remain unchanged. Audited the cited source questions: official PMC3642927 XML identifies a brief-report/Short Communication with original microscopy and places the quoted negative-bending sentence in the first paragraph under Intracellular Reorganization upon Gravistimulation, not a separate Introduction section. Updated add-trait scaffold guidance to require actual touched sections and append-only provenance corrections. No new biological claims, artifacts, or record-count changes are introduced.

    +

    Addresses issue #1674. This record supersedes only the events[0].sections claim in history/records/gravitropism/2026-10-04T153928Z-codex-c87cd2.yaml, which is preserved byte-for-byte under the append-only policy. The correct CREATE sections are identity, evidence, canonical_examples, and discussions: two discussions were added and no causal_graphs slot was written. The TraitRecord and its per-record curation_history remain unchanged. Audited the cited source questions: official PMC3642927 XML identifies a brief-report/Short Communication with original microscopy and places the quoted negative-bending sentence in the first paragraph under Intracellular Reorganization upon Gravistimulation, not a separate Introduction section. Updated add-trait scaffold guidance to require actual touched sections and append-only provenance corrections. No new biological claims, artifacts, or record-count changes are introduced.

    • Read this curation session @@ -340,7 +341,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -369,12 +379,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 16:09 UTC diff --git a/pages/traits/physiology/gyrotaxis.html b/pages/traits/physiology/gyrotaxis.html index 5698c1358f8..e72b127e6c9 100644 --- a/pages/traits/physiology/gyrotaxis.html +++ b/pages/traits/physiology/gyrotaxis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1073/pnas.2206738119
    The orientational response to the gravity-viscous torque balance is known as gyrotaxis
    -

    Introduction, page 1; definition checked against the publisher-formatted article deposited by the authors at https://api.repository.cam.ac.uk/server/api/core/bitstreams/ac9ccafe-f229-477c-9d59-b7a56cd506a0/content (PMID:36219692; PMC9586295). The second of the introduction's three accumulation mechanisms starts 'The second is response to an external field': it describes swimming in still water and gravitational restoration resisted hydrodynamically, then names this response gyrotaxis. This record follows Zeng's broader usage, not a universal requirement or exclusion of imposed shear. Results, Figures 5-7, and Materials and Methods distinguish gravitational reorientation from wall-contact effects in Heterosigma akashiwo GY-H24. Shape asymmetry and density asymmetry are alternatives; bottom-heaviness is not universal. The full main article was read; supplementary material and movies were not inspected. No gravity-sensing receptor is asserted.

    +

    Introduction, page 1; definition checked against the publisher-formatted article deposited by the authors at https://api.repository.cam.ac.uk/server/api/core/bitstreams/ac9ccafe-f229-477c-9d59-b7a56cd506a0/content (PMID:36219692; PMC9586295). The second of the introduction's three accumulation mechanisms starts 'The second is response to an external field': it describes swimming in still water and gravitational restoration resisted hydrodynamically, then names this response gyrotaxis. This record follows Zeng's broader usage, not a universal requirement or exclusion of imposed shear. Results, Figures 5-7, and Materials and Methods distinguish gravitational reorientation from wall-contact effects in Heterosigma akashiwo GY-H24. Shape asymmetry and density asymmetry are alternatives; bottom-heaviness is not universal. The full main article was read; supplementary material and movies were not inspected. No gravity-sensing receptor is asserted.

  • DOI:10.1126/science.1167334
    The swimming direction, θ, is then set by the balance of viscous and gravitactic torques
    -

    Page 1068, left column beneath Figure 2; the typeset theta in the torque-balance sentence was visually checked because PDF extraction substitutes q. This passage concerns imposed shear. Live-cell experiments are on pages 1067-1069 of the full main article at https://stockerlab.ethz.ch/wp-content/uploads/2013/01/17.-DurhamKesslerStocker_Science2009.pdf (PMID:19229037). Chlamydomonas nivalis and Heterosigma akashiwo formed layers in a depth-varying shear chamber; dead cells did not. Gyrotactic trapping is a population consequence under suitable shear, not the definition of the organismal trait or the cause of every oceanic thin layer. Ocean-scale results are model predictions. The supplement and exact culture identities were not verified; no strain or modern C. nivalis taxon identity is inferred.

    +

    Page 1068, left column beneath Figure 2; the typeset theta in the torque-balance sentence was visually checked because PDF extraction substitutes q. This passage concerns imposed shear. Live-cell experiments are on pages 1067-1069 of the full main article at https://stockerlab.ethz.ch/wp-content/uploads/2013/01/17.-DurhamKesslerStocker_Science2009.pdf (PMID:19229037). Chlamydomonas nivalis and Heterosigma akashiwo formed layers in a depth-varying shear chamber; dead cells did not. Gyrotactic trapping is a population consequence under suitable shear, not the definition of the organismal trait or the cause of every oceanic thin layer. Ocean-scale results are model predictions. The supplement and exact culture identities were not verified; no strain or modern C. nivalis taxon identity is inferred.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -278,7 +279,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Anchor gyrotaxis snippets and still-water scope after review -

      Addressed PR 1646 review findings: replaced the Durham abstract population-outcome snippet with a torque-balance span from page 1068, visually preserving the typeset theta rather than the extractor q. Anchored Zeng's broader still-water usage to the specific page-1 introduction passage and qualified the GY-H24 example. Definition and parent unchanged. Updated guarded writer, tests, proposal, add-trait PDF and source-usage guidance, and generated artifacts. Issue 1648: https://github.com/CultureBotAI/TraitMech/issues/1648

    +

    Addressed PR 1646 review findings: replaced the Durham abstract population-outcome snippet with a torque-balance span from page 1068, visually preserving the typeset theta rather than the extractor q. Anchored Zeng's broader still-water usage to the specific page-1 introduction passage and qualified the GY-H24 example. Definition and parent unchanged. Updated guarded writer, tests, proposal, add-trait PDF and source-usage guidance, and generated artifacts. Issue 1648: https://github.com/CultureBotAI/TraitMech/issues/1648

    • Read this curation session @@ -310,7 +311,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -339,12 +349,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 01:43 UTC diff --git a/pages/traits/physiology/haptocyst_discharge.html b/pages/traits/physiology/haptocyst_discharge.html index 5941dac5feb..d814cbd518f 100644 --- a/pages/traits/physiology/haptocyst_discharge.html +++ b/pages/traits/physiology/haptocyst_discharge.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1515/znc-1984-7-821
    The fine structure of haptocysts, characteristic organelles of most suctorians, is described during the resting state and the discharge after contact with the prey.
    -

    Benwitz 1984, English abstract reproduced at https://www.nies.go.jp/chiiki1/protoz/refere/id4999/4538.htm, read directly on 2026-10-10. Crossref confirms the DOI, title, author and original 1984 publication; later online dates are not the experiment year. In Ephelota gemmipara the abstract reports prey-contact discharge, continuity of the haptocyst membrane with the tentacle plasma membrane, and attachment of internal haptocyst structures to the perforated prey pellicle. It explicitly reports no predator-prey plasma-membrane fusion in Ephelota. These observations support release to the cell exterior, not cell-cell fusion or merely possession of haptocysts. The publisher PDF was unavailable; figures and full Methods were not visually audited. No universal cargo chemistry or trigger is inferred.

    +

    Benwitz 1984, English abstract reproduced at https://www.nies.go.jp/chiiki1/protoz/refere/id4999/4538.htm, read directly on 2026-10-10. Crossref confirms the DOI, title, author and original 1984 publication; later online dates are not the experiment year. In Ephelota gemmipara the abstract reports prey-contact discharge, continuity of the haptocyst membrane with the tentacle plasma membrane, and attachment of internal haptocyst structures to the perforated prey pellicle. It explicitly reports no predator-prey plasma-membrane fusion in Ephelota. These observations support release to the cell exterior, not cell-cell fusion or merely possession of haptocysts. The publisher PDF was unavailable; figures and full Methods were not visually audited. No universal cargo chemistry or trigger is inferred.

  • DOI:10.1007/BF00331480
    By these haptocysts the tentacle is attached to the prey.
    -

    Bardele and Grell 1967, PMID:4971424. Publisher English Summary points 1-2 at https://link.springer.com/article/10.1007/BF00331480 read directly on 2026-10-10. The source identifies the tentacular organelles in Acineta tuberosa as haptocysts and describes prey attachment. This is independent organelle-identity and attachment evidence, not a second direct discharge experiment. Its ingestion tube hypothesis is not a demonstrated haptocyst release mechanism. Full text is subscription-only and was not inspected.

    +

    Bardele and Grell 1967, PMID:4971424. Publisher English Summary points 1-2 at https://link.springer.com/article/10.1007/BF00331480 read directly on 2026-10-10. The source identifies the tentacular organelles in Acineta tuberosa as haptocysts and describes prey attachment. This is independent organelle-identity and attachment evidence, not a second direct discharge experiment. Its ingestion tube hypothesis is not a demonstrated haptocyst release mechanism. Full text is subscription-only and was not inspected.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -271,7 +272,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add source-bounded haptocyst discharge phenotype -

      Added PROPOSED traitmech:000686 with Benwitz 1984 DOI:10.1515/znc-1984-7-821 discharge evidence and Bardele and Grell 1967 DOI:10.1007/BF00331480 organelle identity and attachment evidence, using directly read abstract/Summary snippets. Distinguishes organelle-plasma-membrane continuity from predator-prey fusion. Leaves the exocytosis hierarchy, natural canonical exemplars and protein mechanism unresolved. Ignored-and-hidden searches across main, all 22 existing worktrees, CommunityMech and exact open PR heads support novelty and the v562 block METPO:1063900-1063999. The guarded writer validates before explicit apply; no existing trait was changed. No causal graph, xref, synonym, taxon or protein accession is asserted.

    +

    Added PROPOSED traitmech:000686 with Benwitz 1984 DOI:10.1515/znc-1984-7-821 discharge evidence and Bardele and Grell 1967 DOI:10.1007/BF00331480 organelle identity and attachment evidence, using directly read abstract/Summary snippets. Distinguishes organelle-plasma-membrane continuity from predator-prey fusion. Leaves the exocytosis hierarchy, natural canonical exemplars and protein mechanism unresolved. Ignored-and-hidden searches across main, all 22 existing worktrees, CommunityMech and exact open PR heads support novelty and the v562 block METPO:1063900-1063999. The guarded writer validates before explicit apply; no existing trait was changed. No causal graph, xref, synonym, taxon or protein accession is asserted.

    • Read this curation session @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-10 01:52 UTC diff --git a/pages/traits/physiology/heat_shock_response.html b/pages/traits/physiology/heat_shock_response.html index 8a787961355..fa79fb6a699 100644 --- a/pages/traits/physiology/heat_shock_response.html +++ b/pages/traits/physiology/heat_shock_response.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -225,7 +226,7 @@

    Edge evidence

    confers heat shock response - traitmech:000205 + traitmech:000205 METPO:2007700

    Restoration of protein-folding homeostasis realizes the heat-shock-response trait.

      @@ -262,8 +263,8 @@

      Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -292,8 +293,8 @@

    Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -359,9 +360,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -377,7 +378,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -577,7 +578,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -941,12 +951,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 04:58 UTC diff --git a/pages/traits/physiology/heterokaryon_incompatibility.html b/pages/traits/physiology/heterokaryon_incompatibility.html index ea9ca82a13d..78793e9f7aa 100644 --- a/pages/traits/physiology/heterokaryon_incompatibility.html +++ b/pages/traits/physiology/heterokaryon_incompatibility.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1099/mic.0.032284-0
    Incompatible heterokaryons show a macroscopic phenotype of slow growth and diminished conidiation, and a microscopic phenotype of hyphal compartmentation and cell death.
    -

    Hutchison et al. (2009), PMID:19696111. The directly retrieved Europe PMC abstract and publisher abstract identify nonself recognition during fusion between strains differing at het loci, with restricted growth and localized cell death. This supports postfusion heterokaryon incompatibility, not failure to approach or fuse. The study combines transcriptional profiling with functional analysis of het-c pin-c incompatibility in Neurospora crassa. Transcript associations do not establish causal edges; the abstract reports that tested caspase and AIF homologues were not required. Full text, figures and supplements were not retrieved, so no detailed assay or protein-dependency claim beyond the abstract is asserted.

    +

    Hutchison et al. (2009), PMID:19696111. The directly retrieved Europe PMC abstract and publisher abstract identify nonself recognition during fusion between strains differing at het loci, with restricted growth and localized cell death. This supports postfusion heterokaryon incompatibility, not failure to approach or fuse. The study combines transcriptional profiling with functional analysis of het-c pin-c incompatibility in Neurospora crassa. Transcript associations do not establish causal edges; the abstract reports that tested caspase and AIF homologues were not required. Full text, figures and supplements were not retrieved, so no detailed assay or protein-dependency claim beyond the abstract is asserted.

  • DOI:10.1016/s1087-1845(03)00086-0
    Hyphal fusion cells in compatible self-pairings and hyphal cells in het-c compatible transformants were not compartmentalized and rarely showed TUNEL-positive nuclei.
    -

    Marek et al. (2003), PMID:14516765; snippet exact-matched to the directly retrieved Europe PMC abstract. Incompatible Neurospora crassa pairings differing at mat, het-c and het-6 were compared with compatible self-pairings; separate transformant experiments tested incompatible het-c alleles. The abstract reports septal compartmentation and nuclear DNA degradation in incompatible cells, contrasted with the quoted controls. TUNEL and apoptosis-like morphology do not identify a conserved metazoan apoptosis pathway. Death also occurred in older hyphae, so death alone is not specific for this trait. Full text, figures, supplements and original strain provenance were not inspected; no natural canonical exemplar is inferred from the transformed assay.

    +

    Marek et al. (2003), PMID:14516765; snippet exact-matched to the directly retrieved Europe PMC abstract. Incompatible Neurospora crassa pairings differing at mat, het-c and het-6 were compared with compatible self-pairings; separate transformant experiments tested incompatible het-c alleles. The abstract reports septal compartmentation and nuclear DNA degradation in incompatible cells, contrasted with the quoted controls. TUNEL and apoptosis-like morphology do not identify a conserved metazoan apoptosis pathway. Death also occurred in older hyphae, so death alone is not specific for this trait. Full text, figures, supplements and original strain provenance were not inspected; no natural canonical exemplar is inferred from the transformed assay.

  • DOI:10.3852/mycologia.98.1.43
    While clearly forming barrages in mycelial interactions, paired strains with different alleles at vic4 formed stable heterokaryons.
    -

    2006 primary study, PMID:16800303; snippet exact-matched to the directly retrieved Europe PMC abstract. Hygromycin B- and benomyl-resistance forcing markers were used in Cryphonectria parasitica pairings. Differences at vic1, vic2, vic3, vic6 or vic7, but not vic4, produced heterokaryon incompatibility readouts of slow growth or abnormal morphology. The vic4 counterexample separates barrage formation from this trait; the abstract treats heterokaryon incompatibility as a component of a broader vegetative incompatibility system. Vegetative incompatibility is therefore not asserted as an exact synonym. Full text, figures, supplements and marker-strain provenance were not inspected. The DOI and any publisher alias identify one study, not independent replications.

    +

    2006 primary study, PMID:16800303; snippet exact-matched to the directly retrieved Europe PMC abstract. Hygromycin B- and benomyl-resistance forcing markers were used in Cryphonectria parasitica pairings. Differences at vic1, vic2, vic3, vic6 or vic7, but not vic4, produced heterokaryon incompatibility readouts of slow growth or abnormal morphology. The vic4 counterexample separates barrage formation from this trait; the abstract treats heterokaryon incompatibility as a component of a broader vegetative incompatibility system. Vegetative incompatibility is therefore not asserted as an exact synonym. Full text, figures, supplements and marker-strain provenance were not inspected. The DOI and any publisher alias identify one study, not independent replications.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 23:05 UTC diff --git a/pages/traits/physiology/heterothallism.html b/pages/traits/physiology/heterothallism.html index 3c703da2cd7..fe08a85f707 100644 --- a/pages/traits/physiology/heterothallism.html +++ b/pages/traits/physiology/heterothallism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1038/nature07528
    The species has a heterothallic breeding system; isolates of complementary mating types are required for sex to occur.
    -

    O'Gorman et al. (2009), PMID:19043401. Exact scientific-abstract sentence retrieved from Europe PMC core metadata; the publisher abstract was also read. Aspergillus fumigatus produced cleistothecia and ascospores, with recombination between mating type and DNA fingerprint markers in progeny from an Irish environmental subpopulation. This is observed sexual-cycle evidence, not an inference from MAT genes alone. Full methods, figures, supplements and individual isolate provenance remain uninspected; no canonical strain or universal compatibility is asserted. The historical teleomorph name in this abstract is not used as a current taxonomy mapping.

    +

    O'Gorman et al. (2009), PMID:19043401. Exact scientific-abstract sentence retrieved from Europe PMC core metadata; the publisher abstract was also read. Aspergillus fumigatus produced cleistothecia and ascospores, with recombination between mating type and DNA fingerprint markers in progeny from an Irish environmental subpopulation. This is observed sexual-cycle evidence, not an inference from MAT genes alone. Full methods, figures, supplements and individual isolate provenance remain uninspected; no canonical strain or universal compatibility is asserted. The historical teleomorph name in this abstract is not used as a current taxonomy mapping.

  • DOI:10.1534/genetics.111.136358
    Coexpression of pre-2 and ccg-4 in the mat A background leads to self-attraction and development of barren perithecia without ascospores.
    -

    Kim et al. (2012), PMID:22298702. Exact scientific-abstract sentence directly retrieved from Europe PMC core metadata. Neurospora crassa experiments distinguish receptor/pheromone identity from completion of sexual reproduction. The quoted engineered coexpression phenotype is not self-fertility; attraction and fruiting-body initiation alone are insufficient readouts. Forced heterokaryon experiments require mating-type genes in different nuclei for meiosis and sexual sporulation in this study, not a universal fungal architecture. Full text, figures, strain provenance and supplements remain uninspected after PMC access challenges and a full-text API error. This citation supports readout limits, not an independent natural canonical example or a protein-resolved causal graph.

    +

    Kim et al. (2012), PMID:22298702. Exact scientific-abstract sentence directly retrieved from Europe PMC core metadata. Neurospora crassa experiments distinguish receptor/pheromone identity from completion of sexual reproduction. The quoted engineered coexpression phenotype is not self-fertility; attraction and fruiting-body initiation alone are insufficient readouts. Forced heterokaryon experiments require mating-type genes in different nuclei for meiosis and sexual sporulation in this study, not a universal fungal architecture. Full text, figures, strain provenance and supplements remain uninspected after PMC access challenges and a full-text API error. This citation supports readout limits, not an independent natural canonical example or a protein-resolved causal graph.

  • DOI:10.1371/journal.pgen.1006981
    Heterothallic progeny can mate only with homothallic strains, and progeny also segregate 50% homothallic, 50% heterothallic.
    -

    Yun et al. (2017), PMID:28892488. Exact sentence of scientific abstract abstract1 in PMC5608430 full-text XML, distinct from the author summary. Chromocrea spinulosa includes self-fertile and partner-dependent strains: self-sterile here does not mean unable to reproduce sexually with a compatible partner. The stated compatibility and segregation are source-specific, not requirements for all heterothallic fungi. Strain/culture Methods and Conclusions were also read. Cs23 and Cs27 natural provenance, most experiments, actual figures and supplements remain unverified. Nuclear-level heterothallic recognition within a self-fertile organism is not organism-level partner dependence. No canonical example is inferred from unstable Cs27-derived MAT transformants or from reference-strain labels.

    +

    Yun et al. (2017), PMID:28892488. Exact sentence of scientific abstract abstract1 in PMC5608430 full-text XML, distinct from the author summary. Chromocrea spinulosa includes self-fertile and partner-dependent strains: self-sterile here does not mean unable to reproduce sexually with a compatible partner. The stated compatibility and segregation are source-specific, not requirements for all heterothallic fungi. Strain/culture Methods and Conclusions were also read. Cs23 and Cs27 natural provenance, most experiments, actual figures and supplements remain unverified. Nuclear-level heterothallic recognition within a self-fertile organism is not organism-level partner dependence. No canonical example is inferred from unstable Cs27-derived MAT transformants or from reference-strain labels.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 02:11 UTC diff --git a/pages/traits/physiology/heterotrophic.html b/pages/traits/physiology/heterotrophic.html index 34ca5a0c870..a8a489b74fc 100644 --- a/pages/traits/physiology/heterotrophic.html +++ b/pages/traits/physiology/heterotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -413,8 +414,8 @@

    Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -480,11 +481,11 @@

    Parent traits (1)

    Synonyms (3)

      -
    • TT_heterotroph RELATED_SYNONYM · metpo.owl
      • +
    • TT_heterotroph RELATED_SYNONYM · metpo.owl
      • -
    • aerobic_heterotrophy RELATED_SYNONYM · metpo.owl
      • +
    • aerobic_heterotrophy RELATED_SYNONYM · metpo.owl
      • -
    • heterotroph RELATED_SYNONYM · metpo.owl
      • +
    • heterotroph RELATED_SYNONYM · metpo.owl
    @@ -500,7 +501,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -842,7 +843,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1206,12 +1216,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/histidine_arylamidase_activity.html b/pages/traits/physiology/histidine_arylamidase_activity.html index 596c3f8f168..6ce0c010bff 100644 --- a/pages/traits/physiology/histidine_arylamidase_activity.html +++ b/pages/traits/physiology/histidine_arylamidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • histidine arylamidase RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
      • +
    • histidine arylamidase RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
    @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -354,7 +355,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -383,12 +393,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/homeoviscous_adaptation.html b/pages/traits/physiology/homeoviscous_adaptation.html index abdd8f2eb49..06e028eaef9 100644 --- a/pages/traits/physiology/homeoviscous_adaptation.html +++ b/pages/traits/physiology/homeoviscous_adaptation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -206,7 +207,7 @@

    Edge evidence

    METPO:1007505 contributes to homeoviscous adaptation - traitmech:000208 + traitmech:000208 RO:0002326

    Restoration of optimal membrane fluidity is the physiological output of homeoviscous adaptation.

      @@ -243,8 +244,8 @@

      Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -279,8 +280,8 @@

    Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -352,9 +353,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -370,7 +371,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -594,7 +595,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -958,12 +968,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 07:27 UTC diff --git a/pages/traits/physiology/homothallism.html b/pages/traits/physiology/homothallism.html index ce56bfb592d..59a51621455 100644 --- a/pages/traits/physiology/homothallism.html +++ b/pages/traits/physiology/homothallism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.5598/imafungus.2015.06.01.13
    the ability of a single spore to produce a sexually reproducing colony when propagated in complete isolation.
    -

    2015 terminology review, PMID:26203424. Exact contiguous span of the historical operational definition in the Introduction at https://pmc.ncbi.nlm.nih.gov/articles/PMC4500084/. Abstract, Introduction and Conclusions were read as full-text XML; mechanism-specific sections and figures remain uninspected. This is definition authority, not experimental replication. Homothallism is an umbrella encompassing primary homothallism, pseudohomothallism, mating-type switching and unisexual reproduction, not one universal MAT architecture. The snippet is full text, not an abstract quote.

    +

    2015 terminology review, PMID:26203424. Exact contiguous span of the historical operational definition in the Introduction at https://pmc.ncbi.nlm.nih.gov/articles/PMC4500084/. Abstract, Introduction and Conclusions were read as full-text XML; mechanism-specific sections and figures remain uninspected. This is definition authority, not experimental replication. Homothallism is an umbrella encompassing primary homothallism, pseudohomothallism, mating-type switching and unisexual reproduction, not one universal MAT architecture. The snippet is full text, not an abstract quote.

  • DOI:10.1371/journal.pgen.1006981
    The filamentous fungus Chromocrea spinulosa (Trichoderma spinulosum) exhibits both self-fertile (homothallic) and self-sterile (heterothallic) sexual reproductive behavior.
    -

    Yun et al. (2017), PMID:28892488. Exact sentence of the directly retrieved Europe PMC scientific abstract, separate from the author summary. Strain/culture Methods and Conclusions were read at PMC5608430; most main-text experiments, actual figures and supplements remain uninspected. Cs23 and Cs27 are the paper's self-fertile and self-sterile reference strains; their original natural provenance has not been verified. MAT manipulation supports direct-repeat-mediated MAT1-2 loss and recognition between unlike nuclei in a shared cytoplasm. Both intact MAT1-1-1 and MAT1-2-1 in one nucleus are not sufficient for self-fertility. The authors describe a heterothallic strategy at the nuclear level, not primary homothallism, while retaining organism-level self-fertility. Unstable Cs27 transformants were tested directly from transformation plates; do not generalize their stability.

    +

    Yun et al. (2017), PMID:28892488. Exact sentence of the directly retrieved Europe PMC scientific abstract, separate from the author summary. Strain/culture Methods and Conclusions were read at PMC5608430; most main-text experiments, actual figures and supplements remain uninspected. Cs23 and Cs27 are the paper's self-fertile and self-sterile reference strains; their original natural provenance has not been verified. MAT manipulation supports direct-repeat-mediated MAT1-2 loss and recognition between unlike nuclei in a shared cytoplasm. Both intact MAT1-1-1 and MAT1-2-1 in one nucleus are not sufficient for self-fertility. The authors describe a heterothallic strategy at the nuclear level, not primary homothallism, while retaining organism-level self-fertility. Unstable Cs27 transformants were tested directly from transformation plates; do not generalize their stability.

  • DOI:10.7554/elife.79114
    Our findings support C. depauperatus as an obligately sexual, homothallic fungus
    -

    Passer, Clancey et al. (2022), PMID:35713948. Exact independent clause of the scientific abstract in PMC9296135 full-text XML. Europe PMC's abstractText instead returns the eLife digest; a manual scientific-abstract match is not a VERIFIED resolver verdict. Publisher version 2 assets were retrieved through https://api.elifesciences.org/articles/79114. Introduction, strain/culture Methods, deletion-mutant Results and intra-/interstrain crossing and recombination Results were read. Actual Figures 5 and 8 and their captions were inspected; Supplementary file 1 strain rows were read from the publisher's elife-79114-supp1-v2.xlsx. Other figures, supplements and unread Methods remain uninspected. Figure 5 separates wild-type CBS7841 sporulation from pheromone/receptor and DMC1 deletion phenotypes. Hyphal growth alone does not establish meiosis. Figure 8 recombination assays use CBS7841-derived marker strains, including UV-induced and spontaneous mutants, not the unmodified canonical isolate. Drug resistance alone is not evidence of sex; genotyping distinguishes recombination from new mutations. Tested interstrain crosses did not yield PCR-confirmed recombinant progeny, so universal compatibility is not asserted. Obligately sexual describes this source's example, not a requirement for all homothallic fungi.

    +

    Passer, Clancey et al. (2022), PMID:35713948. Exact independent clause of the scientific abstract in PMC9296135 full-text XML. Europe PMC's abstractText instead returns the eLife digest; a manual scientific-abstract match is not a VERIFIED resolver verdict. Publisher version 2 assets were retrieved through https://api.elifesciences.org/articles/79114. Introduction, strain/culture Methods, deletion-mutant Results and intra-/interstrain crossing and recombination Results were read. Actual Figures 5 and 8 and their captions were inspected; Supplementary file 1 strain rows were read from the publisher's elife-79114-supp1-v2.xlsx. Other figures, supplements and unread Methods remain uninspected. Figure 5 separates wild-type CBS7841 sporulation from pheromone/receptor and DMC1 deletion phenotypes. Hyphal growth alone does not establish meiosis. Figure 8 recombination assays use CBS7841-derived marker strains, including UV-induced and spontaneous mutants, not the unmodified canonical isolate. Drug resistance alone is not evidence of sex; genotyping distinguishes recombination from new mutations. Tested interstrain crosses did not yield PCR-confirmed recombinant progeny, so universal compatibility is not asserted. Obligately sexual describes this source's example, not a requirement for all homothallic fungi.

    • @@ -130,7 +131,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -219,7 +220,7 @@

    Canonical examples DOI:10.7554/elife.79114 - Qualified natural-isolate example: wild-type CBS7841, distinguished from its laboratory derivatives in Supplementary file 1. Figure 5A shows basidia and spore chains after one week on V8 medium at room temperature in the dark; Figure 5B assays sporulation after ten days on Murashige-Skoog medium. The paper's composite sexual-cycle evidence includes separate mutant experiments, not all measurements on wild type. Natural provenance is independently documented by https://www.atcc.org/products/36983: B3810 [CBS 7841, TRTC 48044], isolated from a dead spider in Ontario, Canada. This collection record supports provenance, not independent trait replication. NCBI taxonomy 1295531 resolves to this active strain name on 2026-10-04. + Qualified natural-isolate example: wild-type CBS7841, distinguished from its laboratory derivatives in Supplementary file 1. Figure 5A shows basidia and spore chains after one week on V8 medium at room temperature in the dark; Figure 5B assays sporulation after ten days on Murashige-Skoog medium. The paper's composite sexual-cycle evidence includes separate mutant experiments, not all measurements on wild type. Natural provenance is independently documented by https://www.atcc.org/products/36983: B3810 [CBS 7841, TRTC 48044], isolated from a dead spider in Ontario, Canada. This collection record supports provenance, not independent trait replication. NCBI taxonomy 1295531 resolves to this active strain name on 2026-10-04. @@ -345,7 +346,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -374,12 +384,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 01:25 UTC diff --git a/pages/traits/physiology/hydrogenotrophic.html b/pages/traits/physiology/hydrogenotrophic.html index aea351e1d18..09b8e3d0068 100644 --- a/pages/traits/physiology/hydrogenotrophic.html +++ b/pages/traits/physiology/hydrogenotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -364,8 +365,8 @@

    Protein and taxon examples

    		 - Cupriavidus necator H16 -
    NCBITaxon:381666 + Cupriavidus necator H16 +
    NCBITaxon:381666         		REVIEWED
    @@ -438,7 +439,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -771,7 +772,7 @@

    Curation history

  • · REVIEW_EVIDENCE_REFERENCE_CHURN · codex -

    Offline review for issue 520 retained 4 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.2138/gselements.16.1.39 -> DOI:10.21775/cimb.006.159 (1 edge); DOI:10.2138/gselements.16.1.39 -> DOI:10.3390/microorganisms7020053 (3 edges).

    +

    Offline review for issue 520 retained 4 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.2138/gselements.16.1.39 -> DOI:10.21775/cimb.006.159 (1 edge); DOI:10.2138/gselements.16.1.39 -> DOI:10.3390/microorganisms7020053 (3 edges).

  • @@ -810,7 +811,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1174,12 +1184,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/hyphal_anastomosis.html b/pages/traits/physiology/hyphal_anastomosis.html index ee85a96d120..0ee41d004d2 100644 --- a/pages/traits/physiology/hyphal_anastomosis.html +++ b/pages/traits/physiology/hyphal_anastomosis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1128/aem.65.12.5571-5575.1999
    We observed complete fusion of hyphal walls and the migration of a mass of particles in both directions within the hyphal bridges.
    -

    Giovannetti et al. (1999); snippet exact-matched to the directly retrieved Europe PMC abstract, PMID:10584019. Publisher Methods, Results and Discussion were read; actual Figures 1 and 3 were inspected. Cellophane over water agar supported live observations. SDH staining visualized active bridges; time-lapse microscopy showed bidirectional particle passage in Glomus caledonium. The 0-to-2-second image pairs are representative observations, not replication counts or identification of each particle as a nucleus. Same-germling and different-germling/same-isolate fusion were observed. Tested interspecific failures do not establish a universal compatibility rule. Nuclear migration was reported separately; Figure 2 was not visually inspected. This study did not demonstrate genetic recombination.

    +

    Giovannetti et al. (1999); snippet exact-matched to the directly retrieved Europe PMC abstract, PMID:10584019. Publisher Methods, Results and Discussion were read; actual Figures 1 and 3 were inspected. Cellophane over water agar supported live observations. SDH staining visualized active bridges; time-lapse microscopy showed bidirectional particle passage in Glomus caledonium. The 0-to-2-second image pairs are representative observations, not replication counts or identification of each particle as a nucleus. Same-germling and different-germling/same-isolate fusion were observed. Tested interspecific failures do not establish a universal compatibility rule. Nuclear migration was reported separately; Figure 2 was not visually inspected. This study did not demonstrate genetic recombination.

  • DOI:10.1128/ec.00191-12
    Hyphal anastomosis, or vegetative hyphal fusion, establishes the interconnection of individual hyphal strands into an integrated network of a fungal mycelium.
    -

    Charlton et al. (2012); snippet exact-matched to the directly retrieved Europe PMC abstract, PMID:23042130. Publisher Methods and fusion Results were read; actual Figure 3 was inspected. This naming sentence supports the exact synonym. Calcofluor and DIC images compare Epichloe festucae E2368, delta-so268 and complemented 268C53: connections in wild type and complement, but separate apposed walls in delta-so268. Static images indicate apparent cytoplasmic connectivity, not measured flow. Delta-so238 retained a gene signal and was interpreted as a heterokaryon/knockdown, not a clean knockout; complementation of delta-so75 did not restore fusion. Host effects do not prove that fusion universally causes mutualism. Supplements were not inspected; no protein-resolved causal chain is asserted.

    +

    Charlton et al. (2012); snippet exact-matched to the directly retrieved Europe PMC abstract, PMID:23042130. Publisher Methods and fusion Results were read; actual Figure 3 was inspected. This naming sentence supports the exact synonym. Calcofluor and DIC images compare Epichloe festucae E2368, delta-so268 and complemented 268C53: connections in wild type and complement, but separate apposed walls in delta-so268. Static images indicate apparent cytoplasmic connectivity, not measured flow. Delta-so238 retained a gene signal and was interpreted as a heterokaryon/knockdown, not a clean knockout; complementation of delta-so75 did not restore fusion. Host effects do not prove that fusion universally causes mutualism. Supplements were not inspected; no protein-resolved causal chain is asserted.

  • DOI:10.1111/j.1469-8137.2008.02726.x
    We show that genetically distinct AMF, from the same field, anastomose, resulting in viable cytoplasmic connections through which genetic exchange could potentially occur.
    -

    Croll et al. (2009); snippet exact-matched to the directly retrieved Europe PMC abstract, PMID:19140939. Publisher Experiment 1 methods/results and relevant Discussion were read. Five Glomus intraradices isolates from one field population were paired; nine of ten nonself combinations had contacts scored as perfect fusion. That category required subsequent streaming and SDH-positive bridges; it is not a count of all fusion events. Postfusion withdrawal and septation were separate outcomes following anastomosis. Genetic identity is therefore not required. The paper separately reports marker transmission to progeny; its genotyping does not establish nuclear recombination. Figures and supplementary movies were not visually inspected. Table 1's PFI/PrFI column-footnote assignments appear transposed in publisher HTML, so those column-specific rates are not used.

    +

    Croll et al. (2009); snippet exact-matched to the directly retrieved Europe PMC abstract, PMID:19140939. Publisher Experiment 1 methods/results and relevant Discussion were read. Five Glomus intraradices isolates from one field population were paired; nine of ten nonself combinations had contacts scored as perfect fusion. That category required subsequent streaming and SDH-positive bridges; it is not a count of all fusion events. Postfusion withdrawal and septation were separate outcomes following anastomosis. Genetic identity is therefore not required. The paper separately reports marker transmission to progeny; its genotyping does not establish nuclear recombination. Figures and supplementary movies were not visually inspected. Table 1's PFI/PrFI column-footnote assignments appear transposed in publisher HTML, so those column-specific rates are not used.

    • @@ -112,7 +113,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • vegetative hyphal fusion EXACT_SYNONYM · DOI:10.1128/ec.00191-12
      • +
    • vegetative hyphal fusion EXACT_SYNONYM · DOI:10.1128/ec.00191-12
    @@ -128,7 +129,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -330,7 +331,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -359,12 +369,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 22:30 UTC diff --git a/pages/traits/physiology/isogamy.html b/pages/traits/physiology/isogamy.html index dd5a7a55acf..9bbc98186f2 100644 --- a/pages/traits/physiology/isogamy.html +++ b/pages/traits/physiology/isogamy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1038/s42003-022-04275-y
    The gametes of isogamous species are of similar size and appearance.
    -

    Innami et al. (2022), PMID:36473948, PMC9726906. Exact Introduction Sec1 sentence checked against raw Europe PMC XML and publisher HTML; not an abstract or web-summary quote. The paper identifies Chlamydomonas reinhardtii as isogamous while testing mating-structure positioning, not the maintenance of equal gamete size. Similar appearance does not exclude mating-type-specific structural or functional differences. Main text and captions were read; actual Figure 4 and Supplementary Table 2 were visually inspected. The latter lists nit1 nit2 in CC-125 and nit1 nit2 agg1 in CC-124 despite their wild-type names. CC-3712 has a deletion including MID and lacks FUS1; CC-3947 carries a MID transgene. These are qualified laboratory observations, not unqualified natural exemplars. Other actual figures, supplementary figures and the source-data workbook remain uninspected. Phototactic fitness explanations in Discussion remain hypotheses, not measured consequences of isogamy.

    +

    Innami et al. (2022), PMID:36473948, PMC9726906. Exact Introduction Sec1 sentence checked against raw Europe PMC XML and publisher HTML; not an abstract or web-summary quote. The paper identifies Chlamydomonas reinhardtii as isogamous while testing mating-structure positioning, not the maintenance of equal gamete size. Similar appearance does not exclude mating-type-specific structural or functional differences. Main text and captions were read; actual Figure 4 and Supplementary Table 2 were visually inspected. The latter lists nit1 nit2 in CC-125 and nit1 nit2 agg1 in CC-124 despite their wild-type names. CC-3712 has a deletion including MID and lacks FUS1; CC-3947 carries a MID transgene. These are qualified laboratory observations, not unqualified natural exemplars. Other actual figures, supplementary figures and the source-data workbook remain uninspected. Phototactic fitness explanations in Discussion remain hypotheses, not measured consequences of isogamy.

  • DOI:10.1111/evo.13427
    we explored size-speed distributions in vegetative and gamete cells of 10 cell lines, and clonal data from within two cell lines.
    -

    Seed and Tomkins (2018), PMID:29345308. Exact scientific-abstract clause from raw Europe PMC metadata; the author's institutional repository abstract corroborates the content. Its preceding clause identifies C. reinhardtii as isogamous. This independently supports experimental use of an isogamous microalga, not a second direct test of the definition's size-symmetry criterion. The two cell types are vegetative cells and gametes, not plus and minus gametes. Positive size-speed relationships and artificial speed selection do not establish a universal size threshold, identical gamete behaviour, or an evolutionary cause of isogamy. Full text, figures, supplements and strain provenance remain uninspected; the linked author manuscript returned HTTP 403.

    +

    Seed and Tomkins (2018), PMID:29345308. Exact scientific-abstract clause from raw Europe PMC metadata; the author's institutional repository abstract corroborates the content. Its preceding clause identifies C. reinhardtii as isogamous. This independently supports experimental use of an isogamous microalga, not a second direct test of the definition's size-symmetry criterion. The two cell types are vegetative cells and gametes, not plus and minus gametes. Positive size-speed relationships and artificial speed selection do not establish a universal size threshold, identical gamete behaviour, or an evolutionary cause of isogamy. Full text, figures, supplements and strain provenance remain uninspected; the linked author manuscript returned HTTP 403.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -271,7 +272,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed isogamy -

      Added PROPOSED PHYSIOLOGY traitmech:000619 and v496 reservation METPO:1057300 under released phenotype. DOI:10.1038/s42003-022-04275-y supplies the definition; DOI:10.1111/evo.13427 independently documents experimental use of an isogamous microalga, not a second direct size-symmetry test. Both snippets exactly matched authoritative raw source text. The maintained resolver returned NOT_IN_ABSTRACT for the Introduction quote and VERIFIED for the scientific-abstract clause. Actual 2022 Figure 4 and Supplementary Table 2 were visually inspected. Gamete-size similarity, mating-type identity, structural asymmetry and vegetative-versus-gamete comparisons remain distinct. Reference-strain mutations and unread source material are explicit; natural canonical taxa and mechanisms are deferred. Ignored-and-hidden novelty and allocation searches, fresh seed dispositions, upstream issues and open-PR files were checked. Writer dry run, seven writer tests, LinkML and single-record strict validation passed; broader gates and generated artifacts follow before review.

    +

    Added PROPOSED PHYSIOLOGY traitmech:000619 and v496 reservation METPO:1057300 under released phenotype. DOI:10.1038/s42003-022-04275-y supplies the definition; DOI:10.1111/evo.13427 independently documents experimental use of an isogamous microalga, not a second direct size-symmetry test. Both snippets exactly matched authoritative raw source text. The maintained resolver returned NOT_IN_ABSTRACT for the Introduction quote and VERIFIED for the scientific-abstract clause. Actual 2022 Figure 4 and Supplementary Table 2 were visually inspected. Gamete-size similarity, mating-type identity, structural asymmetry and vegetative-versus-gamete comparisons remain distinct. Reference-strain mutations and unread source material are explicit; natural canonical taxa and mechanisms are deferred. Ignored-and-hidden novelty and allocation searches, fresh seed dispositions, upstream issues and open-PR files were checked. Writer dry run, seven writer tests, LinkML and single-record strict validation passed; broader gates and generated artifacts follow before review.

    • Read this curation session @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 11:54 UTC diff --git a/pages/traits/physiology/karyoklepty.html b/pages/traits/physiology/karyoklepty.html index b93cd2d0dd0..abd60a5ec0c 100644 --- a/pages/traits/physiology/karyoklepty.html +++ b/pages/traits/physiology/karyoklepty.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1038/nature05496
    Cytokinesis, plastid performance and their replication are dependent on recurrent stealing of cryptophyte nuclei.
    -

    PMID:17251979. Direct scientific abstract from Europe PMC, cross-checked with the publisher abstract. This naming study reports retained, transcriptionally active prey nuclei in Myrionecta rubra, a synonym of Mesodinium rubrum. The plastid-related dependence is system-specific, not a universal definition requirement. Main text, figures and supplements were not accessed; no protein-resolved mechanism is imported.

    +

    PMID:17251979. Direct scientific abstract from Europe PMC, cross-checked with the publisher abstract. This naming study reports retained, transcriptionally active prey nuclei in Myrionecta rubra, a synonym of Mesodinium rubrum. The plastid-related dependence is system-specific, not a universal definition requirement. Main text, figures and supplements were not accessed; no protein-resolved mechanism is imported.

  • DOI:10.1186/s12864-015-2052-9
    Rather, the ciliate steals the nucleus from cryptophyte prey, a process described as karyoklepty
    -

    PMID:26475598, PMC4609049. Direct Background naming passage, not an abstract quote or independent terminology experiment. Scientific Abstract and Background were read. The abstract reports prey-derived transcription after sequestration; expression and annotation are not native protein perturbations. Methods, Results, actual figures and supplements were not audited, so no additional canonical strain or causal edge is asserted from this study.

    +

    PMID:26475598, PMC4609049. Direct Background naming passage, not an abstract quote or independent terminology experiment. Scientific Abstract and Background were read. The abstract reports prey-derived transcription after sequestration; expression and annotation are not native protein perturbations. Methods, Results, actual figures and supplements were not audited, so no additional canonical strain or causal edge is asserted from this study.

  • DOI:10.3389/fmicb.2017.00423
    Well-fed cells of M. rubrum contained additional nuclei of cryptophyte origin.
    -

    PMID:28377747, PMC5359308. Direct Results passage. Main text and actual Figures 2-5 and 9 were inspected; supplements were not. Fixed-cell microscopy documents retained central and peripheral prey nuclei during starvation/refeeding. Figure 9 is an inheritance model with illustrative micrographs, not continuous lineage tracking. Carbon fixation correlates with nuclear prevalence; starvation is not an isolated nuclear perturbation.

    +

    PMID:28377747, PMC5359308. Direct Results passage. Main text and actual Figures 2-5 and 9 were inspected; supplements were not. Fixed-cell microscopy documents retained central and peripheral prey nuclei during starvation/refeeding. Figure 9 is an inheritance model with illustrative micrographs, not continuous lineage tracking. Carbon fixation correlates with nuclear prevalence; starvation is not an isolated nuclear perturbation.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.3389/fmicb.2017.00423 - Qualified example: MBL-DK2009 fed Teleaulax amphioxeia SCCAP K-0434. The Cultures Methods at https://doi.org/10.3389/fmicb.2017.00423 document single-cell isolation from Helsingor harbor, Denmark, in 2009. Retention is conditional on feeding history; do not generalize nuclear inheritance to every strain. NCBI ESearch and EFetch independently resolved the species and its Myrionecta rubra synonym on 2026-10-05. + Qualified example: MBL-DK2009 fed Teleaulax amphioxeia SCCAP K-0434. The Cultures Methods at https://doi.org/10.3389/fmicb.2017.00423 document single-cell isolation from Helsingor harbor, Denmark, in 2009. Retention is conditional on feeding history; do not generalize nuclear inheritance to every strain. NCBI ESearch and EFetch independently resolved the species and its Myrionecta rubra synonym on 2026-10-05. @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 23:39 UTC diff --git a/pages/traits/physiology/kinetocyst_discharge.html b/pages/traits/physiology/kinetocyst_discharge.html index d84e11f053b..33376defb3c 100644 --- a/pages/traits/physiology/kinetocyst_discharge.html +++ b/pages/traits/physiology/kinetocyst_discharge.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (3)

    DOI:10.1078/0932-4739-00847
    By electron microscopy, we show evidence that the kinetocyst is an extrusive organelle that discharges its contents upon food capture.
    -

    Sakaguchi et al. 2002, scientific Abstract directly read on 2026-10-10 at https://www.researchgate.net/publication/222864147. Electron microscopy of Raphidiophrys contractilis supports release during food capture, with the posterior remaining cell-attached and the anterior directed toward prey. The proposed scaffold role is not demonstrated causality. Crossref identifies the 2002 publication; ResearchGate's date and automatically linked author profile are not used as authority. Publisher access returned 403; full Methods and figures were not inspected. No universal toxin, prey-killing requirement or trigger is inferred.

    +

    Sakaguchi et al. 2002, scientific Abstract directly read on 2026-10-10 at https://www.researchgate.net/publication/222864147. Electron microscopy of Raphidiophrys contractilis supports release during food capture, with the posterior remaining cell-attached and the anterior directed toward prey. The proposed scaffold role is not demonstrated causality. Crossref identifies the 2002 publication; ResearchGate's date and automatically linked author profile are not used as authority. Publisher access returned 403; full Methods and figures were not inspected. No universal toxin, prey-killing requirement or trigger is inferred.

  • DOI:10.1515/znc-1976-3-418
    Freeze-fracture studies reveal that extrusive organelles displaying saltatory particle movements in centrohelidian axopod are attached to highly ordered domains within the plasma membrane.
    -

    Bardele 1976, PMID:134561. Scientific abstract and primary full-text OCR directly read on 2026-10-10 at https://www.researchgate.net/publication/22999924. The snippet supports organelle identity and membrane attachment, not discharge alone. Printed pp191-193 describe formaldehyde-fume-induced release in living whole mounts and negative-stained expelled jacket material. Methods name Acanthocystis erinaceoides and Raphidiophrys ambigua; this observation is not assigned here to just one species. The author interprets kinetocysts as compound motile mucocysts. Food-trapping and movement models remain hypotheses. PDF images were unavailable; no visual audit or OCR-normalized quotation is claimed. The article year is 1976, not the later upload date.

    +

    Bardele 1976, PMID:134561. Scientific abstract and primary full-text OCR directly read on 2026-10-10 at https://www.researchgate.net/publication/22999924. The snippet supports organelle identity and membrane attachment, not discharge alone. Printed pp191-193 describe formaldehyde-fume-induced release in living whole mounts and negative-stained expelled jacket material. Methods name Acanthocystis erinaceoides and Raphidiophrys ambigua; this observation is not assigned here to just one species. The author interprets kinetocysts as compound motile mucocysts. Food-trapping and movement models remain hypotheses. PDF images were unavailable; no visual audit or OCR-normalized quotation is claimed. The article year is 1976, not the later upload date.

  • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-10 04:08 UTC diff --git a/pages/traits/physiology/kleptoplasty.html b/pages/traits/physiology/kleptoplasty.html index 10247fd53b6..753a7d0e2ab 100644 --- a/pages/traits/physiology/kleptoplasty.html +++ b/pages/traits/physiology/kleptoplasty.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.1038/s41598-018-28455-1
    Kleptoplasty is defined as the process in which a cell sequesters algal chloroplasts while discarding or digesting other algal components
    -

    PMID:29973634, PMC6031614. Direct Introduction definition, not an abstract quote or experimental replication. The Introduction also includes aphotic cases. Only the scientific Abstract and Introduction were read for this terminology claim; no canonical example or mechanism is imported from the paper's experiments.

    +

    PMID:29973634, PMC6031614. Direct Introduction definition, not an abstract quote or experimental replication. The Introduction also includes aphotic cases. Only the scientific Abstract and Introduction were read for this terminology claim; no canonical example or mechanism is imported from the paper's experiments.

  • DOI:10.1073/pnas.2220100120
    Rapaza viridis has only kleptoplasts derived from a specific strain of green alga, Tetraselmis sp., but no canonical plastids
    -

    PMID:36927158, PMC10041101. Contiguous scientific-abstract span, not the separate Significance section. Main text and actual Figures 1 and 3 were inspected: prey plastids persist after other material is expelled, and bicarbonate labeling supports photosynthetic carbon use. Plastid subdivision and partition do not establish plastid growth or biogenesis. Supplements were not visually audited. Predicted targeting sequences and transporters are not native protein-function validation.

    +

    PMID:36927158, PMC10041101. Contiguous scientific-abstract span, not the separate Significance section. Main text and actual Figures 1 and 3 were inspected: prey plastids persist after other material is expelled, and bicarbonate labeling supports photosynthetic carbon use. Plastid subdivision and partition do not establish plastid growth or biogenesis. Supplements were not visually audited. Predicted targeting sequences and transporters are not native protein-function validation.

  • DOI:10.1038/s41467-026-70516-x
    In the flagellate, Rapaza viridis, nuclear-encoded proteins support photosynthesis in transient, xenogeneic chloroplasts (kleptoplasts) acquired from the green alga Tetraselmis sp.
    -

    PMID:41876518, PMC13013580. Scientific Abstract (Abs1), not the editorial summary (Abs2). Results, Discussion, relevant culture/perturbation/imaging/physiology Methods, actual Figures 3-5 and Supplementary Figure 4 were inspected. Knockout and knockdown support host-protein contributions in this system. RbcS-like localization uses engineered HA tagging; Rca-like localization uses native-protein antibodies. This is a separate study of the same strain, not independent taxon replication.

    +

    PMID:41876518, PMC13013580. Scientific Abstract (Abs1), not the editorial summary (Abs2). Results, Discussion, relevant culture/perturbation/imaging/physiology Methods, actual Figures 3-5 and Supplementary Figure 4 were inspected. Knockout and knockdown support host-protein contributions in this system. RbcS-like localization uses engineered HA tagging; Rca-like localization uses native-protein antibodies. This is a separate study of the same strain, not independent taxon replication.

  • DOI:10.1111/1462-2920.14433
    These results indicate that the photosynthetic pathways in N. labradorica are not functional.
    -

    PMID:30277305. Direct Europe PMC scientific abstract, published online in 2018 and in the 2019 print issue. The authors call Nonionellina labradorica kleptoplastidic despite absent carbon fixation and oxygen production under their assayed conditions. This supports retaining a photosynthesis-independent definition, not universal functional absence. Full text and figures were not accessed; no canonical example or nitrogen/sulfur mechanism is imported. Host versus plastid assimilation remains unresolved.

    +

    PMID:30277305. Direct Europe PMC scientific abstract, published online in 2018 and in the 2019 print issue. The authors call Nonionellina labradorica kleptoplastidic despite absent carbon fixation and oxygen production under their assayed conditions. This supports retaining a photosynthesis-independent definition, not universal functional absence. Full text and figures were not accessed; no canonical example or nitrogen/sulfur mechanism is imported. Host versus plastid assimilation remains unresolved.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Canonical examples DOI:10.1073/pnas.2220100120 - NIES-4477, fed Tetraselmis sp. NIES-4478, is the qualified example; do not generalize prey compatibility to every isolate. NCBI ESearch and EFetch resolve the species name and identifier on 2026-10-05. Natural tide-pool isolation at Pachena Beach in 2010 is documented in the original Methods at https://doi.org/10.1186/1471-2148-12-29. That paper's canonical-plastid interpretation was superseded by the 2023 study. Collection provenance at https://mcc.nbrp.jp/strainList.do?strainId=4475&strainNumberEn=NIES-4477 conflicts with the primary papers on the ATCC alias; retain NIES-4477 without silently equating the conflicting aliases. + NIES-4477, fed Tetraselmis sp. NIES-4478, is the qualified example; do not generalize prey compatibility to every isolate. NCBI ESearch and EFetch resolve the species name and identifier on 2026-10-05. Natural tide-pool isolation at Pachena Beach in 2010 is documented in the original Methods at https://doi.org/10.1186/1471-2148-12-29. That paper's canonical-plastid interpretation was superseded by the 2023 study. Collection provenance at https://mcc.nbrp.jp/strainList.do?strainId=4475&strainNumberEn=NIES-4477 conflicts with the primary papers on the ATCC alias; retain NIES-4477 without silently equating the conflicting aliases. @@ -370,7 +371,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -399,12 +409,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 22:50 UTC diff --git a/pages/traits/physiology/lecithinase_activity.html b/pages/traits/physiology/lecithinase_activity.html index e391cc26603..0c294930492 100644 --- a/pages/traits/physiology/lecithinase_activity.html +++ b/pages/traits/physiology/lecithinase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,9 +107,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • lecithinase production RELATED_SYNONYM · DOI:10.1128/jb.81.6.939-945.1961
      • +
    • lecithinase production RELATED_SYNONYM · DOI:10.1128/jb.81.6.939-945.1961
      • -
    • lecithinase reaction RELATED_SYNONYM · DOI:10.2147/IDR.S365254
      • +
    • lecithinase reaction RELATED_SYNONYM · DOI:10.2147/IDR.S365254
    @@ -124,7 +125,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -274,7 +275,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two egg-yolk/lecithinase diagnostic assay snippets (DOI:10.2147/IDR.S365254, DOI:10.1128/jb.81.6.939-945.1961) without distinct phospholipid cleavage product quotes.

    +

    The current record carries two egg-yolk/lecithinase diagnostic assay snippets (DOI:10.2147/IDR.S365254, DOI:10.1128/jb.81.6.939-945.1961) without distinct phospholipid cleavage product quotes.

    @@ -356,7 +357,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -385,12 +395,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/lethal_algicidal_activity.html b/pages/traits/physiology/lethal_algicidal_activity.html index e14ac9857b8..336390665ac 100644 --- a/pages/traits/physiology/lethal_algicidal_activity.html +++ b/pages/traits/physiology/lethal_algicidal_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1128/AEM.64.8.2806-2813.1998
    All G. catenatum cells in strain Y-treated wells were dead and most cells had lysed after 2 days.
    -

    Lovejoy et al. 1998, PMID:9687434, PMC106776, Results sec9. Scientific Abstract, algal-culture/toxicity Methods, activity and specificity Results, Discussion, Tables 1/2/4/5 and actual Figure 2 inspected. Other actual figures and remaining Methods unread. Strain Y and filtrate support killing, unlike reversible ecdysis or rounding in other targets. Some dinoflagellate controls also died in separate experiments; raphidophyte controls remained healthy. P. carrageenovora was not uniformly harmless. Close affinity to P. peptidysin is not exact species identification. EXT_ID:9687434 AND SRC:MED matched source, ID, title and DOI on 2026-10-11. Full-text quotation directly matched; abstract matching alone cannot verify this passage.

    +

    Lovejoy et al. 1998, PMID:9687434, PMC106776, Results sec9. Scientific Abstract, algal-culture/toxicity Methods, activity and specificity Results, Discussion, Tables 1/2/4/5 and actual Figure 2 inspected. Other actual figures and remaining Methods unread. Strain Y and filtrate support killing, unlike reversible ecdysis or rounding in other targets. Some dinoflagellate controls also died in separate experiments; raphidophyte controls remained healthy. P. carrageenovora was not uniformly harmless. Close affinity to P. peptidysin is not exact species identification. EXT_ID:9687434 AND SRC:MED matched source, ID, title and DOI on 2026-10-11. Full-text quotation directly matched; abstract matching alone cannot verify this passage.

  • DOI:10.1128/AEM.66.10.4334-4339.2000
    The marine bacterium Pseudoalteromonas sp. strain A28 was able to kill the diatom Skeletonema costatum strain NIES-324.
    -

    Lee et al. 2000, PMID:11010878, PMC92304, scientific Abstract. Abstract, Introduction, Methods, Results, Discussion, Tables 1/2 and actual Figures 1/2 inspected; actual Figures 3/4 unread. Parental A28 culture and supernatant support the capability. Results sec11 reports no regrowth after transfer from cleared agar, distinguishing algicidal from algistatic, but that experiment is data not shown. Protease II lacked algicidal action despite protease activity. Six N-terminal residues do not establish full AprI identity; NH1/NH2 are mutagenized derivatives, not natural exemplars. A separate group from Lovejoy et al., not a replication of strain Y. EXT_ID:11010878 AND SRC:MED matched source, ID, title and DOI on 2026-10-11; quotation matched direct scientific Abstract and qualified API abstract.

    +

    Lee et al. 2000, PMID:11010878, PMC92304, scientific Abstract. Abstract, Introduction, Methods, Results, Discussion, Tables 1/2 and actual Figures 1/2 inspected; actual Figures 3/4 unread. Parental A28 culture and supernatant support the capability. Results sec11 reports no regrowth after transfer from cleared agar, distinguishing algicidal from algistatic, but that experiment is data not shown. Protease II lacked algicidal action despite protease activity. Six N-terminal residues do not establish full AprI identity; NH1/NH2 are mutagenized derivatives, not natural exemplars. A separate group from Lovejoy et al., not a replication of strain Y. EXT_ID:11010878 AND SRC:MED matched source, ID, title and DOI on 2026-10-11; quotation matched direct scientific Abstract and qualified API abstract.

  • DOI:10.3390/toxins15030220
    The cyanobacterial cell walls were severely damaged, leading to the leakage of intracellular components.
    -

    Zhang et al. 2023, PMID:36977111, PMC10058357, Results 2.4. Scientific Abstract, Introduction, Results 2.1-2.4, Discussion, Methods 5.1-5.4/5.8/5.12 and actual Figure 3 with caption inspected; other figures and supplement unread. Filtrate damage/lysis supports cyanobacterial target scope. Methods 5.3 calculates relative cell-density reduction versus controls, not a direct dead-cell fraction; no percentage is adopted. Results 2.1 calls HY #320 from 411 isolates, versus #332/412 in Methods 5.2 and #332 in Figure 1 caption; provenance remains unreconciled. Molecular agents are unidentified; transcription changes alone do not establish causal protein edges. EXT_ID:36977111 AND SRC:MED matched source, ID, title and DOI on 2026-10-11. Quotation directly matched full text.

    +

    Zhang et al. 2023, PMID:36977111, PMC10058357, Results 2.4. Scientific Abstract, Introduction, Results 2.1-2.4, Discussion, Methods 5.1-5.4/5.8/5.12 and actual Figure 3 with caption inspected; other figures and supplement unread. Filtrate damage/lysis supports cyanobacterial target scope. Methods 5.3 calculates relative cell-density reduction versus controls, not a direct dead-cell fraction; no percentage is adopted. Results 2.1 calls HY #320 from 411 isolates, versus #332/412 in Methods 5.2 and #332 in Figure 1 caption; provenance remains unreconciled. Molecular agents are unidentified; transcription changes alone do not establish causal protein edges. EXT_ID:36977111 AND SRC:MED matched source, ID, title and DOI on 2026-10-11. Quotation directly matched full text.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -215,7 +216,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    The lethal qualifier distinguishes this capability from broader algicidal usage. Paul and Pohnert 2011, DOI:10.1371/journal.pone.0021032, Methods Monitoring algicidal activity and Results, uses fluorescence-based growth inhibition as an algicidal readout; those directly read passages provide terminology context, not additional killing evidence. This record requires killing, not reduced fluorescence, reversible growth arrest, ecdysis, passive removal or a protease sequence alone. It denotes the acting microbe's capability, not an algicide molecule, treated alga's susceptibility or assay row. Cyanobacteria are included explicitly, not classified as eukaryotic algae. Activity against some susceptible targets suffices; universal host range is not asserted. Predatory bacterium traitmech:000054 requires killing and consuming bacteria for nutrients, so it is not a parent of this class. Killing may overlap predation but neither consumption, grazing nor nutritional benefit is required or inferred; no organismal disjointness is asserted. No exact synonym or phenotype xref is assigned pending authority and scope review.

    +

    The lethal qualifier distinguishes this capability from broader algicidal usage. Paul and Pohnert 2011, DOI:10.1371/journal.pone.0021032, Methods Monitoring algicidal activity and Results, uses fluorescence-based growth inhibition as an algicidal readout; those directly read passages provide terminology context, not additional killing evidence. This record requires killing, not reduced fluorescence, reversible growth arrest, ecdysis, passive removal or a protease sequence alone. It denotes the acting microbe's capability, not an algicide molecule, treated alga's susceptibility or assay row. Cyanobacteria are included explicitly, not classified as eukaryotic algae. Activity against some susceptible targets suffices; universal host range is not asserted. Predatory bacterium traitmech:000054 requires killing and consuming bacteria for nutrients, so it is not a parent of this class. Killing may overlap predation but neither consumption, grazing nor nutritional benefit is required or inferred; no organismal disjointness is asserted. No exact synonym or phenotype xref is assigned pending authority and scope review.

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-11 08:54 UTC diff --git a/pages/traits/physiology/lethal_nematicidal_activity.html b/pages/traits/physiology/lethal_nematicidal_activity.html index a89f44845fe..adc8a1a0b04 100644 --- a/pages/traits/physiology/lethal_nematicidal_activity.html +++ b/pages/traits/physiology/lethal_nematicidal_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1038/s41598-023-33669-z
    T. asperellum FbMi6 at 80% concentration had the highest (90.3%) juvenile mortality compared to control.
    -

    Saharan et al. 2023, PMID:37088805, Results in vitro activity; native NOT_IN_ABSTRACT, direct publisher HTML match. Actual Figure 4 inspected. This is culture filtrate, not live fungal inoculum: 100 newly hatched M. incognita J2, water/PDB controls, 72 h endpoint, 25 +/- 2 degrees C, two repeats. Methods reports fresh-water recovery confirmation without its duration or scoring criterion. The quote's percentage is source-reported, not independently recalculated. Supplement text/tables and its embedded image were inspected, not rendered document pages. Strain/accession discrepancies prevent a canonical taxon assignment; pot/field efficacy is not imported.

    +

    Saharan et al. 2023, PMID:37088805, Results in vitro activity; native NOT_IN_ABSTRACT, direct publisher HTML match. Actual Figure 4 inspected. This is culture filtrate, not live fungal inoculum: 100 newly hatched M. incognita J2, water/PDB controls, 72 h endpoint, 25 +/- 2 degrees C, two repeats. Methods reports fresh-water recovery confirmation without its duration or scoring criterion. The quote's percentage is source-reported, not independently recalculated. Supplement text/tables and its embedded image were inspected, not rendered document pages. Strain/accession discrepancies prevent a canonical taxon assignment; pot/field efficacy is not imported.

  • DOI:10.1128/spectrum.02577-21
    In this study, three secondary metabolites (SMs) with nematicidal activities were isolated from in vitro cultures of P. luminescens sonorensis strain Caborca
    -

    Producer-origin supporting evidence, not definition authority. The self-contained excerpt establishes microbial origin of nematicidal metabolites; its wording alone does not distinguish death from paralysis. The independently cited Saharan mortality result supplies explicit lethal definition support. Kusakabe et al. 2022, PMID:35138171, Discussion opening clause, printed/PDF page 12; native NOT_IN_ABSTRACT and direct XML/typeset PDF match. The producer is Photorhabdus. Culture-supernatant fractionation links the isolated metabolites to this microorganism. t-CA and PPA caused mortality; indole mainly caused reversible paralysis at lower doses, with killing only at high concentrations. Equipotent synthetic standards were used for dose-response assays. Actual Figures 2/3 and Table 4 inspected. Needle response and morphology distinguished death from paralysis; recovery used washing and 24 h in water. Table 4 tests lower-dose indole, not t-CA/PPA survival. No live-culture lethal concentration is inferred. Some numerical prose conflicts with tables; no potency, selectivity or significance values are adopted. Linked supplemental NMR/statistics files were not audited; figure inspection is not raw-data verification.

    +

    Producer-origin supporting evidence, not definition authority. The self-contained excerpt establishes microbial origin of nematicidal metabolites; its wording alone does not distinguish death from paralysis. The independently cited Saharan mortality result supplies explicit lethal definition support. Kusakabe et al. 2022, PMID:35138171, Discussion opening clause, printed/PDF page 12; native NOT_IN_ABSTRACT and direct XML/typeset PDF match. The producer is Photorhabdus. Culture-supernatant fractionation links the isolated metabolites to this microorganism. t-CA and PPA caused mortality; indole mainly caused reversible paralysis at lower doses, with killing only at high concentrations. Equipotent synthetic standards were used for dose-response assays. Actual Figures 2/3 and Table 4 inspected. Needle response and morphology distinguished death from paralysis; recovery used washing and 24 h in water. Table 4 tests lower-dose indole, not t-CA/PPA survival. No live-culture lethal concentration is inferred. Some numerical prose conflicts with tables; no potency, selectivity or significance values are adopted. Linked supplemental NMR/statistics files were not audited; figure inspection is not raw-data verification.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -369,7 +370,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -398,12 +408,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-13 21:06 UTC diff --git a/pages/traits/physiology/leucine_arylamidase_activity.html b/pages/traits/physiology/leucine_arylamidase_activity.html index 13276d09475..5d1d26504b7 100644 --- a/pages/traits/physiology/leucine_arylamidase_activity.html +++ b/pages/traits/physiology/leucine_arylamidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -345,7 +346,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -374,12 +384,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/leucyl_glycine_arylamidase_activity.html b/pages/traits/physiology/leucyl_glycine_arylamidase_activity.html index ea79e439ee3..5e0d0743293 100644 --- a/pages/traits/physiology/leucyl_glycine_arylamidase_activity.html +++ b/pages/traits/physiology/leucyl_glycine_arylamidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,9 +107,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • leucyl glycine arylamidase RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
      • +
    • leucyl glycine arylamidase RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
      • -
    • leucylglycine arylamidase RELATED_SYNONYM · DOI:10.1128/JCM.40.9.3427-3431.2002
      • +
    • leucylglycine arylamidase RELATED_SYNONYM · DOI:10.1128/JCM.40.9.3427-3431.2002
    @@ -124,7 +125,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -274,7 +275,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two diagnostic API rapid ID32A / species-description snippets (DOI:10.1099/ijsem.0.006017, DOI:10.1128/JCM.40.9.3427-3431.2002) without verbatim catalytic reaction quotes.

    +

    The current record carries two diagnostic API rapid ID32A / species-description snippets (DOI:10.1099/ijsem.0.006017, DOI:10.1128/JCM.40.9.3427-3431.2002) without verbatim catalytic reaction quotes.

    @@ -362,7 +363,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -391,12 +401,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/lipase_activity.html b/pages/traits/physiology/lipase_activity.html index 5cdaf17953c..f43ef98327f 100644 --- a/pages/traits/physiology/lipase_activity.html +++ b/pages/traits/physiology/lipase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,9 +107,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • lipase production RELATED_SYNONYM · DOI:10.22207/JPAM.16.4.27
      • +
    • lipase production RELATED_SYNONYM · DOI:10.22207/JPAM.16.4.27
      • -
    • lipolytic activity RELATED_SYNONYM · DOI:10.1016/j.mex.2018.01.004
      • +
    • lipolytic activity RELATED_SYNONYM · DOI:10.1016/j.mex.2018.01.004
    @@ -124,7 +125,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -274,7 +275,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two tributyrin/screening assay snippets (DOI:10.22207/JPAM.16.4.27, DOI:10.1016/j.mex.2018.01.004) without verbatim catalytic reaction or enzyme-mechanism quotes.

    +

    The current record carries two tributyrin/screening assay snippets (DOI:10.22207/JPAM.16.4.27, DOI:10.1016/j.mex.2018.01.004) without verbatim catalytic reaction or enzyme-mechanism quotes.

    @@ -356,7 +357,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -385,12 +395,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/lipophagy.html b/pages/traits/physiology/lipophagy.html index 5b83d2f9c0d..493d1f0f563 100644 --- a/pages/traits/physiology/lipophagy.html +++ b/pages/traits/physiology/lipophagy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1091/mbc.e13-08-0448
    LDs can also be turned over in vacuoles/lysosomes by a process that morphologically resembles microautophagy.
    -

    PMID:24258026, PMC3890349. Scientific abstract directly read in DOI-matched Europe PMC metadata and XML abstract2, not the precis. Results sec9 and Methods sec12-sec15 were read. Purified, trypsin-treated vacuoles, lipid analysis and TAG-lipase assays separate uptake from breakdown in Saccharomyces cerevisiae. The atg1/atg15 comparisons distinguish delivery, vacuolar catabolism and compensating cytosolic lipolysis. BY4742-derived reporter/mutant hosts are not verified natural exemplars. Actual figures and supplements were not inspected.

    +

    PMID:24258026, PMC3890349. Scientific abstract directly read in DOI-matched Europe PMC metadata and XML abstract2, not the precis. Results sec9 and Methods sec12-sec15 were read. Purified, trypsin-treated vacuoles, lipid analysis and TAG-lipase assays separate uptake from breakdown in Saccharomyces cerevisiae. The atg1/atg15 comparisons distinguish delivery, vacuolar catabolism and compensating cytosolic lipolysis. BY4742-derived reporter/mutant hosts are not verified natural exemplars. Actual figures and supplements were not inspected.

  • DOI:10.1016/j.devcel.2024.01.014
    Upon nutrient exhaustion, cells consume LDs via gradual lipolysis or via lipophagy, the en bloc uptake of LDs into the vacuole.
    -

    PMID:38354739. Scientific abstract directly read in Europe PMC with matching DOI. The LDO/Vac8 vCLIP contact site supports starvation-induced yeast uptake. This source operationally calls en bloc uptake lipophagy; docking or uptake alone is not direct proof of completed lipid degradation. Shared Vac8 use links this route to nuclear microautophagy without equating the cargo phenotypes. Full text, Methods, actual figures and strain provenance were not inspected.

    +

    PMID:38354739. Scientific abstract directly read in Europe PMC with matching DOI. The LDO/Vac8 vCLIP contact site supports starvation-induced yeast uptake. This source operationally calls en bloc uptake lipophagy; docking or uptake alone is not direct proof of completed lipid degradation. Shared Vac8 use links this route to nuclear microautophagy without equating the cargo phenotypes. Full text, Methods, actual figures and strain provenance were not inspected.

  • DOI:10.1080/15548627.2024.2325297
    We find that the degradation of LD surface proteins relies on autophagy and can occur independently of lipophagy.
    -

    PMID:38425021, PMC11210923. Scientific ABSTRACT paragraph directly read and exact-matched in DOI-matched NCBI PMC XML at https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=11210923&retmode=xml. Europe PMC and PubMed abstract fields return only abbreviations; they do not verify this quote. The retrieved XML has no body. The yeast study separates engulfment from surface-protein processing and reports glucose-concentration-dependent, ATG1-independent uptake. This does not establish lipid catabolism from a protein marker alone. Full Methods, figures and supplements were not inspected.

    +

    PMID:38425021, PMC11210923. Scientific ABSTRACT paragraph directly read and exact-matched in DOI-matched NCBI PMC XML at https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=11210923&retmode=xml. Europe PMC and PubMed abstract fields return only abbreviations; they do not verify this quote. The retrieved XML has no body. The yeast study separates engulfment from surface-protein processing and reports glucose-concentration-dependent, ATG1-independent uptake. This does not establish lipid catabolism from a protein marker alone. Full Methods, figures and supplements were not inspected.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -215,7 +216,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    The 2014 study supports vacuolar lipid-droplet catabolism via a microautophagy-like route. The two 2024 abstracts also use lipophagy operationally for uptake; the present phenotype retains the autophagy parent's degradative endpoint, not uptake alone. Current GO:0061724 (https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0061724) restricts lipophagy to selective macroautophagy. GO:0140504 (https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0140504) separately denotes microlipophagy. Both are nonobsolete biological processes, not exact organismal-phenotype xrefs. Preserve this source-attributed scope difference for human review; no universal macro/micro route, selectivity mechanism, starvation trigger or ATG inventory is asserted. Lipolysis traitmech:000190 concerns triacylglycerol hydrolysis: it can overlap lipophagy but is neither an exact synonym nor a necessary broader parent for all droplet cargo. Lipid storage, PHA granules and pigment sequestration are not equivalent degradation phenotypes. No exact synonyms or mappings are added.

    +

    The 2014 study supports vacuolar lipid-droplet catabolism via a microautophagy-like route. The two 2024 abstracts also use lipophagy operationally for uptake; the present phenotype retains the autophagy parent's degradative endpoint, not uptake alone. Current GO:0061724 (https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0061724) restricts lipophagy to selective macroautophagy. GO:0140504 (https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0140504) separately denotes microlipophagy. Both are nonobsolete biological processes, not exact organismal-phenotype xrefs. Preserve this source-attributed scope difference for human review; no universal macro/micro route, selectivity mechanism, starvation trigger or ATG inventory is asserted. Lipolysis traitmech:000190 concerns triacylglycerol hydrolysis: it can overlap lipophagy but is neither an exact synonym nor a necessary broader parent for all droplet cargo. Lipid storage, PHA granules and pigment sequestration are not equivalent degradation phenotypes. No exact synonyms or mappings are added.

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 14:32 UTC diff --git a/pages/traits/physiology/lithoautotrophic.html b/pages/traits/physiology/lithoautotrophic.html index 55522a6d696..96b1cedd8d8 100644 --- a/pages/traits/physiology/lithoautotrophic.html +++ b/pages/traits/physiology/lithoautotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -366,7 +367,7 @@

    Edge evidence

    example of reducing power METPO:1007503 - rdfs:subClassOf + rdfs:subClassOf

    NADH generated by reverse electron flow is reducing power for lithoautotrophic carbon fixation.

      @@ -402,8 +403,8 @@

      Protein and taxon examples

    		 - Nitrosomonas europaea ATCC 19718 -
    NCBITaxon:228410 + Nitrosomonas europaea ATCC 19718 +
    NCBITaxon:228410         		REVIEWED
    @@ -469,7 +470,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • lithoautotroph RELATED_SYNONYM · metpo.owl
      • +
    • lithoautotroph RELATED_SYNONYM · metpo.owl
    @@ -485,7 +486,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -866,7 +867,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1230,12 +1240,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/lithoheterotrophic.html b/pages/traits/physiology/lithoheterotrophic.html index 00a0ac5346f..fd0528af7b6 100644 --- a/pages/traits/physiology/lithoheterotrophic.html +++ b/pages/traits/physiology/lithoheterotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -119,7 +120,7 @@

    Edge evidence

    example of inorganic electron donor METPO:1007502 - rdfs:subClassOf + rdfs:subClassOf

    Fe(II) is an example inorganic electron donor for lithotrophic growth.

      @@ -214,7 +215,7 @@

      Edge evidence

      example of organic carbon CHEBI:50860 - rdfs:subClassOf + rdfs:subClassOf

      Glucose is an experimentally supported organic carbon source.

        @@ -328,7 +329,7 @@

        Edge evidence

        example of inorganic electron donor METPO:1007502 - rdfs:subClassOf + rdfs:subClassOf

        Sulfide is an inorganic electron donor for lithotrophic sulfur oxidation.

          @@ -347,7 +348,7 @@

          Edge evidence

          example of inorganic electron donor METPO:1007502 - rdfs:subClassOf + rdfs:subClassOf

          H2 is a reduced inorganic donor that can supplement energy during organic-carbon-supported growth.

            @@ -404,7 +405,7 @@

            Edge evidence

            example of inorganic electron donor METPO:1007502 - rdfs:subClassOf + rdfs:subClassOf

            Thiosulfate is an inorganic sulfur electron donor for lithotrophic oxidation.

              @@ -459,8 +460,8 @@

              Protein and taxon examples

    		 - Sphingopyxis alaskensis RB2256 -
    NCBITaxon:317655 + Sphingopyxis alaskensis RB2256 +
    NCBITaxon:317655         		UNREVIEWED
    @@ -526,7 +527,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • lithoheterotroph RELATED_SYNONYM · metpo.owl
      • +
    • lithoheterotroph RELATED_SYNONYM · metpo.owl
    @@ -542,7 +543,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -881,7 +882,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1245,12 +1255,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 11:46 UTC diff --git a/pages/traits/physiology/lithotrophic.html b/pages/traits/physiology/lithotrophic.html index aa022f3643a..4398f1e6347 100644 --- a/pages/traits/physiology/lithotrophic.html +++ b/pages/traits/physiology/lithotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -119,7 +120,7 @@

    Edge evidence

    example of inorganic electron donor METPO:1007502 - rdfs:subClassOf + rdfs:subClassOf

    Molecular hydrogen is a representative inorganic electron donor.

      @@ -138,7 +139,7 @@

      Edge evidence

      example of inorganic electron donor METPO:1007502 - rdfs:subClassOf + rdfs:subClassOf

      Reduced sulfur compounds are representative lithotrophic electron donors.

        @@ -459,8 +460,8 @@

        Protein and taxon examples

    		 - Nitrosomonas europaea ATCC 19718 -
    NCBITaxon:228410 + Nitrosomonas europaea ATCC 19718 +
    NCBITaxon:228410         		REVIEWED
    @@ -489,8 +490,8 @@

    Protein and taxon examples

    		 - Nitrosomonas europaea ATCC 19718 -
    NCBITaxon:228410 + Nitrosomonas europaea ATCC 19718 +
    NCBITaxon:228410         		REVIEWED
    @@ -556,9 +557,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • TT_lithotroph RELATED_SYNONYM · metpo.owl
      • +
    • TT_lithotroph RELATED_SYNONYM · metpo.owl
      • -
    • lithotroph RELATED_SYNONYM · metpo.owl
      • +
    • lithotroph RELATED_SYNONYM · metpo.owl
    @@ -574,7 +575,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -895,7 +896,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Added reviewed N. europaea ATCC 19718 HAO protein_example UniProtKB:Q50925 (hao1, v155) on hydroxylamine_oxidoreductase (DOI:10.1128/jb.185.9.2759-2773.2003), updated scope_notes, and refreshed UniProtKB:Q04507 entry_version 126 -> 127 on ammonia_monooxygenase.

    +

    Added reviewed N. europaea ATCC 19718 HAO protein_example UniProtKB:Q50925 (hao1, v155) on hydroxylamine_oxidoreductase (DOI:10.1128/jb.185.9.2759-2773.2003), updated scope_notes, and refreshed UniProtKB:Q04507 entry_version 126 -> 127 on ammonia_monooxygenase.

    • @@ -937,7 +938,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1301,12 +1311,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/lysine_decarboxylase_activity.html b/pages/traits/physiology/lysine_decarboxylase_activity.html index fa2371ad915..506cd747c98 100644 --- a/pages/traits/physiology/lysine_decarboxylase_activity.html +++ b/pages/traits/physiology/lysine_decarboxylase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -82,7 +83,7 @@

    Trait evidence (3)

    Lysine decarboxylation to cadaverine and CadBA proton-consuming acid resistance

    Evidence-backed physiological mechanism sketch linking lysine decarboxylase catalytic activity and cadaverine production to the lysine decarboxylase activity phenotype.

    -

    MECHANISTIC · Mechanistic graph backed by EC 4.1.1.18 and DOI:10.1128/jb.01306-06; exemplified on lysine_decarboxylase_cada with Escherichia coli K-12 (NCBITaxon:83333; UP000000625) inducible lysine decarboxylase CadA (UniProtKB:P0A9H3) and cadaverine/lysine antiporter CadB (UniProtKB:P0AAE8).

    +

    MECHANISTIC · Mechanistic graph backed by EC 4.1.1.18 and DOI:10.1128/jb.01306-06; exemplified on lysine_decarboxylase_cada with Escherichia coli K-12 (NCBITaxon:83333; UP000000625) inducible lysine decarboxylase CadA (UniProtKB:P0A9H3) and cadaverine/lysine antiporter CadB (UniProtKB:P0AAE8).

    Loading graph…

    @@ -105,7 +106,7 @@

    Edge evidence

    GO:0008923 confers lysine decarboxylase activity - traitmech:000153 + traitmech:000153 METPO:2007700

    Inducible CadBA lysine decarboxylase activity consumes a proton and produces cadaverine.

      @@ -180,8 +181,8 @@

      Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -210,8 +211,8 @@

    Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -284,7 +285,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -449,7 +450,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The record's primary literature (EC 4.1.1.18, DOI:10.1128/jb.01306-06) establishes the CadBA lysine-dependent acid-resistance decarboxylation of L-lysine to cadaverine and CO2 in Escherichia coli (NCBITaxon:562), but verified UniProtKB accessions must be curated on a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    +

    The record's primary literature (EC 4.1.1.18, DOI:10.1128/jb.01306-06) establishes the CadBA lysine-dependent acid-resistance decarboxylation of L-lysine to cadaverine and CO2 in Escherichia coli (NCBITaxon:562), but verified UniProtKB accessions must be curated on a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

    @@ -468,7 +469,7 @@

    Evidence

    -

    Resolution: Added canonical_examples entry Escherichia coli K-12 (NCBITaxon:83333; DOI:10.1128/jb.01306-06) and promoted lysine_decarboxylase_cadba_sketch to MECHANISTIC by adding InterPro:IPR011193-grounded GENE_OR_PROTEIN node lysine_decarboxylase_cada with reviewed protein_examples UniProtKB:P0A9H3 (CadA) and UniProtKB:P0AAE8 (CadB).

    +

    Resolution: Added canonical_examples entry Escherichia coli K-12 (NCBITaxon:83333; DOI:10.1128/jb.01306-06) and promoted lysine_decarboxylase_cadba_sketch to MECHANISTIC by adding InterPro:IPR011193-grounded GENE_OR_PROTEIN node lysine_decarboxylase_cada with reviewed protein_examples UniProtKB:P0A9H3 (CadA) and UniProtKB:P0AAE8 (CadB).

    @@ -497,7 +498,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Added Escherichia coli K-12 (NCBITaxon:83333; DOI:10.1128/jb.01306-06) canonical example; promoted lysine_decarboxylase_cadba_sketch to MECHANISTIC with InterPro:IPR011193-grounded GENE_OR_PROTEIN node lysine_decarboxylase_cada and reviewed protein_examples UniProtKB:P0A9H3 (CadA) and UniProtKB:P0AAE8 (CadB); resolved lysine-decarboxylase-activity-protein-example-gap.

    +

    Added Escherichia coli K-12 (NCBITaxon:83333; DOI:10.1128/jb.01306-06) canonical example; promoted lysine_decarboxylase_cadba_sketch to MECHANISTIC with InterPro:IPR011193-grounded GENE_OR_PROTEIN node lysine_decarboxylase_cada and reviewed protein_examples UniProtKB:P0A9H3 (CadA) and UniProtKB:P0AAE8 (CadB); resolved lysine-decarboxylase-activity-protein-example-gap.

    • @@ -539,7 +540,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -903,12 +913,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 11:45 UTC diff --git a/pages/traits/physiology/macropinocytosis.html b/pages/traits/physiology/macropinocytosis.html index 6bad931fdf5..2a0703e4a61 100644 --- a/pages/traits/physiology/macropinocytosis.html +++ b/pages/traits/physiology/macropinocytosis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1242/jcs.213736
    Macropinocytosis is a conserved endocytic process used by Dictyostelium amoebae for feeding on liquid medium.
    -

    PMID:29440238, PMC5897714. Scientific ABSTRACT quote. Introduction supports the ruffle-closure definition. Relevant uptake Results, Methods, Discussion and actual Figure 2 were read at https://pmc.ncbi.nlm.nih.gov/articles/PMC5897714/. Figure 2E reports P=0.057 for DdB formation-rate upregulation; do not call this significant. Diameter measurements use a transgenic reporter, unlike the dextran formation assay. Other figures and supplements were not visually audited.

    +

    PMID:29440238, PMC5897714. Scientific ABSTRACT quote. Introduction supports the ruffle-closure definition. Relevant uptake Results, Methods, Discussion and actual Figure 2 were read at https://pmc.ncbi.nlm.nih.gov/articles/PMC5897714/. Figure 2E reports P=0.057 for DdB formation-rate upregulation; do not call this significant. Diameter measurements use a transgenic reporter, unlike the dextran formation assay. Other figures and supplements were not visually audited.

  • DOI:10.7554/eLife.04940
    These cells can also internalise bulk fluid without the guidance of a particle using a closely related process, macropinocytosis
    -

    PMID:25815683, PMC4374526. Contiguous Introduction quote, not the scientific Abstract or eLife digest. Relevant Results, confocal Methods, Discussion, Table 2 and actual Figure 3 were read at https://pmc.ncbi.nlm.nih.gov/articles/PMC4374526/. Figure 3C measures formation events; Figure 3B single sections cannot quantify cumulative uptake. Other figures and movies were not visually audited.

    +

    PMID:25815683, PMC4374526. Contiguous Introduction quote, not the scientific Abstract or eLife digest. Relevant Results, confocal Methods, Discussion, Table 2 and actual Figure 3 were read at https://pmc.ncbi.nlm.nih.gov/articles/PMC4374526/. Figure 3C measures formation events; Figure 3B single sections cannot quantify cumulative uptake. Other figures and movies were not visually audited.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Canonical examples DOI:10.7554/eLife.04940 - Wild-type parental DdB cells freshly harvested from bacterial growth, observed by dextran imaging in Figure 3C; not Ax2, AX4, NF1 knockouts or reporter transformants. Table 2 links DdB to DdB(Wel). Strain genealogy at https://link.springer.com/article/10.1186/gb-2008-9-4-r75 identifies a laboratory-selected NC4 clone with copy-number differences, not an unchanged original wild isolate. NCBI EFetch verified the name and species rank on 2026-10-06; this ID does not identify the strain. + Wild-type parental DdB cells freshly harvested from bacterial growth, observed by dextran imaging in Figure 3C; not Ax2, AX4, NF1 knockouts or reporter transformants. Table 2 links DdB to DdB(Wel). Strain genealogy at https://link.springer.com/article/10.1186/gb-2008-9-4-r75 identifies a laboratory-selected NC4 clone with copy-number differences, not an unchanged original wild isolate. NCBI EFetch verified the name and species rank on 2026-10-06; this ID does not identify the strain. @@ -342,7 +343,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -371,12 +381,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 05:35 UTC diff --git a/pages/traits/physiology/magnetotaxis.html b/pages/traits/physiology/magnetotaxis.html index a20a8f17939..aeea93a1cd6 100644 --- a/pages/traits/physiology/magnetotaxis.html +++ b/pages/traits/physiology/magnetotaxis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -82,7 +83,7 @@

    Trait evidence (3)

    Magnetosome chain alignment and geomagnetic navigation

    Evidence-backed physiological sketch linking magnetosome chain alignment to magnetoreception and directed motility along geomagnetic field lines.

    -

    NONMECHANISTIC · Organelle-to-behavior sketch backed by DOI:10.1128/JB.00398-20, DOI:10.1038/s41396-018-0098-9, and DOI:10.1128/mbio.01649-23; MamK/MamJ magnetoskeleton protein examples are curated on the companion `data/traits/morphology/magnetosome.yaml` organelle record rather than duplicated here without a protein node.

    +

    NONMECHANISTIC · Organelle-to-behavior sketch backed by DOI:10.1128/JB.00398-20, DOI:10.1038/s41396-018-0098-9, and DOI:10.1128/mbio.01649-23; MamK/MamJ magnetoskeleton protein examples are curated on the companion `data/traits/morphology/magnetosome.yaml` organelle record rather than duplicated here without a protein node.

    Loading graph…

    @@ -143,7 +144,7 @@

    Edge evidence

    GO:0042330 confers magnetotaxis - traitmech:000176 + traitmech:000176 METPO:2007700

    Directed motility guided by Earth's magnetic field confers the magnetotaxis phenotype.

      @@ -203,7 +204,7 @@

      Parent traits (1)

      Synonyms (1)

        -
      • magnetotactic RELATED_SYNONYM · DOI:10.1038/nrmicro842
        • +
      • magnetotactic RELATED_SYNONYM · DOI:10.1038/nrmicro842
    @@ -219,7 +220,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -396,7 +397,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -760,12 +770,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-21 21:12 UTC diff --git a/pages/traits/physiology/mating_type_switching.html b/pages/traits/physiology/mating_type_switching.html index 725e5cb3a3a..44ffa1b99ee 100644 --- a/pages/traits/physiology/mating_type_switching.html +++ b/pages/traits/physiology/mating_type_switching.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.5598/imafungus.2015.06.01.13
    In this mating strategy, an individual of one mating type can undergo a switch to the opposite mating type, either bidirectionally (reversibly) or unidirectionally (irreversibly).
    -

    2015 terminology review, PMID:26203424, PMC4500084. Exact sentence from the directly retrieved full-text XML section MATING TYPE SWITCHING (s3), including both subsections read end-to-end. This is definition authority, not experimental replication or an abstract quote. The umbrella includes reversible yeast switching and irreversible mating-type alteration in filamentous fungi. A single founder can yield a mixed-mating-type colony; cellular mating identity and colony-level self-fertility are distinct. The record does not universalize the review's yeast MAT architecture or require a particular endonuclease. Figure 1 and the other mechanism category sections remain uninspected.

    +

    2015 terminology review, PMID:26203424, PMC4500084. Exact sentence from the directly retrieved full-text XML section MATING TYPE SWITCHING (s3), including both subsections read end-to-end. This is definition authority, not experimental replication or an abstract quote. The umbrella includes reversible yeast switching and irreversible mating-type alteration in filamentous fungi. A single founder can yield a mixed-mating-type colony; cellular mating identity and colony-level self-fertility are distinct. The record does not universalize the review's yeast MAT architecture or require a particular endonuclease. Figure 1 and the other mechanism category sections remain uninspected.

  • DOI:10.1534/genetics.107.076315
    Schizosaccharomyces pombe cells can switch between two mating types, plus (P) and minus (M).
    -

    Yamada-Inagawa et al. (2007), PMID:17660548. Exact first sentence of the scientific abstract directly retrieved from Europe PMC core metadata. The study tests synthesis-dependent strand annealing using strains with two engineered mutant P donor cassettes and recovery of wild-type P information at mat1 through heteroduplex formation and repair. This is an in-vivo mechanistic test, not natural-isolate provenance. Do not require this cassette arrangement, exactly two mating types, or the S. pombe replication program for all fungi. Full text, figures, supplements and original strain provenance remain uninspected: the full-text XML endpoint returned HTTP 500 and the PDF mirror returned HTTP 403. The authoritative abstract is indexed and readable despite those access failures.

    +

    Yamada-Inagawa et al. (2007), PMID:17660548. Exact first sentence of the scientific abstract directly retrieved from Europe PMC core metadata. The study tests synthesis-dependent strand annealing using strains with two engineered mutant P donor cassettes and recovery of wild-type P information at mat1 through heteroduplex formation and repair. This is an in-vivo mechanistic test, not natural-isolate provenance. Do not require this cassette arrangement, exactly two mating types, or the S. pombe replication program for all fungi. Full text, figures, supplements and original strain provenance remain uninspected: the full-text XML endpoint returned HTTP 500 and the PDF mirror returned HTTP 403. The authoritative abstract is indexed and readable despite those access failures.

  • DOI:10.1371/journal.pgen.1006981
    a chromosomal looping out-based mechanism underpins irreversible unidirectional mating-type alteration in filamentous fungi.
    -

    Yun et al. (2017), PMID:28892488, PMC5608430. Exact contiguous clause from Conclusions (sec017), not the scientific abstract or author summary. Scientific abstract, strain/culture Methods, Results sec005-sec007 and Discussion sec013/sec015 were read. Actual Figures 3 and 4 and their captions were inspected. Results and Figure 3 identify DR2 deletion in Cs23-derived T10; Discussion sec013 instead says DR1. Retain the figure-supported DR2 identity, not that conflicting wording. Figure 4 separates fertile Cs23 from T10 aggregates and Cs27-derived transformants that can form perithecia without ascospores. The authors support irreversible MAT loss in C. spinulosa; the detailed nuclear-recognition mechanism remains a model. Original natural provenance, other figures, supplements and unread experimental sections remain unverified. Neither reference-strain labels nor transgenic constructs establish natural canonical examples.

    +

    Yun et al. (2017), PMID:28892488, PMC5608430. Exact contiguous clause from Conclusions (sec017), not the scientific abstract or author summary. Scientific abstract, strain/culture Methods, Results sec005-sec007 and Discussion sec013/sec015 were read. Actual Figures 3 and 4 and their captions were inspected. Results and Figure 3 identify DR2 deletion in Cs23-derived T10; Discussion sec013 instead says DR1. Retain the figure-supported DR2 identity, not that conflicting wording. Figure 4 separates fertile Cs23 from T10 aggregates and Cs27-derived transformants that can form perithecia without ascospores. The authors support irreversible MAT loss in C. spinulosa; the detailed nuclear-recognition mechanism remains a model. Original natural provenance, other figures, supplements and unread experimental sections remain unverified. Neither reference-strain labels nor transgenic constructs establish natural canonical examples.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 02:56 UTC diff --git a/pages/traits/physiology/methanotrophic.html b/pages/traits/physiology/methanotrophic.html index 571961d2fb6..9f0076b86b1 100644 --- a/pages/traits/physiology/methanotrophic.html +++ b/pages/traits/physiology/methanotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -341,7 +342,7 @@

    Edge evidence

    example of methane monooxygenase GO:0015050 - rdfs:subClassOf + rdfs:subClassOf

    Particulate MMO is one of the two methane-monooxygenase enzyme types.

      @@ -396,8 +397,8 @@

      Protein and taxon examples

    		 - Methylococcus capsulatus Bath -
    NCBITaxon:243233 + Methylococcus capsulatus Bath +
    NCBITaxon:243233         		REVIEWED
    @@ -463,7 +464,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • methanotroph RELATED_SYNONYM · metpo.owl
      • +
    • methanotroph RELATED_SYNONYM · metpo.owl
    @@ -479,7 +480,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -833,7 +834,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1197,12 +1207,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/methylotrophic.html b/pages/traits/physiology/methylotrophic.html index 5eda607f9f6..102663b6478 100644 --- a/pages/traits/physiology/methylotrophic.html +++ b/pages/traits/physiology/methylotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -379,7 +380,7 @@

    Edge evidence

    example of PQQ-dependent methanol dehydrogenase - rdfs:subClassOf + rdfs:subClassOf

    The calcium-dependent Mxa enzyme is a PQQ-dependent alcohol dehydrogenase used for methanol oxidation.

      @@ -453,8 +454,8 @@

      Protein and taxon examples

    		 - Methylorubrum extorquens AM1 -
    NCBITaxon:272630 + Methylorubrum extorquens AM1 +
    NCBITaxon:272630         		REVIEWED
    @@ -520,11 +521,11 @@

    Parent traits (1)

    Synonyms (3)

      -
    • TT_methylotroph RELATED_SYNONYM · metpo.owl
      • +
    • TT_methylotroph RELATED_SYNONYM · metpo.owl
      • -
    • methylotroph RELATED_SYNONYM · metpo.owl
      • +
    • methylotroph RELATED_SYNONYM · metpo.owl
      • -
    • methylotrophy RELATED_SYNONYM · metpo.owl
      • +
    • methylotrophy RELATED_SYNONYM · metpo.owl
    @@ -540,7 +541,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -888,7 +889,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1252,12 +1262,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/mitophagy.html b/pages/traits/physiology/mitophagy.html index 793e2fe626e..2f11b485853 100644 --- a/pages/traits/physiology/mitophagy.html +++ b/pages/traits/physiology/mitophagy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.7554/eLife.61245
    Thus, we hereafter refer to the selective autophagic degradation of mitochondria in fission yeast as mitophagy.
    -

    PMID:33138913, PMC7609059. Full-text Results section s2-2, not the scientific Abstract, directly read in Europe PMC XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7609059/fullTextXML. Results s2-1/s2-2, Methods s4-1/s4-5/s4-8 and actual Figure 1 plus its figure supplement 1 were inspected. In Schizosaccharomyces pombe, mitochondrial reporter processing has Atg1 and vacuolar-protease Isp6 controls; Atg43 perturbation and complementation distinguish mitochondrial turnover from bulk, cytoplasmic and ER turnover. atg43-1 is a partial allele, not the complete deletion, which also impairs vegetative growth. Tom70 deletion retains weak processing on long exposure. Other actual figures, complete Methods, Key Resources Table and natural strain provenance were not inspected.

    +

    PMID:33138913, PMC7609059. Full-text Results section s2-2, not the scientific Abstract, directly read in Europe PMC XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7609059/fullTextXML. Results s2-1/s2-2, Methods s4-1/s4-5/s4-8 and actual Figure 1 plus its figure supplement 1 were inspected. In Schizosaccharomyces pombe, mitochondrial reporter processing has Atg1 and vacuolar-protease Isp6 controls; Atg43 perturbation and complementation distinguish mitochondrial turnover from bulk, cytoplasmic and ER turnover. atg43-1 is a partial allele, not the complete deletion, which also impairs vegetative growth. Tom70 deletion retains weak processing on long exposure. Other actual figures, complete Methods, Key Resources Table and natural strain provenance were not inspected.

  • DOI:10.1016/j.devcel.2009.06.014
    This gene is not required for other types of selective autophagy or for nonspecific macroautophagy.
    -

    PMID:19619495, PMC2746076. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. The quoted gene is YIL146C/ECM37, named ATG32 by the authors after a mitophagy-deficient mutant screen. This supports selectivity relative to other autophagy phenotypes in the studied yeast, not a universal ATG32 requirement or a gene-presence trait. Mitochondrial recruitment or vacuolar import alone does not establish completed degradation. Full-text retrieval failed; methods, actual figures and strain provenance were not inspected. Human-disease background is not microbial evidence.

    +

    PMID:19619495, PMC2746076. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. The quoted gene is YIL146C/ECM37, named ATG32 by the authors after a mitophagy-deficient mutant screen. This supports selectivity relative to other autophagy phenotypes in the studied yeast, not a universal ATG32 requirement or a gene-presence trait. Mitochondrial recruitment or vacuolar import alone does not establish completed degradation. Full-text retrieval failed; methods, actual figures and strain provenance were not inspected. Human-disease background is not microbial evidence.

  • DOI:10.1016/j.devcel.2009.06.013
    We propose that Atg32 acts as a mitophagy-specific receptor and regulates selective degradation of mitochondria.
    -

    PMID:19619494. Scientific Abstract directly read in Europe PMC core metadata and PubMed HTML. In post-log respiratory yeast cells, the authors report selective mitochondrial transport to the vacuole and propose an Atg32 receptor mechanism. The quote retains that proposal language. It does not establish that every microbial route uses Atg32, that all cargo must be damaged, or that starvation is always required. Full text, actual figures and natural strain provenance were not inspected.

    +

    PMID:19619494. Scientific Abstract directly read in Europe PMC core metadata and PubMed HTML. In post-log respiratory yeast cells, the authors report selective mitochondrial transport to the vacuole and propose an Atg32 receptor mechanism. The quote retains that proposal language. It does not establish that every microbial route uses Atg32, that all cargo must be damaged, or that starvation is always required. Full text, actual figures and natural strain provenance were not inspected.

  • DOI:10.4161/auto.4034
    The observation of mitochondria degradation showed that both a selective process and a nonselective process of mitochondria autophagy occurred successively.
    -

    PMID:17377488. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. The yeast study reports preferential microautophagy under its nonfermentable growth and nitrogen-starvation conditions, and sequential selective and nonselective turnover. Only selective degradation belongs to this proposed trait; incidental capture during bulk autophagy is insufficient. This supports route-sensitive interpretation, not universal microautophagy or a universal UTH1 requirement. Full text, actual electron micrographs and strain provenance were not inspected.

    +

    PMID:17377488. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. The yeast study reports preferential microautophagy under its nonfermentable growth and nitrogen-starvation conditions, and sequential selective and nonselective turnover. Only selective degradation belongs to this proposed trait; incidental capture during bulk autophagy is insufficient. This supports route-sensitive interpretation, not universal microautophagy or a universal UTH1 requirement. Full text, actual electron micrographs and strain provenance were not inspected.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -221,7 +222,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Use autophagy traitmech:000638 as the direct broader phenotype. This draft uses selective mitochondrial degradation, as named in the fission-yeast Results, without making membrane route universal. The 2007 yeast abstract reports selective and nonselective turnover with preferential microautophagy under its conditions. In contrast, issuing GO:0000423 names mitophagy specifically for selective macroautophagy and lists macromitophagy as exact; GO:0000424 micromitophagy is not its child. GO:0000422 autophagy of mitochondrion is broader and lists mitophagy as narrow. These nonobsolete biological-process records were directly resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0000422,GO%3A0000423,GO%3A0000424. Do not silently impose GO's route-specific usage on every microbial source, or assert an exact phenotype xref. Retain this interpretation for human review; omit exact synonyms including broad mitochondrial autophagy and route-specific macromitophagy. Protein/gene presence, puncta, organelle fragmentation, membrane depolarization, delivery without degradation, and nonspecific bulk capture alone are insufficient. The trait belongs to the microbial cell doing the turnover, not to a bacterium inducing mitophagy in an animal host.

    +

    Use autophagy traitmech:000638 as the direct broader phenotype. This draft uses selective mitochondrial degradation, as named in the fission-yeast Results, without making membrane route universal. The 2007 yeast abstract reports selective and nonselective turnover with preferential microautophagy under its conditions. In contrast, issuing GO:0000423 names mitophagy specifically for selective macroautophagy and lists macromitophagy as exact; GO:0000424 micromitophagy is not its child. GO:0000422 autophagy of mitochondrion is broader and lists mitophagy as narrow. These nonobsolete biological-process records were directly resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0000422,GO%3A0000423,GO%3A0000424. Do not silently impose GO's route-specific usage on every microbial source, or assert an exact phenotype xref. Retain this interpretation for human review; omit exact synonyms including broad mitochondrial autophagy and route-specific macromitophagy. Protein/gene presence, puncta, organelle fragmentation, membrane depolarization, delivery without degradation, and nonspecific bulk capture alone are insufficient. The trait belongs to the microbial cell doing the turnover, not to a bacterium inducing mitophagy in an animal host.

    @@ -283,7 +284,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed microbial mitophagy phenotype -

      Added traitmech:000639 under autophagy traitmech:000638 with four primary DOI citations, three scientific-abstract snippets and one directly matched full-text Results snippet. The maintained resolver reports three VERIFIED at 1.00 and one NOT_IN_ABSTRACT at 0.40; the latter was independently exact-matched to PMC7609059 Results s2-2, not relabeled as an abstract match. Reviewed actual Figure 1 and its first supplement for source-bounded degradation and selectivity claims. Fresh ignored-and-hidden searches, full pinned METPO RDF, seed/release reconciliation and all-state GitHub checks found no exact trait or identifier reservation. Reserved METPO:1059200 in v515 and copied the unchanged v514 autophagy context row for a complete proposal hierarchy. Retained two OPEN discussions about route scope, endpoint interpretation and unverified strain/protein grounding; no canonical examples or causal graph added. Writer dry run, 22 controlled-fixture tests, Ruff and single-record LinkML validation passed. Broad QC, generated artifacts, full tests and PR review are subsequent work and are not claimed complete in this event.

    +

    Added traitmech:000639 under autophagy traitmech:000638 with four primary DOI citations, three scientific-abstract snippets and one directly matched full-text Results snippet. The maintained resolver reports three VERIFIED at 1.00 and one NOT_IN_ABSTRACT at 0.40; the latter was independently exact-matched to PMC7609059 Results s2-2, not relabeled as an abstract match. Reviewed actual Figure 1 and its first supplement for source-bounded degradation and selectivity claims. Fresh ignored-and-hidden searches, full pinned METPO RDF, seed/release reconciliation and all-state GitHub checks found no exact trait or identifier reservation. Reserved METPO:1059200 in v515 and copied the unchanged v514 autophagy context row for a complete proposal hierarchy. Retained two OPEN discussions about route scope, endpoint interpretation and unverified strain/protein grounding; no canonical examples or causal graph added. Writer dry run, 22 controlled-fixture tests, Ruff and single-record LinkML validation passed. Broad QC, generated artifacts, full tests and PR review are subsequent work and are not claimed complete in this event.

    • Read this curation session @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 10:09 UTC diff --git a/pages/traits/physiology/mixotrophic.html b/pages/traits/physiology/mixotrophic.html index 9e141866869..b79316a2515 100644 --- a/pages/traits/physiology/mixotrophic.html +++ b/pages/traits/physiology/mixotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -364,8 +365,8 @@

    Protein and taxon examples

    		 - Paracoccus denitrificans Pd1222 -
    NCBITaxon:318586 + Paracoccus denitrificans Pd1222 +
    NCBITaxon:318586         		REVIEWED
    @@ -431,7 +432,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • mixotroph RELATED_SYNONYM · metpo.owl
      • +
    • mixotroph RELATED_SYNONYM · metpo.owl
    @@ -447,7 +448,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -798,7 +799,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1162,12 +1172,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/mucocyst_discharge.html b/pages/traits/physiology/mucocyst_discharge.html index 165dc77ca6a..10da2aeb530 100644 --- a/pages/traits/physiology/mucocyst_discharge.html +++ b/pages/traits/physiology/mucocyst_discharge.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1371/journal.pgen.1010194
    lysosome-related organelles called mucocysts accumulate at the cell periphery where they secrete their contents in response to extracellular events
    -

    PMID:35587496, PMC9159632. Scientific Abstract, relevant Results/Methods and Discussion read directly in Europe PMC fullTextXML and publisher HTML. Figure 1 and its caption were visually inspected; Figure 4 caption, not image, was read. The snippet is from the scientific Abstract, not the Author summary. Dibucaine stimulates release in Tetrahymena thermophila. Sedimented flocculent volume is a secretion proxy, not a count of discharged organelles; cells can be trapped in that layer. The MN175 missense and MDL1 deletion phenotypes differ. S1 Table DOCX text was inspected, not rendered; laboratory strain names and genotypes do not establish natural provenance.

    +

    PMID:35587496, PMC9159632. Scientific Abstract, relevant Results/Methods and Discussion read directly in Europe PMC fullTextXML and publisher HTML. Figure 1 and its caption were visually inspected; Figure 4 caption, not image, was read. The snippet is from the scientific Abstract, not the Author summary. Dibucaine stimulates release in Tetrahymena thermophila. Sedimented flocculent volume is a secretion proxy, not a count of discharged organelles; cells can be trapped in that layer. The MN175 missense and MDL1 deletion phenotypes differ. S1 Table DOCX text was inspected, not rendered; laboratory strain names and genotypes do not establish natural provenance.

  • DOI:10.1016/0309-1651(77)90012-1
    Synchronous secretion of all available mature mucocysts was induced
    -

    PMID:610868. Scientific Abstract directly retrieved with EXT_ID:610868 AND SRC:MED in Europe PMC; an unqualified numeric query also returns an unrelated database record. The correct MED result matches this DOI and title. Abstract-only access; full Methods and figures were not inspected. The source names Tetrahymena thermophilia (B III). Synchrony and complete release concern late-log cultures treated with dibucaine, not universal requirements for this trait. Fusion-rosette reappearance and new mucocyst precursors are temporally associated, not proof of a universal protein mechanism.

    +

    PMID:610868. Scientific Abstract directly retrieved with EXT_ID:610868 AND SRC:MED in Europe PMC; an unqualified numeric query also returns an unrelated database record. The correct MED result matches this DOI and title. Abstract-only access; full Methods and figures were not inspected. The source names Tetrahymena thermophilia (B III). Synchrony and complete release concern late-log cultures treated with dibucaine, not universal requirements for this trait. Fusion-rosette reappearance and new mucocyst precursors are temporally associated, not proof of a universal protein mechanism.

  • DOI:10.1128/ec.00058-15
    those cores do not undergo normal directional expansion during exocytosis, and they thus fail to efficiently extrude from the cells.
    -

    PMID:26092918, PMC4519746. Scientific Abstract directly retrieved by exact quoted DOI query in Europe PMC. Abstract-only access; full Methods, figures and supplements were not inspected. The snippet refers to CTH4-disrupted Tetrahymena thermophila: crystalline cores assemble but extrusion is inefficient. It is boundary evidence distinguishing assembly from successful release, not a positive mutant exemplar or proof that no cargo is released. CTH4 dependence is not imposed on all mucocysts.

    +

    PMID:26092918, PMC4519746. Scientific Abstract directly retrieved by exact quoted DOI query in Europe PMC. Abstract-only access; full Methods, figures and supplements were not inspected. The snippet refers to CTH4-disrupted Tetrahymena thermophila: crystalline cores assemble but extrusion is inefficient. It is boundary evidence distinguishing assembly from successful release, not a positive mutant exemplar or proof that no cargo is released. CTH4 dependence is not imposed on all mucocysts.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-08 17:20 UTC diff --git a/pages/traits/physiology/myzocytosis.html b/pages/traits/physiology/myzocytosis.html index ecbd546dad2..dcaa26aaf06 100644 --- a/pages/traits/physiology/myzocytosis.html +++ b/pages/traits/physiology/myzocytosis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.3390/microorganisms11081945
    Colpodella sp. (ATCC 50594) obtain nutrients by preying on Parabodo caudatus using myzocytosis.
    -

    PMID:37630505, PMC10458597. Direct scientific Abstract quote. Main text and actual Figures 7-9 were inspected; Figures 1-6 were not visually audited. Introduction and Conclusions describe aspiration through a feeding channel. Fixed-cell TEM supports prey-membrane uptake at the contact, not direct piercing by the pseudoconoid. Unattached nanoparticle uptake is separate endocytosis, not proof of myzocytosis. Intact prey organelles in food vacuoles do not establish functional organelle retention. Posterior vacuole position and encystation are not universal requirements. The mixed culture does not resolve a complete native protein mechanism.

    +

    PMID:37630505, PMC10458597. Direct scientific Abstract quote. Main text and actual Figures 7-9 were inspected; Figures 1-6 were not visually audited. Introduction and Conclusions describe aspiration through a feeding channel. Fixed-cell TEM supports prey-membrane uptake at the contact, not direct piercing by the pseudoconoid. Unattached nanoparticle uptake is separate endocytosis, not proof of myzocytosis. Intact prey organelles in food vacuoles do not establish functional organelle retention. Posterior vacuole position and encystation are not universal requirements. The mixed culture does not resolve a complete native protein mechanism.

  • DOI:10.1111/jeu.13050
    cytoplasm contents were transferred through the peduncle to the dinoflagellate.
    -

    PMID:39019843, PMC11603288. Direct Nutrition and feeding behavior Results passage, not an abstract quote. Scientific Abstract, culture and fluorescence Methods, feeding Results and Discussion, and actual supplementary Figure S6 with its caption were inspected. S6 identifies imaged SPMC98; the molecular-data isolate SPMC100 is different. Panel D shows deformed cryptophyte material passing through the peduncle; attachment in panel E alone is not ingestion. The organism can also use conventional phagocytosis. Trichocyst discharge may be a fixation artifact, not a demonstrated prey-capture mechanism. Other supplementary figures, molecular datasets and movies were not audited.

    +

    PMID:39019843, PMC11603288. Direct Nutrition and feeding behavior Results passage, not an abstract quote. Scientific Abstract, culture and fluorescence Methods, feeding Results and Discussion, and actual supplementary Figure S6 with its caption were inspected. S6 identifies imaged SPMC98; the molecular-data isolate SPMC100 is different. Panel D shows deformed cryptophyte material passing through the peduncle; attachment in panel E alone is not ingestion. The organism can also use conventional phagocytosis. Trichocyst discharge may be a fixation artifact, not a demonstrated prey-capture mechanism. Other supplementary figures, molecular datasets and movies were not audited.

  • DOI:10.1038/ismej.2012.29
    parts are sucked out by a microtubule supported feeding tube or peduncle (myzocytosis)
    -

    PMID:22513533, PMC3446796. Direct Introduction terminology span, not an abstract quote or independent naming experiment. Main text and actual Figure 2 were inspected; other figures and supplementary movies were not visually audited. Results report Karlodinium armiger tube feeding on copepods and polychaete larvae, so the prey need not be unicellular. Nematode feeding was not directly observed. Abstract and later passages call the strain K-0688, whereas initial Methods and Table 1 say K-0668; no canonical strain is assigned from this conflicting record. Proposed toxin and chemotaxis explanations are not molecular demonstrations.

    +

    PMID:22513533, PMC3446796. Direct Introduction terminology span, not an abstract quote or independent naming experiment. Main text and actual Figure 2 were inspected; other figures and supplementary movies were not visually audited. Results report Karlodinium armiger tube feeding on copepods and polychaete larvae, so the prey need not be unicellular. Nematode feeding was not directly observed. Abstract and later passages call the strain K-0688, whereas initial Methods and Table 1 say K-0668; no canonical strain is assigned from this conflicting record. Proposed toxin and chemotaxis explanations are not molecular demonstrations.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1111/jeu.13050 - Qualified example: imaged SPMC98 feeding on cryptophyte prey, not molecular-data isolate SPMC100. Maintenance cultures Methods at https://doi.org/10.1111/jeu.13050 document natural isolation from the Salish Sea near Anacortes, Washington, in 1993, originally identified as Amphidinium longum. SPMC98 was lost in 2004. Actual supplementary Figure S6 names this strain and shows prey material passing through the peduncle. Feeding mode is prey-dependent; this is not a claim about all isolates or exclusive myzocytosis. NCBI ESearch and EFetch resolved the species and its Amphidinium longum synonym on 2026-10-06. + Qualified example: imaged SPMC98 feeding on cryptophyte prey, not molecular-data isolate SPMC100. Maintenance cultures Methods at https://doi.org/10.1111/jeu.13050 document natural isolation from the Salish Sea near Anacortes, Washington, in 1993, originally identified as Amphidinium longum. SPMC98 was lost in 2004. Actual supplementary Figure S6 names this strain and shows prey material passing through the peduncle. Feeding mode is prey-dependent; this is not a claim about all isolates or exclusive myzocytosis. NCBI ESearch and EFetch resolved the species and its Amphidinium longum synonym on 2026-10-06. @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 00:50 UTC diff --git a/pages/traits/physiology/nad_dependent_alcohol_dehydrogenase_activity.html b/pages/traits/physiology/nad_dependent_alcohol_dehydrogenase_activity.html index 235ef0bcde1..7af2cf4b862 100644 --- a/pages/traits/physiology/nad_dependent_alcohol_dehydrogenase_activity.html +++ b/pages/traits/physiology/nad_dependent_alcohol_dehydrogenase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -84,7 +85,7 @@

    Trait evidence (3)

    NAD-dependent alcohol dehydrogenase catalysis and NADH generation

    Evidence-backed physiological mechanism sketch linking NAD-dependent alcohol dehydrogenase catalytic activity and NADH generation to the NAD-dependent alcohol dehydrogenase activity phenotype.

    -

    MECHANISTIC · Mechanistic graph backed by DOI:10.1111/j.1432-1033.1986.tb09366.x and DOI:10.1128/jb.169.6.2591-2597.1987; exemplified on nad_dependent_alcohol_dehydrogenase_adh with Zymomonas mobilis subsp. mobilis ZM4 (NCBITaxon:264203; UP000001173) alcohol dehydrogenase 2 AdhB (UniProtKB:P0DJA2) and alcohol dehydrogenase 1 AdhA (UniProtKB:P20368).

    +

    MECHANISTIC · Mechanistic graph backed by DOI:10.1111/j.1432-1033.1986.tb09366.x and DOI:10.1128/jb.169.6.2591-2597.1987; exemplified on nad_dependent_alcohol_dehydrogenase_adh with Zymomonas mobilis subsp. mobilis ZM4 (NCBITaxon:264203; UP000001173) alcohol dehydrogenase 2 AdhB (UniProtKB:P0DJA2) and alcohol dehydrogenase 1 AdhA (UniProtKB:P20368).

    Loading graph…

    @@ -107,7 +108,7 @@

    Edge evidence

    GO:0004022 confers NAD-dependent alcohol dehydrogenase activity - traitmech:000165 + traitmech:000165 METPO:2007700

    Purified NAD-dependent alcohol dehydrogenase isoenzymes confer the organismal alcohol dehydrogenase activity phenotype.

      @@ -184,8 +185,8 @@

      Protein and taxon examples

    		 - Zymomonas mobilis subsp. mobilis ZM4 -
    NCBITaxon:264203 + Zymomonas mobilis subsp. mobilis ZM4 +
    NCBITaxon:264203         		REVIEWED
    @@ -214,8 +215,8 @@

    Protein and taxon examples

    		 - Zymomonas mobilis subsp. mobilis ZM4 -
    NCBITaxon:264203 + Zymomonas mobilis subsp. mobilis ZM4 +
    NCBITaxon:264203         		REVIEWED
    @@ -281,11 +282,11 @@

    Parent traits (1)

    Synonyms (3)

    @@ -301,7 +302,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -466,7 +467,7 @@

    Discussions and Knowledge Gaps (3)

    -

    The current record carries an IUBMB EC 1.1.1.1 reaction snippet and two Zymomonas mobilis adhB purification/cloning snippets (DOI:10.1111/j.1432-1033.1986.tb09366.x, DOI:10.1128/jb.169.6.2591-2597.1987) that identify AdhB but do not state its physiological acetaldehyde-to-ethanol metabolic role or include verified UniProtKB protein_examples.

    +

    The current record carries an IUBMB EC 1.1.1.1 reaction snippet and two Zymomonas mobilis adhB purification/cloning snippets (DOI:10.1111/j.1432-1033.1986.tb09366.x, DOI:10.1128/jb.169.6.2591-2597.1987) that identify AdhB but do not state its physiological acetaldehyde-to-ethanol metabolic role or include verified UniProtKB protein_examples.

    @@ -511,7 +512,7 @@

    Evidence

    -

    The record's primary literature (EC 1.1.1.1, DOI:10.1111/j.1432-1033.1986.tb09366.x, DOI:10.1128/jb.169.6.2591-2597.1987) establishes NAD-dependent alcohol dehydrogenase catalysis and adhB cloning/purification in Zymomonas mobilis (NCBITaxon:542), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    +

    The record's primary literature (EC 1.1.1.1, DOI:10.1111/j.1432-1033.1986.tb09366.x, DOI:10.1128/jb.169.6.2591-2597.1987) establishes NAD-dependent alcohol dehydrogenase catalysis and adhB cloning/purification in Zymomonas mobilis (NCBITaxon:542), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    @@ -530,7 +531,7 @@

    Evidence

    -

    Resolution: Added canonical_examples entry Zymomonas mobilis subsp. mobilis ZM4 (NCBITaxon:264203; DOI:10.1128/jb.169.6.2591-2597.1987) and promoted nad_dependent_alcohol_dehydrogenase_adh_sketch to MECHANISTIC by adding InterPro:IPR001670-grounded GENE_OR_PROTEIN node nad_dependent_alcohol_dehydrogenase_adh with active reviewed Swiss-Prot protein_examples UniProtKB:P0DJA2 (AdhB; replacing demerged/inactive P06758/P0DTE6) and UniProtKB:P20368 (AdhA).

    +

    Resolution: Added canonical_examples entry Zymomonas mobilis subsp. mobilis ZM4 (NCBITaxon:264203; DOI:10.1128/jb.169.6.2591-2597.1987) and promoted nad_dependent_alcohol_dehydrogenase_adh_sketch to MECHANISTIC by adding InterPro:IPR001670-grounded GENE_OR_PROTEIN node nad_dependent_alcohol_dehydrogenase_adh with active reviewed Swiss-Prot protein_examples UniProtKB:P0DJA2 (AdhB; replacing demerged/inactive P06758/P0DTE6) and UniProtKB:P20368 (AdhA).

    @@ -571,7 +572,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Added Zymomonas mobilis subsp. mobilis ZM4 (NCBITaxon:264203; DOI:10.1128/jb.169.6.2591-2597.1987) canonical example; promoted nad_dependent_alcohol_dehydrogenase_adh_sketch to MECHANISTIC with InterPro:IPR001670-grounded GENE_OR_PROTEIN node nad_dependent_alcohol_dehydrogenase_adh and reviewed protein_examples UniProtKB:P0DJA2 (AdhB) and UniProtKB:P20368 (AdhA); resolved nad-dependent-alcohol-dehydrogenase-activity-protein-example-gap.

    +

    Added Zymomonas mobilis subsp. mobilis ZM4 (NCBITaxon:264203; DOI:10.1128/jb.169.6.2591-2597.1987) canonical example; promoted nad_dependent_alcohol_dehydrogenase_adh_sketch to MECHANISTIC with InterPro:IPR001670-grounded GENE_OR_PROTEIN node nad_dependent_alcohol_dehydrogenase_adh and reviewed protein_examples UniProtKB:P0DJA2 (AdhB) and UniProtKB:P20368 (AdhA); resolved nad-dependent-alcohol-dehydrogenase-activity-protein-example-gap.

    • @@ -619,7 +620,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -983,12 +993,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 08:45 UTC diff --git a/pages/traits/physiology/naphthol_as_bi_phosphohydrolase_activity.html b/pages/traits/physiology/naphthol_as_bi_phosphohydrolase_activity.html index 4ab63260297..5d5bb236e46 100644 --- a/pages/traits/physiology/naphthol_as_bi_phosphohydrolase_activity.html +++ b/pages/traits/physiology/naphthol_as_bi_phosphohydrolase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • naphthol-AS-BI-phosphohydrolase RELATED_SYNONYM · DOI:10.14202/vetworld.2024.143-149
      • +
    • naphthol-AS-BI-phosphohydrolase RELATED_SYNONYM · DOI:10.14202/vetworld.2024.143-149
    @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -272,7 +273,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two API ZYM diagnostic substrate/panel snippets (DOI:10.14202/vetworld.2024.143-149, DOI:10.1128/JCM.43.8.3713-3717.2005) without catalytic product or enzyme-identity quotes.

    +

    The current record carries two API ZYM diagnostic substrate/panel snippets (DOI:10.14202/vetworld.2024.143-149, DOI:10.1128/JCM.43.8.3713-3717.2005) without catalytic product or enzyme-identity quotes.

    @@ -354,7 +355,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -383,12 +393,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/natural_competence.html b/pages/traits/physiology/natural_competence.html index da197e3280c..504c9a2270f 100644 --- a/pages/traits/physiology/natural_competence.html +++ b/pages/traits/physiology/natural_competence.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    GO:0030420 confers natural competence - traitmech:000087 + traitmech:000087 METPO:2007700

    The competence program realizes the natural-competence trait.

      @@ -326,8 +327,8 @@

      Protein and taxon examples

    		 - Streptococcus pneumoniae R6 -
    NCBITaxon:171101 + Streptococcus pneumoniae R6 +
    NCBITaxon:171101         		REVIEWED
    @@ -393,7 +394,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • natural transformation RELATED_SYNONYM · DOI:10.1038/nrmicro3199
      • +
    • natural transformation RELATED_SYNONYM · DOI:10.1038/nrmicro3199
    @@ -409,7 +410,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -709,7 +710,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1073,12 +1083,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/negative_autotropism.html b/pages/traits/physiology/negative_autotropism.html index 6475f93bd1c..1f268548a53 100644 --- a/pages/traits/physiology/negative_autotropism.html +++ b/pages/traits/physiology/negative_autotropism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.3390/biomimetics10050287
    the hyphae often diverted their growth from their initial direction away from each other.
    -

    Montiel-Rubies et al. (2025), Section 3.4.1; exact span in directly retrieved Europe PMC JATS, PMC12109565 (PMID:40422117). Methods and Sections 3.2/3.4.1 were read; Figure 5 and Table 2 were visually inspected in the authors' PDF. This is a retrospective analysis of earlier microfluidic experiments, not a new independent replication of those datasets. Side-by-side Pycnoporus cinnabarinus hyphae redirected laterally where space allowed. Figure 5B instead shows head-on arrest and cytoplasm retreat, not growth away. Armillaria mellea divergence could reflect directional memory. For Neurospora crassa, Table 2 rates side-by-side avoidance strong and head-on avoidance not observed; prose calls the latter extremely rare. These qualitative descriptions are not counts or replication estimates. Supplementary movies were not inspected. The definition uses the directional-growth component of this paper's broader usage.

    +

    Montiel-Rubies et al. (2025), Section 3.4.1; exact span in directly retrieved Europe PMC JATS, PMC12109565 (PMID:40422117). Methods and Sections 3.2/3.4.1 were read; Figure 5 and Table 2 were visually inspected in the authors' PDF. This is a retrospective analysis of earlier microfluidic experiments, not a new independent replication of those datasets. Side-by-side Pycnoporus cinnabarinus hyphae redirected laterally where space allowed. Figure 5B instead shows head-on arrest and cytoplasm retreat, not growth away. Armillaria mellea divergence could reflect directional memory. For Neurospora crassa, Table 2 rates side-by-side avoidance strong and head-on avoidance not observed; prose calls the latter extremely rare. These qualitative descriptions are not counts or replication estimates. Supplementary movies were not inspected. The definition uses the directional-growth component of this paper's broader usage.

  • DOI:10.1093/jxb/19.1.125
    When germinated on agar surfaces the first three species exhibited negative autotropism, B. cinerea being neutral in its autotropic behaviour.
    -

    Robinson, Park and Graham (1968), original publisher abstract directly retrieved from https://oup.silverchair-cdn.com/article-minimal/447341. The first three species are Rhizopus stolonifer, Mucor plumbeus and Trichoderma viride. Spore-pair assays concern orientation of germ-tube emergence, not demonstrated subsequent tip bending. Cellophane increased their negative response; Botrytis cinerea was neutral on agar and positive on Cellophane, so is not a negative exemplar here. Germination timing and cis-ness are separate readouts, not substitutes for orientation. The full paper, figures, strain provenance and sample sizes were not retrieved; proposed mechanisms in the abstract are not established causal pathways.

    +

    Robinson, Park and Graham (1968), original publisher abstract directly retrieved from https://oup.silverchair-cdn.com/article-minimal/447341. The first three species are Rhizopus stolonifer, Mucor plumbeus and Trichoderma viride. Spore-pair assays concern orientation of germ-tube emergence, not demonstrated subsequent tip bending. Cellophane increased their negative response; Botrytis cinerea was neutral on agar and positive on Cellophane, so is not a negative exemplar here. Germination timing and cis-ness are separate readouts, not substitutes for orientation. The full paper, figures, strain provenance and sample sizes were not retrieved; proposed mechanisms in the abstract are not established causal pathways.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 20:21 UTC diff --git a/pages/traits/physiology/nematode_attracting_activity.html b/pages/traits/physiology/nematode_attracting_activity.html index 878d6eef8bb..6ebebbfffea 100644 --- a/pages/traits/physiology/nematode_attracting_activity.html +++ b/pages/traits/physiology/nematode_attracting_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.7554/eLife.20023
    C. elegans and other nematodes were attracted to volatile compounds produced by A. oligospora.
    -

    Hsueh et al. 2017, PMID:28098555, scientific abstract; native VERIFIED and direct original XML match, not an editorial digest. The producer is Arthrobotrys oligospora CBS 115.81. The 2 h assay physically separates fungal material from nematodes and compares fungal volatiles with medium controls. Actual Figure 1B/D inspected: adult responses are stronger than L1/dauer responses, and not every tested nematode species is attracted. Figure 1D, not the capture image 1E, supplies the multispecies behavioral comparison. Sodium azide retains arrivals; it is not microbial killing evidence. No universal host range, evolutionary adaptation or exact pheromone mimicry is inferred.

    +

    Hsueh et al. 2017, PMID:28098555, scientific abstract; native VERIFIED and direct original XML match, not an editorial digest. The producer is Arthrobotrys oligospora CBS 115.81. The 2 h assay physically separates fungal material from nematodes and compares fungal volatiles with medium controls. Actual Figure 1B/D inspected: adult responses are stronger than L1/dauer responses, and not every tested nematode species is attracted. Figure 1D, not the capture image 1E, supplies the multispecies behavioral comparison. Sodium azide retains arrivals; it is not microbial killing evidence. No universal host range, evolutionary adaptation or exact pheromone mimicry is inferred.

  • DOI:10.1038/ismej.2015.134
    We showed that C. elegans is attracted to L. paracasei grown on citrate or yuzu media.
    -

    Choi et al. 2016, online 2015, PMID:26241504, Discussion opening paragraph; native NOT_IN_ABSTRACT and direct publisher HTML match. Lactobacillus paracasei YSM0385-bearing plugs on the lid are compared with matched bacteria-free medium in a 1 h adult C. elegans N2 assay. Citrate medium includes glucose plus citrate. Actual Figures 1-4 and HTML Table 1 inspected; the table's wild co-occurrence observations alone do not establish attraction. Sodium azide retains arrivals, not bacterial toxicity. Wild isolate Y091 is only Lactobacillus sp., not an inferred L. paracasei assignment. Field recruitment, microbial benefit and nematode fitness benefit are not adopted.

    +

    Choi et al. 2016, online 2015, PMID:26241504, Discussion opening paragraph; native NOT_IN_ABSTRACT and direct publisher HTML match. Lactobacillus paracasei YSM0385-bearing plugs on the lid are compared with matched bacteria-free medium in a 1 h adult C. elegans N2 assay. Citrate medium includes glucose plus citrate. Actual Figures 1-4 and HTML Table 1 inspected; the table's wild co-occurrence observations alone do not establish attraction. Sodium azide retains arrivals, not bacterial toxicity. Wild isolate Y091 is only Lactobacillus sp., not an inferred L. paracasei assignment. Field recruitment, microbial benefit and nematode fitness benefit are not adopted.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-13 23:04 UTC diff --git a/pages/traits/physiology/nematode_egg_hatching_inhibitory_activity.html b/pages/traits/physiology/nematode_egg_hatching_inhibitory_activity.html index 4f936fd2792..d7dc3bab296 100644 --- a/pages/traits/physiology/nematode_egg_hatching_inhibitory_activity.html +++ b/pages/traits/physiology/nematode_egg_hatching_inhibitory_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -61,7 +62,7 @@

    Trait evidence (2)

    DOI:10.1038/s41598-023-33669-z
    T. asperellum FbMi6 inhibited egg hatching in all concentrations as compared to control.
    -

    Saharan et al. 2023, PMID:37088805, Results; direct publisher HTML match, native NOT_IN_ABSTRACT. This is its own experiment, not its background account of Meyer. Five surface-sterilized egg masses received spore-checked culture filtrates at 20/40/60/80%, with water and PDB controls; alternate-day counts through ten days, two repeats at 25 +/- 2 degrees C. Actual Figure 3 inspected. Results associates maximum inhibition with 120 h, whereas its legend specifies 2/4/6/8/10 days; no exact maximum/time pairing is adopted. Egg deformation does not prove death. Juvenile water-recovery findings are not transferred to eggs.

    +

    Saharan et al. 2023, PMID:37088805, Results; direct publisher HTML match, native NOT_IN_ABSTRACT. This is its own experiment, not its background account of Meyer. Five surface-sterilized egg masses received spore-checked culture filtrates at 20/40/60/80%, with water and PDB controls; alternate-day counts through ten days, two repeats at 25 +/- 2 degrees C. Actual Figure 3 inspected. Results associates maximum inhibition with 120 h, whereas its legend specifies 2/4/6/8/10 days; no exact maximum/time pairing is adopted. Egg deformation does not prove death. Juvenile water-recovery findings are not transferred to eggs.

    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-14 03:14 UTC diff --git a/pages/traits/physiology/nematode_egg_hatching_stimulatory_activity.html b/pages/traits/physiology/nematode_egg_hatching_stimulatory_activity.html index 3532a2e8674..2de0c0cb142 100644 --- a/pages/traits/physiology/nematode_egg_hatching_stimulatory_activity.html +++ b/pages/traits/physiology/nematode_egg_hatching_stimulatory_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -61,7 +62,7 @@

    Trait evidence (2)

    DOI:10.1186/s13071-015-0986-z
    When incubated with Gram-positive bacteria, only T. muris eggs showed noticeable hatching after 20 h, although with high variability.
    -

    Vejzagic et al. 2015, PMID:26174801, PMCID:PMC4501204, scientific Abstract Results; exact normalized publisher/XML match and native VERIFIED. This is its own bacterial experiment, not a citation of Meyer. Full Results and actual Figure 2 show Enterococcus caccae and Lactobacillus reuteri above bacteria-free controls after 20 h without antimicrobials, with substantial within- and between-run variability. Hatch is released larvae divided by initial embryonated eggs. T. muris and T. suis are Trichuris muris and Trichuris suis; little T. suis hatch in these conditions is not absolute inability. Antimicrobials and egg storage history affect interpretation. The E. coli strain/concentration ANOVA excludes near-zero controls; that analysis is not a statistical contrast against no bacteria. No direct-contact mechanism is inferred from background citations.

    +

    Vejzagic et al. 2015, PMID:26174801, PMCID:PMC4501204, scientific Abstract Results; exact normalized publisher/XML match and native VERIFIED. This is its own bacterial experiment, not a citation of Meyer. Full Results and actual Figure 2 show Enterococcus caccae and Lactobacillus reuteri above bacteria-free controls after 20 h without antimicrobials, with substantial within- and between-run variability. Hatch is released larvae divided by initial embryonated eggs. T. muris and T. suis are Trichuris muris and Trichuris suis; little T. suis hatch in these conditions is not absolute inability. Antimicrobials and egg storage history affect interpretation. The E. coli strain/concentration ANOVA excludes near-zero controls; that analysis is not a statistical contrast against no bacteria. No direct-contact mechanism is inferred from background citations.

    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-14 06:06 UTC diff --git a/pages/traits/physiology/nematode_repelling_activity.html b/pages/traits/physiology/nematode_repelling_activity.html index 9cccffbe0ba..bd08efad9d9 100644 --- a/pages/traits/physiology/nematode_repelling_activity.html +++ b/pages/traits/physiology/nematode_repelling_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1073/pnas.0610281104
    C. elegans specifically avoids certain strains of Serratia based on their production of the cyclic lipodepsipentapeptide serrawettin W2.
    -

    Pradel et al. 2007, PMID:17267603, PMCID:PMC1892944, scientific Abstract; exact normalized PMC match and native VERIFIED. C. elegans denotes Caenorhabditis elegans. Own Results and actual Figures 1-4 distinguish initial entry followed by leaving Serratia marcescens lawns from absence of attraction. A swrA insertion mutant shows reduced lawn leaving but similar multiday killing; reduced avoidance is not loss of pathogenicity. Purified serrawettin W2 on E. coli OP50 lawns and acute drop-induced reversal are separate assays. The 16-hour bacterial-lawn endpoint, 60-minute supplemented-lawn endpoint and acute reversal are not one exposure. Chemical recognition versus a mechanical surfactant cue remains unresolved, and other bacterial cues can contribute. Serratia swrA is not the similarly named Bacillus motility regulator.

    +

    Pradel et al. 2007, PMID:17267603, PMCID:PMC1892944, scientific Abstract; exact normalized PMC match and native VERIFIED. C. elegans denotes Caenorhabditis elegans. Own Results and actual Figures 1-4 distinguish initial entry followed by leaving Serratia marcescens lawns from absence of attraction. A swrA insertion mutant shows reduced lawn leaving but similar multiday killing; reduced avoidance is not loss of pathogenicity. Purified serrawettin W2 on E. coli OP50 lawns and acute drop-induced reversal are separate assays. The 16-hour bacterial-lawn endpoint, 60-minute supplemented-lawn endpoint and acute reversal are not one exposure. Chemical recognition versus a mechanical surfactant cue remains unresolved, and other bacterial cues can contribute. Serratia swrA is not the similarly named Bacillus motility regulator.

  • DOI:10.15252/embj.2020106938
    a specific volatile organic compound, 1‐undecene, produced by the pathogen P. aeruginosa is sensed as an aversive signal by C. elegans.
    -

    Prakash et al. 2021, PMID:34086368, PMCID:PMC8246062, Discussion first paragraph, own-study result; directly matched JATS, PMC and publisher text. Native NOT_IN_ABSTRACT is retained, not relabeled VERIFIED. This is its own experiment, not a citation of Pradel. P. aeruginosa denotes Pseudomonas aeruginosa. Figure 1A-B measures PA14 lawn occupancy over 12 hours. Pure 1-undecene gives negative chemotaxis and omega turns in distinct Figure 2 and Appendix S2 assays. PA14-versus-undA odor choice establishes relative preference, not by itself repulsion or complete loss of bacterial repellence. Peer-review reply page 14 reports reversals but no complete lawn leaving after 1-undecene on OP50; the alternative adjacent-lawn crossing assay is not eviction from an occupied lawn. Roaming or higher mean square displacement alone is not directional avoidance. Recipient sensory genetics is not a microbial causal pathway.

    +

    Prakash et al. 2021, PMID:34086368, PMCID:PMC8246062, Discussion first paragraph, own-study result; directly matched JATS, PMC and publisher text. Native NOT_IN_ABSTRACT is retained, not relabeled VERIFIED. This is its own experiment, not a citation of Pradel. P. aeruginosa denotes Pseudomonas aeruginosa. Figure 1A-B measures PA14 lawn occupancy over 12 hours. Pure 1-undecene gives negative chemotaxis and omega turns in distinct Figure 2 and Appendix S2 assays. PA14-versus-undA odor choice establishes relative preference, not by itself repulsion or complete loss of bacterial repellence. Peer-review reply page 14 reports reversals but no complete lawn leaving after 1-undecene on OP50; the alternative adjacent-lawn crossing assay is not eviction from an occupied lawn. Roaming or higher mean square displacement alone is not directional avoidance. Recipient sensory genetics is not a microbial causal pathway.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-14 09:16 UTC diff --git a/pages/traits/physiology/nucleophagy.html b/pages/traits/physiology/nucleophagy.html index 0e565e3c7b1..95e58f40ad7 100644 --- a/pages/traits/physiology/nucleophagy.html +++ b/pages/traits/physiology/nucleophagy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,31 +56,31 @@

    Trait evidence (5)

    DOI:10.1091/mbc.e02-08-0483
    During PMN, teardrop-like blebs are pinched from the nucleus, released into the vacuole lumen, and degraded by soluble hydrolases.
    -

    PMID:12529432, PMC140233. Scientific Abstract directly read in Europe PMC with matching DOI. Saccharomyces cerevisiae nuclear portions undergo selective microautophagic turnover; Nvj1 degradation supports flux, not just bleb formation. The reported apg7-delta independence was revised by the 2008 follow-up, so it is not a universal absence-of-ATG requirement. Full-text retrieval failed; Methods, actual figures and strain provenance were not inspected.

    +

    PMID:12529432, PMC140233. Scientific Abstract directly read in Europe PMC with matching DOI. Saccharomyces cerevisiae nuclear portions undergo selective microautophagic turnover; Nvj1 degradation supports flux, not just bleb formation. The reported apg7-delta independence was revised by the 2008 follow-up, so it is not a universal absence-of-ATG requirement. Full-text retrieval failed; Methods, actual figures and strain provenance were not inspected.

  • DOI:10.1091/mbc.e08-04-0363
    We conclude that a spectrum of ATG genes is required for the terminal vacuole enclosure and fusion stages of PMN.
    -

    PMID:18701704, PMC2555948. Scientific Abstract directly read in Europe PMC with matching DOI. Two biochemical assays revise the older PMN dependence claim: atg mutants form blebs but rarely release vesicles into the vacuole. Formation, terminal enclosure and degradation are distinct readouts. This is a yeast PMN result, not a gene-inventory definition of all nucleophagy. Full-text retrieval returned HTTP 500; complete Methods and actual figures were not inspected.

    +

    PMID:18701704, PMC2555948. Scientific Abstract directly read in Europe PMC with matching DOI. Two biochemical assays revise the older PMN dependence claim: atg mutants form blebs but rarely release vesicles into the vacuole. Formation, terminal enclosure and degradation are distinct readouts. This is a yeast PMN result, not a gene-inventory definition of all nucleophagy. Full-text retrieval returned HTTP 500; complete Methods and actual figures were not inspected.

  • DOI:10.1007/s00284-024-03838-y
    These results indicate that nuclei are engulfed in the autophagosomes as a whole and transported/released into the vacuolar lumen where they are degraded.
    -

    PMID:39162852, PMC11335778. Scientific Abstract directly read in Europe PMC; matching-DOI XML Methods Sec3/Sec6, Results Sec11/Sec12 and Discussion Sec13 read. Aspergillus oryzae H2B-EGFP processing and Atg1/Atg8/Ypt7/Atg15 perturbations distinguish whole-nucleus uptake, fusion and degradation. Residual carbon-starvation cleavage and possible sample-preparation proteolysis limit interpretation; complementation was incomplete. RIB40 was the DNA donor, not the assayed NSRku70-derived host; Aspergillus nidulans supplied the reporter, not the phenotype. Receptor speculation includes unpublished data. Figure captions, not actual figures or supplements, were inspected.

    +

    PMID:39162852, PMC11335778. Scientific Abstract directly read in Europe PMC; matching-DOI XML Methods Sec3/Sec6, Results Sec11/Sec12 and Discussion Sec13 read. Aspergillus oryzae H2B-EGFP processing and Atg1/Atg8/Ypt7/Atg15 perturbations distinguish whole-nucleus uptake, fusion and degradation. Residual carbon-starvation cleavage and possible sample-preparation proteolysis limit interpretation; complementation was incomplete. RIB40 was the DNA donor, not the assayed NSRku70-derived host; Aspergillus nidulans supplied the reporter, not the phenotype. Receptor speculation includes unpublished data. Figure captions, not actual figures or supplements, were inspected.

  • DOI:10.1371/journal.pone.0033270
    infection-associated nuclear degeneration in M. oryzae instead occurs by non-selective macroautophagy, which is necessary for rice blast disease.
    -

    PMID:22448240, PMC3308974. Scientific Abstract directly read in Europe PMC and PLOS. Results on nuclear degeneration and macroautophagy were read. H1-RFP imaging and Atg1/Atg4 perturbations support infection-associated nuclear loss; MoVac8/MoTsc13 are dispensable for it. Some selective-autophagy mutant comparisons are data not shown. The 2024 study's Discussion includes this route under nucleophagy; retain that attributed usage, not a yeast PMN assignment. Actual figures, full Methods and independent strain provenance were not inspected.

    +

    PMID:22448240, PMC3308974. Scientific Abstract directly read in Europe PMC and PLOS. Results on nuclear degeneration and macroautophagy were read. H1-RFP imaging and Atg1/Atg4 perturbations support infection-associated nuclear loss; MoVac8/MoTsc13 are dispensable for it. Some selective-autophagy mutant comparisons are data not shown. The 2024 study's Discussion includes this route under nucleophagy; retain that attributed usage, not a yeast PMN assignment. Actual figures, full Methods and independent strain provenance were not inspected.

  • DOI:10.1242/jcs.133090
    A selective form of autophagy, known as nucleophagy, can be used to accomplish the degradation of nucleus-derived material.
    -

    PMID:24013549. Scientific Abstract directly read in Europe PMC with matching DOI. This is a review supporting terminology, not an independent experiment. Its selective formulation is narrower than the 2024 Discussion's inclusion of nonselective Magnaporthe nuclear degradation. Preserve that scope question explicitly rather than imposing selectivity universally. Full text and poster were not inspected.

    +

    PMID:24013549. Scientific Abstract directly read in Europe PMC with matching DOI. This is a review supporting terminology, not an independent experiment. Its selective formulation is narrower than the 2024 Discussion's inclusion of nonselective Magnaporthe nuclear degradation. Preserve that scope question explicitly rather than imposing selectivity universally. Full text and poster were not inspected.

    • @@ -131,7 +132,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -227,7 +228,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Include nuclear portions and entire nuclei, micro and macro routes. The 2013 review defines nucleophagy as selective, whereas the 2024 Discussion includes the 2012 nonselective Magnaporthe route. The present cargo-defined phenotype does not require universal selectivity; preserve this attributed difference for human review. GO:0044804, resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0044804, is nonobsolete and includes nuclear parts or entire nuclei without an explicit selectivity restriction. Its biological process scope is not an exact organismal-phenotype xref. The autophagy parent traitmech:000638 is corrected to intracellular cargo in this change (#1754). Nuclear-envelope overlap with ER-phagy traitmech:000642 does not make the records equivalent. No exact synonyms or SSSOM mapping are asserted. Nuclear damage, loss of fluorescence or DNA degradation alone does not prove autophagic delivery and flux.

    +

    Include nuclear portions and entire nuclei, micro and macro routes. The 2013 review defines nucleophagy as selective, whereas the 2024 Discussion includes the 2012 nonselective Magnaporthe route. The present cargo-defined phenotype does not require universal selectivity; preserve this attributed difference for human review. GO:0044804, resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0044804, is nonobsolete and includes nuclear parts or entire nuclei without an explicit selectivity restriction. Its biological process scope is not an exact organismal-phenotype xref. The autophagy parent traitmech:000638 is corrected to intracellular cargo in this change (#1754). Nuclear-envelope overlap with ER-phagy traitmech:000642 does not make the records equivalent. No exact synonyms or SSSOM mapping are asserted. Nuclear damage, loss of fluorescence or DNA degradation alone does not prove autophagic delivery and flux.

    @@ -321,7 +322,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -350,12 +360,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 13:38 UTC diff --git a/pages/traits/physiology/nutrient_adaptation.html b/pages/traits/physiology/nutrient_adaptation.html index f1fa5acbd07..56086ee7057 100644 --- a/pages/traits/physiology/nutrient_adaptation.html +++ b/pages/traits/physiology/nutrient_adaptation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -137,7 +138,7 @@

    Edge evidence

    manifests as copiotrophic - METPO:1000642 + METPO:1000642 METPO:2007400

    Allocation favoring rapid growth machinery yields a copiotrophic phenotype under nutrient-rich conditions.

      @@ -156,7 +157,7 @@

      Edge evidence

      manifests as oligotrophic - METPO:1000654 + METPO:1000654 METPO:2007400

      Allocation favoring high-affinity uptake and streamlining yields an oligotrophic phenotype under nutrient-poor conditions.

        @@ -172,11 +173,11 @@

        Edge evidence

      • copiotrophic - METPO:1000642 + METPO:1000642 is a nutrient adaptation METPO:1000731 - rdfs:subClassOf + rdfs:subClassOf

        Copiotrophy is a child phenotype of nutrient adaptation.

          @@ -191,11 +192,11 @@

          Edge evidence

        • oligotrophic - METPO:1000654 + METPO:1000654 is a nutrient adaptation METPO:1000731 - rdfs:subClassOf + rdfs:subClassOf

          Oligotrophy is a child phenotype of nutrient adaptation.

            @@ -310,7 +311,7 @@

            kg-microbe context

            via direct_metpo.

            512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

            @@ -559,7 +560,7 @@

            Curation history

          • · ADD_CANONICAL_EXAMPLES · codex -

            Added Candidatus Pelagibacter ubique HTCC1062 as a directly characterized nutrient-adaptation example from DOI:10.1038/s41586-024-07924-w; verified the current strain taxon and label through NCBI Taxonomy.

            +

            Added Candidatus Pelagibacter ubique HTCC1062 as a directly characterized nutrient-adaptation example from DOI:10.1038/s41586-024-07924-w; verified the current strain taxon and label through NCBI Taxonomy.

            • @@ -592,7 +593,16 @@

            Identifier

            Term kind
            CLASS
            Status
            -
            REVIEWED
            +
            REVIEWED + + +
            + What this status means +

            Curator has signed off on label / definition / parents.

            +

            Quoted from the schema's status definitions.

            +
            + +
    @@ -956,12 +966,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 11:06 UTC diff --git a/pages/traits/physiology/oligotrophic.html b/pages/traits/physiology/oligotrophic.html index 4dadcb6a4ad..3aa01a786f2 100644 --- a/pages/traits/physiology/oligotrophic.html +++ b/pages/traits/physiology/oligotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -355,9 +356,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • TT_oligotroph RELATED_SYNONYM · metpo.owl
      • +
    • TT_oligotroph RELATED_SYNONYM · metpo.owl
      • -
    • oligotroph RELATED_SYNONYM · metpo.owl
      • +
    • oligotroph RELATED_SYNONYM · metpo.owl
    @@ -373,7 +374,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -661,7 +662,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1025,12 +1035,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-24 21:00 UTC diff --git a/pages/traits/physiology/oogamy.html b/pages/traits/physiology/oogamy.html index f931ca0c448..9ed1fe49d0b 100644 --- a/pages/traits/physiology/oogamy.html +++ b/pages/traits/physiology/oogamy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -61,19 +62,19 @@

    Trait evidence (4)

    DOI:10.1186/s12915-024-01878-1
    Oogamy constitutes a specialized form of anisogamy wherein small male gametes are motile and large female gametes are not
    -

    Lindsey et al. (2024), PMID:38600528, PMC11007952, Background Sec1 clause before the parenthetical, verified in raw XML and publisher HTML. Supports the anisogamy parent and usual motile-male formulation, not a universal rule in view of Vranken et al. The scientific abstract and scope paragraph were read; remaining analyses, actual figures and supplements were not audited. This terminology passage is not independent experimental replication.

    +

    Lindsey et al. (2024), PMID:38600528, PMC11007952, Background Sec1 clause before the parenthetical, verified in raw XML and publisher HTML. Supports the anisogamy parent and usual motile-male formulation, not a universal rule in view of Vranken et al. The scientific abstract and scope paragraph were read; remaining analyses, actual figures and supplements were not audited. This terminology passage is not independent experimental replication.

  • DOI:10.1186/s40529-018-0227-9
    Volvox carteri f. nagariensis is an oogamous species that has heterothallic sexuality
    -

    Nozaki et al. (2018), PMID:29616358, PMC5882469, exact Background clause checked in raw XML. Scientific abstract, Background, Methods, Results, Discussion, Table 1 with row spans, captions and actual Figure 2 were inspected. Panels a-d show male spheroids/sperm packets, e female eggs, f-g mature zygotes. The Results qualify zygote formation as after possible fertilization; individual gamete fusion was not directly tracked. Do not compare packet size with egg size as a gamete-size ratio. Reference strains were induced in VTAC at 25 C with a 14:10 light-dark cycle; sexual spheroids formed after 2-4 days. Table 1's sex column is PCR-based, not 33 independent phenotype experiments. Failure to amplify HMG1f in another strain does not demonstrate deletion: primer polymorphism remains an explicit alternative. Other actual figures, Table 2 and supplements remain uninspected. Heterothallism describes this example, not all oogamy.

    +

    Nozaki et al. (2018), PMID:29616358, PMC5882469, exact Background clause checked in raw XML. Scientific abstract, Background, Methods, Results, Discussion, Table 1 with row spans, captions and actual Figure 2 were inspected. Panels a-d show male spheroids/sperm packets, e female eggs, f-g mature zygotes. The Results qualify zygote formation as after possible fertilization; individual gamete fusion was not directly tracked. Do not compare packet size with egg size as a gamete-size ratio. Reference strains were induced in VTAC at 25 C with a 14:10 light-dark cycle; sexual spheroids formed after 2-4 days. Table 1's sex column is PCR-based, not 33 independent phenotype experiments. Failure to amplify HMG1f in another strain does not demonstrate deletion: primer polymorphism remains an explicit alternative. Other actual figures, Table 2 and supplements remain uninspected. Heterothallism describes this example, not all oogamy.

  • DOI:10.1371/journal.pbio.1001904
    Transgenic female V. carteri expressing male MID produced functional sperm packets during sexual development.
    -

    Geng et al. (2014), PMID:25003332, PMC4086717, scientific-abstract sentence checked in raw XML. The scientific abstract, selected Introduction/Results/Methods passages, actual Figure 2 with its caption and all extracted Table S3 text were inspected. Figure 2B/C/F/H show wild-type egg/sperm controls; D/G/I show the engineered pseudo-male spheroid, its sperm packet and an aberrant sperm cell, respectively. Panel E shows a mature zygote from an Eve::VcMID-BH x Eve cross, not the engineered parent. Table S3 distinguishes Eve (UTEX 1885) and AichiM (NIES-398) from nitA- derivatives E15 and A18 used to generate transgenics. Table S3 was text-extracted, not visually rendered; remaining source material was not fully audited. MID gain/loss supports gamete-development causality in the tested backgrounds, not a universal oogamy mechanism or a natural canonical exemplar for the engineered strains. Resolve native protein accessions before a protein-grounded causal graph.

    +

    Geng et al. (2014), PMID:25003332, PMC4086717, scientific-abstract sentence checked in raw XML. The scientific abstract, selected Introduction/Results/Methods passages, actual Figure 2 with its caption and all extracted Table S3 text were inspected. Figure 2B/C/F/H show wild-type egg/sperm controls; D/G/I show the engineered pseudo-male spheroid, its sperm packet and an aberrant sperm cell, respectively. Panel E shows a mature zygote from an Eve::VcMID-BH x Eve cross, not the engineered parent. Table S3 distinguishes Eve (UTEX 1885) and AichiM (NIES-398) from nitA- derivatives E15 and A18 used to generate transgenics. Table S3 was text-extracted, not visually rendered; remaining source material was not fully audited. MID gain/loss supports gamete-development causality in the tested backgrounds, not a universal oogamy mechanism or a natural canonical exemplar for the engineered strains. Resolve native protein accessions before a protein-grounded causal graph.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Canonical examples DOI:10.1186/s40529-018-0227-9 - Source-observed reference example, not every strain. Natural Taiwan isolates female 2016-0609-v-1 (NIES-4206) and male 2016-tw-nuk-6-1 (NIES-4208) were examined after sex-inducer treatment; see Figure 2, Table 1 and Methods. The Results describe zygotes after possible fertilization, not directly tracked fusion of each pair. Primary collection records at https://mcc.nbrp.jp/strainList.do?strainNumber=NIES-4206 and https://mcc.nbrp.jp/strainList.do?strainNumber=NIES-4208 confirm strain aliases, sex and ITS2 accessions LC376032/LC376034. Both list collection on 2016-05-25, whereas Table 1 lists 2016-06-09 and 2016-06-10 respectively (the collection records' isolation dates). This collection-date conflict remains unresolved; no date is silently corrected. Their March 2022 axenic status is not projected onto 2018. Collection fields establish provenance, not independent phenotype replication or an unmutated genome. The forma-level name and NCBITaxon:3068 were checked at https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3068 on 2026-10-05; no reference genome is assigned to these isolates. + Source-observed reference example, not every strain. Natural Taiwan isolates female 2016-0609-v-1 (NIES-4206) and male 2016-tw-nuk-6-1 (NIES-4208) were examined after sex-inducer treatment; see Figure 2, Table 1 and Methods. The Results describe zygotes after possible fertilization, not directly tracked fusion of each pair. Primary collection records at https://mcc.nbrp.jp/strainList.do?strainNumber=NIES-4206 and https://mcc.nbrp.jp/strainList.do?strainNumber=NIES-4208 confirm strain aliases, sex and ITS2 accessions LC376032/LC376034. Both list collection on 2016-05-25, whereas Table 1 lists 2016-06-09 and 2016-06-10 respectively (the collection records' isolation dates). This collection-date conflict remains unresolved; no date is silently corrected. Their March 2022 axenic status is not projected onto 2018. Collection fields establish provenance, not independent phenotype replication or an unmutated genome. The forma-level name and NCBITaxon:3068 were checked at https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3068 on 2026-10-05; no reference genome is assigned to these isolates. @@ -352,7 +353,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -381,12 +391,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 14:26 UTC diff --git a/pages/traits/physiology/organoheterotrophic.html b/pages/traits/physiology/organoheterotrophic.html index 3e47cef6832..ac0030fc277 100644 --- a/pages/traits/physiology/organoheterotrophic.html +++ b/pages/traits/physiology/organoheterotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -364,8 +365,8 @@

    Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -431,7 +432,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • organoheterotroph RELATED_SYNONYM · metpo.owl
      • +
    • organoheterotroph RELATED_SYNONYM · metpo.owl
    @@ -447,7 +448,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -774,7 +775,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1138,12 +1148,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/organotrophic.html b/pages/traits/physiology/organotrophic.html index 8d61b9db172..b720fd034d8 100644 --- a/pages/traits/physiology/organotrophic.html +++ b/pages/traits/physiology/organotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -119,7 +120,7 @@

    Edge evidence

    example of organic compound CHEBI:50860 - rdfs:subClassOf + rdfs:subClassOf

    Glucose is a representative organic substrate.

      @@ -345,8 +346,8 @@

      Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -412,9 +413,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • TT_organotroph RELATED_SYNONYM · metpo.owl
      • +
    • TT_organotroph RELATED_SYNONYM · metpo.owl
      • -
    • organotroph RELATED_SYNONYM · metpo.owl
      • +
    • organotroph RELATED_SYNONYM · metpo.owl
    @@ -430,7 +431,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -772,7 +773,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1136,12 +1146,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/ornithine_decarboxylase_activity.html b/pages/traits/physiology/ornithine_decarboxylase_activity.html index a6afe652638..fc0b8caf85f 100644 --- a/pages/traits/physiology/ornithine_decarboxylase_activity.html +++ b/pages/traits/physiology/ornithine_decarboxylase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -82,7 +83,7 @@

    Trait evidence (3)

    Ornithine decarboxylase conversion of L-ornithine to putrescine

    Evidence-backed physiological mechanism sketch linking ornithine decarboxylase catalytic activity and putrescine biosynthesis to the ornithine decarboxylase activity phenotype.

    -

    MECHANISTIC · Mechanistic graph backed by DOI:10.1128/jb.124.2.791-799.1975; exemplified on ornithine_decarboxylase_spec with Escherichia coli K-12 (NCBITaxon:83333; UP000000625) constitutive ornithine decarboxylase SpeC (UniProtKB:P21169).

    +

    MECHANISTIC · Mechanistic graph backed by DOI:10.1128/jb.124.2.791-799.1975; exemplified on ornithine_decarboxylase_spec with Escherichia coli K-12 (NCBITaxon:83333; UP000000625) constitutive ornithine decarboxylase SpeC (UniProtKB:P21169).

    Loading graph…

    @@ -105,7 +106,7 @@

    Edge evidence

    GO:0004586 confers ornithine decarboxylase activity - traitmech:000154 + traitmech:000154 METPO:2007700

    Cellular synthesis of active ornithine decarboxylase confers the ornithine decarboxylase activity phenotype, which is abolished in E. coli K-12 OD mutants.

      @@ -180,8 +181,8 @@

      Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -254,7 +255,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -404,7 +405,7 @@

    Discussions and Knowledge Gaps (3)

    -

    The current record pairs one IUBMB EC 4.1.1.17 reaction snippet with one mutant-isolation sentence (DOI:10.1128/jb.124.2.791-799.1975) that does not state the enzyme's physiological pathway link to the organism-level phenotype.

    +

    The current record pairs one IUBMB EC 4.1.1.17 reaction snippet with one mutant-isolation sentence (DOI:10.1128/jb.124.2.791-799.1975) that does not state the enzyme's physiological pathway link to the organism-level phenotype.

    @@ -447,7 +448,7 @@

    Evidence

    -

    The record's primary literature (EC 4.1.1.17, DOI:10.1128/jb.124.2.791-799.1975) establishes L-ornithine decarboxylation to putrescine and CO2 and speC mutant loss of activity in Escherichia coli K-12 (NCBITaxon:83333), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    +

    The record's primary literature (EC 4.1.1.17, DOI:10.1128/jb.124.2.791-799.1975) establishes L-ornithine decarboxylation to putrescine and CO2 and speC mutant loss of activity in Escherichia coli K-12 (NCBITaxon:83333), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    @@ -466,7 +467,7 @@

    Evidence

    -

    Resolution: Promoted ornithine_decarboxylase_spec_sketch to MECHANISTIC by adding InterPro:IPR005308-grounded GENE_OR_PROTEIN node ornithine_decarboxylase_spec with reviewed Escherichia coli K-12 (NCBITaxon:83333; UP000000625) protein_examples UniProtKB:P21169 (SpeC) backed by DOI:10.1128/jb.124.2.791-799.1975.

    +

    Resolution: Promoted ornithine_decarboxylase_spec_sketch to MECHANISTIC by adding InterPro:IPR005308-grounded GENE_OR_PROTEIN node ornithine_decarboxylase_spec with reviewed Escherichia coli K-12 (NCBITaxon:83333; UP000000625) protein_examples UniProtKB:P21169 (SpeC) backed by DOI:10.1128/jb.124.2.791-799.1975.

    @@ -501,7 +502,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Promoted ornithine_decarboxylase_spec_sketch to MECHANISTIC; added InterPro:IPR005308-grounded GENE_OR_PROTEIN node ornithine_decarboxylase_spec with reviewed Escherichia coli K-12 (NCBITaxon:83333) protein_examples UniProtKB:P21169 (SpeC) backed by DOI:10.1128/jb.124.2.791-799.1975; resolved ornithine-decarboxylase-activity-protein-example-gap.

    +

    Promoted ornithine_decarboxylase_spec_sketch to MECHANISTIC; added InterPro:IPR005308-grounded GENE_OR_PROTEIN node ornithine_decarboxylase_spec with reviewed Escherichia coli K-12 (NCBITaxon:83333) protein_examples UniProtKB:P21169 (SpeC) backed by DOI:10.1128/jb.124.2.791-799.1975; resolved ornithine-decarboxylase-activity-protein-example-gap.

    • @@ -543,7 +544,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -907,12 +917,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 08:45 UTC diff --git a/pages/traits/physiology/osmotaxis.html b/pages/traits/physiology/osmotaxis.html index a28a93065e7..7ccd649881c 100644 --- a/pages/traits/physiology/osmotaxis.html +++ b/pages/traits/physiology/osmotaxis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1016/s0014-4894(03)00031-6
    We find that promastigotes move towards concentrations of all substances tested and that this taxis requires the presence of an osmotic gradient.
    -

    Abstract, exact-matched at Europe PMC (PMID:12706748); full text not inspected. The study concerns Leishmania mexicana promastigotes and supports migration requiring an osmotic gradient under the tested conditions. The authors reinterpret those responses as osmotaxis; this is not evidence that all chemical-gradient responses in Leishmania are osmotic, or that every substance or life stage elicits this behavior. No universal preferred osmolarity or natural-strain example is inferred from the abstract.

    +

    Abstract, exact-matched at Europe PMC (PMID:12706748); full text not inspected. The study concerns Leishmania mexicana promastigotes and supports migration requiring an osmotic gradient under the tested conditions. The authors reinterpret those responses as osmotaxis; this is not evidence that all chemical-gradient responses in Leishmania are osmotic, or that every substance or life stage elicits this behavior. No universal preferred osmolarity or natural-strain example is inferred from the abstract.

  • DOI:10.1016/j.exppara.2005.10.005
    These were able to respond to chemotaxic as well as to osmotaxic stimuli.
    -

    Abstract, exact-matched at Europe PMC (PMID:16313904); full text not inspected. The antecedent is Leishmania promastigotes; the article identifies Leishmania amazonensis. The authors report distinguishing chemical from osmotic responses, supporting osmotaxis without collapsing all chemotaxis into it. Their receptor model and possible vector-development role are not established as universal mechanisms or required trait consequences.

    +

    Abstract, exact-matched at Europe PMC (PMID:16313904); full text not inspected. The antecedent is Leishmania promastigotes; the article identifies Leishmania amazonensis. The authors report distinguishing chemical from osmotic responses, supporting osmotaxis without collapsing all chemotaxis into it. Their receptor model and possible vector-development role are not established as universal mechanisms or required trait consequences.

  • DOI:10.1073/pnas.1620945114
    We discuss how the speed changes we observe can lead to steady-state bacterial accumulation.
    -

    Abstract, exact-matched at Europe PMC (PMID:28874571); full text and supplement not systematically inspected. Escherichia coli motor and population-swimming measurements concern stepwise osmotic changes. The snippet states a proposed link from measured speed changes to accumulation, not a direct spatial-gradient migration result from those measurements. Osmokinesis and motor bias may contribute to osmotaxis but are not exact synonyms or sufficient evidence of net migration on their own; no molecular causal edge is inferred.

    +

    Abstract, exact-matched at Europe PMC (PMID:28874571); full text and supplement not systematically inspected. Escherichia coli motor and population-swimming measurements concern stepwise osmotic changes. The snippet states a proposed link from measured speed changes to accumulation, not a direct spatial-gradient migration result from those measurements. Osmokinesis and motor bias may contribute to osmotaxis but are not exact synonyms or sufficient evidence of net migration on their own; no molecular causal edge is inferred.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -277,7 +278,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed osmotaxis -

      Created traitmech:000592 under motile METPO:1000702 with three primary DOI sources: 10.1016/s0014-4894(03)00031-6 (PMID:12706748), 10.1016/j.exppara.2005.10.005 (PMID:16313904), and 10.1073/pnas.1620945114 (PMID:28874571). Exact Europe PMC abstract snippets distinguish spatial migration, chemical/osmotic response coexistence and a proposed speed-to-accumulation link. Fresh seed: 399 IDs, 344 present and 55 absent in the pre-change 986-record corpus. Whole-repository ignored-and-hidden searches and structured OWL review found no exact record or term. Reserved METPO:1054600 in v469. No natural-strain exemplar, molecular graph or external equivalent was inferred; two discussions retain those gaps. Dry-run validated writer and seven focused tests passed.

    +

    Created traitmech:000592 under motile METPO:1000702 with three primary DOI sources: 10.1016/s0014-4894(03)00031-6 (PMID:12706748), 10.1016/j.exppara.2005.10.005 (PMID:16313904), and 10.1073/pnas.1620945114 (PMID:28874571). Exact Europe PMC abstract snippets distinguish spatial migration, chemical/osmotic response coexistence and a proposed speed-to-accumulation link. Fresh seed: 399 IDs, 344 present and 55 absent in the pre-change 986-record corpus. Whole-repository ignored-and-hidden searches and structured OWL review found no exact record or term. Reserved METPO:1054600 in v469. No natural-strain exemplar, molecular graph or external equivalent was inferred; two discussions retain those gaps. Dry-run validated writer and seven focused tests passed.

    • Read this curation session @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 08:48 UTC diff --git a/pages/traits/physiology/oxidase_activity.html b/pages/traits/physiology/oxidase_activity.html index 1e83a497b81..a4c0583ac4c 100644 --- a/pages/traits/physiology/oxidase_activity.html +++ b/pages/traits/physiology/oxidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -137,7 +138,7 @@

    Edge evidence

    GO:0045277 confers oxidase activity - traitmech:000076 + traitmech:000076 METPO:2007700

    Possession of a terminal oxidase confers the oxidase-activity phenotype.

      @@ -271,7 +272,7 @@

      Edge evidence

      example of cytochrome c oxidase GO:0045277 - rdfs:subClassOf + rdfs:subClassOf

      Family A heme-copper oxygen reductases are a class of cytochrome c oxidase.

        @@ -307,8 +308,8 @@

        Protein and taxon examples

    		 - Paracoccus denitrificans -
    NCBITaxon:266 + Paracoccus denitrificans +
    NCBITaxon:266         		REVIEWED
    @@ -374,7 +375,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -390,7 +391,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -681,7 +682,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Added verified verbatim snippet from DOI:10.3390/microorganisms10050926 (already present on causal_graphs[0].edges[9].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-002 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Added verified verbatim snippet from DOI:10.3390/microorganisms10050926 (already present on causal_graphs[0].edges[9].evidence[0]) to record-level evidence[0] to match definition_source (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-002 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -723,7 +724,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1087,12 +1097,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/physiology/oxidative_stress_response.html b/pages/traits/physiology/oxidative_stress_response.html index dfd78664e03..1b34c99fba3 100644 --- a/pages/traits/physiology/oxidative_stress_response.html +++ b/pages/traits/physiology/oxidative_stress_response.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    GO:0006979 confers oxidative stress response - traitmech:000079 + traitmech:000079 METPO:2007700

    The induced defense realizes the oxidative-stress-response trait.

      @@ -212,8 +213,8 @@

      Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -286,7 +287,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -580,7 +581,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -944,12 +954,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/paedogamy.html b/pages/traits/physiology/paedogamy.html index 4cf387a0598..2b1c050a198 100644 --- a/pages/traits/physiology/paedogamy.html +++ b/pages/traits/physiology/paedogamy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (3)

    DOI:10.1080/0269249X.2013.791344
    fusion of two gametes within a single gametangium
    -

    Kaczmarska et al. (2013), p.271, section 5.2.1, contiguous definition phrase in the directly read author-posted full text at https://www.researchgate.net/publication/259079699_Proposals_for_a_terminology_for_diatom_sexual_reproduction_auxospores_and_resting_stages. Cytokinesis distinguishes gametes from the undivided-cell nuclear fusion of section 5.2.2. Section 5.2 treats both as automixis, not equivalent names. This is terminology synthesis, not independent experimental replication of its cited Neidium study. Actual diagrams were not visually inspected. Do not make meiosis-I cytokinesis or immediate gametic-nuclear fusion universal requirements.

    +

    Kaczmarska et al. (2013), p.271, section 5.2.1, contiguous definition phrase in the directly read author-posted full text at https://www.researchgate.net/publication/259079699_Proposals_for_a_terminology_for_diatom_sexual_reproduction_auxospores_and_resting_stages. Cytokinesis distinguishes gametes from the undivided-cell nuclear fusion of section 5.2.2. Section 5.2 treats both as automixis, not equivalent names. This is terminology synthesis, not independent experimental replication of its cited Neidium study. Actual diagrams were not visually inspected. Do not make meiosis-I cytokinesis or immediate gametic-nuclear fusion universal requirements.

  • @@ -67,7 +68,7 @@

    Trait evidence (3)

    DOI:10.1007/s12223-008-0018-x
    The gametic nuclei fused after auxospore expansion had begun.
    -

    Poulickova (2008), PMID:18500631, scientific abstract directly retrieved from Europe PMC and PubMed. Unpaired Neidium cf. ampliatum cells differentiated into gametangia and underwent pedogamy. The quoted timing cautions against conflating gamete fusion with immediate nuclear fusion. Full text, actual figures and strain provenance remain unread. Preserve cf.; no exact species mapping or canonical Neidium example is asserted.

    +

    Poulickova (2008), PMID:18500631, scientific abstract directly retrieved from Europe PMC and PubMed. Unpaired Neidium cf. ampliatum cells differentiated into gametangia and underwent pedogamy. The quoted timing cautions against conflating gamete fusion with immediate nuclear fusion. Full text, actual figures and strain provenance remain unread. Preserve cf.; no exact species mapping or canonical Neidium example is asserted.

    • @@ -112,7 +113,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -128,7 +129,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -217,7 +218,7 @@

    Canonical examples DOI:10.3390/d14121133 - Qualified VCA-7 example, one of the four sexually active clones in Results 3.3, not every tested clone. Table S1 traces VCA-7 to wet ground in Gonduras Cave, Krasnoyarsk Territory, collected 2011-02-19; Methods 2.1 describes single-cell isolation and subsequent culture. Provenance table directly inspected in https://mdpi-res.com/d_attachment/diversity/diversity-14-01133/article_deploy/diversity-14-01133-s001.zip. NCBI https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1302829 and taxonomy EFetch checked on 2026-10-05 resolve this species name; this does not authenticate a genome or current culture accession. + Qualified VCA-7 example, one of the four sexually active clones in Results 3.3, not every tested clone. Table S1 traces VCA-7 to wet ground in Gonduras Cave, Krasnoyarsk Territory, collected 2011-02-19; Methods 2.1 describes single-cell isolation and subsequent culture. Provenance table directly inspected in https://mdpi-res.com/d_attachment/diversity/diversity-14-01133/article_deploy/diversity-14-01133-s001.zip. NCBI https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1302829 and taxonomy EFetch checked on 2026-10-05 resolve this species name; this does not authenticate a genome or current culture accession. @@ -317,7 +318,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add paedogamy with source-backed gamete-fusion scope -

      Added traitmech:000624 with DOI:10.1080/0269249X.2013.791344 terminology, DOI:10.3390/d14121133 publisher XML/PDF and DOI:10.1007/s12223-008-0018-x scientific abstract; each has a directly checked snippet. Inspected actual Figure 3 and supplementary Table S1 of the 2022 study, and NCBI taxonomy for the qualified natural VCA-7 example. Ignored-and-hidden repository and proposal searches preceded fresh METPO:1057700 allocation in v500. Distinguished terminology synthesis from primary observations, retained negative clones and delayed nuclear-fusion timing, and deferred unsupported mappings and molecular graphs. Writer dry run and 50 focused tests passed before application; broader gates follow.

    +

    Added traitmech:000624 with DOI:10.1080/0269249X.2013.791344 terminology, DOI:10.3390/d14121133 publisher XML/PDF and DOI:10.1007/s12223-008-0018-x scientific abstract; each has a directly checked snippet. Inspected actual Figure 3 and supplementary Table S1 of the 2022 study, and NCBI taxonomy for the qualified natural VCA-7 example. Ignored-and-hidden repository and proposal searches preceded fresh METPO:1057700 allocation in v500. Distinguished terminology synthesis from primary observations, retained negative clones and delayed nuclear-fusion timing, and deferred unsupported mappings and molecular graphs. Writer dry run and 50 focused tests passed before application; broader gates follow.

    • Read this curation session
  • @@ -355,7 +356,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -384,12 +394,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 18:22 UTC diff --git a/pages/traits/physiology/pallium_feeding.html b/pages/traits/physiology/pallium_feeding.html index f7033575550..e4a5bde2a64 100644 --- a/pages/traits/physiology/pallium_feeding.html +++ b/pages/traits/physiology/pallium_feeding.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1111/j.1529-8817.1986.tb00021.x
    The contents of the phytoplankton prey are liquified and transported through the pallium
    -

    Direct scientific Abstract quote, printed p. 249; original spelling retained. Institutional scan: https://www.whoi.edu/cms/files/Jacobson_%26_Anderson_1986_JP_feeding_30828.pdf. All seven available pages (249-252, 256-258), Table 1 and actual Figures 1, 2 and 23 were inspected. Pages 253-255 and Figures 3-22 are missing from this copy and were not audited. Figure 2B shows Oblea rotunda feeding on Pyramimonas sp. Discussion p. 256 distinguishes complete from partial enclosure; Table 1 also lists detrital food. Neither living prey nor a particular prey size, taxon, capture filament or digestion time is a universal requirement.

    +

    Direct scientific Abstract quote, printed p. 249; original spelling retained. Institutional scan: https://www.whoi.edu/cms/files/Jacobson_%26_Anderson_1986_JP_feeding_30828.pdf. All seven available pages (249-252, 256-258), Table 1 and actual Figures 1, 2 and 23 were inspected. Pages 253-255 and Figures 3-22 are missing from this copy and were not audited. Figure 2B shows Oblea rotunda feeding on Pyramimonas sp. Discussion p. 256 distinguishes complete from partial enclosure; Table 1 also lists detrital food. Neither living prey nor a particular prey size, taxon, capture filament or digestion time is a universal requirement.

  • DOI:10.1111/j.0022-3646.1992.00069.x
    the prey cytoplasm is liquified within the pallium
    -

    Direct Introduction quote, printed p. 69, not an abstract quote. Complete 14-page institutional scan and actual Figures 1-46 inspected at https://www.whoi.edu/cms/files/Jacobson%26Anderson_1992_Proto-ultrastructrure_31161.pdf. Results describe five feeding cells named Protoperidinium spinulosum by the authors. Figures 9-12 show the pallium and degraded diatom contents outside the main cell body; Figures 1 and 46 are reconstructions. Discussion p. 81 leaves inner-membrane loss during fixation versus in vivo reorganization unresolved. Morphology does not demonstrate specific digestive proteins or a complete transport mechanism. No canonical taxon assignment is made from this culture.

    +

    Direct Introduction quote, printed p. 69, not an abstract quote. Complete 14-page institutional scan and actual Figures 1-46 inspected at https://www.whoi.edu/cms/files/Jacobson%26Anderson_1992_Proto-ultrastructrure_31161.pdf. Results describe five feeding cells named Protoperidinium spinulosum by the authors. Figures 9-12 show the pallium and degraded diatom contents outside the main cell body; Figures 1 and 46 are reconstructions. Discussion p. 81 leaves inner-membrane loss during fixation versus in vivo reorganization unresolved. Morphology does not demonstrate specific digestive proteins or a complete transport mechanism. No canonical taxon assignment is made from this culture.

  • DOI:10.4319/lo.1993.38.5.0965
    Laboratory experiments were performed to determine the growth and grazing capabilities of Oblea rotunda, a pallium-feeding dinoflagellate.
    -

    Direct scientific Abstract from the publisher page at https://aslopubs.onlinelibrary.wiley.com/doi/10.4319/lo.1993.38.5.0965. Supports the feeding-mode name and growth on several phytoplankton foods. Only the abstract was inspected; Methods, figures and culture provenance were not audited. The laboratory culture is not equated with the field specimens in the 1986 canonical example. Behavioral responses do not identify a molecular receptor.

    +

    Direct scientific Abstract from the publisher page at https://aslopubs.onlinelibrary.wiley.com/doi/10.4319/lo.1993.38.5.0965. Supports the feeding-mode name and growth on several phytoplankton foods. Only the abstract was inspected; Methods, figures and culture provenance were not audited. The laboratory culture is not equated with the field specimens in the 1986 canonical example. Behavioral responses do not identify a molecular receptor.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1111/j.1529-8817.1986.tb00021.x - Qualified example: naturally collected specimens in the 1986 study, Table 1 and Figure 2B, not all isolates. Methods p. 249 at https://www.whoi.edu/cms/files/Jacobson_%26_Anderson_1986_JP_feeding_30828.pdf report net tows from Perch Pond or Vineyard Sound, Massachusetts, followed by short laboratory incubation and microscopy. No strain identifier or single collection site is assigned to this example. Figure 2B depicts pallium deployment around Pyramimonas sp. NCBI ESearch and EFetch verified the species name, rank and Peridiniopsis rotunda synonym on 2026-10-06. + Qualified example: naturally collected specimens in the 1986 study, Table 1 and Figure 2B, not all isolates. Methods p. 249 at https://www.whoi.edu/cms/files/Jacobson_%26_Anderson_1986_JP_feeding_30828.pdf report net tows from Perch Pond or Vineyard Sound, Massachusetts, followed by short laboratory incubation and microscopy. No strain identifier or single collection site is assigned to this example. Figure 2B depicts pallium deployment around Pyramimonas sp. NCBI ESearch and EFetch verified the species name, rank and Peridiniopsis rotunda synonym on 2026-10-06. @@ -340,7 +341,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -369,12 +379,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 01:55 UTC diff --git a/pages/traits/physiology/parasexuality.html b/pages/traits/physiology/parasexuality.html index 133806273f2..84db172bfcd 100644 --- a/pages/traits/physiology/parasexuality.html +++ b/pages/traits/physiology/parasexuality.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1093/emboj/cdg235
    Thus, an efficient parasexual cycle can be performed in C.albicans, one that leads to the reassortment of genetic material in this organism.
    -

    Bennett and Johnson (2003), PMID:12743044. The snippet is an exact span of the directly retrieved Europe PMC abstract. Main-text experiments and Figures 1-9 were inspected in the author-hosted PDF: https://static1.squarespace.com/static/56463117e4b0770d2cd2d163/t/564e4d55e4b04412d33a3036/1447972181154/the%2Bembo%2Bjournal%2B2003%2Bbennett.pdf. Marked CAI4-derived Candida albicans strains formed tetraploid mating products; chromosome loss yielded diploid or near-diploid progeny that could mate again. Flow cytometry and multiple marker/MTL readouts support ploidy reduction; marker loss alone can also arise by recombination. The cycle need not reach haploidy. The paper leaves conventional meiosis possible under untested conditions. Its supplementary media, mating and PCR details remain unread, and its unpublished meiotic-gene deletion observations are not used as mechanistic proof.

    +

    Bennett and Johnson (2003), PMID:12743044. The snippet is an exact span of the directly retrieved Europe PMC abstract. Main-text experiments and Figures 1-9 were inspected in the author-hosted PDF: https://static1.squarespace.com/static/56463117e4b0770d2cd2d163/t/564e4d55e4b04412d33a3036/1447972181154/the%2Bembo%2Bjournal%2B2003%2Bbennett.pdf. Marked CAI4-derived Candida albicans strains formed tetraploid mating products; chromosome loss yielded diploid or near-diploid progeny that could mate again. Flow cytometry and multiple marker/MTL readouts support ploidy reduction; marker loss alone can also arise by recombination. The cycle need not reach haploidy. The paper leaves conventional meiosis possible under untested conditions. Its supplementary media, mating and PCR details remain unread, and its unpublished meiotic-gene deletion observations are not used as mechanistic proof.

  • DOI:10.1128/ec.00128-13
    The diploid products are themselves mating competent, thereby establishing a parasexual cycle in this species for the first time.
    -

    Seervai et al. (2013), PMID:24123269. The snippet exact-matches the directly retrieved Europe PMC abstract. Publisher Methods, Results, Discussion and strain tables were read, and Figures 3 and 4 were visually inspected. Marked Candida tropicalis tetraploids produced near-diploid progeny on sorbose; remating, MTL genotyping and DNA-content measurements support a repeatable cycle. 2-DOG resistance selects GAL1 loss, not necessarily chromosome loss. The Figure 4 caption's wild-type wording does not erase the CAY2060 arg4/arg4 tester genotype reported in Table 1 and Methods. The response to presporulation medium differs from C. albicans. The supplementary Figure S1 caption and labels were read as PDF text, but the actual supplemental plot was not visually inspected. No natural canonical example is inferred from these marker-strain experiments.

    +

    Seervai et al. (2013), PMID:24123269. The snippet exact-matches the directly retrieved Europe PMC abstract. Publisher Methods, Results, Discussion and strain tables were read, and Figures 3 and 4 were visually inspected. Marked Candida tropicalis tetraploids produced near-diploid progeny on sorbose; remating, MTL genotyping and DNA-content measurements support a repeatable cycle. 2-DOG resistance selects GAL1 loss, not necessarily chromosome loss. The Figure 4 caption's wild-type wording does not erase the CAY2060 arg4/arg4 tester genotype reported in Table 1 and Methods. The response to presporulation medium differs from C. albicans. The supplementary Figure S1 caption and labels were read as PDF text, but the actual supplemental plot was not visually inspected. No natural canonical example is inferred from these marker-strain experiments.

  • DOI:10.1038/s41467-019-12376-2
    These results indicate that C. albicans CCL represents a 'parameiosis' that blurs the conventional boundaries between mitosis and meiosis.
    -

    Anderson et al. (2019), PMID:31558727. The snippet is an exact span of the directly retrieved Europe PMC abstract. Publisher Introduction and Results were read, but full Methods, actual figures and supplements were not inspected. Concerted chromosome loss (CCL) in C. albicans includes high inter-homolog recombination and functions of Spo11 and Rec8. Their effects on chromosome stability and recombination are different endpoints: loss of SPO11 increases marker loss while reducing recombination, whereas loss of REC8 reduces both in the tested CCL assays. Absence of conventional meiosis does not mean absence of meiosis-associated proteins. Neither homologue presence alone nor these assays establish a conventional meiotic cycle. Protein identities, native strain provenance and assay-specific causal edges remain uncurated.

    +

    Anderson et al. (2019), PMID:31558727. The snippet is an exact span of the directly retrieved Europe PMC abstract. Publisher Introduction and Results were read, but full Methods, actual figures and supplements were not inspected. Concerted chromosome loss (CCL) in C. albicans includes high inter-homolog recombination and functions of Spo11 and Rec8. Their effects on chromosome stability and recombination are different endpoints: loss of SPO11 increases marker loss while reducing recombination, whereas loss of REC8 reduces both in the tested CCL assays. Absence of conventional meiosis does not mean absence of meiosis-associated proteins. Neither homologue presence alone nor these assays establish a conventional meiotic cycle. Protein identities, native strain provenance and assay-specific causal edges remain uncurated.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 23:47 UTC diff --git a/pages/traits/physiology/persister_cell_formation.html b/pages/traits/physiology/persister_cell_formation.html index ca9d145f995..5aba9da867b 100644 --- a/pages/traits/physiology/persister_cell_formation.html +++ b/pages/traits/physiology/persister_cell_formation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -124,7 +125,7 @@

    Edge evidence

    GO:0022611 confers persister cell formation - traitmech:000082 + traitmech:000082 METPO:2007700

    Dormancy underlies stochastic persister formation.

      @@ -140,7 +141,7 @@

      Edge evidence

    • persister cell formation - traitmech:000082 + traitmech:000082 enables antibiotic tolerance @@ -159,7 +160,7 @@

      Edge evidence

    • persister cell formation - traitmech:000082 + traitmech:000082 characterized by biphasic killing curve @@ -178,7 +179,7 @@

      Edge evidence

    • persister cell formation - traitmech:000082 + traitmech:000082 has characteristic minimum inhibitory concentration of susceptible cells @@ -235,7 +236,7 @@

      Edge evidence

    • persister cell formation - traitmech:000082 + traitmech:000082 enables oxidative phosphorylation GO:0006119 @@ -276,7 +277,7 @@

      Edge evidence

      is distinct from persister cell formation - traitmech:000082 + traitmech:000082

      Genetic antibiotic resistance is explicitly distinct from the phenotypic persistence trait.

        @@ -313,8 +314,8 @@

        Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -380,7 +381,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -396,7 +397,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -702,7 +703,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1066,12 +1076,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/pexophagy.html b/pages/traits/physiology/pexophagy.html index 9d50670562d..49c7c30d720 100644 --- a/pages/traits/physiology/pexophagy.html +++ b/pages/traits/physiology/pexophagy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.1038/emboj.2012.151
    Peroxisomes undergo rapid, selective autophagic degradation (pexophagy) when the metabolic pathways they contain are no longer required for cellular metabolism.
    -

    PMID:22643220, PMC3395097. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. Results sec3/sec4 and Methods sec16/sec20/sec23 were also directly read in https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3395097/fullTextXML. In Saccharomyces cerevisiae, Pex11-GFP processing and peroxisomal reporters, with Atg1 and vacuolar-protease controls, support degradation rather than puncta alone. Atg36 perturbation distinguishes peroxisome turnover from mitophagy, Cvt and bulk autophagy in the tested conditions. Post-log turnover also occurs in glucose, glycerol and oleate media; starvation is not a universal requirement. Pex14 deletion retains pexophagy in this species. The abstract's mitochondrial Pex3 redirection is engineered, not native Atg36 mitophagy evidence. Figure 1/2 captions were read, but actual figures, supplements, complete Methods and natural strain provenance were not inspected.

    +

    PMID:22643220, PMC3395097. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. Results sec3/sec4 and Methods sec16/sec20/sec23 were also directly read in https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3395097/fullTextXML. In Saccharomyces cerevisiae, Pex11-GFP processing and peroxisomal reporters, with Atg1 and vacuolar-protease controls, support degradation rather than puncta alone. Atg36 perturbation distinguishes peroxisome turnover from mitophagy, Cvt and bulk autophagy in the tested conditions. Post-log turnover also occurs in glucose, glycerol and oleate media; starvation is not a universal requirement. Pex14 deletion retains pexophagy in this species. The abstract's mitochondrial Pex3 redirection is engineered, not native Atg36 mitophagy evidence. Figure 1/2 captions were read, but actual figures, supplements, complete Methods and natural strain provenance were not inspected.

  • DOI:10.1016/j.devcel.2007.12.011
    It is necessary for pexophagy, but not for other selective and nonselective autophagy-related processes.
    -

    PMID:18331717, PMC3763908. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. The quoted protein is PpAtg30 in historically named Pichia pastoris. The abstract explicitly uses pexophagy for selective peroxisome turnover through micropexophagy and macropexophagy, and reports cargo selection and delivery. This supports route-inclusive terminology and selectivity in the tested yeast, not a universal Atg30 requirement or a gene-presence trait. The opening nonselective description of autophagy is not imposed on the broader local parent, which includes selective turnover. Full-text retrieval failed; methods, actual figures and strain-specific modern taxonomy were not inspected.

    +

    PMID:18331717, PMC3763908. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. The quoted protein is PpAtg30 in historically named Pichia pastoris. The abstract explicitly uses pexophagy for selective peroxisome turnover through micropexophagy and macropexophagy, and reports cargo selection and delivery. This supports route-inclusive terminology and selectivity in the tested yeast, not a universal Atg30 requirement or a gene-presence trait. The opening nonselective description of autophagy is not imposed on the broader local parent, which includes selective turnover. Full-text retrieval failed; methods, actual figures and strain-specific modern taxonomy were not inspected.

  • DOI:10.1242/jcs.108.1.25
    there exist in P. pastoris at least two pathways for the sequestration of peroxisomes into the vacuole for degradation.
    -

    PMID:7738102. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. Methanol-to-ethanol adaptation elicits individual wrapping and vacuolar fusion; glucose adaptation elicits vacuolar engulfment of peroxisome clusters and also turnover of a cytosolic enzyme. Morphology, enzyme measurements and mutant controls support distinct routes; vacuolar-proteinase mutants accumulate undegraded peroxisomes. Enzyme loss or delivery alone is not completed organelle degradation. These conditions are not universal trait requirements. Full methods, actual figures and natural strain provenance were not inspected.

    +

    PMID:7738102. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. Methanol-to-ethanol adaptation elicits individual wrapping and vacuolar fusion; glucose adaptation elicits vacuolar engulfment of peroxisome clusters and also turnover of a cytosolic enzyme. Morphology, enzyme measurements and mutant controls support distinct routes; vacuolar-proteinase mutants accumulate undegraded peroxisomes. Enzyme loss or delivery alone is not completed organelle degradation. These conditions are not universal trait requirements. Full methods, actual figures and natural strain provenance were not inspected.

  • DOI:10.1080/15548627.2019.1603546
    the cytosolic pools of PTS receptors and their cargoes are degraded via a pexophagy-independent, selective autophagy pathway under pexophagy conditions.
    -

    PMID:31007124, PMC6984484. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. This is boundary evidence, not a positive whole-peroxisome turnover experiment: cytosolic Pex5/Pex7 and cargo pools undergo Atg30-independent selective autophagy in Pichia pastoris. Peroxisomal-protein turnover outside the organelle must not be equated with pexophagy. The background's damaged-or-redundant wording does not make damage obligatory. Full text, actual figures and strain provenance were not inspected.

    +

    PMID:31007124, PMC6984484. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. This is boundary evidence, not a positive whole-peroxisome turnover experiment: cytosolic Pex5/Pex7 and cargo pools undergo Atg30-independent selective autophagy in Pichia pastoris. Peroxisomal-protein turnover outside the organelle must not be equated with pexophagy. The background's damaged-or-redundant wording does not make damage obligatory. Full text, actual figures and strain provenance were not inspected.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -221,7 +222,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Use autophagy traitmech:000638 as the direct broader phenotype. The 2008 PpAtg30 scientific abstract uses pexophagy for both micropexophagy and macropexophagy. In contrast, issuing GO:0000425 names pexophagy specifically for selective macroautophagy and lists macropexophagy as exact; GO:0000426 micropexophagy is its sibling under GO:0030242 autophagy of peroxisome, which lists pexophagy as related. These nonobsolete biological-process records were resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0000425,GO%3A0000426,GO%3A0030242. Retain the source-attributed route-inclusive interpretation for human review and omit exact phenotype xrefs and synonyms. Bulk incidental capture, peroxisome presence, import defects, puncta, protein abundance and delivery without degradation alone are insufficient. Cytosolic peroxisomal-protein autophagy is a separate endpoint. The microbial cell doing the degradation carries the trait, not an organism merely inducing an animal host response.

    +

    Use autophagy traitmech:000638 as the direct broader phenotype. The 2008 PpAtg30 scientific abstract uses pexophagy for both micropexophagy and macropexophagy. In contrast, issuing GO:0000425 names pexophagy specifically for selective macroautophagy and lists macropexophagy as exact; GO:0000426 micropexophagy is its sibling under GO:0030242 autophagy of peroxisome, which lists pexophagy as related. These nonobsolete biological-process records were resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0000425,GO%3A0000426,GO%3A0030242. Retain the source-attributed route-inclusive interpretation for human review and omit exact phenotype xrefs and synonyms. Bulk incidental capture, peroxisome presence, import defects, puncta, protein abundance and delivery without degradation alone are insufficient. Cytosolic peroxisomal-protein autophagy is a separate endpoint. The microbial cell doing the degradation carries the trait, not an organism merely inducing an animal host response.

    @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 11:08 UTC diff --git a/pages/traits/physiology/ph_taxis.html b/pages/traits/physiology/ph_taxis.html index 0bf707d57a5..c060e15a3f5 100644 --- a/pages/traits/physiology/ph_taxis.html +++ b/pages/traits/physiology/ph_taxis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1128/jb.00491-19
    This bacterium was found to perform bidirectional taxis in response to external pH gradients, enabling it to preferentially migrate to neutral environments.
    -

    Abstract, exact-matched at Europe PMC (PMID:31685537). The antecedent is Bacillus subtilis. This observation supports external-gradient-directed movement, including responses from both acidic and alkaline environments in this study. It does not establish neutral pH as a universal preferred destination. Full text was not systematically inspected; receptor-chimera findings in the abstract are not converted into a molecular causal graph or an unqualified natural-strain example.

    +

    Abstract, exact-matched at Europe PMC (PMID:31685537). The antecedent is Bacillus subtilis. This observation supports external-gradient-directed movement, including responses from both acidic and alkaline environments in this study. It does not establish neutral pH as a universal preferred destination. Full text was not systematically inspected; receptor-chimera findings in the abstract are not converted into a molecular causal graph or an unqualified natural-strain example.

  • DOI:10.1128/jb.188.7.2656-2665.2006
    Bacteria in more-alkaline regions did not swim toward the acid, suggesting the pH taxis is a form of negative chemotaxis.
    -

    Abstract, exact-matched at Europe PMC (PMID:16547053); full text not inspected. The preceding observation describes Helicobacter pylori moving away from strong acid in a microscope-slide pH gradient. This supports an acid-avoidance response without requiring every pH-tactic organism to show bidirectional attraction to a neutral optimum. Strain-specific mutant, receptor and host-colonization findings are not generalized into the trait definition or mechanism.

    +

    Abstract, exact-matched at Europe PMC (PMID:16547053); full text not inspected. The preceding observation describes Helicobacter pylori moving away from strong acid in a microscope-slide pH gradient. This supports an acid-avoidance response without requiring every pH-tactic organism to show bidirectional attraction to a neutral optimum. Strain-specific mutant, receptor and host-colonization findings are not generalized into the trait definition or mechanism.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -271,7 +272,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed pH taxis -

      Created traitmech:000591 with DOI:10.1128/jb.00491-19 (PMID:31685537) and DOI:10.1128/jb.188.7.2656-2665.2006 (PMID:16547053), each with an exact Europe PMC abstract snippet. Fresh seed comparison: 399 identifiers, 344 present and 55 absent; pre-change corpus 985 records. Ignored-and-hidden repository searches and structured OWL review found no exact record or METPO term. Reserved METPO:1054500 in proposal v468 under motile METPO:1000702. Deferred natural-strain examples, protein-resolved mechanisms and equivalent mappings; did not impose universal neutral preference or bidirectionality. Authored via dry-run validated writer and record_curation_event; focused writer tests passed.

    +

    Created traitmech:000591 with DOI:10.1128/jb.00491-19 (PMID:31685537) and DOI:10.1128/jb.188.7.2656-2665.2006 (PMID:16547053), each with an exact Europe PMC abstract snippet. Fresh seed comparison: 399 identifiers, 344 present and 55 absent; pre-change corpus 985 records. Ignored-and-hidden repository searches and structured OWL review found no exact record or METPO term. Reserved METPO:1054500 in proposal v468 under motile METPO:1000702. Deferred natural-strain examples, protein-resolved mechanisms and equivalent mappings; did not impose universal neutral preference or bidirectionality. Authored via dry-run validated writer and record_curation_event; focused writer tests passed.

    • Read this curation session @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 08:05 UTC diff --git a/pages/traits/physiology/ph_tropism.html b/pages/traits/physiology/ph_tropism.html index 27eff11b8e0..b75abd6f1a8 100644 --- a/pages/traits/physiology/ph_tropism.html +++ b/pages/traits/physiology/ph_tropism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1128/mbio.00285-23
    F. oxysporum hyphae exposed to a pH gradient displayed robust tropism toward acid.
    -

    Fernandes et al. (2023), Discussion; exact span in directly retrieved Europe PMC JATS, PMC10128062 (PMID:36861989). Results and Methods were read; Figure 1B and Table S1 (10.1128/mbio.00285-23.7) were visually inspected. Opposing 25 mM HCl/NaOH wells tested germ-tube direction after 8 h, with at least three experiments and 500 germ tubes per experiment. Mpk1 deletion reversed direction; complementation restored acidward growth, not necessarily wild-type magnitude. Panel A measures invasion, not tropism. The assay does not by itself resolve the local pH profile or exclude every co-varying ionic effect. The higher-pH response is an engineered-mutant observation, not a natural exemplar.

    +

    Fernandes et al. (2023), Discussion; exact span in directly retrieved Europe PMC JATS, PMC10128062 (PMID:36861989). Results and Methods were read; Figure 1B and Table S1 (10.1128/mbio.00285-23.7) were visually inspected. Opposing 25 mM HCl/NaOH wells tested germ-tube direction after 8 h, with at least three experiments and 500 germ tubes per experiment. Mpk1 deletion reversed direction; complementation restored acidward growth, not necessarily wild-type magnitude. Panel A measures invasion, not tropism. The assay does not by itself resolve the local pH profile or exclude every co-varying ionic effect. The higher-pH response is an engineered-mutant observation, not a natural exemplar.

  • DOI:10.1371/journal.pbio.3002726
    These outcomes indicate that the hyphae exhibit chemotropism towards pH 4 within the pH range of 3 to 8.
    -

    Yamamoto et al. (2024), Results, Chemotropism to low pH; exact span in directly retrieved Europe PMC JATS, PMC11288418 (PMID:39078817). Figure 3 and Table S1 (10.1371/journal.pbio.3002726.s002) were visually inspected. Aspergillus nidulans tip trajectories near the pH 6.5/8 interface support reorientation. Figure 3D reports n=1 experiment with 40-50 hyphae; hypha counts are not independent experimental replication. Growth inhibition at pH 3 confounds the 3/4 comparison. The separate summary abstract's acidic-pH avoidance wording conflicts with the main Results. This is not a universal pH-4 setpoint. Strains are engineered; movies and remaining supplements were not inspected.

    +

    Yamamoto et al. (2024), Results, Chemotropism to low pH; exact span in directly retrieved Europe PMC JATS, PMC11288418 (PMID:39078817). Figure 3 and Table S1 (10.1371/journal.pbio.3002726.s002) were visually inspected. Aspergillus nidulans tip trajectories near the pH 6.5/8 interface support reorientation. Figure 3D reports n=1 experiment with 40-50 hyphae; hypha counts are not independent experimental replication. Growth inhibition at pH 3 confounds the 3/4 comparison. The separate summary abstract's acidic-pH avoidance wording conflicts with the main Results. This is not a universal pH-4 setpoint. Strains are engineered; movies and remaining supplements were not inspected.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -271,7 +272,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add pH-directed polarized growth with primary evidence -

      Added traitmech:000602 pH tropism under local chemotropism after whole-repository ignored/hidden novelty and ID searches and structured OWL inspection. Two snippets exactly match directly retrieved Europe PMC JATS (PMC10128062, PMC11288418); inspected Fernandes Figure 1B and Table S1 and Yamamoto Figure 3 and Table S1 as images. Distinguished gradient-directed growth from locomotion, pH tolerance, uniform shifts and invasion; retained mutant direction limits, single-experiment counts, growth inhibition, conflicting summary wording and collection-label discrepancy. Deferred canonical strains and accession-level causal graphs. Reserved METPO:1055600 in v479 with the released phenotype parent and pending chemotropism reconciliation. Guarded writer dry run and seven focused tests pass; broader checks and rendered artifacts follow before submission. No older source YAML or QC baseline changed.

    +

    Added traitmech:000602 pH tropism under local chemotropism after whole-repository ignored/hidden novelty and ID searches and structured OWL inspection. Two snippets exactly match directly retrieved Europe PMC JATS (PMC10128062, PMC11288418); inspected Fernandes Figure 1B and Table S1 and Yamamoto Figure 3 and Table S1 as images. Distinguished gradient-directed growth from locomotion, pH tolerance, uniform shifts and invasion; retained mutant direction limits, single-experiment counts, growth inhibition, conflicting summary wording and collection-label discrepancy. Deferred canonical strains and accession-level causal graphs. Reserved METPO:1055600 in v479 with the released phenotype parent and pending chemotropism reconciliation. Guarded writer dry run and seven focused tests pass; broader checks and rendered artifacts follow before submission. No older source YAML or QC baseline changed.

    • Read this curation session @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 19:14 UTC diff --git a/pages/traits/physiology/phagocytosis.html b/pages/traits/physiology/phagocytosis.html index d40d2235a0f..271f4e70f5e 100644 --- a/pages/traits/physiology/phagocytosis.html +++ b/pages/traits/physiology/phagocytosis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1371/journal.pone.0095577
    remodeling of the collar membrane to engulf the prey, and transport of engulfed bacteria into the cell.
    -

    Dayel and King (2014), PMID:24806026, PMC4012994, scientific Abstract directly checked in Europe PMC XML and the PLOS article. Results, Discussion and Methods were read; actual Figures 1 and 4 were inspected. Live-cell images and SEM/TEM support collar-associated engulfment and internalization in Salpingoeca rosetta. Mere contact or retention on the collar is not ingestion. Nutrient assimilation and the molecular identity of collar links are not established by these images. Actual supplements and movies were not inspected. The culture-provenance papers cited by the Methods were not followed, so this study is retained as trait evidence without a canonical strain assignment.

    +

    Dayel and King (2014), PMID:24806026, PMC4012994, scientific Abstract directly checked in Europe PMC XML and the PLOS article. Results, Discussion and Methods were read; actual Figures 1 and 4 were inspected. Live-cell images and SEM/TEM support collar-associated engulfment and internalization in Salpingoeca rosetta. Mere contact or retention on the collar is not ingestion. Nutrient assimilation and the molecular identity of collar links are not established by these images. Actual supplements and movies were not inspected. The culture-provenance papers cited by the Methods were not followed, so this study is retained as trait evidence without a canonical strain assignment.

  • DOI:10.1111/nph.20388
    We found cells ingested proxy (up to 2 μm diameter) and natural (bacteria and cyanobacteria) prey particles
    -

    Scientific Summary directly checked in Europe PMC full-text XML and PMC11982794; PMID:40035416. Results, Discussion and Methods were read, and actual Figures 5, 6, 9 and 10 were inspected. Scyphosphaera apsteinii RCC1456 cultures internalized particles and labeled bacteria into a prominent vacuole. Distinguish pHrodo Escherichia coli BioParticles from Acridine Orange-labeled marine bacteria and from inert beads. Acidic-organelle staining alone is not prey uptake; some imaging used EGTA decalcification. The paper uses phagotrophy for the nutritional interpretation; this record asserts particle engulfment, not a measured carbon assimilation rate. Figure 10 is a conceptual sequence-based model, not native protein validation: its S. apsteinii transcripts come from RCC1455, not the assayed RCC1456, and some candidates are from Gephyrocapsa huxleyi. Actual supplements and movies were not inspected. No negative comparator-species claim, bead-degrading enzyme assignment or inferred nutrient quota is imported.

    +

    Scientific Summary directly checked in Europe PMC full-text XML and PMC11982794; PMID:40035416. Results, Discussion and Methods were read, and actual Figures 5, 6, 9 and 10 were inspected. Scyphosphaera apsteinii RCC1456 cultures internalized particles and labeled bacteria into a prominent vacuole. Distinguish pHrodo Escherichia coli BioParticles from Acridine Orange-labeled marine bacteria and from inert beads. Acidic-organelle staining alone is not prey uptake; some imaging used EGTA decalcification. The paper uses phagotrophy for the nutritional interpretation; this record asserts particle engulfment, not a measured carbon assimilation rate. Figure 10 is a conceptual sequence-based model, not native protein validation: its S. apsteinii transcripts come from RCC1455, not the assayed RCC1456, and some candidates are from Gephyrocapsa huxleyi. Actual supplements and movies were not inspected. No negative comparator-species claim, bead-degrading enzyme assignment or inferred nutrient quota is imported.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Canonical examples DOI:10.1111/nph.20388 - Strain-qualified example: diploid RCC1456, also AC504, TW15 and NIES-3344. Mid- to late-exponential nonaxenic cultures ingested labeled marine bacteria and particles under the reported incubation conditions; Figures 5 and 6 were inspected. The species taxon ID and scientific name were independently verified at NCBI on 2026-10-05; this is not a strain-level taxon ID or a claim about every isolate. Natural isolation from the Spanish coast of the Balearic Sea by single-cell micropipetting on 2001-02-01 was checked directly in the collection record https://www.roscoff-culture-collection.org/rcc-strain-details/1456. The transcript-source strain RCC1455 (AC505/TW16) is distinct and is not substituted for this exemplar. + Strain-qualified example: diploid RCC1456, also AC504, TW15 and NIES-3344. Mid- to late-exponential nonaxenic cultures ingested labeled marine bacteria and particles under the reported incubation conditions; Figures 5 and 6 were inspected. The species taxon ID and scientific name were independently verified at NCBI on 2026-10-05; this is not a strain-level taxon ID or a claim about every isolate. Natural isolation from the Spanish coast of the Balearic Sea by single-cell micropipetting on 2001-02-01 was checked directly in the collection record https://www.roscoff-culture-collection.org/rcc-strain-details/1456. The transcript-source strain RCC1455 (AC505/TW16) is distinct and is not substituted for this exemplar. @@ -340,7 +341,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -369,12 +379,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 06:50 UTC diff --git a/pages/traits/physiology/phagotrophy.html b/pages/traits/physiology/phagotrophy.html index 53ac25a8cae..102db8b180d 100644 --- a/pages/traits/physiology/phagotrophy.html +++ b/pages/traits/physiology/phagotrophy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1038/ismej.2017.68
    NanoSIMS and bulk IRMS isotope analyses revealed that Ochromonas obtained 84-99% of its carbon and 88-95% of its nitrogen from consumed bacteria.
    -

    PMID:28524870, PMC5563956. This contiguous scientific-abstract quote uses the directly retrieved Europe PMC abstract's ASCII range hyphens; the full-text XML uses en dashes. The maintained resolver verifies the API form but flags the en-dash form as LIKELY_PARAPHRASE solely for that typography difference. Full Introduction, Methods, Results and Discussion were read, and actual Figures 1 and 4 were inspected. Axenic Ochromonas sp. BG-1 cultures received washed heat-killed bacterial prey or labeled inorganic substrates in triplicate light/dark treatments with unlabeled controls. Isotope incorporation and prey-dependent growth support nutritional use, not merely particle uptake. The percentages describe the nutrient source under these conditions, not a universal rate or an exclusively direct organic-carbon assimilation route: bacterial carbon can be respired and refixed, and uncontrolled pH/atmospheric exchange may underestimate inorganic carbon fixation. NanoSIMS and bulk carbon estimates differ. Actual Figures 2, 3 and 5 and supplements were not visually audited; no unique claims from those panels are imported. Heat-killed prey do not demonstrate that the consumer kills living prey.

    +

    PMID:28524870, PMC5563956. This contiguous scientific-abstract quote uses the directly retrieved Europe PMC abstract's ASCII range hyphens; the full-text XML uses en dashes. The maintained resolver verifies the API form but flags the en-dash form as LIKELY_PARAPHRASE solely for that typography difference. Full Introduction, Methods, Results and Discussion were read, and actual Figures 1 and 4 were inspected. Axenic Ochromonas sp. BG-1 cultures received washed heat-killed bacterial prey or labeled inorganic substrates in triplicate light/dark treatments with unlabeled controls. Isotope incorporation and prey-dependent growth support nutritional use, not merely particle uptake. The percentages describe the nutrient source under these conditions, not a universal rate or an exclusively direct organic-carbon assimilation route: bacterial carbon can be respired and refixed, and uncontrolled pH/atmospheric exchange may underestimate inorganic carbon fixation. NanoSIMS and bulk carbon estimates differ. Actual Figures 2, 3 and 5 and supplements were not visually audited; no unique claims from those panels are imported. Heat-killed prey do not demonstrate that the consumer kills living prey.

  • DOI:10.1007/s00248-001-1024-6
    nutrient acquisition for this species in the presence of bacteria was accomplished primarily via ingestion of bacteria.
    -

    Sanders et al. (2001), PMID:12024234. Scientific Abstract and full Introduction, Methods, Results, Discussion and Conclusions were directly read from the author-institution PDF. Actual PDF pages 2 and 7, including Figure 4, were inspected. The study compares axenic and bacterized BG-1 cultures with light, dissolved-organic and nutrient treatments. Live Pasteurella sp. prey in this experiment are distinct from the 2017 heat-killed prey treatment. Population abundance and biovolume are separate readouts; cell division alone need not mean biomass increase. Authors cannot exclude contributions from bacterial trace compounds or nutrient recycling. Fluorescent prey added above ambient prey abundance can inflate grazing estimates, while prey-disappearance estimates omit bacterial growth. No unqualified grazing rate, specific MES assimilation or BG-1 cannibalism claim is imported. This is a separate study of the same strain, not independent taxon replication.

    +

    Sanders et al. (2001), PMID:12024234. Scientific Abstract and full Introduction, Methods, Results, Discussion and Conclusions were directly read from the author-institution PDF. Actual PDF pages 2 and 7, including Figure 4, were inspected. The study compares axenic and bacterized BG-1 cultures with light, dissolved-organic and nutrient treatments. Live Pasteurella sp. prey in this experiment are distinct from the 2017 heat-killed prey treatment. Population abundance and biovolume are separate readouts; cell division alone need not mean biomass increase. Authors cannot exclude contributions from bacterial trace compounds or nutrient recycling. Fluorescent prey added above ambient prey abundance can inflate grazing estimates, while prey-disappearance estimates omit bacterial growth. No unqualified grazing rate, specific MES assimilation or BG-1 cannibalism claim is imported. This is a separate study of the same strain, not independent taxon replication.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Canonical examples DOI:10.1038/ismej.2017.68 - Strain-qualified BG-1 example: washed heat-killed bacterial prey supported growth and supplied cellular carbon and nitrogen in the 2017 isotope experiments; actual Figures 1 and 4 were inspected. This is not a claim that every Ochromonas isolate has the same trophic dependence. NCBI ESearch and EFetch independently resolve the exact name and identifier on 2026-10-05; NCBI assigns species rank despite the BG-1 name. Natural isolation from a Malaysian freshwater pond after dark organic enrichment, followed by single-cell transfers and antibiotic axenization, is documented in the 2001 primary Methods (DOI:10.1007/s00248-001-1024-6), directly read at https://dornsife.usc.edu/caron/wp-content/uploads/sites/263/2023/11/2001_Sanders_etal_ME.pdf. Antibiotic axenization is not evidence of genetic engineering. Nutrient-source fractions do not identify the complete intracellular assimilation pathway. + Strain-qualified BG-1 example: washed heat-killed bacterial prey supported growth and supplied cellular carbon and nitrogen in the 2017 isotope experiments; actual Figures 1 and 4 were inspected. This is not a claim that every Ochromonas isolate has the same trophic dependence. NCBI ESearch and EFetch independently resolve the exact name and identifier on 2026-10-05; NCBI assigns species rank despite the BG-1 name. Natural isolation from a Malaysian freshwater pond after dark organic enrichment, followed by single-cell transfers and antibiotic axenization, is documented in the 2001 primary Methods (DOI:10.1007/s00248-001-1024-6), directly read at https://dornsife.usc.edu/caron/wp-content/uploads/sites/263/2023/11/2001_Sanders_etal_ME.pdf. Antibiotic axenization is not evidence of genetic engineering. Nutrient-source fractions do not identify the complete intracellular assimilation pathway. @@ -328,7 +329,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -357,12 +367,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 21:50 UTC diff --git a/pages/traits/physiology/phenylalanine_arylamidase_activity.html b/pages/traits/physiology/phenylalanine_arylamidase_activity.html index 8d670da6c89..a2b8edff513 100644 --- a/pages/traits/physiology/phenylalanine_arylamidase_activity.html +++ b/pages/traits/physiology/phenylalanine_arylamidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • phenylalanine arylamidase RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
      • +
    • phenylalanine arylamidase RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
    @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -272,7 +273,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two diagnostic enzyme-panel survey snippets (DOI:10.1099/ijsem.0.006017, DOI:10.1128/JCM.40.9.3427-3431.2002) without verbatim catalytic reaction quotes.

    +

    The current record carries two diagnostic enzyme-panel survey snippets (DOI:10.1099/ijsem.0.006017, DOI:10.1128/JCM.40.9.3427-3431.2002) without verbatim catalytic reaction quotes.

    @@ -354,7 +355,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -383,12 +393,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/photoautotrophic.html b/pages/traits/physiology/photoautotrophic.html index 63af43dcdb9..8de08a3bae1 100644 --- a/pages/traits/physiology/photoautotrophic.html +++ b/pages/traits/physiology/photoautotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -408,8 +409,8 @@

    Protein and taxon examples

    		 - Synechocystis sp. PCC 6803 -
    NCBITaxon:1111708 + Synechocystis sp. PCC 6803 +
    NCBITaxon:1111708         		REVIEWED
    @@ -475,17 +476,17 @@

    Parent traits (1)

    Synonyms (6)

      -
    • anoxygenic_photoautotrophy RELATED_SYNONYM · metpo.owl
      • +
    • anoxygenic_photoautotrophy RELATED_SYNONYM · metpo.owl
      • -
    • anoxygenic_photoautotrophy_hydrogen_oxidation RELATED_SYNONYM · metpo.owl
      • +
    • anoxygenic_photoautotrophy_hydrogen_oxidation RELATED_SYNONYM · metpo.owl
      • -
    • anoxygenic_photoautotrophy_iron_oxidation RELATED_SYNONYM · metpo.owl
      • +
    • anoxygenic_photoautotrophy_iron_oxidation RELATED_SYNONYM · metpo.owl
      • -
    • anoxygenic_photoautotrophy_sulfur_oxidation RELATED_SYNONYM · metpo.owl
      • +
    • anoxygenic_photoautotrophy_sulfur_oxidation RELATED_SYNONYM · metpo.owl
      • -
    • photoautotroph RELATED_SYNONYM · metpo.owl
      • +
    • photoautotroph RELATED_SYNONYM · metpo.owl
      • -
    • photoautotrophy RELATED_SYNONYM · metpo.owl
      • +
    • photoautotrophy RELATED_SYNONYM · metpo.owl
    @@ -501,7 +502,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -861,7 +862,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1225,12 +1235,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/photoheterotrophic.html b/pages/traits/physiology/photoheterotrophic.html index 14c2e404a02..793e853d427 100644 --- a/pages/traits/physiology/photoheterotrophic.html +++ b/pages/traits/physiology/photoheterotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -305,7 +306,7 @@

    Edge evidence

  • aerobic anoxygenic phototrophs - traitmech:000194 + traitmech:000194 perform photophosphorylation @@ -343,7 +344,7 @@

    Edge evidence

  • aerobic anoxygenic phototrophs - traitmech:000194 + traitmech:000194 relies primarily on dissolved organic matter @@ -402,8 +403,8 @@

    Protein and taxon examples

    		•  - Rhodospirillum rubrum -
    NCBITaxon:1085 + Rhodospirillum rubrum +
    NCBITaxon:1085         		REVIEWED
    @@ -478,9 +479,9 @@

    Children (1)

    Synonyms (2)

      -
    • photoheterotroph RELATED_SYNONYM · metpo.owl
      • +
    • photoheterotroph RELATED_SYNONYM · metpo.owl
      • -
    • photoheterotrophy RELATED_SYNONYM · metpo.owl
      • +
    • photoheterotrophy RELATED_SYNONYM · metpo.owl
    @@ -496,7 +497,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -844,7 +845,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1208,12 +1218,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/photokinesis.html b/pages/traits/physiology/photokinesis.html index 3dd26dc9cd1..2beab898e37 100644 --- a/pages/traits/physiology/photokinesis.html +++ b/pages/traits/physiology/photokinesis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1128/AEM.67.12.5410-5419.2001
    swimming velocities are correlated to the illumination intensity.
    -

    Introduction's photokinesis definition; publisher full text at https://journals.asm.org/doi/10.1128/AEM.67.12.5410-5419.2001 and Figure 2A-B with caption inspected. In Marichromatium gracile CE2205, the anoxic 1 mM total-sulfide preparation shows lower speed at low irradiance; oxic controls (>100 micromolar oxygen, no free sulfide) show no significant irradiance dependence. Reported irradiance is visible-region scalar irradiance (400-700 nm), with a fixed visible:near-infrared photon ratio of 1:8.3. Measurements use two-dimensional cell tracks after 60 s at each irradiance. Exponential-phase cells with sulfur globules were sampled above bottom aggregates. The collection-supplied strain is not assigned an independently verified natural lineage here. The separate gradient-migration results are attributed to phobic responses, not used to infer directional photokinesis.

    +

    Introduction's photokinesis definition; publisher full text at https://journals.asm.org/doi/10.1128/AEM.67.12.5410-5419.2001 and Figure 2A-B with caption inspected. In Marichromatium gracile CE2205, the anoxic 1 mM total-sulfide preparation shows lower speed at low irradiance; oxic controls (>100 micromolar oxygen, no free sulfide) show no significant irradiance dependence. Reported irradiance is visible-region scalar irradiance (400-700 nm), with a fixed visible:near-infrared photon ratio of 1:8.3. Measurements use two-dimensional cell tracks after 60 s at each irradiance. Exponential-phase cells with sulfur globules were sampled above bottom aggregates. The collection-supplied strain is not assigned an independently verified natural lineage here. The separate gradient-migration results are attributed to phobic responses, not used to infer directional photokinesis.

  • DOI:10.1016/S0176-1617(00)80045-0
    Photosynthetically active continuous red light reversibly enhances the swimming velocity and increases or decreases the precision of gravitaxis, depending on its initial level.
    -

    Abstract, PMID:12090268, exact-matched at Europe PMC. This primary study of Chlamydomonas reinhardtii supports light-dependent speed modulation alongside a distinct orientation response. Its blue-light responses have different kinetics; proposed chlamy-rhodopsin participation is explicitly inferential. Subscription full text was not inspected; no strain lineage, protein accession or full-text-only result is inferred.

    +

    Abstract, PMID:12090268, exact-matched at Europe PMC. This primary study of Chlamydomonas reinhardtii supports light-dependent speed modulation alongside a distinct orientation response. Its blue-light responses have different kinetics; proposed chlamy-rhodopsin participation is explicitly inferential. Subscription full text was not inspected; no strain lineage, protein accession or full-text-only result is inferred.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 04:48 UTC diff --git a/pages/traits/physiology/photolithoautotrophic.html b/pages/traits/physiology/photolithoautotrophic.html index 69fef1b7c2f..a9fe590acfd 100644 --- a/pages/traits/physiology/photolithoautotrophic.html +++ b/pages/traits/physiology/photolithoautotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -353,7 +354,7 @@

    Edge evidence

    example of inorganic electron donor METPO:1007502 - rdfs:subClassOf + rdfs:subClassOf

    Sulfide is a reduced inorganic electron donor used by anoxygenic photolithoautotrophs.

      @@ -408,8 +409,8 @@

      Protein and taxon examples

    		 - Synechococcus elongatus PCC 7942 -
    NCBITaxon:1140 + Synechococcus elongatus PCC 7942 +
    NCBITaxon:1140         		REVIEWED
    @@ -475,7 +476,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • photolithoautotroph RELATED_SYNONYM · metpo.owl
      • +
    • photolithoautotroph RELATED_SYNONYM · metpo.owl
    @@ -491,7 +492,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -887,7 +888,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1251,12 +1261,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/photolithotrophic.html b/pages/traits/physiology/photolithotrophic.html index 3f39532e475..5cba49bed13 100644 --- a/pages/traits/physiology/photolithotrophic.html +++ b/pages/traits/physiology/photolithotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -138,7 +139,7 @@

    Edge evidence

    example of inorganic electron donor METPO:1007502 - rdfs:subClassOf + rdfs:subClassOf

    Hydrogen sulfide is a representative inorganic electron donor.

      @@ -157,7 +158,7 @@

      Edge evidence

      example of inorganic electron donor METPO:1007502 - rdfs:subClassOf + rdfs:subClassOf

      Fe(II) is a representative inorganic electron donor in photoferrotrophy.

        @@ -327,7 +328,7 @@

        Edge evidence

        defines photoferrotrophy - traitmech:000193 + traitmech:000193 METPO:2007500

        Photoferrotrophy is the oxidation of reduced iron via anoxygenic photosynthesis.

          @@ -402,8 +403,8 @@

          Protein and taxon examples

    		 - Chlorobaculum tepidum TLS -
    NCBITaxon:194439 + Chlorobaculum tepidum TLS +
    NCBITaxon:194439         		REVIEWED
    @@ -469,7 +470,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • photolithotroph RELATED_SYNONYM · metpo.owl
      • +
    • photolithotroph RELATED_SYNONYM · metpo.owl
    @@ -485,7 +486,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -845,7 +846,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1209,12 +1219,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/photoorganoheterotrophic.html b/pages/traits/physiology/photoorganoheterotrophic.html index d86e275d3ed..85d8e03b6cf 100644 --- a/pages/traits/physiology/photoorganoheterotrophic.html +++ b/pages/traits/physiology/photoorganoheterotrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -389,8 +390,8 @@

    Protein and taxon examples

    		 - Rhodospirillum rubrum -
    NCBITaxon:1085 + Rhodospirillum rubrum +
    NCBITaxon:1085         		REVIEWED
    @@ -456,7 +457,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • photoorganoheterotroph RELATED_SYNONYM · metpo.owl
      • +
    • photoorganoheterotroph RELATED_SYNONYM · metpo.owl
    @@ -472,7 +473,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -568,15 +569,15 @@

    Deep research

    | Mechanism / edge family | Generic vs taxon-specific status | Strongest DOI | Evidence strength | Recommended TraitMech action | |---|---|---|---|---| -| Reaction-center phototrophy: light captured by bacteriochlorophyll-based RC systems generates proton-motive force and ATP; applicable to RC-bearing photoorganoheterotrophs | Generic within RC-based photoheterotrophs; not universal to rhodopsin-based cases | 10.1016/j.tim.2006.09.001 | Strong review-level mechanistic support; foundational, not 2023–2024 (bryant2006prokaryoticphotosynthesisand pages 2-3, thiel2018diversityofchlorophototrophic pages 2-3) | Curate as core mechanism for an RC-based subclass/branch of photoorganoheterotrophy; avoid asserting universality for all METPO:1000659 instances | -| Proteorhodopsin phototrophy: PR + retinal light-driven proton pumping supplements ATP production without full photosynthetic electron transport | Taxon/mechanism-specific; applies to PR-bearing bacteria, not RC-based phototrophs | 10.4014/jmb.2410.10034 | Strong for specific strain physiology; recent primary data, but strain-context dependent (oh2024effectoflight pages 13-14, oh2024effectoflight pages 1-2) | Curate as alternative mechanistic branch under photoorganoheterotrophy with uncertainty/generalization note | -| Organic carbon dependence: organisms obtain carbon from organic compounds; light supplements energy rather than replacing organic carbon requirement | Generic trait-defining feature | 10.1038/nbt923 | Strong definition-level evidence plus recent physiological support (larimer2004completegenomesequence pages 1-2, tinguely2023diurnalcyclesdrive pages 1-2, oh2024effectoflight pages 13-14) | Curate as core defining edge(s): organic compounds support biomass carbon; do not over-specify a single substrate set | -| Oxygen boundary: aerobic anoxygenic photoheterotrophs function under oxic conditions, while many anaerobic anoxygenic phototrophs suppress photosystem biosynthesis in oxygen | Boundary is clade/mechanism-specific, not universal | 10.1146/annurev-arplant-042817-040500 | Moderate-to-strong review evidence, but not globally applicable across all photoorganoheterotrophs (thiel2018diversityofchlorophototrophic pages 10-11) | Curate only as contextual/environmental qualifiers on specific branches (e.g., AAP vs anaerobic purple bacteria), not as a global trait constraint | -| CBB/anaplerotic redox balancing: CO2 fixation can act as electron sink during photoheterotrophic growth | Strongly supported in purple phototrophic bacteria; not yet generic to all photoorganoheterotrophs | 10.1038/s42003-024-07188-0 | Strong recent mechanistic support in mixed PPB biofilms and related PPB literature, but lineage-specific (edreira2024elucidatingmetabolictuning pages 1-2, edreira2024elucidatingmetabolictuning pages 5-6) | Curate as taxon-specific/uncertain edge set for PPB-focused branch; do not make obligatory for the whole trait | -| PHA accumulation as excess-reductant sink under photoheterotrophic/redox-stress conditions | Taxon- and condition-specific | 10.1038/s42003-024-07188-0 | Strong recent application/mechanistic support in PPB biocathodes; clearly conditional on substrate/redox state (edreira2024elucidatingmetabolictuning pages 1-2, edreira2024elucidatingmetabolictuning pages 9-10) | Curate only as conditional, PPB-specific downstream edge; mark uncertain and context dependent | -| Nutrient/light effects: carbon limitation, diel cycling, and nutrient status modulate growth, ATP use, survival, and competitive fitness | Broad but not universal; effects differ by mechanism and taxon | 10.1093/femsec/fiae090 | Strong recent ecological/physiological evidence, but outcomes differ across AAPB and PR systems (tinguely2023diurnalcyclesdrive pages 1-2, tinguely2023diurnalcyclesdrive pages 9-10, oh2024effectoflight pages 13-14, oh2024effectoflight pages 14-15) | Curate as environmental modulation edges with explicit assay/context notes; avoid a single directional rule for all taxa | -| Applications: wastewater treatment, bioremediation, biomass/single-cell protein, pigments, PHA, biohydrogen, photo-bioelectrochemical CO2 upcycling | Application-level evidence is strong for PPB/PNSB, not trait-universal biology | 10.1007/s11274-023-03729-7 | Strong recent applied literature and quantitative implementations, but mostly consortium/taxon-specific engineering evidence (dhar2023anoxygenicphototrophicpurple pages 1-3, sepulvedamunoz2023wastewatertreatmentusing pages 1-2, wada2023valorizationofpurple pages 1-2, wada2023valorizationofpurple pages 11-12, edreira2024elucidatingmetabolictuning pages 1-2) | Do not curate as intrinsic causal edges of the trait; keep as downstream use-cases or annotation notes outside core TraitMech graph | -| Photosynthesis genes/proteins (e.g., pufL, pufM, bchH/bchM, RuBisCO/cbbL in some taxa) | Taxon-specific markers of RC-based subtypes; not universal trait markers | 10.1038/s43705-023-00334-5 | Moderate-to-strong primary support for specific taxa and gene sets (tinguely2023diurnalcyclesdrive pages 2-2, yabe2022vulcanimicrobiumalpinusgen. pages 7-8) | Curate as candidate grounded nodes on subtype branches only; avoid using any single gene as universal biomarker for METPO:1000659 | +| Reaction-center phototrophy: light captured by bacteriochlorophyll-based RC systems generates proton-motive force and ATP; applicable to RC-bearing photoorganoheterotrophs | Generic within RC-based photoheterotrophs; not universal to rhodopsin-based cases | 10.1016/j.tim.2006.09.001 | Strong review-level mechanistic support; foundational, not 2023–2024 (bryant2006prokaryoticphotosynthesisand pages 2-3, thiel2018diversityofchlorophototrophic pages 2-3) | Curate as core mechanism for an RC-based subclass/branch of photoorganoheterotrophy; avoid asserting universality for all METPO:1000659 instances | +| Proteorhodopsin phototrophy: PR + retinal light-driven proton pumping supplements ATP production without full photosynthetic electron transport | Taxon/mechanism-specific; applies to PR-bearing bacteria, not RC-based phototrophs | 10.4014/jmb.2410.10034 | Strong for specific strain physiology; recent primary data, but strain-context dependent (oh2024effectoflight pages 13-14, oh2024effectoflight pages 1-2) | Curate as alternative mechanistic branch under photoorganoheterotrophy with uncertainty/generalization note | +| Organic carbon dependence: organisms obtain carbon from organic compounds; light supplements energy rather than replacing organic carbon requirement | Generic trait-defining feature | 10.1038/nbt923 | Strong definition-level evidence plus recent physiological support (larimer2004completegenomesequence pages 1-2, tinguely2023diurnalcyclesdrive pages 1-2, oh2024effectoflight pages 13-14) | Curate as core defining edge(s): organic compounds support biomass carbon; do not over-specify a single substrate set | +| Oxygen boundary: aerobic anoxygenic photoheterotrophs function under oxic conditions, while many anaerobic anoxygenic phototrophs suppress photosystem biosynthesis in oxygen | Boundary is clade/mechanism-specific, not universal | 10.1146/annurev-arplant-042817-040500 | Moderate-to-strong review evidence, but not globally applicable across all photoorganoheterotrophs (thiel2018diversityofchlorophototrophic pages 10-11) | Curate only as contextual/environmental qualifiers on specific branches (e.g., AAP vs anaerobic purple bacteria), not as a global trait constraint | +| CBB/anaplerotic redox balancing: CO2 fixation can act as electron sink during photoheterotrophic growth | Strongly supported in purple phototrophic bacteria; not yet generic to all photoorganoheterotrophs | 10.1038/s42003-024-07188-0 | Strong recent mechanistic support in mixed PPB biofilms and related PPB literature, but lineage-specific (edreira2024elucidatingmetabolictuning pages 1-2, edreira2024elucidatingmetabolictuning pages 5-6) | Curate as taxon-specific/uncertain edge set for PPB-focused branch; do not make obligatory for the whole trait | +| PHA accumulation as excess-reductant sink under photoheterotrophic/redox-stress conditions | Taxon- and condition-specific | 10.1038/s42003-024-07188-0 | Strong recent application/mechanistic support in PPB biocathodes; clearly conditional on substrate/redox state (edreira2024elucidatingmetabolictuning pages 1-2, edreira2024elucidatingmetabolictuning pages 9-10) | Curate only as conditional, PPB-specific downstream edge; mark uncertain and context dependent | +| Nutrient/light effects: carbon limitation, diel cycling, and nutrient status modulate growth, ATP use, survival, and competitive fitness | Broad but not universal; effects differ by mechanism and taxon | 10.1093/femsec/fiae090 | Strong recent ecological/physiological evidence, but outcomes differ across AAPB and PR systems (tinguely2023diurnalcyclesdrive pages 1-2, tinguely2023diurnalcyclesdrive pages 9-10, oh2024effectoflight pages 13-14, oh2024effectoflight pages 14-15) | Curate as environmental modulation edges with explicit assay/context notes; avoid a single directional rule for all taxa | +| Applications: wastewater treatment, bioremediation, biomass/single-cell protein, pigments, PHA, biohydrogen, photo-bioelectrochemical CO2 upcycling | Application-level evidence is strong for PPB/PNSB, not trait-universal biology | 10.1007/s11274-023-03729-7 | Strong recent applied literature and quantitative implementations, but mostly consortium/taxon-specific engineering evidence (dhar2023anoxygenicphototrophicpurple pages 1-3, sepulvedamunoz2023wastewatertreatmentusing pages 1-2, wada2023valorizationofpurple pages 1-2, wada2023valorizationofpurple pages 11-12, edreira2024elucidatingmetabolictuning pages 1-2) | Do not curate as intrinsic causal edges of the trait; keep as downstream use-cases or annotation notes outside core TraitMech graph | +| Photosynthesis genes/proteins (e.g., pufL, pufM, bchH/bchM, RuBisCO/cbbL in some taxa) | Taxon-specific markers of RC-based subtypes; not universal trait markers | 10.1038/s43705-023-00334-5 | Moderate-to-strong primary support for specific taxa and gene sets (tinguely2023diurnalcyclesdrive pages 2-2, yabe2022vulcanimicrobiumalpinusgen. pages 7-8) | Curate as candidate grounded nodes on subtype branches only; avoid using any single gene as universal biomarker for METPO:1000659 | *Table: This table summarizes which mechanism families are safe to curate as core TraitMech content for photoorganoheterotrophy versus which should remain branch-specific, conditional, or outside the core graph. It helps separate trait-defining biology from taxon-limited mechanisms and engineering applications.* @@ -784,7 +785,7 @@

    Curation history

  • · ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE · claude -

    Appended record-level evidence entry for definition_source DOI:10.1016/B978-012373944-5.00083-3 using the verified verbatim snippet already present on causal_graphs[0].edges[0].evidence[0] (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-001 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    +

    Appended record-level evidence entry for definition_source DOI:10.1016/B978-012373944-5.00083-3 using the verified verbatim snippet already present on causal_graphs[0].edges[0].evidence[0] (Cycle 3 Stage 5 remediation of F-C3S4-DEF-SRC-001 in group G-C3S4-RECORD-LEVEL-DEFINITION-SOURCE-SNIPPETS, issue #2002).

    • @@ -826,7 +827,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1190,12 +1200,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-24 02:45 UTC diff --git a/pages/traits/physiology/phototaxis.html b/pages/traits/physiology/phototaxis.html index f7bfa6124e7..9fe0076124e 100644 --- a/pages/traits/physiology/phototaxis.html +++ b/pages/traits/physiology/phototaxis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.7554/eLife.12620
    the majority of motile cells switched direction within about 1 min, and then moved directly towards the light source
    -

    Results, first subsection, Figure 1c-d and methods; publisher version 2, posted 2022-04-22, originally published 2016-02-09 (PMID:26858197). Version-specific full text: https://cdn.elifesciences.org/articles/12620/elife-12620-v2.xml. Figure 1 and both optical figure supplements visually inspected. Motile Synechocystis sp. PCC 6803 PCC-M cells on agarose move toward oblique RGB illumination (470/525/625 nm, equal intensity; 10 micromol photons per square metre per second). The projected white-light intensity gradient does not produce significant directional bias in this experiment. Cells were sampled from moving colony fronts; analysis excludes immotile cells. These observations are separate from torA-gfp optical reporter assays and from the proposed PixJ1-to-pilus signaling model. They do not establish one universal directional-sensing mechanism.

    +

    Results, first subsection, Figure 1c-d and methods; publisher version 2, posted 2022-04-22, originally published 2016-02-09 (PMID:26858197). Version-specific full text: https://cdn.elifesciences.org/articles/12620/elife-12620-v2.xml. Figure 1 and both optical figure supplements visually inspected. Motile Synechocystis sp. PCC 6803 PCC-M cells on agarose move toward oblique RGB illumination (470/525/625 nm, equal intensity; 10 micromol photons per square metre per second). The projected white-light intensity gradient does not produce significant directional bias in this experiment. Cells were sampled from moving colony fronts; analysis excludes immotile cells. These observations are separate from torA-gfp optical reporter assays and from the proposed PixJ1-to-pilus signaling model. They do not establish one universal directional-sensing mechanism.

  • DOI:10.1105/tpc.108.057919
    Chlamydomonas cells with low CHR2 content exhibit photophobic and phototactic responses that strictly depend on the availability of CHR1.
    -

    Abstract exact-matched at Europe PMC (PMID:18552201). The PMC introduction distinguishes directional swimming toward or away from light from transient photophobic reversal; the beginning of Results identifies the cell-wall-deficient CW2 strain. Evidence concerns Chlamydomonas reinhardtii under the stated receptor-content conditions, not every algal strain or a universal CHR1 requirement. Xenopus ion-conductance assays are heterologous. Remaining full-text sections and supplements were not inspected; no natural algal exemplar or complete protein-resolved pathway is inferred.

    +

    Abstract exact-matched at Europe PMC (PMID:18552201). The PMC introduction distinguishes directional swimming toward or away from light from transient photophobic reversal; the beginning of Results identifies the cell-wall-deficient CW2 strain. Evidence concerns Chlamydomonas reinhardtii under the stated receptor-content conditions, not every algal strain or a universal CHR1 requirement. Xenopus ion-conductance assays are heterologous. Remaining full-text sections and supplements were not inspected; no natural algal exemplar or complete protein-resolved pathway is inferred.

  • DOI:10.1093/dnares/dss024
    ‘PCC-M and PCC-P’ are strains that both exhibit the native positive phototaxis, whereas ‘PCC-N’ strain shows negative phototaxis.
    -

    Results, section 3.1, exact-matched to Europe PMC full-text XML (PMID:23069868). Methods trace PCC-M to the Shestakov laboratory in 1993 and maintenance of motile colonies, matching the Schuergers study. The strain descends from the original PCC isolate but has undergone laboratory microevolution; it is not asserted genetically identical to the original isolate. Discussion also reports no blue-light phototaxis for PCC-M. This supports a substrain-qualified exemplar, not a statement that every PCC 6803 lineage or illumination gives the same response.

    +

    Results, section 3.1, exact-matched to Europe PMC full-text XML (PMID:23069868). Methods trace PCC-M to the Shestakov laboratory in 1993 and maintenance of motile colonies, matching the Schuergers study. The strain descends from the original PCC isolate but has undergone laboratory microevolution; it is not asserted genetically identical to the original isolate. Discussion also reports no blue-light phototaxis for PCC-M. This supports a substrain-qualified exemplar, not a statement that every PCC 6803 lineage or illumination gives the same response.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.7554/eLife.12620 - Motile wild-type PCC-M substrain, not the torA-gfp reporter. Figure 1c-d shows positive phototaxis on agarose under oblique RGB illumination after sampling moving colony fronts. Independent provenance: DOI:10.1093/dnares/dss024, Methods 2.1 and Results 3.1; PCC-M retains native positive phototaxis but has laboratory sequence differences and lacks blue-light phototaxis in the cited comparison. NCBI:1148 was resolved at NCBI on 2026-10-04; it is species-level, not a PCC-M-specific accession. No universal substrain, wavelength or sign claim. + Motile wild-type PCC-M substrain, not the torA-gfp reporter. Figure 1c-d shows positive phototaxis on agarose under oblique RGB illumination after sampling moving colony fronts. Independent provenance: DOI:10.1093/dnares/dss024, Methods 2.1 and Results 3.1; PCC-M retains native positive phototaxis but has laboratory sequence differences and lacks blue-light phototaxis in the cited comparison. NCBI:1148 was resolved at NCBI on 2026-10-04; it is species-level, not a PCC-M-specific accession. No universal substrain, wavelength or sign claim. @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 05:23 UTC diff --git a/pages/traits/physiology/phototrophic.html b/pages/traits/physiology/phototrophic.html index 2d810b4a357..9f22e93bdfc 100644 --- a/pages/traits/physiology/phototrophic.html +++ b/pages/traits/physiology/phototrophic.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -364,8 +365,8 @@

    Protein and taxon examples

    		 - Rhodospirillum rubrum -
    NCBITaxon:1085 + Rhodospirillum rubrum +
    NCBITaxon:1085         		REVIEWED
    @@ -431,9 +432,9 @@

    Parent traits (1)

    Synonyms (2)

      -
    • TT_phototroph RELATED_SYNONYM · metpo.owl
      • +
    • TT_phototroph RELATED_SYNONYM · metpo.owl
      • -
    • phototroph RELATED_SYNONYM · metpo.owl
      • +
    • phototroph RELATED_SYNONYM · metpo.owl
    @@ -449,7 +450,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -827,7 +828,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1191,12 +1201,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/phototropism.html b/pages/traits/physiology/phototropism.html index ab526c532f6..2be44dd08f1 100644 --- a/pages/traits/physiology/phototropism.html +++ b/pages/traits/physiology/phototropism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1073/pnas.0600633103
    it exhibits phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths
    -

    Abstract, exact-matched at Europe PMC (PMID:16537433; PMC1450208); it refers to Phycomyces blakesleeanus sporangiophore growth. The institutional full-text PDF and Figure 1A were inspected: the wild-type control bends toward white light, unlike the reduced response of madA mutants. The abstract's far-UV response is not measured in that panel. Methods identify NRRL1555 as the wild-type background and distinguish chemically mutagenized derivatives and isogenic A56. Genetic cosegregation supports madA involvement, not a complete growth-polarity pathway.

    +

    Abstract, exact-matched at Europe PMC (PMID:16537433; PMC1450208); it refers to Phycomyces blakesleeanus sporangiophore growth. The institutional full-text PDF and Figure 1A were inspected: the wild-type control bends toward white light, unlike the reduced response of madA mutants. The abstract's far-UV response is not measured in that panel. Methods identify NRRL1555 as the wild-type background and distinguish chemically mutagenized derivatives and isogenic A56. Genetic cosegregation supports madA involvement, not a complete growth-polarity pathway.

  • DOI:10.1073/pnas.0900879106
    Phototropism, growth toward light, shares many features in fungi and plants but the molecular mechanisms remain to be fully elucidated.
    -

    Abstract, exact-matched at Europe PMC (PMID:19380729; PMC2678449). This passage describes the positive case; the Idnurm source establishes the broader directional scope. The institutional full-text PDF and Figures 2B and 4 were inspected. Phototropic responses cosegregate with madB alleles; MADA-MADB interaction assays use yeast and E. coli, not the native fungus. The Discussion leaves rapid bending mechanisms unresolved. Transcription measurements are not themselves directional-growth readouts. The supplementary strain table and figures were not accessible and were not inspected.

    +

    Abstract, exact-matched at Europe PMC (PMID:19380729; PMC2678449). This passage describes the positive case; the Idnurm source establishes the broader directional scope. The institutional full-text PDF and Figures 2B and 4 were inspected. Phototropic responses cosegregate with madB alleles; MADA-MADB interaction assays use yeast and E. coli, not the native fungus. The Discussion leaves rapid bending mechanisms unresolved. Transcription measurements are not themselves directional-growth readouts. The supplementary strain table and figures were not accessible and were not inspected.

  • DOI:10.1128/EC.00203-13
    These strains are wild isolates, except for A56.
    -

    Materials and Methods, Strains and growth conditions; exact contiguous raw PMC HTML text (PMID:24243797; PMC3910969). The preceding sentence includes NRRL1555 in the named strains; the following sentence distinguishes backcrossed A56. This supports natural-isolate provenance for the NRRL1555 exemplar, not an independent phototropism experiment.

    +

    Materials and Methods, Strains and growth conditions; exact contiguous raw PMC HTML text (PMID:24243797; PMC3910969). The preceding sentence includes NRRL1555 in the named strains; the following sentence distinguishes backcrossed A56. This supports natural-isolate provenance for the NRRL1555 exemplar, not an independent phototropism experiment.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -208,7 +209,7 @@

    Canonical examples DOI:10.1073/pnas.0600633103 - Wild-type sporangiophore growth toward white light in Figure 1A, with NRRL1555 background identified in Methods; not the madA mutants or backcrossed A56. Independent natural-isolate provenance: DOI:10.1128/EC.00203-13, Materials and Methods (https://pmc.ncbi.nlm.nih.gov/articles/PMC3910969/). Strain-level identity and exact name resolved at NCBI Taxonomy on 2026-10-04. No invariant wavelength or response direction is asserted. + Wild-type sporangiophore growth toward white light in Figure 1A, with NRRL1555 background identified in Methods; not the madA mutants or backcrossed A56. Independent natural-isolate provenance: DOI:10.1128/EC.00203-13, Materials and Methods (https://pmc.ncbi.nlm.nih.gov/articles/PMC3910969/). Strain-level identity and exact name resolved at NCBI Taxonomy on 2026-10-04. No invariant wavelength or response direction is asserted. @@ -334,7 +335,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -363,12 +373,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 14:41 UTC diff --git a/pages/traits/physiology/pinocytosis.html b/pages/traits/physiology/pinocytosis.html index 812912bf6f4..9cb799cf3cb 100644 --- a/pages/traits/physiology/pinocytosis.html +++ b/pages/traits/physiology/pinocytosis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1083/jcb.53.3.681
    HRP activity was found exclusively within membrane profiles within the cytoplasm, confirming the pinocytotic mode of uptake.
    -

    PMID:5028259, PMC2108769. Scientific Abstract directly read in Europe PMC XML. The full-text OCR, including Introduction, Methods, Results and Discussion, was read at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC2108769/fullTextXML. Tracer uptake and author-reported intracellular HRP support vesicular fluid uptake in Neff cells. OCR is not a visual figure audit: the PDF/figures were unavailable. The authors qualify the vesicle sample as nonrandom and membrane turnover as estimated; no size distribution, numerical rate or exclusive transport route is generalized here.

    +

    PMID:5028259, PMC2108769. Scientific Abstract directly read in Europe PMC XML. The full-text OCR, including Introduction, Methods, Results and Discussion, was read at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC2108769/fullTextXML. Tracer uptake and author-reported intracellular HRP support vesicular fluid uptake in Neff cells. OCR is not a visual figure audit: the PDF/figures were unavailable. The authors qualify the vesicle sample as nonrandom and membrane turnover as estimated; no size distribution, numerical rate or exclusive transport route is generalized here.

  • DOI:10.1099/00221287-92-2-246
    The reduced pinocytotic activity of stationary-phase cells remains sensitive to respiratory inhibitors.
    -

    PMID:1255130. Scientific Abstract directly read at the publisher and in NCBI PubMed XML. This independent study reports reduced inulin uptake in stationary-phase Acanthamoeba trophozoites while bead phagocytosis essentially ceases. It supports a condition-dependent fluid-uptake phenotype, not organismal disjointness or a specific protein mechanism. Full text and figures were unavailable; no unread methods or strain accession is inferred.

    +

    PMID:1255130. Scientific Abstract directly read at the publisher and in NCBI PubMed XML. This independent study reports reduced inulin uptake in stationary-phase Acanthamoeba trophozoites while bead phagocytosis essentially ceases. It supports a condition-dependent fluid-uptake phenotype, not organismal disjointness or a specific protein mechanism. Full text and figures were unavailable; no unread methods or strain accession is inferred.

    • @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -211,7 +212,7 @@

    Canonical examples DOI:10.1083/jcb.53.3.681 - Laboratory-maintained Neff cells studied in the 1972 paper, with fluid tracers and author-reported intracellular HRP. NCBI EFetch verified this exact strain-rank name on 2026-10-06. ATCC Neff provenance at https://www.atcc.org/products/30010 gives soil from Pacific Grove, California. The paper supplies no collection accession; this does not establish vial or genome identity with ATCC 30010 or an unchanged original isolate. The legacy NCBI name is retained despite the transfer of Neff to A. terricola in DOI:10.1016/j.ejop.2024.126091; see the open taxonomy discussion. This is not a species-wide assertion. + Laboratory-maintained Neff cells studied in the 1972 paper, with fluid tracers and author-reported intracellular HRP. NCBI EFetch verified this exact strain-rank name on 2026-10-06. ATCC Neff provenance at https://www.atcc.org/products/30010 gives soil from Pacific Grove, California. The paper supplies no collection accession; this does not establish vial or genome identity with ATCC 30010 or an unchanged original isolate. The legacy NCBI name is retained despite the transfer of Neff to A. terricola in DOI:10.1016/j.ejop.2024.126091; see the open taxonomy discussion. This is not a species-wide assertion. @@ -355,7 +356,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed pinocytosis phenotype -

      Added traitmech:000635 with DOI:10.1083/jcb.53.3.681 and DOI:10.1099/00221287-92-2-246, exact scientific-abstract snippets, strain-qualified Neff NCBITaxon:1257118 and explicit source-access limits. Discussion-only DOI:10.1016/j.ejop.2024.126091 qualifies the conflicting Neff name. Reserved METPO:1058800 in v511; ignored-and-hidden searches, full pinned RDF search and seed reconciliation found no exact record. All three abstract spans were directly matched. The guarded dry run and 26 focused tests passed before application. Corpus, generated-artifact and CI validation follow separately; no causal graph was added.

    +

    Added traitmech:000635 with DOI:10.1083/jcb.53.3.681 and DOI:10.1099/00221287-92-2-246, exact scientific-abstract snippets, strain-qualified Neff NCBITaxon:1257118 and explicit source-access limits. Discussion-only DOI:10.1016/j.ejop.2024.126091 qualifies the conflicting Neff name. Reserved METPO:1058800 in v511; ignored-and-hidden searches, full pinned RDF search and seed reconciliation found no exact record. All three abstract spans were directly matched. The guarded dry run and 26 focused tests passed before application. Corpus, generated-artifact and CI validation follow separately; no causal graph was added.

    • Read this curation session
  • @@ -393,7 +394,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -422,12 +432,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 06:50 UTC diff --git a/pages/traits/physiology/positive_autotropism.html b/pages/traits/physiology/positive_autotropism.html index bcf9be9435d..0b39b77cb6c 100644 --- a/pages/traits/physiology/positive_autotropism.html +++ b/pages/traits/physiology/positive_autotropism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1093/jxb/19.1.125
    the positive germ-tube, i.e. one beginning more nearly towards its neighbour
    -

    Robinson, Park and Graham (1968), original publisher abstract directly retrieved from https://oup.silverchair-cdn.com/article-minimal/447341. The abstract reports positive autotropism in Botrytis cinerea on Cellophane over agar and neutrality on agar alone. The quoted orientation definition occurs in the mixed-orientation spore-pair timing comparison for Rhizopus stolonifer and Mucor plumbeus, both described as exhibiting marked negative autotropism. Earlier emergence of the positive germ-tube in those pairs does not establish a net positive response in either species. The abstract defines positive germ-tube orientation relative to the neighboring spore. This supports the terminology and emergence component, not later tip bending or completed fusion. Germination timing and cis-ness are separate readouts. The full paper, strain provenance and sample sizes were not retrieved. No universal chemical mechanism is inferred from the abstract's proposed explanations.

    +

    Robinson, Park and Graham (1968), original publisher abstract directly retrieved from https://oup.silverchair-cdn.com/article-minimal/447341. The abstract reports positive autotropism in Botrytis cinerea on Cellophane over agar and neutrality on agar alone. The quoted orientation definition occurs in the mixed-orientation spore-pair timing comparison for Rhizopus stolonifer and Mucor plumbeus, both described as exhibiting marked negative autotropism. Earlier emergence of the positive germ-tube in those pairs does not establish a net positive response in either species. The abstract defines positive germ-tube orientation relative to the neighboring spore. This supports the terminology and emergence component, not later tip bending or completed fusion. Germination timing and cis-ness are separate readouts. The full paper, strain provenance and sample sizes were not retrieved. No universal chemical mechanism is inferred from the abstract's proposed explanations.

  • DOI:10.1039/d3lc00859b
    The hyphae approach each other from opposing directions with occasional arrestation of growth and readjustment of the growth direction.
    -

    Richter et al. (2024), Results section on stop-and-go growth before anastomosis; directly retrieved Europe PMC full-text JATS, PMC10964749 (PMID:38416560). Culture and image-analysis methods, corresponding Discussion and actual Figure 5 were inspected. Figure 5a-c shows Rhizophagus irregularis MUCL 43194 approaching before fusion; the 21-hour trace is a representative pair, not a replication count. This is independent extension evidence interpreted within the directional definition, not an assertion that this paper uses the autotropism label. Supplementary methods and movies were not retrieved; attachment requests returned access-check HTML or HTTP errors.

    +

    Richter et al. (2024), Results section on stop-and-go growth before anastomosis; directly retrieved Europe PMC full-text JATS, PMC10964749 (PMID:38416560). Culture and image-analysis methods, corresponding Discussion and actual Figure 5 were inspected. Figure 5a-c shows Rhizophagus irregularis MUCL 43194 approaching before fusion; the 21-hour trace is a representative pair, not a replication count. This is independent extension evidence interpreted within the directional definition, not an assertion that this paper uses the autotropism label. Supplementary methods and movies were not retrieved; attachment requests returned access-check HTML or HTTP errors.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -277,13 +278,13 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed positive autotropism -

      Added traitmech:000604 under phenotype with DOI:10.1093/jxb/19.1.125 and DOI:10.1039/d3lc00859b and exact snippets checked against directly retrieved publisher abstract and Europe PMC full text. Inspected Figure 5; retained emergence versus extension, approach versus fusion, representative-pair and unread-supplement limitations. Ignored-and-hidden novelty searches and structured pinned-METPO review found no exact existing record. Added guarded writer and tests, v481 proposal reserving METPO:1055800, and explicit strain-provenance and mechanism TODOs; no canonical taxa or graph asserted.

    +

    Added traitmech:000604 under phenotype with DOI:10.1093/jxb/19.1.125 and DOI:10.1039/d3lc00859b and exact snippets checked against directly retrieved publisher abstract and Europe PMC full text. Inspected Figure 5; retained emergence versus extension, approach versus fusion, representative-pair and unread-supplement limitations. Ignored-and-hidden novelty searches and structured pinned-METPO review found no exact existing record. Added guarded writer and tests, v481 proposal reserving METPO:1055800, and explicit strain-provenance and mechanism TODOs; no canonical taxa or graph asserted.

    • Read this curation session
  • · codex
    • EDIT — Quote the germ-tube orientation readout directly -

      Corrects the evidence quotation added in history/records/positive_autotropism/2026-10-04T210708Z-codex-cda643.yaml. Replaced the 1968 label-only snippet with an exact 11-word contiguous orientation definition from the directly retrieved original publisher abstract at https://oup.silverchair-cdn.com/article-minimal/447341 (DOI:10.1093/jxb/19.1.125). Notes distinguish its mixed-orientation Rhizopus stolonifer and Mucor plumbeus pair-timing context from their net negative response and the separate substrate-dependent positive Botrytis cinerea result. Preserved the mint event and appended a new curation event through the validated writer after a SHA256 preimage guard. Regression assertions now require the directional quote and species/response qualification. The existing add-trait skill already requires specific, self-contained source claims, so no skill change is needed.

    +

    Corrects the evidence quotation added in history/records/positive_autotropism/2026-10-04T210708Z-codex-cda643.yaml. Replaced the 1968 label-only snippet with an exact 11-word contiguous orientation definition from the directly retrieved original publisher abstract at https://oup.silverchair-cdn.com/article-minimal/447341 (DOI:10.1093/jxb/19.1.125). Notes distinguish its mixed-orientation Rhizopus stolonifer and Mucor plumbeus pair-timing context from their net negative response and the separate substrate-dependent positive Botrytis cinerea result. Preserved the mint event and appended a new curation event through the validated writer after a SHA256 preimage guard. Regression assertions now require the directional quote and species/response qualification. The existing add-trait skill already requires specific, self-contained source claims, so no skill change is needed.

    • Read this curation session @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 21:36 UTC diff --git a/pages/traits/physiology/primary_homothallism.html b/pages/traits/physiology/primary_homothallism.html index c297c92a208..d61650483a7 100644 --- a/pages/traits/physiology/primary_homothallism.html +++ b/pages/traits/physiology/primary_homothallism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.1371/journal.pgen.1006110
    co-occurrence in the genome of a single individual of all the MAT alleles required to trigger sexual development
    -

    David-Palma et al. (2016), PMID:27327578, PMC4915694. Exact Introduction sec001 clause defining primary homothallism, not an abstract quote. Abstract sections, Introduction, all Results and Methods sec011/sec014/sec015 were read. Actual Figures 1, 3 and 4, Table 1 and supplementary Table S3 were inspected. Methods/tables/images identify CBS 6938; prose also says CBS 6838, a retained source inconsistency. Single receptor deletions retain sporulation; double deletion blocks it and rescue restores it. HD2 deletion retains vestigial sporulation; an obligatory HD1/HD2 heterodimer is not established. Figure 3's caption swaps C/D: the actual C is the count plot. Table S3's Figure 2 E/G pointers correspond to actual Figure 1 E/F. SPO11-mutant basidia counts are not significantly reduced; spore viability is. Other figures, supplements and unread Methods/Discussion remain uninspected. Functional genetics supports the model, not MAT sequence presence alone.

    +

    David-Palma et al. (2016), PMID:27327578, PMC4915694. Exact Introduction sec001 clause defining primary homothallism, not an abstract quote. Abstract sections, Introduction, all Results and Methods sec011/sec014/sec015 were read. Actual Figures 1, 3 and 4, Table 1 and supplementary Table S3 were inspected. Methods/tables/images identify CBS 6938; prose also says CBS 6838, a retained source inconsistency. Single receptor deletions retain sporulation; double deletion blocks it and rescue restores it. HD2 deletion retains vestigial sporulation; an obligatory HD1/HD2 heterodimer is not established. Figure 3's caption swaps C/D: the actual C is the count plot. Table S3's Figure 2 E/G pointers correspond to actual Figure 1 E/F. SPO11-mutant basidia counts are not significantly reduced; spore viability is. Other figures, supplements and unread Methods/Discussion remain uninspected. Functional genetics supports the model, not MAT sequence presence alone.

  • DOI:10.5598/imafungus.2015.06.01.13
    combined expression of MAT1-1 and MAT1-2 genes in a single genome
    -

    2015 terminology review, PMID:26203424, PMC4500084. Exact contiguous phrase from section s2a Primary homothallism, read end-to-end in full-text XML. This is terminology authority, not experimental replication. Its MAT1-1/MAT1-2 formulation describes the ascomycete framework; do not impose that nomenclature on basidiomycetes. The section permits linked or unlinked loci and distinguishes other routes to self-fertility. Its Aspergillus example does not require eight uninucleate spores in every primary-homothallic fungus. Actual Figure 1 remains uninspected.

    +

    2015 terminology review, PMID:26203424, PMC4500084. Exact contiguous phrase from section s2a Primary homothallism, read end-to-end in full-text XML. This is terminology authority, not experimental replication. Its MAT1-1/MAT1-2 formulation describes the ascomycete framework; do not impose that nomenclature on basidiomycetes. The section permits linked or unlinked loci and distinguishes other routes to self-fertility. Its Aspergillus example does not require eight uninucleate spores in every primary-homothallic fungus. Actual Figure 1 remains uninspected.

  • DOI:10.1016/j.cub.2007.07.012
    self-fertilization does not bypass requirements for outcrossing sex but instead requires activation of these pathways within a single individual.
    -

    Paoletti et al. (2007), PMID:17669651. Exact contiguous clause from the directly retrieved Europe PMC scientific abstract. In Aspergillus nidulans, alpha- and HMG-domain MAT gene expression is required for normal sexual development and ascospore production; balanced overexpression and an mpkB mutant test distinct perturbations. This does not establish universal dependence on every MAT gene in other fungi. Full text, methods, figures, supplements and original strain provenance remain uninspected; no canonical example is inferred.

    +

    Paoletti et al. (2007), PMID:17669651. Exact contiguous clause from the directly retrieved Europe PMC scientific abstract. In Aspergillus nidulans, alpha- and HMG-domain MAT gene expression is required for normal sexual development and ascospore production; balanced overexpression and an mpkB mutant test distinct perturbations. This does not establish universal dependence on every MAT gene in other fungi. Full text, methods, figures, supplements and original strain provenance remain uninspected; no canonical example is inferred.

  • DOI:10.1128/EC.00019-10
    produced the same number of perithecia as the WT, containing mature, viable ascospores at day 7 of development.
    -

    Klix et al. (2010), PMID:20435701, PMC2901639. Exact first Results subsection clause, whose subjects are the SmtA-1 and SmtA-3 deletion strains. Author-institution published PDF at https://www.uni-goettingen.de/de/document/download/a343d8aa3ca6ea7528fe002c2281f0fb.pdf/60.pdf was read after Europe PMC full-text failure; NCBI efetch returned front matter only. Abstract, Introduction, first two Results subsections, strain/culture and microscopy Methods were read; actual Figures 1/2 were inspected. On SWG at 24 C, SmtA-2 deletion instead arrests development at protoperithecia; rescue restores fertility. Thus all MAT genes are not individually essential. The abstract calls SmtA-3 an alpha-domain protein, whereas Introduction/Figure 1 report no known functional domain; do not infer an HMG domain from its MAT1-1-3 relationship. Other experiments, Discussion, supplements and natural provenance of S48977 remain unverified.

    +

    Klix et al. (2010), PMID:20435701, PMC2901639. Exact first Results subsection clause, whose subjects are the SmtA-1 and SmtA-3 deletion strains. Author-institution published PDF at https://www.uni-goettingen.de/de/document/download/a343d8aa3ca6ea7528fe002c2281f0fb.pdf/60.pdf was read after Europe PMC full-text failure; NCBI efetch returned front matter only. Abstract, Introduction, first two Results subsections, strain/culture and microscopy Methods were read; actual Figures 1/2 were inspected. On SWG at 24 C, SmtA-2 deletion instead arrests development at protoperithecia; rescue restores fertility. Thus all MAT genes are not individually essential. The abstract calls SmtA-3 an alpha-domain protein, whereas Introduction/Figure 1 report no known functional domain; do not infer an HMG domain from its MAT1-1-3 relationship. Other experiments, Discussion, supplements and natural provenance of S48977 remain unverified.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Canonical examples DOI:10.1371/journal.pgen.1006110 - Qualified example: wild-type CBS 6938, not engineered derivatives. Natural provenance is reported in Table 1 at https://pmc.ncbi.nlm.nih.gov/articles/PMC5103461/: UCD 77-61, sap of Betula stumps in Finland; this is provenance, not independent trait replication. The reproductive study's Methods, Table 1 and figure images support 6938 despite 6838 in parts of the prose. Figure 1D shows basidia and basidiospores; sec014 assays DWR (2.5% agar, 0.5% ribitol) at 18 C for 10 days. Figure 4B reports 32 of 41 wild-type basidiospores germinated. Keep basidia counts and spore viability distinct. NCBI 264483 resolves to this species on 2026-10-04; do not generalize the assay to every strain. + Qualified example: wild-type CBS 6938, not engineered derivatives. Natural provenance is reported in Table 1 at https://pmc.ncbi.nlm.nih.gov/articles/PMC5103461/: UCD 77-61, sap of Betula stumps in Finland; this is provenance, not independent trait replication. The reproductive study's Methods, Table 1 and figure images support 6938 despite 6838 in parts of the prose. Figure 1D shows basidia and basidiospores; sec014 assays DWR (2.5% agar, 0.5% ribitol) at 18 C for 10 days. Figure 4B reports 32 of 41 wild-type basidiospores germinated. Keep basidia counts and spore viability distinct. NCBI 264483 resolves to this species on 2026-10-04; do not generalize the assay to every strain. @@ -340,7 +341,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -369,12 +379,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 05:53 UTC diff --git a/pages/traits/physiology/prolyl_aminopeptidase_activity.html b/pages/traits/physiology/prolyl_aminopeptidase_activity.html index cd81cd5ac63..d301915c595 100644 --- a/pages/traits/physiology/prolyl_aminopeptidase_activity.html +++ b/pages/traits/physiology/prolyl_aminopeptidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -88,7 +89,7 @@

    Trait evidence (4)

    Prolyl aminopeptidase (Pip) hydrolytic release of N-terminal L-proline

    Evidence-backed physiological mechanism sketch linking prolyl aminopeptidase catalytic activity and N-terminal L-proline release from peptides to the prolyl aminopeptidase activity phenotype.

    -

    MECHANISTIC · Mechanistic graph backed by EC 3.4.11.5 and DOI:10.1111/j.1365-2958.1993.tb01249.x; exemplified on prolyl_aminopeptidase_pip with Neisseria gonorrhoeae (NCBITaxon:485) proline iminopeptidase Pip (UniProtKB:P42786).

    +

    MECHANISTIC · Mechanistic graph backed by EC 3.4.11.5 and DOI:10.1111/j.1365-2958.1993.tb01249.x; exemplified on prolyl_aminopeptidase_pip with Neisseria gonorrhoeae (NCBITaxon:485) proline iminopeptidase Pip (UniProtKB:P42786).

    Loading graph…

    @@ -111,7 +112,7 @@

    Edge evidence

    GO:0004177 confers prolyl aminopeptidase activity - traitmech:000166 + traitmech:000166 METPO:2007700

    Elaboration of proline iminopeptidase (Pip) hydrolase activity selectively removing N-terminal proline residues from peptides confers the prolyl aminopeptidase activity phenotype.

      @@ -186,8 +187,8 @@

      Protein and taxon examples

    		 - Neisseria gonorrhoeae -
    NCBITaxon:485 + Neisseria gonorrhoeae +
    NCBITaxon:485         		REVIEWED
    @@ -253,13 +254,13 @@

    Parent traits (1)

    Synonyms (4)

    @@ -275,7 +276,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -425,7 +426,7 @@

    Discussions and Knowledge Gaps (3)

    -

    The current record carries an IUBMB EC 3.4.11.5 reaction snippet, one sentence noting that Pip is a hydrolase elaborated by Neisseria gonorrhoeae (DOI:10.1111/j.1365-2958.1993.tb01249.x), and a diagnostic enzyme list (DOI:10.1099/ijsem.0.006017), without a second non-redundant mechanistic step or UniProtKB protein_examples.

    +

    The current record carries an IUBMB EC 3.4.11.5 reaction snippet, one sentence noting that Pip is a hydrolase elaborated by Neisseria gonorrhoeae (DOI:10.1111/j.1365-2958.1993.tb01249.x), and a diagnostic enzyme list (DOI:10.1099/ijsem.0.006017), without a second non-redundant mechanistic step or UniProtKB protein_examples.

    @@ -468,7 +469,7 @@

    Evidence

    -

    The record's primary literature (EC 3.4.11.5, DOI:10.1111/j.1365-2958.1993.tb01249.x) establishes N-terminal proline release from peptides by proline iminopeptidase (Pip) in Neisseria gonorrhoeae (NCBITaxon:485), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    +

    The record's primary literature (EC 3.4.11.5, DOI:10.1111/j.1365-2958.1993.tb01249.x) establishes N-terminal proline release from peptides by proline iminopeptidase (Pip) in Neisseria gonorrhoeae (NCBITaxon:485), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    @@ -487,7 +488,7 @@

    Evidence

    -

    Resolution: Promoted prolyl_aminopeptidase_pip_sketch to MECHANISTIC by adding InterPro:IPR005944-grounded GENE_OR_PROTEIN node prolyl_aminopeptidase_pip with reviewed Neisseria gonorrhoeae (NCBITaxon:485) protein_examples UniProtKB:P42786 (Pip) backed by DOI:10.1111/j.1365-2958.1993.tb01249.x (replacing prompt candidate P40051, which is Saccharomyces cerevisiae ICP55).

    +

    Resolution: Promoted prolyl_aminopeptidase_pip_sketch to MECHANISTIC by adding InterPro:IPR005944-grounded GENE_OR_PROTEIN node prolyl_aminopeptidase_pip with reviewed Neisseria gonorrhoeae (NCBITaxon:485) protein_examples UniProtKB:P42786 (Pip) backed by DOI:10.1111/j.1365-2958.1993.tb01249.x (replacing prompt candidate P40051, which is Saccharomyces cerevisiae ICP55).

    @@ -522,7 +523,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Promoted prolyl_aminopeptidase_pip_sketch to MECHANISTIC; added InterPro:IPR005944-grounded GENE_OR_PROTEIN node prolyl_aminopeptidase_pip with reviewed Neisseria gonorrhoeae (NCBITaxon:485) protein_examples UniProtKB:P42786 (Pip) backed by DOI:10.1111/j.1365-2958.1993.tb01249.x; resolved prolyl-aminopeptidase-activity-protein-example-gap.

    +

    Promoted prolyl_aminopeptidase_pip_sketch to MECHANISTIC; added InterPro:IPR005944-grounded GENE_OR_PROTEIN node prolyl_aminopeptidase_pip with reviewed Neisseria gonorrhoeae (NCBITaxon:485) protein_examples UniProtKB:P42786 (Pip) backed by DOI:10.1111/j.1365-2958.1993.tb01249.x; resolved prolyl-aminopeptidase-activity-protein-example-gap.

    • @@ -564,7 +565,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -928,12 +938,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-25 08:45 UTC diff --git a/pages/traits/physiology/proteaphagy.html b/pages/traits/physiology/proteaphagy.html index 2bb0197ce06..f5e817c11a7 100644 --- a/pages/traits/physiology/proteaphagy.html +++ b/pages/traits/physiology/proteaphagy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1074/jbc.M115.699124
    Here we show that in yeast, upon nitrogen starvation, proteasomes are targeted for vacuolar degradation through autophagy.
    -

    PMID:26670610, PMC4751371. Scientific abstract directly read in DOI-matched Europe PMC metadata and XML. Yeast-strain and immunoblot Methods, autophagy-dependence and core/regulatory-particle Results, Table 1 and relevant captions were read. Saccharomyces cerevisiae reporter processing and vacuolar localization support degradation; native gels address incorporation into complexes. The core and regulatory particles can be targeted separately, with different Ubp3 dependence; intact 26S uptake is not required by the definition. Figure 6D's caption conflicts with its title and body concerning Rpn10, so no Rpn10 requirement is curated. Actual figures, supplements and independent natural-strain provenance were not inspected.

    +

    PMID:26670610, PMC4751371. Scientific abstract directly read in DOI-matched Europe PMC metadata and XML. Yeast-strain and immunoblot Methods, autophagy-dependence and core/regulatory-particle Results, Table 1 and relevant captions were read. Saccharomyces cerevisiae reporter processing and vacuolar localization support degradation; native gels address incorporation into complexes. The core and regulatory particles can be targeted separately, with different Ubp3 dependence; intact 26S uptake is not required by the definition. Figure 6D's caption conflicts with its title and body concerning Rpn10, so no Rpn10 requirement is curated. Actual figures, supplements and independent natural-strain provenance were not inspected.

  • DOI:10.1016/j.celrep.2016.07.015
    Here, we define two proteaphagy routes in yeast that respond to either nitrogen starvation or particle inactivation.
    -

    PMID:27477278. Scientific abstract directly read in Europe PMC with matching DOI. The yeast study distinguishes starvation from quality-control turnover of inactive proteasomes; Cue5 and Hsp42 support the latter route, not a universal microbial gene inventory. Correction DOI:10.1016/j.celrep.2022.110552 (PMID:35294886) is linked by the source metadata. Its text was directly read at https://profiles.wustl.edu/en/publications/erratum-autophagic-turnover-of-inactive-26s-proteasomes-in-yeast-/: a duplicated anti-histone H3 control blot in Figure S3 was replaced; the authors state their conclusions are unchanged. The corrected figure, original full Methods, actual figures and strain provenance were not inspected. The correction is not independent trait evidence.

    +

    PMID:27477278. Scientific abstract directly read in Europe PMC with matching DOI. The yeast study distinguishes starvation from quality-control turnover of inactive proteasomes; Cue5 and Hsp42 support the latter route, not a universal microbial gene inventory. Correction DOI:10.1016/j.celrep.2022.110552 (PMID:35294886) is linked by the source metadata. Its text was directly read at https://profiles.wustl.edu/en/publications/erratum-autophagic-turnover-of-inactive-26s-proteasomes-in-yeast-/: a duplicated anti-histone H3 control blot in Figure S3 was replaced; the authors state their conclusions are unchanged. The corrected figure, original full Methods, actual figures and strain provenance were not inspected. The correction is not independent trait evidence.

  • DOI:10.1016/j.jbc.2021.101494
    Indeed, we found that several conditions that activated general autophagy did not induce proteaphagy, further distinguishing proteaphagy from general autophagy.
    -

    PMID:34919962, PMC8732087. Scientific abstract directly read in DOI-matched Europe PMC metadata and XML; Results sec1.1-sec1.3, Discussion sec2 and Methods sec3.1-sec3.4 were read. Proteasome GFP processing, native gels and vacuolar microscopy distinguish cargo turnover from general autophagy. In sec1.3, ATG11 deletion abolishes residual nitrogen-starvation turnover in an ATG17 deletion background, not all proteaphagy in every condition. Rapamycin yields no detected difference in the ATG11 single deletion, with a stated detection-limit caveat. Thus the later result does not establish a blanket contradiction of the 2016 single-deletion result. Methods identify W303-derived SUB61/SUB62 reporter and deletion strains. Captions were read; actual figures, supplements and independent strain provenance were not inspected.

    +

    PMID:34919962, PMC8732087. Scientific abstract directly read in DOI-matched Europe PMC metadata and XML; Results sec1.1-sec1.3, Discussion sec2 and Methods sec3.1-sec3.4 were read. Proteasome GFP processing, native gels and vacuolar microscopy distinguish cargo turnover from general autophagy. In sec1.3, ATG11 deletion abolishes residual nitrogen-starvation turnover in an ATG17 deletion background, not all proteaphagy in every condition. Rapamycin yields no detected difference in the ATG11 single deletion, with a stated detection-limit caveat. Thus the later result does not establish a blanket contradiction of the 2016 single-deletion result. Methods identify W303-derived SUB61/SUB62 reporter and deletion strains. Captions were read; actual figures, supplements and independent strain provenance were not inspected.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -215,7 +216,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Proteasomes are the autophagic cargo, not the machinery degrading unrelated substrates. Ordinary proteasome-mediated proteolysis, proteasome biogenesis, storage granules, free-subunit loss or gene presence alone does not establish this phenotype. The 2016 starvation study includes separately targeted core and regulatory particles, so do not require intact holoenzyme uptake. GO:0061816, directly resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0061816, is a nonobsolete biological process restricted to selective macroautophagy, not an exact organismal phenotype. The cargo-defined local term does not impose a universal route, trigger or selectivity mechanism; retain this scope difference for human review and omit exact xrefs and synonyms. Ribophagy traitmech:000641 and nuclear-cargo degradation traitmech:000643 are distinct: shared machinery or prior nuclear localization does not equate these cargo phenotypes.

    +

    Proteasomes are the autophagic cargo, not the machinery degrading unrelated substrates. Ordinary proteasome-mediated proteolysis, proteasome biogenesis, storage granules, free-subunit loss or gene presence alone does not establish this phenotype. The 2016 starvation study includes separately targeted core and regulatory particles, so do not require intact holoenzyme uptake. GO:0061816, directly resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0061816, is a nonobsolete biological process restricted to selective macroautophagy, not an exact organismal phenotype. The cargo-defined local term does not impose a universal route, trigger or selectivity mechanism; retain this scope difference for human review and omit exact xrefs and synonyms. Ribophagy traitmech:000641 and nuclear-cargo degradation traitmech:000643 are distinct: shared machinery or prior nuclear localization does not equate these cargo phenotypes.

    @@ -245,7 +246,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Keep starvation and inactive-particle quality-control routes distinct. The later ATG11 result concerns residual turnover in an ATG17 deletion background; neither an abstract's general wording nor a single deletion establishes universal necessity. Do not turn reduced efficiency, a detection limit or partial turnover into complete absence. Resolve the 2016 Figure 6D Rpn10 caption/body discrepancy and inspect the corrected Figure S3 associated with DOI:10.1016/j.celrep.2022.110552 before relying on those panels. Canonical examples remain unset pending independent natural-strain provenance. The microbial cell performing degradation carries the phenotype, not a bacterium eliciting an animal host response. Native taxon-paired protein accessions and functional evidence are required before a causal graph is added; ATG presence, puncta or loss of total proteasome abundance alone is not proof of autophagic flux.

    +

    Keep starvation and inactive-particle quality-control routes distinct. The later ATG11 result concerns residual turnover in an ATG17 deletion background; neither an abstract's general wording nor a single deletion establishes universal necessity. Do not turn reduced efficiency, a detection limit or partial turnover into complete absence. Resolve the 2016 Figure 6D Rpn10 caption/body discrepancy and inspect the corrected Figure S3 associated with DOI:10.1016/j.celrep.2022.110552 before relying on those panels. Canonical examples remain unset pending independent natural-strain provenance. The microbial cell performing degradation carries the phenotype, not a bacterium eliciting an animal host response. Native taxon-paired protein accessions and functional evidence are required before a causal graph is added; ATG presence, puncta or loss of total proteasome abundance alone is not proof of autophagic flux.

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 15:33 UTC diff --git a/pages/traits/physiology/pseudobipolar_mating_system.html b/pages/traits/physiology/pseudobipolar_mating_system.html index 452239e937a..9a799d597c1 100644 --- a/pages/traits/physiology/pseudobipolar_mating_system.html +++ b/pages/traits/physiology/pseudobipolar_mating_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1371/journal.pgen.1001052
    occasional disruptions of the genetic cohesion of the bipolar MAT locus originate new mating types.
    -

    Coelho et al. (2010), PMID:20700437, PMC2916851. Exact clause in scientific abstract abstract1, checked against raw Europe PMC metadata and full-text XML, not the author summary. Results/Discussion and Methods were read, with actual Figures 3-5, Figure S5 and both pages of Table S1 inspected. Sporidiobolus salmonicolor CBS 6832 x ML 2241 yielded the recombinant T7.1, incompatible with either parent but compatible with CBS 490 in Figure 4. The scored endpoint is clamp-bearing mycelium and teliospores after four days on corn meal agar at 25 C; normal germination after compatible T7 crosses is reported in prose as results not shown. Eight teliospores came from one parental cross; colonies from a teliospore are mostly mitotic clones, and T8 was apparently diploid. The authors require larger samples for statistically significant linkage and precise recombination frequencies. Figure 5 partly assumes S. roseus synteny, not a complete S. salmonicolor chromosome assembly. Table S1 and Figures 3/4 label CBS 6832 A2-15, whereas the germination and micromanipulation Methods say A2-6; strain identity is kept without silently reconciling that discrepancy. Table S1 gives CBS 6832 a clinical origin but only names ML 2241's isolator, so full parental provenance and active taxonomy remain unresolved. Other actual figures and supplements remain uninspected. This is native crossing evidence, not solely MAT sequence annotation or a precise population rate.

    +

    Coelho et al. (2010), PMID:20700437, PMC2916851. Exact clause in scientific abstract abstract1, checked against raw Europe PMC metadata and full-text XML, not the author summary. Results/Discussion and Methods were read, with actual Figures 3-5, Figure S5 and both pages of Table S1 inspected. Sporidiobolus salmonicolor CBS 6832 x ML 2241 yielded the recombinant T7.1, incompatible with either parent but compatible with CBS 490 in Figure 4. The scored endpoint is clamp-bearing mycelium and teliospores after four days on corn meal agar at 25 C; normal germination after compatible T7 crosses is reported in prose as results not shown. Eight teliospores came from one parental cross; colonies from a teliospore are mostly mitotic clones, and T8 was apparently diploid. The authors require larger samples for statistically significant linkage and precise recombination frequencies. Figure 5 partly assumes S. roseus synteny, not a complete S. salmonicolor chromosome assembly. Table S1 and Figures 3/4 label CBS 6832 A2-15, whereas the germination and micromanipulation Methods say A2-6; strain identity is kept without silently reconciling that discrepancy. Table S1 gives CBS 6832 a clinical origin but only names ML 2241's isolator, so full parental provenance and active taxonomy remain unresolved. Other actual figures and supplements remain uninspected. This is native crossing evidence, not solely MAT sequence annotation or a precise population rate.

  • DOI:10.1371/journal.pbio.3003417
    In the pseudobipolar configuration, the P/R and HD loci remained on the same chromosome but genetically unlinked
    -

    Coelho et al. (2025), PMID:41042803, PMC12510652. Exact scientific-abstract clause checked against raw Europe PMC metadata, full-text XML and publisher HTML. Supports the broader same-chromosome, recombination-permitting usage, not an independent functional replication in Kwoniella europaea. Abstract, Introduction, first two Results subsections, the relevant Discussion paragraph in sec017 and actual Figure 1 were read. Figure 1B classifies its breeding system as likely heterothallic; Figure 1E shows separated loci in PYCC6329. Despite the abstract's declarative wording, sec017 says crosses have not yielded sexual reproduction and treats persistent recombination as conditional. Physical distance alone does not exclude long-range recombination suppression. Its inferred configuration therefore does not establish observed mating or fertility. The C. decagattii and K. mangrovensis sexual results cannot be transferred to K. europaea. Other Results, Methods, figures and supplements remain uninspected.

    +

    Coelho et al. (2025), PMID:41042803, PMC12510652. Exact scientific-abstract clause checked against raw Europe PMC metadata, full-text XML and publisher HTML. Supports the broader same-chromosome, recombination-permitting usage, not an independent functional replication in Kwoniella europaea. Abstract, Introduction, first two Results subsections, the relevant Discussion paragraph in sec017 and actual Figure 1 were read. Figure 1B classifies its breeding system as likely heterothallic; Figure 1E shows separated loci in PYCC6329. Despite the abstract's declarative wording, sec017 says crosses have not yielded sexual reproduction and treats persistent recombination as conditional. Physical distance alone does not exclude long-range recombination suppression. Its inferred configuration therefore does not establish observed mating or fertility. The C. decagattii and K. mangrovensis sexual results cannot be transferred to K. europaea. Other Results, Methods, figures and supplements remain uninspected.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -271,7 +272,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed pseudobipolar mating system -

      Added traitmech:000617 with DOI:10.1371/journal.pgen.1001052 and DOI:10.1371/journal.pbio.3003417, exact scientific-abstract snippets, qualified native-cross evidence, and explicit limits on genomic prediction, recombination statistics, strain provenance and allele labels. Used the guarded validated writer and curation-event helper, with no canonical taxon or protein graph asserted. Added proposal v494 reserving METPO:1057100 under released phenotype; ignored-and-hidden novelty searches and current seed/release checks found no exact duplicate. Generated artifacts and full validation follow this creation event.

    +

    Added traitmech:000617 with DOI:10.1371/journal.pgen.1001052 and DOI:10.1371/journal.pbio.3003417, exact scientific-abstract snippets, qualified native-cross evidence, and explicit limits on genomic prediction, recombination statistics, strain provenance and allele labels. Used the guarded validated writer and curation-event helper, with no canonical taxon or protein graph asserted. Added proposal v494 reserving METPO:1057100 under released phenotype; ignored-and-hidden novelty searches and current seed/release checks found no exact duplicate. Generated artifacts and full validation follow this creation event.

    • Read this curation session @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 09:49 UTC diff --git a/pages/traits/physiology/pseudohomothallism.html b/pages/traits/physiology/pseudohomothallism.html index a857af3664f..ec8eefc4a9b 100644 --- a/pages/traits/physiology/pseudohomothallism.html +++ b/pages/traits/physiology/pseudohomothallism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.5598/imafungus.2015.06.01.13
    self-fertility is the result of the packaging of two independent and opposite mating type nuclei within a single spore
    -

    2015 terminology review, PMID:26203424, PMC4500084. Exact contiguous clause from section s2b Pseudohomothallism, read end-to-end in directly retrieved full-text XML. This supplies definition and homothallism-parent authority, not experimental replication or an abstract quote. The review describes single-spore self-fertility arising from compatible partners packaged as separate nuclei. Its two-nucleus description is not a fixed count for every subsequent spore or mycelial stage; the comparative primary study below documents developmental variation. Occasional self-sterile propagules allow outcrossing. Figure 1 remains uninspected.

    +

    2015 terminology review, PMID:26203424, PMC4500084. Exact contiguous clause from section s2b Pseudohomothallism, read end-to-end in directly retrieved full-text XML. This supplies definition and homothallism-parent authority, not experimental replication or an abstract quote. The review describes single-spore self-fertility arising from compatible partners packaged as separate nuclei. Its two-nucleus description is not a fixed count for every subsequent spore or mycelial stage; the comparative primary study below documents developmental variation. Occasional self-sterile propagules allow outcrossing. Figure 1 remains uninspected.

  • DOI:10.1093/genetics/143.2.789
    Ascospores of Neurospora tetrasperma normally contain nuclei of both mating-type idiomorphs (a and A), resulting in self-fertile heterokaryons
    -

    Merino et al. (1996), PMID:8725227. Exact opening clause of the scientific abstract directly retrieved from Europe PMC core metadata. The following parenthesis names this sexual system pseudohomothallism. The study compares mating-type chromosome and autosomal sequences from wild-collected self-fertile strains, while distinguishing occasional homokaryotic self-sterile strains capable of outcrossing. Recombination suppression is an evolutionary association in this system, not the definition of every pseudohomothallic fungus. Full text, figures, supplements and strain-level provenance in this paper remain uninspected.

    +

    Merino et al. (1996), PMID:8725227. Exact opening clause of the scientific abstract directly retrieved from Europe PMC core metadata. The following parenthesis names this sexual system pseudohomothallism. The study compares mating-type chromosome and autosomal sequences from wild-collected self-fertile strains, while distinguishing occasional homokaryotic self-sterile strains capable of outcrossing. Recombination suppression is an evolutionary association in this system, not the definition of every pseudohomothallic fungus. Full text, figures, supplements and strain-level provenance in this paper remain uninspected.

  • DOI:10.1002/dvg.1020150111
    Two basically different modes underlie the delivery of opposite mating type nuclei into each of the four ascospores in the different genera.
    -

    Raju and Perkins (1994), PMID:8187347. Exact sentence of the directly retrieved Europe PMC scientific abstract, which is explicitly truncated at 400 words. Comparative cytology covers N. tetrasperma, G. tetrasperma, P. anserina and P. tetraspora. First-division segregation in Neurospora differs from the second-division program in Podospora and Gelasinospora. The mat-centromere crossover is established for P. anserina but inferred for the other two latter species. Following postmeiotic development, germinating P. anserina ascospores retain three functional nuclei, two of one mating type and one of the other. Do not require exactly two nuclei, four spores, a fixed nuclear ratio, suppressed crossing over or one spindle geometry for the whole trait. Full text, original methods, actual figures and strain provenance remain unread.

    +

    Raju and Perkins (1994), PMID:8187347. Exact sentence of the directly retrieved Europe PMC scientific abstract, which is explicitly truncated at 400 words. Comparative cytology covers N. tetrasperma, G. tetrasperma, P. anserina and P. tetraspora. First-division segregation in Neurospora differs from the second-division program in Podospora and Gelasinospora. The mat-centromere crossover is established for P. anserina but inferred for the other two latter species. Following postmeiotic development, germinating P. anserina ascospores retain three functional nuclei, two of one mating type and one of the other. Do not require exactly two nuclei, four spores, a fixed nuclear ratio, suppressed crossing over or one spindle geometry for the whole trait. Full text, original methods, actual figures and strain provenance remain unread.

  • DOI:10.1371/journal.pgen.1000030
    recombination was assessed in individual sexual progeny originating from a selfed cross of the heterokaryotic mycelia.
    -

    Menkis et al. (2008), PMID:18369449, PMC2268244. Exact contiguous clause of Methods s4d, not an abstract quote. Scientific abstract, Introduction, Results s2b/s2c, Methods s4a/s4c/s4d/s4e and Table 1 including footnotes were read in the full-text XML. Results s2b and Methods s4d assay 152 heterokaryotic sexual progeny of a selfed P581 cross; that selected assay denominator is not the frequency of all heterokaryotic offspring. Table 1 identifies P581 as a wild-type heterokaryon from Lihue, Hawaii, and its P-prefix footnote identifies the Perkins collection from nature. FGSC 2508/2509 are homokaryotic components, not alternative identifiers for the natural heterokaryon. The separate 83-progeny N. crassa introgression experiment is not the native P581 selfing assay. Figures, supplements, Discussion and unread experimental sections remain uninspected; inferred evolutionary history is not a demonstrated universal developmental mechanism.

    +

    Menkis et al. (2008), PMID:18369449, PMC2268244. Exact contiguous clause of Methods s4d, not an abstract quote. Scientific abstract, Introduction, Results s2b/s2c, Methods s4a/s4c/s4d/s4e and Table 1 including footnotes were read in the full-text XML. Results s2b and Methods s4d assay 152 heterokaryotic sexual progeny of a selfed P581 cross; that selected assay denominator is not the frequency of all heterokaryotic offspring. Table 1 identifies P581 as a wild-type heterokaryon from Lihue, Hawaii, and its P-prefix footnote identifies the Perkins collection from nature. FGSC 2508/2509 are homokaryotic components, not alternative identifiers for the natural heterokaryon. The separate 83-progeny N. crassa introgression experiment is not the native P581 selfing assay. Figures, supplements, Discussion and unread experimental sections remain uninspected; inferred evolutionary history is not a demonstrated universal developmental mechanism.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -214,7 +215,7 @@

    Canonical examples DOI:10.1371/journal.pgen.1000030 - Qualified natural example: heterokaryon P581 from Lihue, Hawaii. Provenance is Table 1 and its Perkins-collection footnote at https://pmc.ncbi.nlm.nih.gov/articles/PMC2268244/. Results s2b and Methods s4d analyze 152 heterokaryotic sexual progeny from selfed P581; this is a selected assay set, not a claim that every spore is heterokaryotic or self-fertile. Methods s4a specifies synthetic cross medium at 25 C for crosses. FGSC 2508 and 2509 are its isolated homokaryotic components and are not the example. Do not extend this observation to every strain or life stage. NCBI taxonomy 40127 resolves to the active species name on 2026-10-04. + Qualified natural example: heterokaryon P581 from Lihue, Hawaii. Provenance is Table 1 and its Perkins-collection footnote at https://pmc.ncbi.nlm.nih.gov/articles/PMC2268244/. Results s2b and Methods s4d analyze 152 heterokaryotic sexual progeny from selfed P581; this is a selected assay set, not a claim that every spore is heterokaryotic or self-fertile. Methods s4a specifies synthetic cross medium at 25 C for crosses. FGSC 2508 and 2509 are its isolated homokaryotic components and are not the example. Do not extend this observation to every strain or life stage. NCBI taxonomy 40127 resolves to the active species name on 2026-10-04. @@ -340,7 +341,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -369,12 +379,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 03:56 UTC diff --git a/pages/traits/physiology/pyrazinamidase_activity.html b/pages/traits/physiology/pyrazinamidase_activity.html index a333227b634..51dda08e112 100644 --- a/pages/traits/physiology/pyrazinamidase_activity.html +++ b/pages/traits/physiology/pyrazinamidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -82,7 +83,7 @@

    Trait evidence (3)

    Nicotinamidase/pyrazinamidase (PncA) hydrolysis of nicotinamide and pyrazinamide

    Evidence-backed physiological mechanism sketch linking nicotinamidase/pyrazinamidase catalytic activity, nicotinamide hydrolysis to nicotinate, and pyrazinamide conversion to pyrazinoic acid to the pyrazinamidase activity phenotype.

    -

    MECHANISTIC · Mechanistic graph backed by DOI:10.1111/j.1742-4658.2007.06241.x and DOI:10.1371/journal.pone.0015785; exemplified on pyrazinamidase_pnca with Mycobacterium tuberculosis H37Rv (NCBITaxon:83332; UP000001584) nicotinamidase/pyrazinamidase PncA (UniProtKB:I6XD65).

    +

    MECHANISTIC · Mechanistic graph backed by DOI:10.1111/j.1742-4658.2007.06241.x and DOI:10.1371/journal.pone.0015785; exemplified on pyrazinamidase_pnca with Mycobacterium tuberculosis H37Rv (NCBITaxon:83332; UP000001584) nicotinamidase/pyrazinamidase PncA (UniProtKB:I6XD65).

    Loading graph…

    @@ -105,7 +106,7 @@

    Edge evidence

    GO:0008936 confers pyrazinamidase activity - traitmech:000163 + traitmech:000163 METPO:2007700

    Nicotinamidase/pyrazinamidase (PncA) catalytic activity converts pyrazinamide into pyrazinoic acid and confers the pyrazinamidase activity phenotype.

      @@ -180,8 +181,8 @@

      Protein and taxon examples

    		 - Mycobacterium tuberculosis H37Rv -
    NCBITaxon:83332 + Mycobacterium tuberculosis H37Rv +
    NCBITaxon:83332         		REVIEWED
    @@ -247,13 +248,13 @@

    Parent traits (1)

    Synonyms (4)

    @@ -269,7 +270,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -434,7 +435,7 @@

    Discussions and Knowledge Gaps (3)

    -

    The current record carries an IUBMB EC 3.5.1.19 reaction snippet and two Mycobacterium tuberculosis PncA nicotinamidase/pyrazinamidase snippets (DOI:10.1111/j.1742-4658.2007.06241.x, DOI:10.1371/journal.pone.0015785), but requires verified strain-matched UniProtKB protein_examples on PncA to represent the enzyme-resolved mechanism.

    +

    The current record carries an IUBMB EC 3.5.1.19 reaction snippet and two Mycobacterium tuberculosis PncA nicotinamidase/pyrazinamidase snippets (DOI:10.1111/j.1742-4658.2007.06241.x, DOI:10.1371/journal.pone.0015785), but requires verified strain-matched UniProtKB protein_examples on PncA to represent the enzyme-resolved mechanism.

    @@ -477,7 +478,7 @@

    Evidence

    -

    The record's primary literature (EC 3.5.1.19, DOI:10.1111/j.1742-4658.2007.06241.x, DOI:10.1371/journal.pone.0015785) establishes nicotinamide hydrolysis to nicotinate and pyrazinamide activation to pyrazinoic acid by PncA in Mycobacterium tuberculosis (NCBITaxon:1773), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    +

    The record's primary literature (EC 3.5.1.19, DOI:10.1111/j.1742-4658.2007.06241.x, DOI:10.1371/journal.pone.0015785) establishes nicotinamide hydrolysis to nicotinate and pyrazinamide activation to pyrazinoic acid by PncA in Mycobacterium tuberculosis (NCBITaxon:1773), but a verified UniProtKB accession on a GENE_OR_PROTEIN node must be curated before marking the graph MECHANISTIC.

    @@ -496,7 +497,7 @@

    Evidence

    -

    Resolution: Added canonical_examples entry Mycobacterium tuberculosis H37Rv (NCBITaxon:83332; DOI:10.1371/journal.pone.0015785) and promoted pyrazinamidase_activity_pnca_sketch to MECHANISTIC by adding InterPro:IPR000868-grounded GENE_OR_PROTEIN node pyrazinamidase_pnca with reviewed protein_examples UniProtKB:I6XD65 (PncA).

    +

    Resolution: Added canonical_examples entry Mycobacterium tuberculosis H37Rv (NCBITaxon:83332; DOI:10.1371/journal.pone.0015785) and promoted pyrazinamidase_activity_pnca_sketch to MECHANISTIC by adding InterPro:IPR000868-grounded GENE_OR_PROTEIN node pyrazinamidase_pnca with reviewed protein_examples UniProtKB:I6XD65 (PncA).

    @@ -531,7 +532,7 @@

    Curation history

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Added Mycobacterium tuberculosis H37Rv (NCBITaxon:83332; DOI:10.1371/journal.pone.0015785) canonical example; promoted pyrazinamidase_activity_pnca_sketch to MECHANISTIC with InterPro:IPR000868-grounded GENE_OR_PROTEIN node pyrazinamidase_pnca and reviewed protein_examples UniProtKB:I6XD65 (PncA); resolved pyrazinamidase-activity-protein-example-gap.

    +

    Added Mycobacterium tuberculosis H37Rv (NCBITaxon:83332; DOI:10.1371/journal.pone.0015785) canonical example; promoted pyrazinamidase_activity_pnca_sketch to MECHANISTIC with InterPro:IPR000868-grounded GENE_OR_PROTEIN node pyrazinamidase_pnca and reviewed protein_examples UniProtKB:I6XD65 (PncA); resolved pyrazinamidase-activity-protein-example-gap.

    • @@ -573,7 +574,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -937,12 +947,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 22:45 UTC diff --git a/pages/traits/physiology/pyrrolidonyl_arylamidase_activity.html b/pages/traits/physiology/pyrrolidonyl_arylamidase_activity.html index faf45ea54b5..4270bdd3746 100644 --- a/pages/traits/physiology/pyrrolidonyl_arylamidase_activity.html +++ b/pages/traits/physiology/pyrrolidonyl_arylamidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -263,7 +264,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record pairs one IUBMB EC 3.4.19.3 reaction snippet with a diagnostic strain-phenotyping list (DOI:10.1128/JCM.37.11.3443-3447.1999), leaving only one mechanistic quote.

    +

    The current record pairs one IUBMB EC 3.4.19.3 reaction snippet with a diagnostic strain-phenotyping list (DOI:10.1128/JCM.37.11.3443-3447.1999), leaving only one mechanistic quote.

    @@ -345,7 +346,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -374,12 +384,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/quorum_quenching.html b/pages/traits/physiology/quorum_quenching.html index be432f19322..c96980e19f8 100644 --- a/pages/traits/physiology/quorum_quenching.html +++ b/pages/traits/physiology/quorum_quenching.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1128/AEM.70.2.954-960.2004
    However, no AHL was detected in the culture supernatant of SCG1 cocultured with either COT1 or B1, which produce AHL-lactonase.
    -

    Dong et al. 2004, PMID:14766576, PMC348924, first Results subsection. Introduction explicitly calls signal interference quorum quenching. Scientific Abstract, Introduction, Methods, Results and early Discussion read; actual Figure 1 and Tables 1/2 inspected. Other actual figures unread. COT1/B1 cocultures support AHL loss with comparable growth in this setting, not universal growth neutrality. Table 2 retains residual protection after aiiA disruption. B23 is plasmidless; SCG1-GFP is engineered. COT1 species assignment partly uses an unshown crystal-protein observation. EXT_ID:14766576 AND SRC:MED confirmed ID, title and DOI on 2026-10-11. Native resolver: NOT_IN_ABSTRACT; quotation separately matched directly retrieved PMC full text.

    +

    Dong et al. 2004, PMID:14766576, PMC348924, first Results subsection. Introduction explicitly calls signal interference quorum quenching. Scientific Abstract, Introduction, Methods, Results and early Discussion read; actual Figure 1 and Tables 1/2 inspected. Other actual figures unread. COT1/B1 cocultures support AHL loss with comparable growth in this setting, not universal growth neutrality. Table 2 retains residual protection after aiiA disruption. B23 is plasmidless; SCG1-GFP is engineered. COT1 species assignment partly uses an unshown crystal-protein observation. EXT_ID:14766576 AND SRC:MED confirmed ID, title and DOI on 2026-10-11. Native resolver: NOT_IN_ABSTRACT; quotation separately matched directly retrieved PMC full text.

  • DOI:10.1128/AEM.68.4.1754-1759.2002
    Here we report identification of more than 20 bacterial isolates capable of enzymatic inactivation of AHLs from different sources.
    -

    Dong et al. 2002, PMID:11916693, PMC123891, scientific Abstract. Abstract, Introduction, Methods, Results and selected Discussion read; actual Figure 2 and Table 1 inspected. Other actual figures unread. Whole-cell OHHL inactivation and live-versus-boiled controls support activity, not just aiiA sequence homology. Activity units use culture OD600, not molecular turnover. Restricted isolate sampling does not establish universal species activity. Plasmidless derivatives and recombinant E. coli are not unqualified natural exemplars. Authors overlap the 2004 study, not independent-laboratory replication. EXT_ID:11916693 AND SRC:MED confirmed ID, title and DOI on 2026-10-11; native resolver VERIFIED, also matched directly retrieved scientific Abstract.

    +

    Dong et al. 2002, PMID:11916693, PMC123891, scientific Abstract. Abstract, Introduction, Methods, Results and selected Discussion read; actual Figure 2 and Table 1 inspected. Other actual figures unread. Whole-cell OHHL inactivation and live-versus-boiled controls support activity, not just aiiA sequence homology. Activity units use culture OD600, not molecular turnover. Restricted isolate sampling does not establish universal species activity. Plasmidless derivatives and recombinant E. coli are not unqualified natural exemplars. Authors overlap the 2004 study, not independent-laboratory replication. EXT_ID:11916693 AND SRC:MED confirmed ID, title and DOI on 2026-10-11; native resolver VERIFIED, also matched directly retrieved scientific Abstract.

  • DOI:10.1126/scitranslmed.aat8329
    clinical isolates of different coagulase-negative staphylococci (CoNS) species residing on normal skin produced autoinducing peptides that inhibited the S. aureus agr system
    -

    Williams et al. 2019, PMID:31043573, PMC7106486, scientific Abstract. Direct PMC Abstract, Results S4-S6, Methods S9-S11/S18 and actual Figures 2-4 with captions inspected. Other actual figures unread. Natural isolate supernatants and live S. hominis C5 support non-AHL interference. Figure 4 separates culture-product identification from synthetic-peptide assays; synthetic potency is not a whole-cell threshold. Figure 2A shows modest type-II/III effects despite prose describing little effect. Growth controls are condition-specific; nonsignificance is not equivalence. Supplement returned HTML, not PDF; supplemental figures and Table S1 unread. EXT_ID:31043573 AND SRC:MED confirmed ID, title and DOI on 2026-10-11; native resolver VERIFIED, also matched directly retrieved scientific Abstract. A separate author group and mechanism, not direct replication of the Bacillus experiments.

    +

    Williams et al. 2019, PMID:31043573, PMC7106486, scientific Abstract. Direct PMC Abstract, Results S4-S6, Methods S9-S11/S18 and actual Figures 2-4 with captions inspected. Other actual figures unread. Natural isolate supernatants and live S. hominis C5 support non-AHL interference. Figure 4 separates culture-product identification from synthetic-peptide assays; synthetic potency is not a whole-cell threshold. Figure 2A shows modest type-II/III effects despite prose describing little effect. Growth controls are condition-specific; nonsignificance is not equivalence. Supplement returned HTML, not PDF; supplemental figures and Table S1 unread. EXT_ID:31043573 AND SRC:MED confirmed ID, title and DOI on 2026-10-11; native resolver VERIFIED, also matched directly retrieved scientific Abstract. A separate author group and mechanism, not direct replication of the Bacillus experiments.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -277,7 +278,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add source-bounded quorum-quenching phenotype and METPO proposal v570 -

      Added traitmech:000694 as a PROPOSED PHYSIOLOGY CLASS under METPO:1000059 through the guarded validated writer. DOI:10.1128/AEM.70.2.954-960.2004, DOI:10.1128/AEM.68.4.1754-1759.2002 and DOI:10.1126/scitranslmed.aat8329 support signal interference; each has a directly matched contiguous snippet. Qualified MED metadata confirmed source, PMID, title and DOI. Native resolver verdicts are NOT_IN_ABSTRACT for the manually checked 2004 Results quote and VERIFIED for the two scientific-abstract quotes. Record notes delimit reading coverage, experimental conditions, derivatives, synthetic-peptide assays and the unread 2019 supplement. No canonical examples, synonyms, xrefs or graph are asserted; two OPEN discussions retain gaps. Quorum-sensing protein and chemical nodes are not retyped as phenotype nodes. Ignored-and-hidden searches covered all 22 pre-existing worktrees, CommunityMech and all five open PR heads including draft 924; no exact trait or conflicting reservation was found. METPO, current seed projection and prior release-review dispositions were inspected. Reserve v570 and METPO:1064700-1064799, with only 1064700 populated. Writer dry run and 20 focused tests passed; full validation and immutable review follow. Existing records including protected spore germination remain unchanged. No paid research was used.

    +

    Added traitmech:000694 as a PROPOSED PHYSIOLOGY CLASS under METPO:1000059 through the guarded validated writer. DOI:10.1128/AEM.70.2.954-960.2004, DOI:10.1128/AEM.68.4.1754-1759.2002 and DOI:10.1126/scitranslmed.aat8329 support signal interference; each has a directly matched contiguous snippet. Qualified MED metadata confirmed source, PMID, title and DOI. Native resolver verdicts are NOT_IN_ABSTRACT for the manually checked 2004 Results quote and VERIFIED for the two scientific-abstract quotes. Record notes delimit reading coverage, experimental conditions, derivatives, synthetic-peptide assays and the unread 2019 supplement. No canonical examples, synonyms, xrefs or graph are asserted; two OPEN discussions retain gaps. Quorum-sensing protein and chemical nodes are not retyped as phenotype nodes. Ignored-and-hidden searches covered all 22 pre-existing worktrees, CommunityMech and all five open PR heads including draft 924; no exact trait or conflicting reservation was found. METPO, current seed projection and prior release-review dispositions were inspected. Reserve v570 and METPO:1064700-1064799, with only 1064700 populated. Writer dry run and 20 focused tests passed; full validation and immutable review follow. Existing records including protected spore germination remain unchanged. No paid research was used.

    • Read this curation session @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-11 02:49 UTC diff --git a/pages/traits/physiology/quorum_sensing.html b/pages/traits/physiology/quorum_sensing.html index 3e00fb838ba..71d3cdc6c03 100644 --- a/pages/traits/physiology/quorum_sensing.html +++ b/pages/traits/physiology/quorum_sensing.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -137,7 +138,7 @@

    Edge evidence

    GO:0009372 confers quorum sensing - traitmech:000084 + traitmech:000084 METPO:2007700

    The sensing process realizes the quorum-sensing trait.

      @@ -250,8 +251,8 @@

      Protein and taxon examples

    		 - Aliivibrio fischeri -
    NCBITaxon:668 + Aliivibrio fischeri +
    NCBITaxon:668         		REVIEWED
    @@ -280,8 +281,8 @@

    Protein and taxon examples

    		 - Pseudomonas aeruginosa PAO1 -
    NCBITaxon:208964 + Pseudomonas aeruginosa PAO1 +
    NCBITaxon:208964         		REVIEWED
    @@ -310,8 +311,8 @@

    Protein and taxon examples

    		 - Pseudomonas aeruginosa PAO1 -
    NCBITaxon:208964 + Pseudomonas aeruginosa PAO1 +
    NCBITaxon:208964         		REVIEWED
    @@ -340,8 +341,8 @@

    Protein and taxon examples

    		 - Chromobacterium violaceum ATCC 12472 -
    NCBITaxon:243365 + Chromobacterium violaceum ATCC 12472 +
    NCBITaxon:243365         		UNREVIEWED
    @@ -370,8 +371,8 @@

    Protein and taxon examples

    		 - Bacillus thuringiensis subsp. kurstaki -
    NCBITaxon:29339 + Bacillus thuringiensis subsp. kurstaki +
    NCBITaxon:29339         		REVIEWED
    @@ -437,9 +438,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -462,7 +463,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -573,25 +574,25 @@

    Deep research

    | module/taxon | subject | predicate | object | evidence strength | DOI | |---|---|---|---|---|---| -| General QS | autoinducer | accumulates to threshold concentration in extracellular milieu | cognate QS perception/activation | Strong review consensus (2024) (juszczukkubiak2024molecularaspectsof pages 2-3, hu2024nanomaterialsregulatebacterial pages 1-2) | 10.3390/ijms25052655; 10.1002/advs.202306070 | -| General QS | cognate autoinducer perception | activates | QS-responsive gene regulation | Strong review consensus (2024) (juszczukkubiak2024molecularaspectsof pages 2-3, hu2024nanomaterialsregulatebacterial pages 1-2) | 10.3390/ijms25052655; 10.1002/advs.202306070 | -| LuxI/LuxR (Aliivibrio/Vibrio model) | LuxI | synthesizes | AHL (e.g., 3-oxo-C6-HSL) | Strong canonical mechanism (juszczukkubiak2024molecularaspectsof pages 2-3, chan2015inhibitingnacylhomoserinelactone pages 1-2) | 10.3390/ijms25052655; 10.3389/fmicb.2015.01173 | -| LuxI/LuxR (Aliivibrio/Vibrio model) | AHL | binds | LuxR | Strong canonical mechanism (juszczukkubiak2024molecularaspectsof pages 2-3, chan2015inhibitingnacylhomoserinelactone pages 1-2) | 10.3390/ijms25052655; 10.3389/fmicb.2015.01173 | -| LuxI/LuxR (Aliivibrio/Vibrio model) | LuxR-AHL complex | binds promoter of | lux-box target genes | Strong canonical mechanism (juszczukkubiak2024molecularaspectsof pages 2-3) | 10.3390/ijms25052655 | -| LuxI/LuxR (Aliivibrio/Vibrio model) | LuxR-AHL complex | activates transcription of | luxI | Strong canonical positive-feedback edge (juszczukkubiak2024molecularaspectsof pages 2-3, chan2015inhibitingnacylhomoserinelactone pages 1-2) | 10.3390/ijms25052655; 10.3389/fmicb.2015.01173 | -| Vibrio harveyi/cholerae | LuxN/LuxPQ/CqsS receptors at low AI | phosphorylate via phosphorelay | LuxU | Strong primary/review support (eickhoff2021luxtcontrolsspecific pages 1-2, walker2023asimplemechanism pages 1-2) | 10.1371/journal.pgen.1009336; 10.7554/eLife.86699 | -| Vibrio harveyi/cholerae | LuxU | transfers phosphate to | LuxO | Strong primary/review support (eickhoff2021luxtcontrolsspecific pages 1-2, walker2023asimplemechanism pages 1-2) | 10.1371/journal.pgen.1009336; 10.7554/eLife.86699 | -| Vibrio harveyi/cholerae | LuxO-P + sigma-54 | activates transcription of | qrr sRNAs | Strong primary/review support (eickhoff2021luxtcontrolsspecific pages 1-2, walker2023asimplemechanism pages 1-2) | 10.1371/journal.pgen.1009336; 10.7554/eLife.86699 | -| Vibrio harveyi/cholerae | Qrr sRNAs | activate translation of | AphA | Strong primary/review support (eickhoff2021luxtcontrolsspecific pages 1-2, walker2023asimplemechanism pages 1-2) | 10.1371/journal.pgen.1009336; 10.7554/eLife.86699 | -| Vibrio harveyi/cholerae | Qrr sRNAs | repress translation/expression of | HapR/LuxR | Strong primary/review support (eickhoff2021luxtcontrolsspecific pages 1-2, walker2023asimplemechanism pages 1-2) | 10.1371/journal.pgen.1009336; 10.7554/eLife.86699 | -| Vibrio cholerae high-cell-density state | high autoinducer abundance | permits expression of | HapR | Strong primary support (walker2023asimplemechanism pages 1-2) | 10.7554/eLife.86699 | -| Staphylococcus aureus agr | AgrD | is precursor of | AIP | Strong canonical mechanism (juszczukkubiak2024molecularaspectsof pages 5-7, green2023modelledmicrogravityreducesvirulence pages 1-2) | 10.3390/ijms25052655; 10.3390/ijms242115997 | -| Staphylococcus aureus agr | AgrB | processes/matures | AgrD into AIP | Strong canonical mechanism (juszczukkubiak2024molecularaspectsof pages 5-7) | 10.3390/ijms25052655 | -| Staphylococcus aureus agr | AIP | binds/activates | AgrC | Strong primary/review support (green2023modelledmicrogravityreducesvirulence pages 1-2, juszczukkubiak2024molecularaspectsof pages 5-7) | 10.3390/ijms242115997; 10.3390/ijms25052655 | -| Staphylococcus aureus agr | AgrC | phosphorylates | AgrA | Strong canonical mechanism (green2023modelledmicrogravityreducesvirulence pages 1-2) | 10.3390/ijms242115997 | -| Staphylococcus aureus agr | AgrA | activates transcription of | RNAIII | Strong canonical mechanism (juszczukkubiak2024molecularaspectsof pages 5-7) | 10.3390/ijms25052655 | -| Staphylococcus aureus agr | RNAIII | inhibits translation/activity of | Rot | Strong canonical mechanism (juszczukkubiak2024molecularaspectsof pages 5-7) | 10.3390/ijms25052655 | -| Staphylococcus aureus agr | reduced AIP production under modeled microgravity | delays | agr activation | Strong 2023 condition-specific evidence; environment-specific (green2023modelledmicrogravityreducesvirulence pages 1-2) | 10.3390/ijms242115997 | +| General QS | autoinducer | accumulates to threshold concentration in extracellular milieu | cognate QS perception/activation | Strong review consensus (2024) (juszczukkubiak2024molecularaspectsof pages 2-3, hu2024nanomaterialsregulatebacterial pages 1-2) | 10.3390/ijms25052655; 10.1002/advs.202306070 | +| General QS | cognate autoinducer perception | activates | QS-responsive gene regulation | Strong review consensus (2024) (juszczukkubiak2024molecularaspectsof pages 2-3, hu2024nanomaterialsregulatebacterial pages 1-2) | 10.3390/ijms25052655; 10.1002/advs.202306070 | +| LuxI/LuxR (Aliivibrio/Vibrio model) | LuxI | synthesizes | AHL (e.g., 3-oxo-C6-HSL) | Strong canonical mechanism (juszczukkubiak2024molecularaspectsof pages 2-3, chan2015inhibitingnacylhomoserinelactone pages 1-2) | 10.3390/ijms25052655; 10.3389/fmicb.2015.01173 | +| LuxI/LuxR (Aliivibrio/Vibrio model) | AHL | binds | LuxR | Strong canonical mechanism (juszczukkubiak2024molecularaspectsof pages 2-3, chan2015inhibitingnacylhomoserinelactone pages 1-2) | 10.3390/ijms25052655; 10.3389/fmicb.2015.01173 | +| LuxI/LuxR (Aliivibrio/Vibrio model) | LuxR-AHL complex | binds promoter of | lux-box target genes | Strong canonical mechanism (juszczukkubiak2024molecularaspectsof pages 2-3) | 10.3390/ijms25052655 | +| LuxI/LuxR (Aliivibrio/Vibrio model) | LuxR-AHL complex | activates transcription of | luxI | Strong canonical positive-feedback edge (juszczukkubiak2024molecularaspectsof pages 2-3, chan2015inhibitingnacylhomoserinelactone pages 1-2) | 10.3390/ijms25052655; 10.3389/fmicb.2015.01173 | +| Vibrio harveyi/cholerae | LuxN/LuxPQ/CqsS receptors at low AI | phosphorylate via phosphorelay | LuxU | Strong primary/review support (eickhoff2021luxtcontrolsspecific pages 1-2, walker2023asimplemechanism pages 1-2) | 10.1371/journal.pgen.1009336; 10.7554/eLife.86699 | +| Vibrio harveyi/cholerae | LuxU | transfers phosphate to | LuxO | Strong primary/review support (eickhoff2021luxtcontrolsspecific pages 1-2, walker2023asimplemechanism pages 1-2) | 10.1371/journal.pgen.1009336; 10.7554/eLife.86699 | +| Vibrio harveyi/cholerae | LuxO-P + sigma-54 | activates transcription of | qrr sRNAs | Strong primary/review support (eickhoff2021luxtcontrolsspecific pages 1-2, walker2023asimplemechanism pages 1-2) | 10.1371/journal.pgen.1009336; 10.7554/eLife.86699 | +| Vibrio harveyi/cholerae | Qrr sRNAs | activate translation of | AphA | Strong primary/review support (eickhoff2021luxtcontrolsspecific pages 1-2, walker2023asimplemechanism pages 1-2) | 10.1371/journal.pgen.1009336; 10.7554/eLife.86699 | +| Vibrio harveyi/cholerae | Qrr sRNAs | repress translation/expression of | HapR/LuxR | Strong primary/review support (eickhoff2021luxtcontrolsspecific pages 1-2, walker2023asimplemechanism pages 1-2) | 10.1371/journal.pgen.1009336; 10.7554/eLife.86699 | +| Vibrio cholerae high-cell-density state | high autoinducer abundance | permits expression of | HapR | Strong primary support (walker2023asimplemechanism pages 1-2) | 10.7554/eLife.86699 | +| Staphylococcus aureus agr | AgrD | is precursor of | AIP | Strong canonical mechanism (juszczukkubiak2024molecularaspectsof pages 5-7, green2023modelledmicrogravityreducesvirulence pages 1-2) | 10.3390/ijms25052655; 10.3390/ijms242115997 | +| Staphylococcus aureus agr | AgrB | processes/matures | AgrD into AIP | Strong canonical mechanism (juszczukkubiak2024molecularaspectsof pages 5-7) | 10.3390/ijms25052655 | +| Staphylococcus aureus agr | AIP | binds/activates | AgrC | Strong primary/review support (green2023modelledmicrogravityreducesvirulence pages 1-2, juszczukkubiak2024molecularaspectsof pages 5-7) | 10.3390/ijms242115997; 10.3390/ijms25052655 | +| Staphylococcus aureus agr | AgrC | phosphorylates | AgrA | Strong canonical mechanism (green2023modelledmicrogravityreducesvirulence pages 1-2) | 10.3390/ijms242115997 | +| Staphylococcus aureus agr | AgrA | activates transcription of | RNAIII | Strong canonical mechanism (juszczukkubiak2024molecularaspectsof pages 5-7) | 10.3390/ijms25052655 | +| Staphylococcus aureus agr | RNAIII | inhibits translation/activity of | Rot | Strong canonical mechanism (juszczukkubiak2024molecularaspectsof pages 5-7) | 10.3390/ijms25052655 | +| Staphylococcus aureus agr | reduced AIP production under modeled microgravity | delays | agr activation | Strong 2023 condition-specific evidence; environment-specific (green2023modelledmicrogravityreducesvirulence pages 1-2) | 10.3390/ijms242115997 | *Table: This table summarizes the strongest, curation-ready causal edges for quorum sensing across general, LuxI/LuxR, Vibrio, and staphylococcal agr modules. It is designed as a compact graph blueprint highlighting well-supported mechanistic nodes and edges with direct literature grounding.* @@ -717,13 +718,13 @@

    Curation history

  • · REVIEW_EVIDENCE_REFERENCE_CHURN · codex -

    Offline review for issue 520 retained 5 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1146/annurev.cellbio.21.012704.131001 -> DOI:10.1007/s10867-010-9186-4 (1 edge); DOI:10.1146/annurev.micro.55.1.165 -> DOI:10.1007/s10867-010-9186-4 (1 edge); DOI:10.3390/ijms25052655 -> DOI:10.1016/j.molcel.2011.04.003 (1 edge); DOI:10.3390/ijms25052655 -> DOI:10.1073/pnas.0504996102 (1 edge); DOI:10.3390/ijms25052655 -> DOI:10.1128/mbio.01079-17 (1 edge).

    +

    Offline review for issue 520 retained 5 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1146/annurev.cellbio.21.012704.131001 -> DOI:10.1007/s10867-010-9186-4 (1 edge); DOI:10.1146/annurev.micro.55.1.165 -> DOI:10.1007/s10867-010-9186-4 (1 edge); DOI:10.3390/ijms25052655 -> DOI:10.1016/j.molcel.2011.04.003 (1 edge); DOI:10.3390/ijms25052655 -> DOI:10.1073/pnas.0504996102 (1 edge); DOI:10.3390/ijms25052655 -> DOI:10.1128/mbio.01079-17 (1 edge).

  • · CURATE_PROTEIN_TAXON_EXAMPLE · claude -

    Added LuxR-family receptor protein_examples UniProtKB:P25084 (LasR, v177), UniProtKB:P54292 (RhlR, v151) in P. aeruginosa PAO1 (DOI:10.1128/mbio.01079-17) and UniProtKB:Q7NQP7 (CviR, v143) in C. violaceum ATCC 12472 (DOI:10.1016/j.molcel.2011.04.003) on signal_receptor, updated scope_notes, and refreshed entry_version on UniProtKB:P12747 (97 -> 98 on autoinducer_synthase) and UniProtKB:P0CJ63 (47 -> 48 on quorum_quenching_enzyme).

    +

    Added LuxR-family receptor protein_examples UniProtKB:P25084 (LasR, v177), UniProtKB:P54292 (RhlR, v151) in P. aeruginosa PAO1 (DOI:10.1128/mbio.01079-17) and UniProtKB:Q7NQP7 (CviR, v143) in C. violaceum ATCC 12472 (DOI:10.1016/j.molcel.2011.04.003) on signal_receptor, updated scope_notes, and refreshed entry_version on UniProtKB:P12747 (97 -> 98 on autoinducer_synthase) and UniProtKB:P0CJ63 (47 -> 48 on quorum_quenching_enzyme).

    • @@ -765,7 +766,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1129,12 +1139,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/rapid_axopodial_contraction.html b/pages/traits/physiology/rapid_axopodial_contraction.html index 977ef18b828..5b0d1dc5e06 100644 --- a/pages/traits/physiology/rapid_axopodial_contraction.html +++ b/pages/traits/physiology/rapid_axopodial_contraction.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.2108/zsj.20.1367
    Axopodial contraction of the centrohelid heliozoon Raphidiophrys contractilis was induced by mechanical or electrical stimulation.
    -

    Khan et al. (2003), scientific Abstract, directly retrieved from Europe PMC for PMID:14624035 at https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A14624035%20AND%20SRC%3AMED&resultType=core&format=json. Abstract-only access; full Methods and figures were not inspected. The study reports contraction faster than 3.0 mm/sec, followed by re-elongation initially about 0.30 microm/sec, and a microtubule bundle in each axopodium. Extracellular calcium dependence is restricted to this stimulation assay, not a universal defining threshold. Failure to detect other filaments with the reported fixation method does not prove their biological absence. Source taxon spelling is retained; natural culture provenance and current taxonomic identity are not established here.

    +

    Khan et al. (2003), scientific Abstract, directly retrieved from Europe PMC for PMID:14624035 at https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A14624035%20AND%20SRC%3AMED&resultType=core&format=json. Abstract-only access; full Methods and figures were not inspected. The study reports contraction faster than 3.0 mm/sec, followed by re-elongation initially about 0.30 microm/sec, and a microtubule bundle in each axopodium. Extracellular calcium dependence is restricted to this stimulation assay, not a universal defining threshold. Failure to detect other filaments with the reported fixation method does not prove their biological absence. Source taxon spelling is retained; natural culture provenance and current taxonomic identity are not established here.

  • DOI:10.1111/j.1550-7408.2001.tb00187.x
    Upon food uptake, the tubules shorten and transform into a mass of small granules when rapid axopodial contraction occurs
    -

    Kinoshita et al. (2001), scientific Abstract, directly read at https://pubmed.ncbi.nlm.nih.gov/11596916/ and cross-checked against Europe PMC's scientific abstract. Abstract-only access; full Methods and figures were not inspected. The study concerns Actinophrys sol. Contractile-tubule shortening and granulation accompany the food-uptake response; the authors suggest, rather than prove, a causal role. Cold and colchicine both induce microtubule disassembly, but only cold induces tubule granulation in the reported comparison. Neither intervention alone defines the natural rapid-contraction phenotype. No protein identity, effect size or strain provenance is inferred.

    +

    Kinoshita et al. (2001), scientific Abstract, directly read at https://pubmed.ncbi.nlm.nih.gov/11596916/ and cross-checked against Europe PMC's scientific abstract. Abstract-only access; full Methods and figures were not inspected. The study concerns Actinophrys sol. Contractile-tubule shortening and granulation accompany the food-uptake response; the authors suggest, rather than prove, a causal role. Cold and colchicine both induce microtubule disassembly, but only cold induces tubule granulation in the reported comparison. Neither intervention alone defines the natural rapid-contraction phenotype. No protein identity, effect size or strain provenance is inferred.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -347,7 +348,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -376,12 +386,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-14 22:39 UTC diff --git a/pages/traits/physiology/replicative_aging.html b/pages/traits/physiology/replicative_aging.html index 88a394563da..bb1fdc2fdde 100644 --- a/pages/traits/physiology/replicative_aging.html +++ b/pages/traits/physiology/replicative_aging.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.1098/rstb.2018.0442
    For both cell types, division time progressively increased over successive generations
    -

    Lapinska et al. 2019, PMID:31587633, PMC6792439; Figure 2 caption, directly checked in primary full-text XML and the author-hosted PDF. The Introduction defines aging by declining performance. Figure 2 was visually inspected: the early division-time trend approaches a plateau in the longer run, not indefinite deterioration. Methods separate brightfield aging measurements from fluorescent uptake/aggregation assays. Methods name BW25113, but the Introduction says BW21113; that discrepancy is unresolved. Starting-condition effects remain a limitation. No universal protein mechanism is established.

    +

    Lapinska et al. 2019, PMID:31587633, PMC6792439; Figure 2 caption, directly checked in primary full-text XML and the author-hosted PDF. The Introduction defines aging by declining performance. Figure 2 was visually inspected: the early division-time trend approaches a plateau in the longer run, not indefinite deterioration. Methods separate brightfield aging measurements from fluorescent uptake/aggregation assays. Methods name BW25113, but the Introduction says BW21113; that discrepancy is unresolved. Starting-condition effects remain a limitation. No universal protein mechanism is established.

  • DOI:10.1186/1471-2148-7-126
    Aging refers to a decline in reproduction and survival with increasing age.
    -

    Ackermann et al. 2007, PMID:17662151, PMC2174458; scientific abstract Background, directly checked against MED and primary full-text XML. Caulobacter stalked-cell cohorts showed age-dependent loss of reproductive function, with both faster and slower aging among evolved clones. This endpoint combines survival and reproduction and cannot separate them. UJ590 is a pilA-deletion derivative, not an unmodified natural exemplar. Its elapsed-time assay complements, rather than replaces, the division-indexed evidence above.

    +

    Ackermann et al. 2007, PMID:17662151, PMC2174458; scientific abstract Background, directly checked against MED and primary full-text XML. Caulobacter stalked-cell cohorts showed age-dependent loss of reproductive function, with both faster and slower aging among evolved clones. This endpoint combines survival and reproduction and cannot separate them. UJ590 is a pilA-deletion derivative, not an unmodified natural exemplar. Its elapsed-time assay complements, rather than replaces, the division-indexed evidence above.

  • DOI:10.7554/eLife.20340
    Surprisingly, cells die without the classic hallmarks of cellular aging, such as progressive changes in size, doubling time, or sibling health.
    -

    Spivey et al. 2017, PMID:28139976, PMC5332158; scientific abstract, not the eLife digest, directly checked against MED and primary full-text XML. Boundary evidence: finite replicative lifespan and its extension do not alone demonstrate age-dependent deterioration. The reported age-independent mortality applies to the measured fission-yeast conditions, not all strains and environments. The abstract and Discussion were assessed, not all experiments or figure images.

    +

    Spivey et al. 2017, PMID:28139976, PMC5332158; scientific abstract, not the eLife digest, directly checked against MED and primary full-text XML. Boundary evidence: finite replicative lifespan and its extension do not alone demonstrate age-dependent deterioration. The reported age-independent mortality applies to the measured fission-yeast conditions, not all strains and environments. The abstract and Discussion were assessed, not all experiments or figure images.

  • DOI:10.1371/journal.pbio.3002245
    This occurs without an increase in lifespan, proving that at least in yeast, lifespan is distinct from senescence and loss of fitness.
    -

    Horkai et al. 2023, PMID:37643155, PMC10464975; Results, Suppression of age-linked phenotypic change, directly checked against publisher text and primary XML. Galactose-aged diploid MEP cells retained better performance without longer lifespan. This engineered mother-enrichment system and its platform-dependent results are not universal natural-taxon claims. The authors also use replicative ageing for passage through divisions without senescent decline; that broader usage is not the operational phenotype defined here.

    +

    Horkai et al. 2023, PMID:37643155, PMC10464975; Results, Suppression of age-linked phenotypic change, directly checked against publisher text and primary XML. Galactose-aged diploid MEP cells retained better performance without longer lifespan. This engineered mother-enrichment system and its platform-dependent results are not universal natural-taxon claims. The authors also use replicative ageing for passage through divisions without senescent decline; that broader usage is not the operational phenotype defined here.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -327,7 +328,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -356,12 +366,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-12 10:31 UTC diff --git a/pages/traits/physiology/reversible_nematode_paralyzing_activity.html b/pages/traits/physiology/reversible_nematode_paralyzing_activity.html index 33a8bcfadbe..5594df5142a 100644 --- a/pages/traits/physiology/reversible_nematode_paralyzing_activity.html +++ b/pages/traits/physiology/reversible_nematode_paralyzing_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-14 01:05 UTC diff --git a/pages/traits/physiology/rheotaxis.html b/pages/traits/physiology/rheotaxis.html index f9bb9287d4f..1be682c53fe 100644 --- a/pages/traits/physiology/rheotaxis.html +++ b/pages/traits/physiology/rheotaxis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1073/pnas.1120955109
    Rheotaxis is the directed movement resulting from fluid velocity gradients
    -

    Abstract and Results, https://pmc.ncbi.nlm.nih.gov/articles/PMC3324032/ (PMID:22411815). Smooth-swimming Bacillus subtilis OI4139 exhibits transverse swimming in bulk shear flow. Physical reorientation couples to active propulsion; passive advection alone is insufficient. This is not restricted to upstream migration or receptor-mediated sensing. OI4139 is a mutant that almost never tumbles, not a wild-type canonical exemplar; no strain accession is inferred.

    +

    Abstract and Results, https://pmc.ncbi.nlm.nih.gov/articles/PMC3324032/ (PMID:22411815). Smooth-swimming Bacillus subtilis OI4139 exhibits transverse swimming in bulk shear flow. Physical reorientation couples to active propulsion; passive advection alone is insufficient. This is not restricted to upstream migration or receptor-mediated sensing. OI4139 is a mutant that almost never tumbles, not a wild-type canonical exemplar; no strain accession is inferred.

  • DOI:10.1016/j.bpj.2012.03.001
    positive rheotaxis (rapid and continuous upstream motility) in wild-type Escherichia coli freely swimming over a surface
    -

    Abstract, with strain and preparation in Materials and Methods, Bacteria preparation; behavioral regimes in Results and Figures 3-6. The publisher-formatted article was read at https://sacredheart.elsevierpure.com/ws/portalfiles/portal/39998836/Kaya_BJ12_Bacteria.pdf (PMID:22500751). K12 cells underwent 3-5 rounds of motility selection. Moderate shear supported upstream swimming near the channel ceiling; higher shear produced sideways swimming and downstream drag. The study does not establish universal upstream motion, a universal shear threshold, or in-vivo infection. Supplementary movies were not viewed.

    +

    Abstract, with strain and preparation in Materials and Methods, Bacteria preparation; behavioral regimes in Results and Figures 3-6. The publisher-formatted article was read at https://sacredheart.elsevierpure.com/ws/portalfiles/portal/39998836/Kaya_BJ12_Bacteria.pdf (PMID:22500751). K12 cells underwent 3-5 rounds of motility selection. Moderate shear supported upstream swimming near the channel ceiling; higher shear produced sideways swimming and downstream drag. The study does not establish universal upstream motion, a universal shear threshold, or in-vivo infection. Supplementary movies were not viewed.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -266,7 +267,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add rheotaxis with context-qualified primary evidence -

      Added traitmech:000582 under motile, with DOI:10.1073/pnas.1120955109 and DOI:10.1016/j.bpj.2012.03.001, contiguous snippets and an NCBI-resolved K-12 example qualified by motility selection and near-surface shear. Bulk transverse motion is not conflated with upstream motion or passive advection. Deferred a protein-resolved graph pending a verified experimental strain/accession link. Whole-repository searches included ignored and hidden files. Reserved METPO:1053600 in proposal v459; writer is dry-run by default and refuses output drift. No older trait was edited.

    +

    Added traitmech:000582 under motile, with DOI:10.1073/pnas.1120955109 and DOI:10.1016/j.bpj.2012.03.001, contiguous snippets and an NCBI-resolved K-12 example qualified by motility selection and near-surface shear. Bulk transverse motion is not conflated with upstream motion or passive advection. Deferred a protein-resolved graph pending a verified experimental strain/accession link. Whole-repository searches included ignored and hidden files. Reserved METPO:1053600 in proposal v459; writer is dry-run by default and refuses output drift. No older trait was edited.

    • Read this curation session @@ -298,7 +299,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -327,12 +337,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 00:20 UTC diff --git a/pages/traits/physiology/rheotropism.html b/pages/traits/physiology/rheotropism.html index b58cbe6f768..b5c3cdef670 100644 --- a/pages/traits/physiology/rheotropism.html +++ b/pages/traits/physiology/rheotropism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1016/S0006-3495(65)86719-4
    Sparsely sowed, hence independent Botrytis spores, which are fixed to the wall of a laminar flow chamber, tend to germinate downstream.
    -

    Abstract, exact-matched at Europe PMC (PMID:19431336). The author-hosted full text was inspected at https://mterasaki.us/cellbio/lfjaffe/reprints/65bj2.pdf. Methods identify Botrytis cinerea without a strain accession. Figures 3 and 4 (pages 322 and 324) measure downstream outgrowth orientation, not simply germination rate. Tables VI and VII (page 329) test viscosity and rotation confounds; these figures and tables were visually checked. The proposed self-emitted diffusible stimulator is an indirect mechanistic inference, not an identified molecule or receptor. Initial outgrowth localization is not evidence of later tip reorientation.

    +

    Abstract, exact-matched at Europe PMC (PMID:19431336). The author-hosted full text was inspected at https://mterasaki.us/cellbio/lfjaffe/reprints/65bj2.pdf. Methods identify Botrytis cinerea without a strain accession. Figures 3 and 4 (pages 322 and 324) measure downstream outgrowth orientation, not simply germination rate. Tables VI and VII (page 329) test viscosity and rotation confounds; these figures and tables were visually checked. The proposed self-emitted diffusible stimulator is an indirect mechanistic inference, not an identified molecule or receptor. Initial outgrowth localization is not evidence of later tip reorientation.

  • DOI:10.1016/S0168-1656(97)00147-8
    Hyphal tips quickly reoriented towards the upstream of the flowing medium and became aligned parallel to the flow axis as they grew larger.
    -

    Abstract, exact-matched at Europe PMC (PMID:9470224). Attached Aspergillus niger hyphae were tested in flowing liquid medium. Other tested fungi showed upstream hyphal and branch growth without polarized germ-tube emergence. The inlet/outlet pH and oxygen measurements do not exclude every local chemical gradient or identify a flow receptor. Strain identity, full text and figures were not verified; claims are abstract-limited.

    +

    Abstract, exact-matched at Europe PMC (PMID:9470224). Attached Aspergillus niger hyphae were tested in flowing liquid medium. Other tested fungi showed upstream hyphal and branch growth without polarized germ-tube emergence. The inlet/outlet pH and oxygen measurements do not exclude every local chemical gradient or identify a flow receptor. Strain identity, full text and figures were not verified; claims are abstract-limited.

  • DOI:10.1007/BF00397538
    When the spph was placed in a laminar flow of air, it grew into the wind within 2-4 min.
    -

    Abstract, exact-matched at Europe PMC (PMID:24258181). The sporangiophore (spph) of Phycomyces blakesleeanus exhibits upstream growth in air, establishing that this usage of rheotropism is not limited to liquid currents. Added ethylene did not remove the response; that result does not identify its mediator or establish a universal ethylene-independent mechanism. The barrier-avoidance assay is distinct from the wind assay. Strain identity, full text and figures were not verified; claims are abstract-limited.

    +

    Abstract, exact-matched at Europe PMC (PMID:24258181). The sporangiophore (spph) of Phycomyces blakesleeanus exhibits upstream growth in air, establishing that this usage of rheotropism is not limited to liquid currents. Added ethylene did not remove the response; that result does not identify its mediator or establish a universal ethylene-independent mechanism. The barrier-avoidance assay is distinct from the wind assay. Strain identity, full text and figures were not verified; claims are abstract-limited.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 16:46 UTC diff --git a/pages/traits/physiology/ribophagy.html b/pages/traits/physiology/ribophagy.html index 87591a0f05c..3a5f776b8c3 100644 --- a/pages/traits/physiology/ribophagy.html +++ b/pages/traits/physiology/ribophagy.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.1038/ncb1723
    A genetic screen revealed that selective degradation of ribosomes requires catalytic activity of the Ubp3p/Bre5p ubiquitin protease.
    -

    PMID:18391941. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. Saccharomyces cerevisiae degrades mature ribosomes during nutrient starvation by both nonselective autophagy and a selective component named ribophagy. The deletion phenotype concerns 60S particles despite retained starvation sensing and general autophagy; do not transfer the same dependence to 40S subunits. Enriched ubiquitination suggests direct regulation rather than proving every substrate or step. Full text, actual figures and natural strain provenance were not inspected.

    +

    PMID:18391941. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. Saccharomyces cerevisiae degrades mature ribosomes during nutrient starvation by both nonselective autophagy and a selective component named ribophagy. The deletion phenotype concerns 60S particles despite retained starvation sensing and general autophagy; do not transfer the same dependence to 40S subunits. Enriched ubiquitination suggests direct regulation rather than proving every substrate or step. Full text, actual figures and natural strain provenance were not inspected.

  • DOI:10.1083/jcb.201308139
    Its ubiquitylation is Ltn1 dependent and Ubp3 reversed, and mutation of its ubiquitylation site rendered ribophagy less dependent on Ubp3.
    -

    PMID:24616224, PMC3998797. Scientific Abstract directly read in Europe PMC core metadata and XML, distinct from the precis. The quoted substrate is Rpl25. Introduction, the LTN1-deletion Results and strain/culture Methods were also read. This yeast study explicitly treats 60S subunit turnover as ribophagy; Rpl5/Rpl25-GFP processing and vacuolar localization support degradation. LTN1 deletion rescues the delayed reporter cleavage in ubp3 mutants, so Ubp3 is not an unconditional presence criterion. Table 1 identifies the reference as BY4741 with auxotrophic deletions, not an independently verified natural exemplar. Figure 1 caption was read; actual figures, supplements, complete Methods and independent strain provenance were not inspected.

    +

    PMID:24616224, PMC3998797. Scientific Abstract directly read in Europe PMC core metadata and XML, distinct from the precis. The quoted substrate is Rpl25. Introduction, the LTN1-deletion Results and strain/culture Methods were also read. This yeast study explicitly treats 60S subunit turnover as ribophagy; Rpl5/Rpl25-GFP processing and vacuolar localization support degradation. LTN1 deletion rescues the delayed reporter cleavage in ubp3 mutants, so Ubp3 is not an unconditional presence criterion. Table 1 identifies the reference as BY4741 with auxotrophic deletions, not an independently verified natural exemplar. Figure 1 caption was read; actual figures, supplements, complete Methods and independent strain provenance were not inspected.

  • DOI:10.15252/embj.201489083
    Under nutrient starvation, a portion of the cytoplasm is non-selectively sequestered into autophagosomes.
    -

    PMID:25468960, PMC4337068. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. This is boundary evidence, not a positive selective-ribophagy observation: the study frames yeast vacuolar RNA catabolism as bulk nonselective autophagy. Rny1-mediated RNA cleavage, downstream nucleotide metabolism or ribosome delivery alone does not establish cargo selectivity. Full-text retrieval returned HTTP 500; full Methods and actual figures were not inspected.

    +

    PMID:25468960, PMC4337068. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. This is boundary evidence, not a positive selective-ribophagy observation: the study frames yeast vacuolar RNA catabolism as bulk nonselective autophagy. Rny1-mediated RNA cleavage, downstream nucleotide metabolism or ribosome delivery alone does not establish cargo selectivity. Full-text retrieval returned HTTP 500; full Methods and actual figures were not inspected.

  • DOI:10.1016/j.jbc.2025.108554
    We discovered that most ribosomes are selectively degraded, whose mechanism differs from the previously reported selective degradation process called "ribophagy."
    -

    PMID:40294649, PMC12152620. Scientific Abstract directly read in Europe PMC core metadata and XML. Results sec1.1-sec1.3, Discussion sec2 and Methods sec3.1/sec3.7-sec3.11/sec3.13 were read. The authors distinguish Rsa1-dependent turnover from previously named Ubp3/Ufd3/Cdc48-dependent ribophagy; this is terminology/mechanism boundary evidence, not an unqualified canonical ribophagy assignment. Rpl25-GFP processing, Atg2 controls and rRNA measurements support degradation; RNA accumulation in rny1 mutants alone does not. Residual turnover in rsa1 mutants is retained. The Results support mature rRNA turnover, while the Discussion also hypothesizes nascent nuclear cargo; that cargo choice is not established. Rpl8 contact and Atg8-binding motifs are modeled, not experimentally mapped. Captions were read, but actual figures, supplements, complete Methods and independent natural strain provenance were not inspected.

    +

    PMID:40294649, PMC12152620. Scientific Abstract directly read in Europe PMC core metadata and XML. Results sec1.1-sec1.3, Discussion sec2 and Methods sec3.1/sec3.7-sec3.11/sec3.13 were read. The authors distinguish Rsa1-dependent turnover from previously named Ubp3/Ufd3/Cdc48-dependent ribophagy; this is terminology/mechanism boundary evidence, not an unqualified canonical ribophagy assignment. Rpl25-GFP processing, Atg2 controls and rRNA measurements support degradation; RNA accumulation in rny1 mutants alone does not. Residual turnover in rsa1 mutants is retained. The Results support mature rRNA turnover, while the Discussion also hypothesizes nascent nuclear cargo; that cargo choice is not established. Rpl8 contact and Atg8-binding motifs are modeled, not experimentally mapped. Captions were read, but actual figures, supplements, complete Methods and independent natural strain provenance were not inspected.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -221,7 +222,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    Use autophagy traitmech:000638 as the broader phenotype. The 2008 paper names selective mature-ribosome turnover ribophagy; the 2014 paper explicitly includes 60S subunits. Neither ribosome protection in dormancy nor bulk RNA decay, free ribosomal-protein degradation, ribosome biogenesis, gene presence or puncta alone establishes this phenotype. The 2025 Rsa1 paper distinguishes its pathway from known ribophagy and notes differing mammalian usage. Retain that source-attributed distinction for human review; do not silently equate Rsa1-dependent turnover with the historically named pathway or make Ubp3 universal. GO:0034517, resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0034517, is a nonobsolete biological process for selective mature ribosome degradation by macroautophagy, not an exact organismal phenotype. Preserve that route qualifier and omit exact xrefs and synonyms.

    +

    Use autophagy traitmech:000638 as the broader phenotype. The 2008 paper names selective mature-ribosome turnover ribophagy; the 2014 paper explicitly includes 60S subunits. Neither ribosome protection in dormancy nor bulk RNA decay, free ribosomal-protein degradation, ribosome biogenesis, gene presence or puncta alone establishes this phenotype. The 2025 Rsa1 paper distinguishes its pathway from known ribophagy and notes differing mammalian usage. Retain that source-attributed distinction for human review; do not silently equate Rsa1-dependent turnover with the historically named pathway or make Ubp3 universal. GO:0034517, resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0034517, is a nonobsolete biological process for selective mature ribosome degradation by macroautophagy, not an exact organismal phenotype. Preserve that route qualifier and omit exact xrefs and synonyms.

    @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 12:00 UTC diff --git a/pages/traits/physiology/serine_arylamidase_activity.html b/pages/traits/physiology/serine_arylamidase_activity.html index b597fd3ae99..9c2d0c5a449 100644 --- a/pages/traits/physiology/serine_arylamidase_activity.html +++ b/pages/traits/physiology/serine_arylamidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • serine arylamidase RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
      • +
    • serine arylamidase RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
    @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -272,7 +273,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two diagnostic enzyme-panel survey snippets (DOI:10.1099/ijsem.0.006017, DOI:10.1128/JCM.40.9.3427-3431.2002) without verbatim catalytic reaction quotes.

    +

    The current record carries two diagnostic enzyme-panel survey snippets (DOI:10.1099/ijsem.0.006017, DOI:10.1128/JCM.40.9.3427-3431.2002) without verbatim catalytic reaction quotes.

    @@ -354,7 +355,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -383,12 +393,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/siderophore_production.html b/pages/traits/physiology/siderophore_production.html index 0452509a72a..84faaad8bc1 100644 --- a/pages/traits/physiology/siderophore_production.html +++ b/pages/traits/physiology/siderophore_production.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -88,7 +89,7 @@

    Trait evidence (4)

    Siderophore biosynthesis, extracellular secretion, and iron scavenging

    Evidence-backed physiological mechanism sketch linking siderophore biosynthesis, extracellular siderophore secretion, and high-affinity iron scavenging to siderophore production.

    -

    NONMECHANISTIC · Biosynthesis-and-transport sketch backed by DOI:10.1111/1462-2920.14937, DOI:10.15698/mic2018.10.649, and DOI:10.1073/pnas.0908760106; strain-matched UniProtKB protein examples for Pseudomonas aeruginosa pyoverdine synthetases (PvdL/PvdI/PvdJ/PvdD) and TonB-dependent receptor FpvA remain to be curated.

    +

    NONMECHANISTIC · Biosynthesis-and-transport sketch backed by DOI:10.1111/1462-2920.14937, DOI:10.15698/mic2018.10.649, and DOI:10.1073/pnas.0908760106; strain-matched UniProtKB protein examples for Pseudomonas aeruginosa pyoverdine synthetases (PvdL/PvdI/PvdJ/PvdD) and TonB-dependent receptor FpvA remain to be curated.

    Loading graph…

    @@ -111,7 +112,7 @@

    Edge evidence

    GO:0019290 confers siderophore production - traitmech:000186 + traitmech:000186 METPO:2007700

    Biosynthesis of iron-chelating siderophores such as pyoverdine under iron-limiting conditions confers the siderophore production trait.

      @@ -216,7 +217,7 @@

      kg-microbe context

      via parent_proxy.

        -
      • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
        • +
      • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

      512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

      @@ -366,7 +367,7 @@

      Discussions and Knowledge Gaps (2)

      -

      The record's primary literature (DOI:10.1111/1462-2920.14937, DOI:10.15698/mic2018.10.649, DOI:10.1073/pnas.0908760106) establishes pyoverdine siderophore biosynthesis and extracellular iron scavenging in Pseudomonas aeruginosa (NCBITaxon:287), but verified UniProtKB accessions must be curated on a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

      +

      The record's primary literature (DOI:10.1111/1462-2920.14937, DOI:10.15698/mic2018.10.649, DOI:10.1073/pnas.0908760106) establishes pyoverdine siderophore biosynthesis and extracellular iron scavenging in Pseudomonas aeruginosa (NCBITaxon:287), but verified UniProtKB accessions must be curated on a GENE_OR_PROTEIN node before marking the graph MECHANISTIC.

      @@ -390,7 +391,7 @@

      Evidence

      Provenance -

      Cycle 2 Stage 3 UniProt audit: canonical_examples cites species-level Pseudomonas aeruginosa (NCBITaxon:287; DOI:10.1073/pnas.0908760106) and Pseudomonas fluorescens (NCBITaxon:294; DOI:10.15698/mic2018.10.649), whereas reviewed Swiss-Prot pyoverdine biosynthesis/transport proteins (e.g., PvdA UniProtKB:Q51548, FpvA UniProtKB:P48632) are annotated on strain Pseudomonas aeruginosa PAO1 (NCBITaxon:208964; UP000002438) and current record evidence snippets do not name individual pvd/fpv gene products. Keeping graph NONMECHANISTIC and discussion OPEN until a PAO1-specific primary source snippet and canonical_examples entry are added.

      +

      Cycle 2 Stage 3 UniProt audit: canonical_examples cites species-level Pseudomonas aeruginosa (NCBITaxon:287; DOI:10.1073/pnas.0908760106) and Pseudomonas fluorescens (NCBITaxon:294; DOI:10.15698/mic2018.10.649), whereas reviewed Swiss-Prot pyoverdine biosynthesis/transport proteins (e.g., PvdA UniProtKB:Q51548, FpvA UniProtKB:P48632) are annotated on strain Pseudomonas aeruginosa PAO1 (NCBITaxon:208964; UP000002438) and current record evidence snippets do not name individual pvd/fpv gene products. Keeping graph NONMECHANISTIC and discussion OPEN until a PAO1-specific primary source snippet and canonical_examples entry are added.

    @@ -427,7 +428,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add siderophore production trait -

      Minted traitmech:000186 for the bacterial siderophore production physiology trait with DOI-backed siderophore synthesis and release evidence from 10.1111/1462-2920.14937, 10.15698/mic2018.10.649, and 10.1073/pnas.0908760106; added Pseudomonas aeruginosa as a canonical pyoverdine-producing example; and reserved METPO:1014000 in proposals/metpo_traitmech_v63.

    +

    Minted traitmech:000186 for the bacterial siderophore production physiology trait with DOI-backed siderophore synthesis and release evidence from 10.1111/1462-2920.14937, 10.15698/mic2018.10.649, and 10.1073/pnas.0908760106; added Pseudomonas aeruginosa as a canonical pyoverdine-producing example; and reserved METPO:1014000 in proposals/metpo_traitmech_v63.

    • Read this curation session @@ -459,7 +460,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -823,12 +833,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 11:45 UTC diff --git a/pages/traits/physiology/siliceous_scale_production.html b/pages/traits/physiology/siliceous_scale_production.html index 637f6cc0935..46ae59de99f 100644 --- a/pages/traits/physiology/siliceous_scale_production.html +++ b/pages/traits/physiology/siliceous_scale_production.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1016/j.protis.2016.05.002
    Scales were formed one by one in silica deposition vesicles (SDVs)
    -

    Nomura and Ishida 2016, PMID:27348459. Scientific abstract directly read on 2026-10-10 at https://rrc.nbrp.jp/references/56432?lang=en and Europe PMC CORE, using EXT_ID:27348459 AND SRC:MED and checking the returned source, title and DOI together. The study describes scale formation in Paulinella chromatophora under its historical name and detects silicon in vesicles with immature scales. Microtubule involvement in determining scale geometry is proposed, not demonstrated molecular necessity. Publisher access returned 403; full Methods and figures were not inspected. Scale production and subsequent shell assembly are distinct observations.

    +

    Nomura and Ishida 2016, PMID:27348459. Scientific abstract directly read on 2026-10-10 at https://rrc.nbrp.jp/references/56432?lang=en and Europe PMC CORE, using EXT_ID:27348459 AND SRC:MED and checking the returned source, title and DOI together. The study describes scale formation in Paulinella chromatophora under its historical name and detects silicon in vesicles with immature scales. Microtubule involvement in determining scale geometry is proposed, not demonstrated molecular necessity. Publisher access returned 403; full Methods and figures were not inspected. Scale production and subsequent shell assembly are distinct observations.

  • DOI:10.1111/j.0022-3646.1996.00675.x
    The first new scales appeared within 2 h after the silica addition
    -

    Sandgren, Hall and Barlow 1996, scientific ABSTRACT directly read on 2026-10-10 in publisher-deposited Crossref JATS at https://api.crossref.org/works/10.1111%2Fj.0022-3646.1996.00675.x. Silica-limited Synura petersenii cultures suppressed scale deposition, and scale-free cells regenerated scales after dissolved silica addition. This supports production rather than possession alone. The quoted recovery timing is specific to that culture experiment, not a universal threshold or rate. Scale production could be uncoupled from cell division in this system; no obligatory growth dependence is inferred. Crossref print date is August 1996; its June 2008 online date is not a second study. Full Methods and figures were not inspected.

    +

    Sandgren, Hall and Barlow 1996, scientific ABSTRACT directly read on 2026-10-10 in publisher-deposited Crossref JATS at https://api.crossref.org/works/10.1111%2Fj.0022-3646.1996.00675.x. Silica-limited Synura petersenii cultures suppressed scale deposition, and scale-free cells regenerated scales after dissolved silica addition. This supports production rather than possession alone. The quoted recovery timing is specific to that culture experiment, not a universal threshold or rate. Scale production could be uncoupled from cell division in this system; no obligatory growth dependence is inferred. Crossref print date is August 1996; its June 2008 online date is not a second study. Full Methods and figures were not inspected.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -241,7 +242,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    No canonical examples are assigned until primary assay Methods, strain provenance and current taxonomy are jointly reconciled. NIES-4060 is currently catalogued as Paulinella micropora (MYN1) at https://mcc.next.nbrp.jp/strainList.do?strainNumber=NIES-4060; its reference list links the 2016 historical chromatophora paper, but this collection association is not an independent production experiment or authority to rename every historical observation. The two primary abstracts support a reusable phenotype through different methods, not one conserved molecular pathway. Ultrastructure and cytoskeletal association alone cannot establish causal protein requirements. Separate deposition, vesicle transport, extrusion and assembly before adding causal edges. A protein mechanism needs functional evidence and taxon-paired accessions; sequence features alone cannot supply that support. Mechanism is deferred, not claimed absent.

    +

    No canonical examples are assigned until primary assay Methods, strain provenance and current taxonomy are jointly reconciled. NIES-4060 is currently catalogued as Paulinella micropora (MYN1) at https://mcc.next.nbrp.jp/strainList.do?strainNumber=NIES-4060; its reference list links the 2016 historical chromatophora paper, but this collection association is not an independent production experiment or authority to rename every historical observation. The two primary abstracts support a reusable phenotype through different methods, not one conserved molecular pathway. Ultrastructure and cytoskeletal association alone cannot establish causal protein requirements. Separate deposition, vesicle transport, extrusion and assembly before adding causal edges. A protein mechanism needs functional evidence and taxon-paired accessions; sequence features alone cannot supply that support. Mechanism is deferred, not claimed absent.

    @@ -317,7 +318,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -346,12 +356,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-10 08:07 UTC diff --git a/pages/traits/physiology/sos_response.html b/pages/traits/physiology/sos_response.html index b04a925fb40..57a0bd1d3b5 100644 --- a/pages/traits/physiology/sos_response.html +++ b/pages/traits/physiology/sos_response.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -225,7 +226,7 @@

    Edge evidence

    confers SOS response - traitmech:000207 + traitmech:000207 METPO:2007700

    The induced repair and damage-tolerance program realizes the SOS-response trait.

      @@ -262,8 +263,8 @@

      Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -292,8 +293,8 @@

    Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -359,7 +360,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • SOS system RELATED_SYNONYM · DOI:10.1002/em.22267
      • +
    • SOS system RELATED_SYNONYM · DOI:10.1002/em.22267
    @@ -375,7 +376,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -560,7 +561,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -924,12 +934,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-09-15 06:23 UTC diff --git a/pages/traits/physiology/spore_germination.html b/pages/traits/physiology/spore_germination.html index f6266a96764..116dd930633 100644 --- a/pages/traits/physiology/spore_germination.html +++ b/pages/traits/physiology/spore_germination.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -116,7 +117,7 @@

    Edge evidence

    GO:0009847 confers spore germination - traitmech:000083 + traitmech:000083 METPO:2007700

    The germination process realizes the spore-germination trait.

      @@ -192,7 +193,7 @@

      Edge evidence

      confers spore germination - traitmech:000083 + traitmech:000083 METPO:2007700

      Core rehydration and outgrowth complete realization of the spore-germination trait.

        @@ -252,7 +253,7 @@

        Parent traits (1)

        Synonyms (1)

    @@ -275,7 +276,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -521,7 +522,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -885,12 +895,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 01:15 UTC diff --git a/pages/traits/physiology/stalk_contraction.html b/pages/traits/physiology/stalk_contraction.html index 88fae3b92b4..080ccc2ebaa 100644 --- a/pages/traits/physiology/stalk_contraction.html +++ b/pages/traits/physiology/stalk_contraction.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.2142/biophysics.8.1
    The stalk is straight at the initial stage. Then, it bends and coils into a helix near the zooid.
    -

    Kamiguri et al. 2012, PMID:27857602, PMCID:PMC5070450, printed page 3, Results and Discussion first paragraph, left column. Direct contiguous PDF match with whitespace-only line-wrap normalization and actual typeset passage inspected; native NOT_IN_ABSTRACT retained. Junko Kamiguri is the first author; the running header says Hashimoto et al. Living source-named Vorticella sp. from activated sludge attached to glass rods was stimulated by hitting the dish; eight cells were observed at 6000 frames/s. Figures 3 and 5 show coiling and decreased end-to-end extension. The same paragraph says contour length does not change. All nine main-paper pages were inspected; raw videos were not reanalyzed. Model fits are not molecular proof. The primary PDF came from J-STAGE; an acquisition-helper failure left no original request timestamp or header receipt. Those missing fields are not reconstructed. Current taxonomic and culture identities remain unresolved.

    +

    Kamiguri et al. 2012, PMID:27857602, PMCID:PMC5070450, printed page 3, Results and Discussion first paragraph, left column. Direct contiguous PDF match with whitespace-only line-wrap normalization and actual typeset passage inspected; native NOT_IN_ABSTRACT retained. Junko Kamiguri is the first author; the running header says Hashimoto et al. Living source-named Vorticella sp. from activated sludge attached to glass rods was stimulated by hitting the dish; eight cells were observed at 6000 frames/s. Figures 3 and 5 show coiling and decreased end-to-end extension. The same paragraph says contour length does not change. All nine main-paper pages were inspected; raw videos were not reanalyzed. Model fits are not molecular proof. The primary PDF came from J-STAGE; an acquisition-helper failure left no original request timestamp or header receipt. Those missing fields are not reconstructed. Current taxonomic and culture identities remain unresolved.

  • DOI:10.1016/j.bpj.2012.07.038
    The stalk contraction was stalled more as the fluid viscosity and/or flow rate increased.
    -

    Ryu et al. 2012, PMID:23009835, PMCID:PMC3433611, printed page 862, Figure 2A caption, sentence beginning The stalk contraction. Direct contiguous PDF match and actual typeset passage inspected; native NOT_IN_ABSTRACT retained. The primary PDF was retrieved from the Vanderbilt Lang Lab mirror. Source-named Vorticella convallaria contracted in microfluidic channels under varied flow and viscosity. Four to five contractions per cell per condition are not independent cells. Figure 3 uses six cells; Figure 4C uses fifteen in a separate analysis. Isometric force is extrapolated through a hydrodynamic model, not directly measured zero-shortening force. All eight main-paper pages and actual Figures 1-5 were inspected; the supplement was not. Projection and geometry assumptions remain relevant. Some extracted micrometre symbols appear as mm; no such numeric extraction is quoted. Culture/taxonomy correspondence is unresolved. No universal rate, force, calcium threshold, ATP independence or protein mechanism follows.

    +

    Ryu et al. 2012, PMID:23009835, PMCID:PMC3433611, printed page 862, Figure 2A caption, sentence beginning The stalk contraction. Direct contiguous PDF match and actual typeset passage inspected; native NOT_IN_ABSTRACT retained. The primary PDF was retrieved from the Vanderbilt Lang Lab mirror. Source-named Vorticella convallaria contracted in microfluidic channels under varied flow and viscosity. Four to five contractions per cell per condition are not independent cells. Figure 3 uses six cells; Figure 4C uses fifteen in a separate analysis. Isometric force is extrapolated through a hydrodynamic model, not directly measured zero-shortening force. All eight main-paper pages and actual Figures 1-5 were inspected; the supplement was not. Projection and geometry assumptions remain relevant. Some extracted micrometre symbols appear as mm; no such numeric extraction is quoted. Culture/taxonomy correspondence is unresolved. No universal rate, force, calcium threshold, ATP independence or protein mechanism follows.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -345,7 +346,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -374,12 +384,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-15 03:55 UTC diff --git a/pages/traits/physiology/stress_response.html b/pages/traits/physiology/stress_response.html index ff5e966149b..e480b3f54e0 100644 --- a/pages/traits/physiology/stress_response.html +++ b/pages/traits/physiology/stress_response.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    GO:0006950 confers stress response - traitmech:000078 + traitmech:000078 METPO:2007700

    The induced program realizes the stress-response trait.

      @@ -270,7 +271,7 @@

      Edge evidence

      confers stress response - traitmech:000078 + traitmech:000078 METPO:2007700

      General stress resistance realizes the stress-response trait.

        @@ -307,8 +308,8 @@

        Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -391,7 +392,7 @@

    Children (5)

    Synonyms (1)

    @@ -407,7 +408,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -713,7 +714,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1077,12 +1087,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/tetrapolar_mating_system.html b/pages/traits/physiology/tetrapolar_mating_system.html index 5a0bd752c5f..d79d542fba8 100644 --- a/pages/traits/physiology/tetrapolar_mating_system.html +++ b/pages/traits/physiology/tetrapolar_mating_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1371/journal.pgen.1002528
    None of these MAT recombinant progeny mated with either parent, further confirming that C. amylolentus possesses a tetrapolar mating system
    -

    Findley et al. (2012), PMID:22359516, PMC3280970. Exact Results s2g clause, not an abstract quote. The preceding sentences report interfertility of complementary recombinants; parent sterility alone is insufficient. Introduction defines the two unlinked factors and differences at both. Actual Figures 8/9 were inspected: sexual structures and the mating matrix support the functional phenotype. Figure 9A is a conceptual model, not an observed equal-ratio result. Results s2b/s2e, direct prose of s2f/s2g and Methods s4a/s4m were read. Mixed F1 progeny include blastospores; frequent infertility and biased mating types make this a modified tetrapolar cycle. Complete Text S1 was text-extracted, not page-rendered: filamentation is not successful mating. Its description of F1S2 #16 as sterile must not override s2g's successful crosses with some partners. Tables 1/2, other figures and other supplements remain uninspected. Physical MAT separation alone in T. wingfieldii does not establish its reproductive phenotype.

    +

    Findley et al. (2012), PMID:22359516, PMC3280970. Exact Results s2g clause, not an abstract quote. The preceding sentences report interfertility of complementary recombinants; parent sterility alone is insufficient. Introduction defines the two unlinked factors and differences at both. Actual Figures 8/9 were inspected: sexual structures and the mating matrix support the functional phenotype. Figure 9A is a conceptual model, not an observed equal-ratio result. Results s2b/s2e, direct prose of s2f/s2g and Methods s4a/s4m were read. Mixed F1 progeny include blastospores; frequent infertility and biased mating types make this a modified tetrapolar cycle. Complete Text S1 was text-extracted, not page-rendered: filamentation is not successful mating. Its description of F1S2 #16 as sterile must not override s2g's successful crosses with some partners. Tables 1/2, other figures and other supplements remain uninspected. Physical MAT separation alone in T. wingfieldii does not establish its reproductive phenotype.

  • DOI:10.1534/genetics.115.177717
    independent assortment of MAT alleles was observed in the meiotic progeny of a test cross.
    -

    Maia et al. (2015), PMID:26178967, PMC4566278. Exact scientific abstract clause, directly retrieved from Europe PMC core metadata and checked against NCBI efetch front matter. Leucosporidium scottii has physically unlinked HD and P/R regions; the reported meiotic segregation supports functional tetrapolarity independently of sequence annotation. Natural population linkage disequilibrium does not contradict the test-cross result. The abstract reports fertile progeny of four mating types but approximately two thirds nonhaploid; do not impose universal haploidy or equal ratios. Full-text XML/PDF endpoints failed with HTTP 500/403 and NCBI returned no body. Methods, figures, supplements and natural strain provenance remain uninspected; no canonical example is inferred.

    +

    Maia et al. (2015), PMID:26178967, PMC4566278. Exact scientific abstract clause, directly retrieved from Europe PMC core metadata and checked against NCBI efetch front matter. Leucosporidium scottii has physically unlinked HD and P/R regions; the reported meiotic segregation supports functional tetrapolarity independently of sequence annotation. Natural population linkage disequilibrium does not contradict the test-cross result. The abstract reports fertile progeny of four mating types but approximately two thirds nonhaploid; do not impose universal haploidy or equal ratios. Full-text XML/PDF endpoints failed with HTTP 500/403 and NCBI returned no body. Methods, figures, supplements and natural strain provenance remain uninspected; no canonical example is inferred.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Canonical examples DOI:10.1371/journal.pgen.1002528 - Qualified to the CBS6039 x CBS6273 cross, not every strain or laboratory-derived progeny. Natural provenance: Methods Strains and media at https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002528 reports both isolates from insect frass in South Africa. Mating used V8 pH 5 in the dark at 24 C; actual Figure 8 shows two-week sexual structures and Figure 9 compares complementary mating combinations. Recombinant fertility, not hyphae alone, supports the modified tetrapolar classification. NCBI taxonomy 104669 resolves to this species on 2026-10-05. + Qualified to the CBS6039 x CBS6273 cross, not every strain or laboratory-derived progeny. Natural provenance: Methods Strains and media at https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002528 reports both isolates from insect frass in South Africa. Mating used V8 pH 5 in the dark at 24 C; actual Figure 8 shows two-week sexual structures and Figure 9 compares complementary mating combinations. Recombinant fertility, not hyphae alone, supports the modified tetrapolar classification. NCBI taxonomy 104669 resolves to this species on 2026-10-05. @@ -328,7 +329,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -357,12 +367,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 07:17 UTC diff --git a/pages/traits/physiology/thermotaxis.html b/pages/traits/physiology/thermotaxis.html index 07ab0bd0e54..9ebd40a8472 100644 --- a/pages/traits/physiology/thermotaxis.html +++ b/pages/traits/physiology/thermotaxis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,7 +56,7 @@

    Trait evidence (2)

    DOI:10.7554/eLife.26607
    detect and follow environmental temperature gradients
    -

    Paulick et al., Introduction; version 2, Version of Record dated 2017-08-31, https://cdn.elifesciences.org/articles/26607/elife-26607-v2.pdf. Figures 1-3 and their figure supplements distinguish behavioral gradients from FRET reporters and chemical adaptation. Temperature preference for movement is not a growth-temperature class.

    +

    Paulick et al., Introduction; version 2, Version of Record dated 2017-08-31, https://cdn.elifesciences.org/articles/26607/elife-26607-v2.pdf. Figures 1-3 and their figure supplements distinguish behavioral gradients from FRET reporters and chemical adaptation. Temperature preference for movement is not a growth-temperature class.

  • @@ -175,7 +176,7 @@

    Edge evidence

    GO:0043052 confers thermotaxis - traitmech:000580 + traitmech:000580 METPO:2007700

    Temperature-guided migration realizes the organismal thermotaxis phenotype.

      @@ -212,8 +213,8 @@

      Protein and taxon examples

    		•  - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -286,7 +287,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -407,7 +408,7 @@

    Discussions and Knowledge Gaps (1)

    mechanism it concerns.

    -

    DOI:10.1073/pnas.0709903105 reports thermal-response inversion under its tethered-cell conditions. DOI:10.7554/eLife.26607 instead finds continued warm-seeking in buffer under flow; its Discussion suggests residual chemical stimulation as one explanation of earlier results, not a proven correction. Retain medium, adaptation, strain and assay context. Growth optima, passive thermophoresis and temperature-dependent speed alone do not establish thermotaxis. GO:0043052 is a biological process (QuickGO checked 2026-10-03), so it grounds the process node rather than an equivalent xref on the disposition. The Tar arm does not describe every thermotactic microbe.

    +

    DOI:10.1073/pnas.0709903105 reports thermal-response inversion under its tethered-cell conditions. DOI:10.7554/eLife.26607 instead finds continued warm-seeking in buffer under flow; its Discussion suggests residual chemical stimulation as one explanation of earlier results, not a proven correction. Retain medium, adaptation, strain and assay context. Growth optima, passive thermophoresis and temperature-dependent speed alone do not establish thermotaxis. GO:0043052 is a biological process (QuickGO checked 2026-10-03), so it grounds the process node rather than an equivalent xref on the disposition. The Tar arm does not describe every thermotactic microbe.

    @@ -439,7 +440,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add temperature-guided active movement as thermotaxis -

      Added traitmech:000580 using primary DOI:10.7554/eLife.26607 version 2, DOI:10.1073/pnas.0709903105, DOI:10.1074/jbc.271.30.17932 and DOI:10.1128/jb.179.21.6573-6580.1997. Verified exact snippets, K-12 behavioral assay scope, NCBITaxon:83333, reviewed UniProtKB:P07017 and GO:0043052 as a process-only grounding. The graph describes the Tar-mediated arm, not a universal or complete Tar/Tsr mechanism; an open discussion preserves assay-context uncertainty. Ignored-and-hidden novelty searches found no exact record or METPO term. Reserved METPO:1053400 in proposal v457 and updated README counts. Existing traits and the protected spore-germination record are untouched.

    +

    Added traitmech:000580 using primary DOI:10.7554/eLife.26607 version 2, DOI:10.1073/pnas.0709903105, DOI:10.1074/jbc.271.30.17932 and DOI:10.1128/jb.179.21.6573-6580.1997. Verified exact snippets, K-12 behavioral assay scope, NCBITaxon:83333, reviewed UniProtKB:P07017 and GO:0043052 as a process-only grounding. The graph describes the Tar-mediated arm, not a universal or complete Tar/Tsr mechanism; an open discussion preserves assay-context uncertainty. Ignored-and-hidden novelty searches found no exact record or METPO term. Reserved METPO:1053400 in proposal v457 and updated README counts. Existing traits and the protected spore-germination record are untouched.

    • Read this curation session @@ -471,7 +472,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -835,12 +845,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-03 22:20 UTC diff --git a/pages/traits/physiology/thigmotropism.html b/pages/traits/physiology/thigmotropism.html index 1cebe4f260a..b64b29b0cbb 100644 --- a/pages/traits/physiology/thigmotropism.html +++ b/pages/traits/physiology/thigmotropism.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.1080/02681219280000621
    The response was likely to be due to contact guidance (thigmotropism) and not chemotropism towards the nutrients
    -

    Abstract, exact-matched at Europe PMC (PMID:1287165); full text not inspected. Candida albicans hyphae entered membrane pores after contacting their lips, including from the underside while growing away from nutrient agar. This supports the authors' contact-guidance interpretation, not exclusion of every chemical influence or proof of tissue invasion in vivo.

    +

    Abstract, exact-matched at Europe PMC (PMID:1287165); full text not inspected. Candida albicans hyphae entered membrane pores after contacting their lips, including from the underside while growing away from nutrient agar. This supports the authors' contact-guidance interpretation, not exclusion of every chemical influence or proof of tissue invasion in vivo.

  • DOI:10.1099/00221287-144-3-689
    both compounds reduced the percentage of hyphae reorienting on contact with a ridge without markedly affecting hyphal extension rate
    -

    Abstract, exact-matched at Europe PMC (PMID:9534238); full text not inspected. The compounds are GdCl3 and verapamil at the tested low concentrations. Reorientation and extension rate are distinct readouts. Pharmacological attenuation and membrane channel recordings suggest channel involvement but do not identify a unique molecular mechanosensor.

    +

    Abstract, exact-matched at Europe PMC (PMID:9534238); full text not inspected. The compounds are GdCl3 and verapamil at the tested low concentrations. Reorientation and extension rate are distinct readouts. Pharmacological attenuation and membrane channel recordings suggest channel involvement but do not identify a unique molecular mechanosensor.

  • DOI:10.1016/j.cub.2006.12.043
    The establishment and maintenance of directional growth in relation to these environmental cues was Ca(2+) dependent.
    -

    Abstract, exact-matched at Europe PMC (PMID:17275302). PMC1885950 full text distinguishes contact-dependent thigmotropism from electric-field galvanotropism. In the reported ridge assays, channel-component mutations reduced reorientation without reducing hyphal extension rates. Calcineurin was required for cathodal emergence but not thigmotropism; do not transfer that pathway requirement between the two responses. Localized channel activation and calcium influx remain a proposed model, not a universal mechanism established in every microbe. Supplement not inspected.

    +

    Abstract, exact-matched at Europe PMC (PMID:17275302). PMC1885950 full text distinguishes contact-dependent thigmotropism from electric-field galvanotropism. In the reported ridge assays, channel-component mutations reduced reorientation without reducing hyphal extension rates. Calcineurin was required for cathodal emergence but not thigmotropism; do not transfer that pathway requirement between the two responses. Localized channel activation and calcium influx remain a proposed model, not a universal mechanism established in every microbe. Supplement not inspected.

  • DOI:10.1111/cmi.12369
    In vitro, hyphal tips reorient thigmotropically on contact with small obstacles.
    -

    Abstract, exact-matched at Europe PMC (PMID:25262778). PMC4371639 full text, Fig. 6 and supplementary Table S1 were inspected. Adhesion or friction sufficient to oppose forward growth supported acute tip reorientation; less constrained hyphae instead bent subapically. Tip contact alone was insufficient in these assays. Table S1 lists CAI4/CIp10, BWP17 and engineered derivatives, including fluorescent reporters and an rsr1 deletion; the paper's wild-type designation is not proof of natural strain provenance. Spitzenkorper position correlated with growth but was not an absolute predictor. Force magnitudes are not curated because main-text and supplementary Fig. S2 units disagree. Movies were not inspected.

    +

    Abstract, exact-matched at Europe PMC (PMID:25262778). PMC4371639 full text, Fig. 6 and supplementary Table S1 were inspected. Adhesion or friction sufficient to oppose forward growth supported acute tip reorientation; less constrained hyphae instead bent subapically. Tip contact alone was insufficient in these assays. Table S1 lists CAI4/CIp10, BWP17 and engineered derivatives, including fluorescent reporters and an rsr1 deletion; the paper's wild-type designation is not proof of natural strain provenance. Spitzenkorper position correlated with growth but was not an absolute predictor. Force magnitudes are not curated because main-text and supplementary Fig. S2 units disagree. Movies were not inspected.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -283,7 +284,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed thigmotropism -

      Created traitmech:000594 under phenotype METPO:1000059 with four primary DOI sources: 10.1080/02681219280000621 (PMID:1287165), 10.1099/00221287-144-3-689 (PMID:9534238), 10.1016/j.cub.2006.12.043 (PMID:17275302; PMCID:PMC1885950), and 10.1111/cmi.12369 (PMID:25262778; PMCID:PMC4371639). Read authoritative abstracts, two full texts, Thomson Fig. 6 and supplementary Table S1. Distinguish contact-directed polarized growth from locomotion and passive bending; retain calcium-model limitations and do not transfer calcineurin dependence from galvanotropism. Engineered backgrounds and reporters do not establish natural canonical examples; taxon-paired protein mechanisms remain deferred. Main-text and supplementary force units disagree, so magnitudes were omitted. Fresh seed: 399 IDs, 344 present and 55 absent in the pre-change 988-record corpus. Ignored-and-hidden whole-repository searches, frozen release review and structured OWL found no exact trait or identifier collision. Reserved METPO:1054800 in v471. Seven writer tests and validated dry run passed. Added a focused growth-tropism interpretation rule to the add-trait skill.

    +

    Created traitmech:000594 under phenotype METPO:1000059 with four primary DOI sources: 10.1080/02681219280000621 (PMID:1287165), 10.1099/00221287-144-3-689 (PMID:9534238), 10.1016/j.cub.2006.12.043 (PMID:17275302; PMCID:PMC1885950), and 10.1111/cmi.12369 (PMID:25262778; PMCID:PMC4371639). Read authoritative abstracts, two full texts, Thomson Fig. 6 and supplementary Table S1. Distinguish contact-directed polarized growth from locomotion and passive bending; retain calcium-model limitations and do not transfer calcineurin dependence from galvanotropism. Engineered backgrounds and reporters do not establish natural canonical examples; taxon-paired protein mechanisms remain deferred. Main-text and supplementary force units disagree, so magnitudes were omitted. Fresh seed: 399 IDs, 344 present and 55 absent in the pre-change 988-record corpus. Ignored-and-hidden whole-repository searches, frozen release review and structured OWL found no exact trait or identifier collision. Reserved METPO:1054800 in v471. Seven writer tests and validated dry run passed. Added a focused growth-tropism interpretation rule to the add-trait skill.

    • Read this curation session @@ -315,7 +316,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -344,12 +354,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 10:26 UTC diff --git a/pages/traits/physiology/toxicyst_discharge.html b/pages/traits/physiology/toxicyst_discharge.html index 888814c433c..51a1393e25e 100644 --- a/pages/traits/physiology/toxicyst_discharge.html +++ b/pages/traits/physiology/toxicyst_discharge.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1111/jeu.12106
    we isolated the discharge of the toxicysts from living cells
    -

    PMID:24512001. Scientific Abstract read directly in PubMed and Europe PMC (EXT_ID:24512001 AND SRC:MED); source, title and DOI agree. Coleps hirtus discharge was collected and tested against other ciliates. This supports extracellular release from living cells, not merely possession of an organelle or toxicity of a whole-cell extract. Abstract-only access: full Methods and figures were not inspected; the institutional postprint at https://hdl.handle.net/11393/192287 is access-restricted. The reported chemical mixture is not a universal toxicyst cargo.

    +

    PMID:24512001. Scientific Abstract read directly in PubMed and Europe PMC (EXT_ID:24512001 AND SRC:MED); source, title and DOI agree. Coleps hirtus discharge was collected and tested against other ciliates. This supports extracellular release from living cells, not merely possession of an organelle or toxicity of a whole-cell extract. Abstract-only access: full Methods and figures were not inspected; the institutional postprint at https://hdl.handle.net/11393/192287 is access-restricted. The reported chemical mixture is not a universal toxicyst cargo.

  • DOI:10.1007/BF01279249
    Injection of Ca2+ evoked discharge of toxicysts, if the site of the injection was the periphery region of the proboscis.
    -

    Scientific Summary read directly on the publisher page; Ca2+ represents its rendered superscript charge. Methods, Results and captions also read in the author-upload full-text transcript at https://www.researchgate.net/publication/227062328_Ca2_triggers_toxicyst_discharge_in_Didinium_nasutum. Figures were not visually inspected. Didinium nasutum pressure injection near the proboscis periphery produced discharge in 8/11 cells versus 1/11 calcium-free controls; cell-body and central-proboscis injections did not. Iontophoretic injection caused damage and cytoplasm outflow, motivating pressure injection. These are assay-specific observations, not a universal calcium requirement or proof of a particular fusion protein. No PMID was resolved by the exact DOI query.

    +

    Scientific Summary read directly on the publisher page; Ca2+ represents its rendered superscript charge. Methods, Results and captions also read in the author-upload full-text transcript at https://www.researchgate.net/publication/227062328_Ca2_triggers_toxicyst_discharge_in_Didinium_nasutum. Figures were not visually inspected. Didinium nasutum pressure injection near the proboscis periphery produced discharge in 8/11 cells versus 1/11 calcium-free controls; cell-body and central-proboscis injections did not. Iontophoretic injection caused damage and cytoplasm outflow, motivating pressure injection. These are assay-specific observations, not a universal calcium requirement or proof of a particular fusion protein. No PMID was resolved by the exact DOI query.

  • DOI:10.1186/s12915-024-01904-2
    However, our understanding of the genetic processes and specific toxins involved in toxicyst formation and discharge is still limited.
    -

    PMID:38715037, PMC11077807. Scientific Abstract, Background, morphology Results, Discussion and collection/TEM Methods read in primary HTML/fullTextXML. Figure 1 was visually inspected: A-C are drawings, whereas D-F are TEM images of fixed Litonotus. The drawing of discharge is not direct imaging of release. Sequence and expression associations motivate toxin/transport hypotheses, not experimentally resolved discharge mechanisms. Genomics supplements were not inspected and are not used for accessions, prevalence or functional assignments.

    +

    PMID:38715037, PMC11077807. Scientific Abstract, Background, morphology Results, Discussion and collection/TEM Methods read in primary HTML/fullTextXML. Figure 1 was visually inspected: A-C are drawings, whereas D-F are TEM images of fixed Litonotus. The drawing of discharge is not direct imaging of release. Sequence and expression associations motivate toxin/transport hypotheses, not experimentally resolved discharge mechanisms. Genomics supplements were not inspected and are not used for accessions, prevalence or functional assignments.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -277,7 +278,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add source-bounded toxicyst discharge -

      Created traitmech:000685 with DOI:10.1111/jeu.12106, DOI:10.1007/BF01279249 and DOI:10.1186/s12915-024-01904-2; directly checked scientific Abstract/Summary snippets. Reserved v561 and METPO:1063800-1063899 after ignored-and-hidden worktree and open-head checks. Retained phenotype parent with explicit unresolved exocytosis classification. Distinguished discharge from injury, organelle possession and sequence predictions. No canonical examples, xrefs or protein graph without verified provenance and mechanism. Existing records unchanged.

    +

    Created traitmech:000685 with DOI:10.1111/jeu.12106, DOI:10.1007/BF01279249 and DOI:10.1186/s12915-024-01904-2; directly checked scientific Abstract/Summary snippets. Reserved v561 and METPO:1063800-1063899 after ignored-and-hidden worktree and open-head checks. Retained phenotype parent with explicit unresolved exocytosis classification. Distinguished discharge from injury, organelle possession and sequence predictions. No canonical examples, xrefs or protein graph without verified provenance and mechanism. Existing records unchanged.

    • Read this curation session @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-08 18:24 UTC diff --git a/pages/traits/physiology/trichocyst_discharge.html b/pages/traits/physiology/trichocyst_discharge.html index 49e03afabd0..46cd357049f 100644 --- a/pages/traits/physiology/trichocyst_discharge.html +++ b/pages/traits/physiology/trichocyst_discharge.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1083/jcb.111.6.2527
    A Paramecium possesses secretory organelles called trichocysts which are docked beneath the plasma membrane awaiting an external stimulus that triggers their exocytosis.
    -

    PMID:1703537, PMC2116420. Scientific Abstract and relevant Methods/Results OCR read directly in Europe PMC fullTextXML. The snippet is from the scientific Abstract; figures were not inspected. AED-triggered release was studied in Paramecium tetraurelia stock d4-2, a stock 51 derivative, and mutants. Calcium influx and concentration requirements concern this assay, not a universal discharge threshold or proven channel identity. The Methods distinguish low-calcium membrane injury from secretion; calcium influx alone does not demonstrate release.

    +

    PMID:1703537, PMC2116420. Scientific Abstract and relevant Methods/Results OCR read directly in Europe PMC fullTextXML. The snippet is from the scientific Abstract; figures were not inspected. AED-triggered release was studied in Paramecium tetraurelia stock d4-2, a stock 51 derivative, and mutants. Calcium influx and concentration requirements concern this assay, not a universal discharge threshold or proven channel identity. The Methods distinguish low-calcium membrane injury from secretion; calcium influx alone does not demonstrate release.

  • DOI:10.1016/s0143-4160(98)90030-6
    but only wt cells release trichocysts (t).
    -

    PMID:9681197. Primary PDF at https://d-nb.info/1107191386/34, Figures 1-4 caption, printed page 351. Pages 351-352 were visually inspected, including paired fluorescence/transmitted-light panels and Table 1. Wildtype Paramecium caudatum releases trichocysts after local AED or caffeine stimulation; tnd1 shows calcium transients and membrane fusion without contents release. Most trichocysts remain in wildtype cells during the illustrated local response, so total emptying is not required. Mutant tnd1 is boundary evidence, not a positive discharge exemplar. Reduced calcium binding is a proposed explanation, not a proven protein lesion. Natural strain provenance is unresolved.

    +

    PMID:9681197. Primary PDF at https://d-nb.info/1107191386/34, Figures 1-4 caption, printed page 351. Pages 351-352 were visually inspected, including paired fluorescence/transmitted-light panels and Table 1. Wildtype Paramecium caudatum releases trichocysts after local AED or caffeine stimulation; tnd1 shows calcium transients and membrane fusion without contents release. Most trichocysts remain in wildtype cells during the illustrated local response, so total emptying is not required. Mutant tnd1 is boundary evidence, not a positive discharge exemplar. Reduced calcium binding is a proposed explanation, not a proven protein lesion. Natural strain provenance is unresolved.

  • DOI:10.1016/0143-4160(93)90065-e
    trichocyst contents were slowly extruded
    -

    PMID:7684653. Scientific Abstract retrieved directly using an exact quoted DOI query in Europe PMC. Abstract-only access; full Methods and figures were not inspected. Slow extrusion under AED and low-calcium conditions shows why rapid expansion is not mandatory in this definition. The abstract distinguishes fusion, contents release and resealing; prolonged calcium removal is followed by cell death. Do not infer calcium irrelevance to all stages or treat terminal damage as secretion.

    +

    PMID:7684653. Scientific Abstract retrieved directly using an exact quoted DOI query in Europe PMC. Abstract-only access; full Methods and figures were not inspected. Slow extrusion under AED and low-calcium conditions shows why rapid expansion is not mandatory in this definition. The abstract distinguishes fusion, contents release and resealing; prolonged calcium removal is followed by cell death. Do not infer calcium irrelevance to all stages or treat terminal damage as secretion.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-08 16:06 UTC diff --git a/pages/traits/physiology/tripolar_mating_system.html b/pages/traits/physiology/tripolar_mating_system.html index 75d86fbeeaa..357522fa842 100644 --- a/pages/traits/physiology/tripolar_mating_system.html +++ b/pages/traits/physiology/tripolar_mating_system.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1128/ec.00271-08
    one of the parents has one contiguous MAT locus (one pole) while the other has two unlinked sex-determining regions (two poles).
    -

    Hsueh et al. (2008), PMID:18723606, PMC2568056. Exact clause in the first tripolar-cross Results subsection, checked against raw PMC HTML; not an abstract quote. Engineered Cryptococcus neoformans strains relocate a homeodomain determinant from MAT to unlinked URA5. Reciprocal crosses with wild-type partners yielded germinating, segregating progeny (Tables 2/3). Actual Figures 1/2 were inspected: Figure 1 shows colony-edge filamentation, whereas Figure 2 is a genotype model, not an observed segregation ratio. Methods, relevant Results and Discussion were read; other actual figures and supplements remain uninspected. These engineered crosses establish functional feasibility, not natural prevalence or a proven ancestral intermediate. The theoretical fertility fractions are not universal measured rates; JF289 also carries multiple SXI2a copies.

    +

    Hsueh et al. (2008), PMID:18723606, PMC2568056. Exact clause in the first tripolar-cross Results subsection, checked against raw PMC HTML; not an abstract quote. Engineered Cryptococcus neoformans strains relocate a homeodomain determinant from MAT to unlinked URA5. Reciprocal crosses with wild-type partners yielded germinating, segregating progeny (Tables 2/3). Actual Figures 1/2 were inspected: Figure 1 shows colony-edge filamentation, whereas Figure 2 is a genotype model, not an observed segregation ratio. Methods, relevant Results and Discussion were read; other actual figures and supplements remain uninspected. These engineered crosses establish functional feasibility, not natural prevalence or a proven ancestral intermediate. The theoretical fertility fractions are not universal measured rates; JF289 also carries multiple SXI2a copies.

  • DOI:10.1128/mbio.00059-26
    the MAT-fused strains were able to successfully mate with the strains in which the P/R and HD are unlinked, constituting a “tripolar” mating.
    -

    Xiong et al. (2026), PMID:41841731, PMC13059729. Exact Results s2-2 clause checked against raw Europe PMC full-text XML; not a scientific-abstract or IMPORTANCE quote. In Cryptococcus amylolentus, engineered MAT-fused derivatives of CBS6039 or CBS6273 mate with an opposite wild-type partner retaining unlinked P/R and HD loci. Results s2-2 reports sexual structures and genotyped germinating progeny; s2-4 reports genome-wide meiotic recombination in 26 tripolar progeny, within a 42-progeny analysis also containing bipolar progeny. Relevant construction, mating and sequencing Methods were read. Figure 2/4 captions were read, but actual figures and supplements remain uninspected after image access failed. Other source sections remain unread. Reduced fusion in bilateral MAT-fused bipolar crosses must not be transferred to these unilateral tripolar crosses.

    +

    Xiong et al. (2026), PMID:41841731, PMC13059729. Exact Results s2-2 clause checked against raw Europe PMC full-text XML; not a scientific-abstract or IMPORTANCE quote. In Cryptococcus amylolentus, engineered MAT-fused derivatives of CBS6039 or CBS6273 mate with an opposite wild-type partner retaining unlinked P/R and HD loci. Results s2-2 reports sexual structures and genotyped germinating progeny; s2-4 reports genome-wide meiotic recombination in 26 tripolar progeny, within a 42-progeny analysis also containing bipolar progeny. Relevant construction, mating and sequencing Methods were read. Figure 2/4 captions were read, but actual figures and supplements remain uninspected after image access failed. Other source sections remain unread. Reduced fusion in bilateral MAT-fused bipolar crosses must not be transferred to these unilateral tripolar crosses.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -271,7 +272,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed tripolar mating system -

      Added PROPOSED PHYSIOLOGY traitmech:000618 and v495 reservation METPO:1057200 under released phenotype. Two primary sources, DOI:10.1128/ec.00271-08 and DOI:10.1128/mbio.00059-26, support a cross-level phenotype with one linked and one unlinked partner. Both snippets were exact-matched to raw full text; the maintained resolver returned NOT_IN_ABSTRACT twice, not VERIFIED. Actual 2008 Figures 1/2 were inspected; 2026 figures and supplements remain unread after image access failed. Engineered provenance, no natural canonical examples, no fixed fertility fraction, and deferred protein mechanisms are explicit. Ignored-and-hidden novelty and allocation searches, fresh seed classification and open-PR inventories were checked. Writer dry run, seven focused tests, LinkML and strict validation passed; broader validation and regenerated artifacts follow before PR review.

    +

    Added PROPOSED PHYSIOLOGY traitmech:000618 and v495 reservation METPO:1057200 under released phenotype. Two primary sources, DOI:10.1128/ec.00271-08 and DOI:10.1128/mbio.00059-26, support a cross-level phenotype with one linked and one unlinked partner. Both snippets were exact-matched to raw full text; the maintained resolver returned NOT_IN_ABSTRACT twice, not VERIFIED. Actual 2008 Figures 1/2 were inspected; 2026 figures and supplements remain unread after image access failed. Engineered provenance, no natural canonical examples, no fixed fertility fraction, and deferred protein mechanisms are explicit. Ignored-and-hidden novelty and allocation searches, fresh seed classification and open-PR inventories were checked. Writer dry run, seven focused tests, LinkML and strict validation passed; broader validation and regenerated artifacts follow before PR review.

    • Read this curation session @@ -303,7 +304,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -332,12 +342,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 10:53 UTC diff --git a/pages/traits/physiology/trogocytosis.html b/pages/traits/physiology/trogocytosis.html index 227670d367f..6f2efd1479a 100644 --- a/pages/traits/physiology/trogocytosis.html +++ b/pages/traits/physiology/trogocytosis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,13 +56,13 @@

    Trait evidence (2)

    DOI:10.1038/nature13242
    amoebae kill by ingesting distinct pieces of living human cells
    -

    PMID:24717428, PMC4006097. Direct scientific Abstract quote from the final Nature/PubMed version, not the differently worded PMC author-manuscript Summary. Author-manuscript Results and Discussion, relevant imaging and cell-culture Methods, and actual Figures 1-2 were inspected at https://pmc.ncbi.nlm.nih.gov/articles/PMC4006097/. Uptake precedes target-cell death; attachment alone is not uptake. Internalization and fragmentation gates are distinct measurements. Other figures and movies were not visually audited. No universal killing threshold, nutritional benefit or complete protein mechanism is inferred.

    +

    PMID:24717428, PMC4006097. Direct scientific Abstract quote from the final Nature/PubMed version, not the differently worded PMC author-manuscript Summary. Author-manuscript Results and Discussion, relevant imaging and cell-culture Methods, and actual Figures 1-2 were inspected at https://pmc.ncbi.nlm.nih.gov/articles/PMC4006097/. Uptake precedes target-cell death; attachment alone is not uptake. Internalization and fragmentation gates are distinct measurements. Other figures and movies were not visually audited. No universal killing threshold, nutritional benefit or complete protein mechanism is inferred.

  • DOI:10.1128/mBio.00068-19
    Protection from human serum occurs only after amoebae have undergone trogocytosis of live cells but not phagocytosis of dead cells.
    -

    PMID:31040235, PMC6495370. Direct scientific Abstract quote, not the separate Importance/precis block. Cell-culture Methods, membrane-display and live/dead-cell Results, Discussion, and actual Figures 1, 6 and 8 were inspected at https://pmc.ncbi.nlm.nih.gov/articles/PMC6495370/. Figure 6B measures the percentage of internalizing amoebae, not material mass per cell. Figure 8 is a proposed model, not direct proof of a membrane-fusion or trafficking route. Other figures and supplements were not visually audited. Serum protection is condition-specific, not definitional.

    +

    PMID:31040235, PMC6495370. Direct scientific Abstract quote, not the separate Importance/precis block. Cell-culture Methods, membrane-display and live/dead-cell Results, Discussion, and actual Figures 1, 6 and 8 were inspected at https://pmc.ncbi.nlm.nih.gov/articles/PMC6495370/. Figure 6B measures the percentage of internalizing amoebae, not material mass per cell. Figure 8 is a proposed model, not direct proof of a membrane-fusion or trafficking route. Other figures and supplements were not visually audited. Serum protection is condition-specific, not definitional.

    • @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -202,7 +203,7 @@

    Canonical examples DOI:10.1128/mBio.00068-19 - Strain-qualified HM1:IMSS parental trophozoites interacting with live Jurkat cells in the 2019 study, not engineered knockdowns, vector controls or every isolate. Cell-culture Methods name ATCC as the supplier, without a catalog or lot number. The matching HM-1:IMSS collection record at https://www.atcc.org/products/30459 documents natural clinical isolation from a colonic biopsy; it does not establish an exact study lot or clone. NCBI ESearch/EFetch verified the scientific name and species rank on 2026-10-06. This taxon ID is species-level, not strain-level. + Strain-qualified HM1:IMSS parental trophozoites interacting with live Jurkat cells in the 2019 study, not engineered knockdowns, vector controls or every isolate. Cell-culture Methods name ATCC as the supplier, without a catalog or lot number. The matching HM-1:IMSS collection record at https://www.atcc.org/products/30459 documents natural clinical isolation from a colonic biopsy; it does not establish an exact study lot or clone. NCBI ESearch/EFetch verified the scientific name and species rank on 2026-10-06. This taxon ID is species-level, not strain-level. @@ -296,7 +297,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add microbial trogocytosis with bounded primary evidence -

      Added traitmech:000633 and v509 reservation METPO:1058600 using DOI:10.1038/nature13242 and DOI:10.1128/mBio.00068-19. Both scientific-abstract snippets were checked directly; inspected 2014 Figures 1-2 and 2019 Figures 1,6,8, distinguishing percentage internalizing from material mass and proposed models from observations. NCBITaxon:5759 was resolved at NCBI; the canonical example is qualified to parental HM1:IMSS and ATCC natural clinical provenance, not an engineered derivative or exact study lot. Ignored-and-hidden searches plus structured pinned ontology and full release-review parsing found no exact record or collision. Dry run and 12 focused writer tests passed before application. Full-corpus checks and artifact regeneration follow; no broader pass is claimed here. No existing trait, baseline or prior history was edited.

    +

    Added traitmech:000633 and v509 reservation METPO:1058600 using DOI:10.1038/nature13242 and DOI:10.1128/mBio.00068-19. Both scientific-abstract snippets were checked directly; inspected 2014 Figures 1-2 and 2019 Figures 1,6,8, distinguishing percentage internalizing from material mass and proposed models from observations. NCBITaxon:5759 was resolved at NCBI; the canonical example is qualified to parental HM1:IMSS and ATCC natural clinical provenance, not an engineered derivative or exact study lot. Ignored-and-hidden searches plus structured pinned ontology and full release-review parsing found no exact record or collision. Dry run and 12 focused writer tests passed before application. Full-corpus checks and artifact regeneration follow; no broader pass is claimed here. No existing trait, baseline or prior history was edited.

    • Read this curation session @@ -328,7 +329,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -357,12 +367,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 03:17 UTC diff --git a/pages/traits/physiology/trophic_type.html b/pages/traits/physiology/trophic_type.html index 8cb94dddd20..1e48573a713 100644 --- a/pages/traits/physiology/trophic_type.html +++ b/pages/traits/physiology/trophic_type.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -172,11 +173,11 @@

    Edge evidence

  • autotrophic - METPO:1000632 + METPO:1000632 is a trophic type METPO:1000631 - rdfs:subClassOf + rdfs:subClassOf

    Autotrophy is a child phenotype of trophic type.

      @@ -191,11 +192,11 @@

      Edge evidence

    • heterotrophic - METPO:1000644 + METPO:1000644 is a trophic type METPO:1000631 - rdfs:subClassOf + rdfs:subClassOf

      Heterotrophy is a child phenotype of trophic type.

        @@ -210,11 +211,11 @@

        Edge evidence

      • phototrophic - METPO:1000660 + METPO:1000660 is a trophic type METPO:1000631 - rdfs:subClassOf + rdfs:subClassOf

        Phototrophy is a child phenotype of trophic type.

          @@ -229,11 +230,11 @@

          Edge evidence

        • chemotrophic - METPO:1000641 + METPO:1000641 is a trophic type METPO:1000631 - rdfs:subClassOf + rdfs:subClassOf

          Chemotrophy is a child phenotype of trophic type.

            @@ -450,11 +451,11 @@

            Children (28)

            Synonyms (3)

              -
            • Physiology and metabolism.nutrition type.type RELATED_SYNONYM · metpo.owl
              • +
            • Physiology and metabolism.nutrition type.type RELATED_SYNONYM · metpo.owl
              • -
            • nutritional type RELATED_SYNONYM · metpo.owl
              • +
            • nutritional type RELATED_SYNONYM · metpo.owl
              • -
            • pathways RELATED_SYNONYM · metpo.owl
              • +
            • pathways RELATED_SYNONYM · metpo.owl
    • @@ -470,7 +471,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -716,7 +717,7 @@

    Curation history

  • · ADD_CANONICAL_EXAMPLES · codex -

    Resolved issue #444 after the #591 source/bin policy with 2 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; PMID:9278503), Synechocystis sp. PCC 6803 (NCBITaxon:1148; DOI:10.3390/md11082894). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    +

    Resolved issue #444 after the #591 source/bin policy with 2 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; PMID:9278503), Synechocystis sp. PCC 6803 (NCBITaxon:1148; DOI:10.3390/md11082894). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

    • @@ -749,7 +750,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1113,12 +1123,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-31 04:43 UTC diff --git a/pages/traits/physiology/trypsin_activity.html b/pages/traits/physiology/trypsin_activity.html index 11c3b390dea..6947d072fcb 100644 --- a/pages/traits/physiology/trypsin_activity.html +++ b/pages/traits/physiology/trypsin_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -128,7 +129,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -278,7 +279,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record pairs IUBMB EC 3.4.21.4 cleavage/vertebrate-pancreas snippets with an API ZYM diagnostic survey list (DOI:10.1371/journal.pone.0322500), lacking a second microbial mechanistic quote.

    +

    The current record pairs IUBMB EC 3.4.21.4 cleavage/vertebrate-pancreas snippets with an API ZYM diagnostic survey list (DOI:10.1371/journal.pone.0322500), lacking a second microbial mechanistic quote.

    @@ -384,7 +385,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -413,12 +423,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/tyrosine_arylamidase_activity.html b/pages/traits/physiology/tyrosine_arylamidase_activity.html index 210aebad65a..2c9aecc4634 100644 --- a/pages/traits/physiology/tyrosine_arylamidase_activity.html +++ b/pages/traits/physiology/tyrosine_arylamidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -106,7 +107,7 @@

    Parent traits (1)

    Synonyms (1)

      -
    • tyrosine arylamidase RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
      • +
    • tyrosine arylamidase RELATED_SYNONYM · DOI:10.1099/ijsem.0.006017
    @@ -122,7 +123,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -272,7 +273,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two diagnostic enzyme-panel survey snippets (DOI:10.1099/ijsem.0.006017, DOI:10.1128/JCM.40.9.3427-3431.2002) without verbatim catalytic reaction quotes.

    +

    The current record carries two diagnostic enzyme-panel survey snippets (DOI:10.1099/ijsem.0.006017, DOI:10.1128/JCM.40.9.3427-3431.2002) without verbatim catalytic reaction quotes.

    @@ -354,7 +355,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -383,12 +393,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/unconventional_protein_secretion.html b/pages/traits/physiology/unconventional_protein_secretion.html index 97a667e29f2..21ebe0b923c 100644 --- a/pages/traits/physiology/unconventional_protein_secretion.html +++ b/pages/traits/physiology/unconventional_protein_secretion.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.3389/fcell.2022.852028
    Our results show that neosynthesized PmaA and PalI are translocated to the PM via Golgi-bypass, similar to nutrient transporters.
    -

    PMID:35465316, PMC9021693. Scientific Abstract and selected Introduction, Results and Methods directly read in Europe PMC XML. The paper includes membrane-cargo delivery within unconventional protein secretion. Aspergillus nidulans fluorescent cargo, conditional trafficking repression and localization assays support Golgi bypass after COPII-dependent ER exit, not soluble extracellular release or universal ER independence. The reporters and promoter replacements are engineered; no natural canonical exemplar is inferred. Actual panels, supplements and independent recipient-strain provenance were not inspected.

    +

    PMID:35465316, PMC9021693. Scientific Abstract and selected Introduction, Results and Methods directly read in Europe PMC XML. The paper includes membrane-cargo delivery within unconventional protein secretion. Aspergillus nidulans fluorescent cargo, conditional trafficking repression and localization assays support Golgi bypass after COPII-dependent ER exit, not soluble extracellular release or universal ER independence. The reporters and promoter replacements are engineered; no natural canonical exemplar is inferred. Actual panels, supplements and independent recipient-strain provenance were not inspected.

  • DOI:10.7554/eLife.16299
    Under these conditions Acb1, but not Cof1, was detected in the cell wall extract of starving cells
    -

    PMID:27115345, PMC4868542. Contiguous full-text Results s2-1 span, directly read in Europe PMC XML, not an abstract quote. Mild extraction detects intact Acb1 outside the plasma membrane of starved Saccharomyces cerevisiae with Cof1 leakage and Bgl2 extraction controls. This is cell-wall/periplasmic recovery, not direct detection in culture medium. Harsh extraction, some mutants, heat and DMSO can invalidate the assay through leakage. The direct assay differs from earlier SDF-2 bioactivity assays and does not support a Vps4 requirement. Static CUPS images do not prove a temporal sequence. Actual panels and strain provenance remain uninspected.

    +

    PMID:27115345, PMC4868542. Contiguous full-text Results s2-1 span, directly read in Europe PMC XML, not an abstract quote. Mild extraction detects intact Acb1 outside the plasma membrane of starved Saccharomyces cerevisiae with Cof1 leakage and Bgl2 extraction controls. This is cell-wall/periplasmic recovery, not direct detection in culture medium. Harsh extraction, some mutants, heat and DMSO can invalidate the assay through leakage. The direct assay differs from earlier SDF-2 bioactivity assays and does not support a Vps4 requirement. Static CUPS images do not prove a temporal sequence. Actual panels and strain provenance remain uninspected.

  • DOI:10.1083/jcb.201407119
    Altogether our findings indicate that CUPS are not specialized autophagosomes as suggested previously.
    -

    PMID:25512390, PMC4274258. Scientific Abstract abstract2, distinct from the precis, and Introduction directly read in Europe PMC XML. The authors revise the earlier autophagosome interpretation of yeast CUPS. This is compartment-identity boundary evidence, not proof that every unconventional route excludes all autophagy-related machinery. Actual panels, full Methods and strain provenance were not inspected.

    +

    PMID:25512390, PMC4274258. Scientific Abstract abstract2, distinct from the precis, and Introduction directly read in Europe PMC XML. The authors revise the earlier autophagosome interpretation of yeast CUPS. This is compartment-identity boundary evidence, not proof that every unconventional route excludes all autophagy-related machinery. Actual panels, full Methods and strain provenance were not inspected.

  • DOI:10.1083/jcb.202312120
    Notably, while CUPS remain stable, the modified TGN undergoes remodeling during the later stages of unconventional secretion.
    -

    PMID:40015244, PMC11867701. Scientific Abstract, not the teaser, and selected Results, Discussion and Methods directly read in Europe PMC XML. Yeast CUPS contact a modified trans-Golgi network; this argues against defining the phenotype by absence of all Golgi-derived membranes. Rcy1 and v-SNARE perturbations reduce cell-wall recovery of Acb1, SOD1 and Trx2 with Cof1 controls. Drs2-deleted cells could not be assayed because of lysis concerns. Cargo collection and final delivery through the proposed CUPS-TGN route remain a model. BY4741 derivatives include engineered reporters and mutants. Actual panels and supplements were not visually inspected.

    +

    PMID:40015244, PMC11867701. Scientific Abstract, not the teaser, and selected Results, Discussion and Methods directly read in Europe PMC XML. Yeast CUPS contact a modified trans-Golgi network; this argues against defining the phenotype by absence of all Golgi-derived membranes. Rcy1 and v-SNARE perturbations reduce cell-wall recovery of Acb1, SOD1 and Trx2 with Cof1 controls. Drs2-deleted cells could not be assayed because of lysis concerns. Cargo collection and final delivery through the proposed CUPS-TGN route remain a model. BY4741 derivatives include engineered reporters and mutants. Actual panels and supplements were not visually inspected.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -221,7 +222,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    The broad usage in DOI:10.3389/fcell.2022.852028 includes plasma-membrane delivery after ER entry; DOI:10.7554/eLife.16299 describes an ER-bypassing soluble-cargo route. Preserve both, rather than treating leaderless secretion, Golgi bypass or secretory autophagy as exact synonyms. This concerns traffic performed by a eukaryotic microbe, not its animal or plant host. An absent predicted signal peptide, ATG dependence, CUPS formation or protein detected after lysis alone is insufficient. Membrane localization does not establish soluble release. The degradative autophagy record traitmech:000638 is not a broader parent; exocytosis traitmech:000637 specifies fusion-pore release rather than an unconventional itinerary. Overlap is not disjointness. Obsolete METPO secretion classes do not supply an active exact term. Keep METPO:1000059 as parent and leave ontology equivalences and finer route hierarchy for human review.

    +

    The broad usage in DOI:10.3389/fcell.2022.852028 includes plasma-membrane delivery after ER entry; DOI:10.7554/eLife.16299 describes an ER-bypassing soluble-cargo route. Preserve both, rather than treating leaderless secretion, Golgi bypass or secretory autophagy as exact synonyms. This concerns traffic performed by a eukaryotic microbe, not its animal or plant host. An absent predicted signal peptide, ATG dependence, CUPS formation or protein detected after lysis alone is insufficient. Membrane localization does not establish soluble release. The degradative autophagy record traitmech:000638 is not a broader parent; exocytosis traitmech:000637 specifies fusion-pore release rather than an unconventional itinerary. Overlap is not disjointness. Obsolete METPO secretion classes do not supply an active exact term. Keep METPO:1000059 as parent and leave ontology equivalences and finer route hierarchy for human review.

    @@ -339,7 +340,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -368,12 +378,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-06 18:53 UTC diff --git a/pages/traits/physiology/unequal_protein_aggregate_inheritance.html b/pages/traits/physiology/unequal_protein_aggregate_inheritance.html index e97472ef437..febd2d15f9a 100644 --- a/pages/traits/physiology/unequal_protein_aggregate_inheritance.html +++ b/pages/traits/physiology/unequal_protein_aggregate_inheritance.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.1073/pnas.0708931105
    their position in the mother cell determines which offspring inherits the inclusion body and where it will be located within it
    -

    Lindner et al. 2008, PMID:18287048, PMC2268587; Results, Inclusion Bodies Are Formed in Discrete Cellular Positions and Accumulate in Old Poles Under Nonstressing Conditions. Primary PMC Results and Methods directly read. The quoted position is that of an IbpA-YFP focus. MGAY is an engineered MG1655 reporter strain, grown on LB-agarose at 37 C without imposed stress. Figure 2 is the inspected localization measurement; Figure 3 is an inspected lineage schematic, not another experiment. Pole identity changes across divisions. These observations describe reporter-focus inheritance and eventual older-pole accumulation. Govers et al. 2018 (DOI:10.1371/journal.pbio.2003853) subsequently demonstrated label-induced clustering with IbpA-YFP. The older readout is not independent proof of endogenous unstressed aggregation; naming the engineered strain alone does not resolve this assay bias. Neither active transport, universal aggregate toxicity nor a natural canonical exemplar is established. Supplements were not inspected. The full-text span retains the native abstract resolver verdict NOT_IN_ABSTRACT.

    +

    Lindner et al. 2008, PMID:18287048, PMC2268587; Results, Inclusion Bodies Are Formed in Discrete Cellular Positions and Accumulate in Old Poles Under Nonstressing Conditions. Primary PMC Results and Methods directly read. The quoted position is that of an IbpA-YFP focus. MGAY is an engineered MG1655 reporter strain, grown on LB-agarose at 37 C without imposed stress. Figure 2 is the inspected localization measurement; Figure 3 is an inspected lineage schematic, not another experiment. Pole identity changes across divisions. These observations describe reporter-focus inheritance and eventual older-pole accumulation. Govers et al. 2018 (DOI:10.1371/journal.pbio.2003853) subsequently demonstrated label-induced clustering with IbpA-YFP. The older readout is not independent proof of endogenous unstressed aggregation; naming the engineered strain alone does not resolve this assay bias. Neither active transport, universal aggregate toxicity nor a natural canonical exemplar is established. Supplements were not inspected. The full-text span retains the native abstract resolver verdict NOT_IN_ABSTRACT.

  • DOI:10.1371/journal.pbio.1001886
    We experimentally confirmed that fusion increases segregation asymmetry, for a range of stresses, and identified Hsp16 as a fusion factor.
    -

    Coelho et al. 2014, PMID:24936793, PMC4061010; scientific abstract, not Author Summary. Primary XML and actual Figures 3, 4 and S4 were inspected. Hsp104-GFP fission-yeast imaging supports stress-associated unequal inheritance without consistent old/new-pole bias. Figure 3C measures an absolute sibling difference in aggregate-associated fluorescence, not concentration; S4I measures count asymmetry. Figure 4B is fusion and 4C is nucleation: the caption reverses them. A Results pointer to 4C for stress-dependent asymmetry disagrees with the plotted endpoints. Figure 3C describes continuous 40 C, whereas Methods describes 40 C for one hour followed by 37 C; this remains unresolved. Text S1 experimental methods and strain table were text-extracted, not visually rendered. No universal transport, death threshold or rejuvenation mechanism is inferred. The scientific-abstract span matches the native resolver text (VERIFIED).

    +

    Coelho et al. 2014, PMID:24936793, PMC4061010; scientific abstract, not Author Summary. Primary XML and actual Figures 3, 4 and S4 were inspected. Hsp104-GFP fission-yeast imaging supports stress-associated unequal inheritance without consistent old/new-pole bias. Figure 3C measures an absolute sibling difference in aggregate-associated fluorescence, not concentration; S4I measures count asymmetry. Figure 4B is fusion and 4C is nucleation: the caption reverses them. A Results pointer to 4C for stress-dependent asymmetry disagrees with the plotted endpoints. Figure 3C describes continuous 40 C, whereas Methods describes 40 C for one hour followed by 37 C; this remains unresolved. Text S1 experimental methods and strain table were text-extracted, not visually rendered. No universal transport, death threshold or rejuvenation mechanism is inferred. The scientific-abstract span matches the native resolver text (VERIFIED).

  • DOI:10.1111/mmi.14228
    Noticeably, stalked cells always inherited more aggregates (75%) than swarmer cells (25%).
    -

    Schramm et al. 2019, PMID:30779464, PMC6850343; Results, The aggregate load does not sort to swarmer or stalked daughter cells in C. crescentus. Primary XML Results, Discussion and relevant Methods were read; actual Figure 6 was inspected. DnaK-mVenus, delta-clpB cells recovered at 30 C after 10 minutes at 40 C. Figure 6G reports aggregate allocation across daughter cell types over successive divisions, not the fraction of all sibling pairs with unequal counts. Figure 6F measures projected cell area, not volume. Unequal shared inheritance is compatible with the broad phenotype; it contradicts neither sharing nor a stable allocation ratio. The paper limits universal exclusive old-pole retention, not every form of quantitative inequality. Supplements and independent strain provenance were not inspected; no natural canonical example is asserted. The full-text span retains the native abstract resolver verdict NOT_IN_ABSTRACT.

    +

    Schramm et al. 2019, PMID:30779464, PMC6850343; Results, The aggregate load does not sort to swarmer or stalked daughter cells in C. crescentus. Primary XML Results, Discussion and relevant Methods were read; actual Figure 6 was inspected. DnaK-mVenus, delta-clpB cells recovered at 30 C after 10 minutes at 40 C. Figure 6G reports aggregate allocation across daughter cell types over successive divisions, not the fraction of all sibling pairs with unequal counts. Figure 6F measures projected cell area, not volume. Unequal shared inheritance is compatible with the broad phenotype; it contradicts neither sharing nor a stable allocation ratio. The paper limits universal exclusive old-pole retention, not every form of quantitative inequality. Supplements and independent strain provenance were not inspected; no natural canonical example is asserted. The full-text span retains the native abstract resolver verdict NOT_IN_ABSTRACT.

  • DOI:10.1371/journal.pbio.2003853
    the polarly deposited PA was subjected to limited disaggregation and therefore became asymmetrically inherited for a large number of generations
    -

    Govers et al. 2018, PMID:30153247, PMC6112618; scientific abstract, directly matched in primary XML and source-qualified MED. Results on reporter validation and post-stress inheritance, relevant Methods and actual Figures 1 and 3 were inspected. Figure 1 shows reporter-dependent clustering; Figure 3 separately follows engineered MG1655 IbpA-msfGFP lineages after 47 C for 15 minutes, with microscopy at 37 C. Focus inheritance is distinct from the fluorescence concentration and growth readouts. This does not validate unstressed IbpA-YFP foci as endogenous aggregates or imply universal harm, benefit, aging or rejuvenation. Supplementary controls were read only where described in Results; their images, raw data and independent strain provenance were not assessed.

    +

    Govers et al. 2018, PMID:30153247, PMC6112618; scientific abstract, directly matched in primary XML and source-qualified MED. Results on reporter validation and post-stress inheritance, relevant Methods and actual Figures 1 and 3 were inspected. Figure 1 shows reporter-dependent clustering; Figure 3 separately follows engineered MG1655 IbpA-msfGFP lineages after 47 C for 15 minutes, with microscopy at 37 C. Focus inheritance is distinct from the fluorescence concentration and growth readouts. This does not validate unstressed IbpA-YFP foci as endogenous aggregates or imply universal harm, benefit, aging or rejuvenation. Supplementary controls were read only where described in Results; their images, raw data and independent strain provenance were not assessed.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -325,7 +326,7 @@

    Recorded curation sessions

  • · codex
    • EDIT — Qualify aggregate-inheritance reporter evidence -

      Corrected the older IbpA-YFP evidence interpretation against Govers 2018, DOI:10.1371/journal.pbio.2003853. Retained the historical snippet as reporter-focus evidence, added a checked scientific-abstract snippet and separate post-stress IbpA-msfGFP inheritance context, and preserved definition, identity, PROPOSED status and original event. Primary Results, relevant Methods and actual Figures 1 and 3 were inspected. The source sidecar appends a correction to its historical assessment; the proposal sources and skill are updated. The guarded correction and 32 focused tests passed before application. Further native validation and linked review outcomes are recorded separately. This succeeds history/records/unequal_protein_aggregate_inheritance/2026-10-12T144228Z-codex-c658f7.yaml without rewriting it.

    +

    Corrected the older IbpA-YFP evidence interpretation against Govers 2018, DOI:10.1371/journal.pbio.2003853. Retained the historical snippet as reporter-focus evidence, added a checked scientific-abstract snippet and separate post-stress IbpA-msfGFP inheritance context, and preserved definition, identity, PROPOSED status and original event. Primary Results, relevant Methods and actual Figures 1 and 3 were inspected. The source sidecar appends a correction to its historical assessment; the proposal sources and skill are updated. The guarded correction and 32 focused tests passed before application. Further native validation and linked review outcomes are recorded separately. This succeeds history/records/unequal_protein_aggregate_inheritance/2026-10-12T144228Z-codex-c658f7.yaml without rewriting it.

    • Read this curation session @@ -357,7 +358,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -386,12 +396,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-12 18:26 UTC diff --git a/pages/traits/physiology/unisexual_reproduction.html b/pages/traits/physiology/unisexual_reproduction.html index 623616b5abe..b987b7deb63 100644 --- a/pages/traits/physiology/unisexual_reproduction.html +++ b/pages/traits/physiology/unisexual_reproduction.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,25 +56,25 @@

    Trait evidence (4)

    DOI:10.1371/journal.pgen.1003688
    Sexual reproduction involves cells of either opposite (bisexual) or one (unisexual) mating type.
    -

    Feretzaki and Heitman (2013), PMID:23966871, PMC3744442. Exact sentence of the directly retrieved scientific abstract (abstract1), not the separate Author Summary. Introduction s1 also includes Candida unisexual reproduction and helper-cell stimulation. Results s2g/s2h and Methods s4a/s4f were read in XML: reduced sporulation in Spo11/Ubc5 mutants is distinct from hyphal growth, and Ubc5's precise role remains unresolved. Do not universalize one diploidization route or timing. Actual figures, complete tables, supplements and other experimental sections remain uninspected; no protein-level dependency is asserted here. Species names follow the paper.

    +

    Feretzaki and Heitman (2013), PMID:23966871, PMC3744442. Exact sentence of the directly retrieved scientific abstract (abstract1), not the separate Author Summary. Introduction s1 also includes Candida unisexual reproduction and helper-cell stimulation. Results s2g/s2h and Methods s4a/s4f were read in XML: reduced sporulation in Spo11/Ubc5 mutants is distinct from hyphal growth, and Ubc5's precise role remains unresolved. Do not universalize one diploidization route or timing. Actual figures, complete tables, supplements and other experimental sections remain uninspected; no protein-level dependency is asserted here. Species names follow the paper.

  • DOI:10.1038/nature03448
    Furthermore, fusion and meiosis can occur between non-isogenic alpha strains, enabling genetic exchange.
    -

    Lin, Hull and Heitman (2005), PMID:15846346. Exact sentence from the scientific abstract directly retrieved through Europe PMC core metadata. The API uses the word alpha. Cryptococcus same-type partners need not be genetically identical: this supports outcrossing within a mating type, not obligatory clonal selfing. Diploidization and meiosis distinguish the reported fruiting from purely mitotic growth. Full text, methods, figures, supplements and natural strain provenance remain uninspected; no canonical example is inferred.

    +

    Lin, Hull and Heitman (2005), PMID:15846346. Exact sentence from the scientific abstract directly retrieved through Europe PMC core metadata. The API uses the word alpha. Cryptococcus same-type partners need not be genetically identical: this supports outcrossing within a mating type, not obligatory clonal selfing. Diploidization and meiosis distinguish the reported fruiting from purely mitotic growth. Full text, methods, figures, supplements and natural strain provenance remain uninspected; no canonical example is inferred.

  • DOI:10.1038/nature08252
    could be induced to undergo chromosome loss to produce diploid cells, thereby completing a parasexual mating cycle
    -

    Alby et al. (2009), PMID:19675652, PMC2866515. Exact main-text clause retrieved via NCBI PMC efetch after Europe PMC full-text failure, not an abstract quote. All main-text paragraphs and Methods Summary were read; Figures 3/4 and Supplementary Figure 7 were visually inspected. Marked opaque Candida a-a partners form tetraploids. Supplement pp. 6-7/15 reports sorbose-induced ploidy reduction, including near-diploid and intermediate progeny, not uniform restoration of euploidy. Bar1-deletion assays and helper-stimulated wild-type mating are distinct: opposite-type pheromone helpers need not contribute genomes. Other figures and supplement sections remain uninspected. Engineered or marked strains are not promoted to natural canonical examples.

    +

    Alby et al. (2009), PMID:19675652, PMC2866515. Exact main-text clause retrieved via NCBI PMC efetch after Europe PMC full-text failure, not an abstract quote. All main-text paragraphs and Methods Summary were read; Figures 3/4 and Supplementary Figure 7 were visually inspected. Marked opaque Candida a-a partners form tetraploids. Supplement pp. 6-7/15 reports sorbose-induced ploidy reduction, including near-diploid and intermediate progeny, not uniform restoration of euploidy. Bar1-deletion assays and helper-stimulated wild-type mating are distinct: opposite-type pheromone helpers need not contribute genomes. Other figures and supplement sections remain uninspected. Engineered or marked strains are not promoted to natural canonical examples.

  • DOI:10.1371/journal.pbio.1001653
    generates abundant hyphae, homozygous diploid intermediates, and haploid meiotic spores when grown on mating-inducing media all by itself.
    -

    Ni et al. (2013), PMID:24058295, PMC3769227. Exact Results s2a clause, not an abstract quote; its subject is XL280alpha. Scientific abstract, author summary, Results s2a and Methods s4b were read directly in XML. Solo culture on V8 or filament agar followed by spore isolation supports selfing in this laboratory F1 derivative of B3501alpha and JEC20a. Natural ancestral isolates do not make XL280 a natural exemplar. The paper does not resolve cell fusion versus endoreplication into one obligatory route. Actual figures, supplements including Table S4, and other experimental sections remain uninspected. Aneuploidy and adaptive benefit are not defining requirements of the whole trait.

    +

    Ni et al. (2013), PMID:24058295, PMC3769227. Exact Results s2a clause, not an abstract quote; its subject is XL280alpha. Scientific abstract, author summary, Results s2a and Methods s4b were read directly in XML. Solo culture on V8 or filament agar followed by spore isolation supports selfing in this laboratory F1 derivative of B3501alpha and JEC20a. Natural ancestral isolates do not make XL280 a natural exemplar. The paper does not resolve cell fusion versus endoreplication into one obligatory route. Actual figures, supplements including Table S4, and other experimental sections remain uninspected. Aneuploidy and adaptive benefit are not defining requirements of the whole trait.

    • @@ -125,7 +126,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -221,7 +222,7 @@

    Discussions and Knowledge Gaps (2)

    mechanism it concerns.

    -

    One mating type does not mean one strain: non-isogenic same-type partners can exchange genetic material. Solo selfing overlaps homothallism (traitmech:000609), but the whole class is not restricted to single-isolate self-fertility. It is not a subclass of parasexuality (traitmech:000607), because meiotic cycles are also included. Pheromone-producing opposite-type helper cells are not necessarily genetic contributors, so do not require their physical absence. Use released phenotype METPO:1000059 in both record and proposal; PHYSIOLOGY is only a filesystem category. MAT sequence content, population mating-type bias or hyphae alone do not establish reproductive completion. Do not require universal meiosis, spores, cell fusion, clonality or absence of outcrossing. Resolve context-dependent same-sex mating terminology and external phenotype/process mappings before adding synonyms or xrefs. The existing homothallism evidence note, citing DOI:10.5598/imafungus.2015.06.01.13, groups unisexual reproduction within a homothallism umbrella. That wording conflicts with interpreting the current single-isolate self-fertility definition as a universal superclass here. Our scope decision interprets the umbrella as including unisexual selfing, not as evidence that every same-type outcrossing partner is independently self-fertile. Preserve the older source attribution and retain phenotype while the operational and umbrella scopes await curator reconciliation; issue #1703 records this explicit distinction.

    +

    One mating type does not mean one strain: non-isogenic same-type partners can exchange genetic material. Solo selfing overlaps homothallism (traitmech:000609), but the whole class is not restricted to single-isolate self-fertility. It is not a subclass of parasexuality (traitmech:000607), because meiotic cycles are also included. Pheromone-producing opposite-type helper cells are not necessarily genetic contributors, so do not require their physical absence. Use released phenotype METPO:1000059 in both record and proposal; PHYSIOLOGY is only a filesystem category. MAT sequence content, population mating-type bias or hyphae alone do not establish reproductive completion. Do not require universal meiosis, spores, cell fusion, clonality or absence of outcrossing. Resolve context-dependent same-sex mating terminology and external phenotype/process mappings before adding synonyms or xrefs. The existing homothallism evidence note, citing DOI:10.5598/imafungus.2015.06.01.13, groups unisexual reproduction within a homothallism umbrella. That wording conflicts with interpreting the current single-isolate self-fertility definition as a universal superclass here. Our scope decision interprets the umbrella as including unisexual selfing, not as evidence that every same-type outcrossing partner is independently self-fertile. Preserve the older source attribution and retain phenotype while the operational and umbrella scopes await curator reconciliation; issue #1703 records this explicit distinction.

    @@ -327,7 +328,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -356,12 +366,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-05 05:05 UTC diff --git a/pages/traits/physiology/urease_activity.html b/pages/traits/physiology/urease_activity.html index fe0a128e5d3..75162d9a2a1 100644 --- a/pages/traits/physiology/urease_activity.html +++ b/pages/traits/physiology/urease_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -156,7 +157,7 @@

    Edge evidence

    GO:0009039 manifests as urease activity - traitmech:000077 + traitmech:000077 METPO:2007400

    Urease enzymatic activity manifests as the observable urease-activity phenotype scored by the diagnostic urease test.

      @@ -307,8 +308,8 @@

      Protein and taxon examples

    		 - Sporosarcina pasteurii -
    NCBITaxon:1474 + Sporosarcina pasteurii +
    NCBITaxon:1474         		REVIEWED
    @@ -337,8 +338,8 @@

    Protein and taxon examples

    		 - Sporosarcina pasteurii -
    NCBITaxon:1474 + Sporosarcina pasteurii +
    NCBITaxon:1474         		REVIEWED
    @@ -367,8 +368,8 @@

    Protein and taxon examples

    		 - Sporosarcina pasteurii -
    NCBITaxon:1474 + Sporosarcina pasteurii +
    NCBITaxon:1474         		REVIEWED
    @@ -434,9 +435,9 @@

    Parent traits (1)

    Synonyms (2)

    @@ -452,7 +453,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -752,7 +753,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1116,12 +1126,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/valine_arylamidase_activity.html b/pages/traits/physiology/valine_arylamidase_activity.html index f5e92b9bdf8..70d75e186ef 100644 --- a/pages/traits/physiology/valine_arylamidase_activity.html +++ b/pages/traits/physiology/valine_arylamidase_activity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -263,7 +264,7 @@

    Discussions and Knowledge Gaps (2)

    -

    The current record carries two API ZYM diagnostic survey snippets (DOI:10.3389/fmicb.2022.1034816, DOI:10.1099/ijsem.0.002327) without verbatim catalytic reaction quotes.

    +

    The current record carries two API ZYM diagnostic survey snippets (DOI:10.3389/fmicb.2022.1034816, DOI:10.1099/ijsem.0.002327) without verbatim catalytic reaction quotes.

    @@ -345,7 +346,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -374,12 +384,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-23 09:40 UTC diff --git a/pages/traits/physiology/viable_but_nonculturable_state.html b/pages/traits/physiology/viable_but_nonculturable_state.html index 404ce824ee8..26bb1866dd5 100644 --- a/pages/traits/physiology/viable_but_nonculturable_state.html +++ b/pages/traits/physiology/viable_but_nonculturable_state.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    causes viable but nonculturable state - traitmech:000081 + traitmech:000081 biolink:causes

    Stress drives cells into the viable-but-nonculturable state.

      @@ -118,7 +119,7 @@

      Edge evidence

      GO:0022611 confers viable but nonculturable state - traitmech:000081 + traitmech:000081 METPO:2007700

      The VBNC state is a form of microbial dormancy.

        @@ -137,7 +138,7 @@

        Edge evidence

        promotes viable but nonculturable state - traitmech:000081 + traitmech:000081 RO:0002213

        Oxidative stress / ROS accumulation promotes entry into the VBNC state.

          @@ -175,7 +176,7 @@

          Edge evidence

          contributes to viable but nonculturable state - traitmech:000081 + traitmech:000081 RO:0002326

          Enhanced stress resistance supports maintenance of the VBNC state.

            @@ -213,7 +214,7 @@

            Edge evidence

            InterPro:IPR012761 promotes viable but nonculturable state - traitmech:000081 + traitmech:000081 RO:0002213

            RpoS promotes persistence and retained resuscitation competence in the E. coli VBNC state.

              @@ -307,8 +308,8 @@

              Protein and taxon examples

    		 - Escherichia coli K-12 -
    NCBITaxon:83333 + Escherichia coli K-12 +
    NCBITaxon:83333         		REVIEWED
    @@ -374,7 +375,7 @@

    Parent traits (1)

    Synonyms (1)

    @@ -390,7 +391,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
      • +
    • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -487,7 +488,7 @@

    Deep research

    - **Exhibit reduced metabolic activity** with decreased nutrient transport and respiration rates (pazosrojas2023theviablebut pages 1-2). - **Express genes continuously**, distinguishing VBNC from spore-forming states (pazosrojas2023theviablebut pages 1-2). -Published: Pazos-Rojas et al., *Microorganisms*, December 2023, https://doi.org/10.3390/microorganisms12010039; Prosdocimi et al., *Annals of Microbiology*, January 2023, https://doi.org/10.1186/s13213-022-01703-6. +Published: Pazos-Rojas et al., *Microorganisms*, December 2023, https://doi.org/10.3390/microorganisms12010039; Prosdocimi et al., *Annals of Microbiology*, January 2023, https://doi.org/10.1186/s13213-022-01703-6. ### 1.2 Boundary Conditions @@ -500,7 +501,7 @@

    Deep research

    **Experimental distinction** from moribund cells: VBNC cells remain "sterile but metabolically active" and "intact" (nystrom2003nonculturablebacteriaprogrammed pages 1-2), whereas moribund cells in the death phase will eventually lose viability. -Published: Nyström, *BioEssays*, March 2003, https://doi.org/10.1002/bies.10233. +Published: Nyström, *BioEssays*, March 2003, https://doi.org/10.1002/bies.10233. ### 1.3 Phenotypic Characteristics @@ -518,7 +519,7 @@

    Deep research

    - Reduced DNA quantity (flow cytometry) (prosdocimi2023cellphenotypechanges pages 1-2). - Altered membrane permeability and fatty acid composition (pazosrojas2023theviablebut pages 11-13). -Published: Santos et al., *Frontiers in Cellular and Infection Microbiology*, March 2023, https://doi.org/10.3389/fcimb.2023.1122450; Cantlay et al., *Frontiers in Microbiology*, February 2024, https://doi.org/10.3389/fmicb.2024.1347488. +Published: Santos et al., *Frontiers in Cellular and Infection Microbiology*, March 2023, https://doi.org/10.3389/fcimb.2023.1122450; Cantlay et al., *Frontiers in Microbiology*, February 2024, https://doi.org/10.3389/fmicb.2024.1347488. --- @@ -663,7 +664,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -1027,12 +1037,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-22 01:35 UTC diff --git a/pages/traits/physiology/viscotaxis.html b/pages/traits/physiology/viscotaxis.html index abf53390916..227d910d041 100644 --- a/pages/traits/physiology/viscotaxis.html +++ b/pages/traits/physiology/viscotaxis.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -55,19 +56,19 @@

    Trait evidence (3)

    DOI:10.1099/00221287-109-1-113
    We have designated this positive response to a viscosity gradient as 'viscotaxis'.
    -

    Abstract, exact-matched at Europe PMC (PMID:731206); full text not inspected. The antecedent is preferential migration into the more viscous region by the paper's historically named Leptospira interrogans (biflexa) strain B16. This supports positive viscotaxis under the reported conditions, not a universal direction of response. The historical name has not been reconciled to a modern species or strain taxon; no modern Leptospira identity or pathogenicity is inferred.

    +

    Abstract, exact-matched at Europe PMC (PMID:731206); full text not inspected. The antecedent is preferential migration into the more viscous region by the paper's historically named Leptospira interrogans (biflexa) strain B16. This supports positive viscotaxis under the reported conditions, not a universal direction of response. The historical name has not been reconciled to a modern species or strain taxon; no modern Leptospira identity or pathogenicity is inferred.

  • DOI:10.1038/s41598-020-79887-7
    they concentrate in the region of low viscosity or maintain a uniform concentration profile, depending on the viscosity ratio between the two regions.
    -

    Abstract, exact-matched at Europe PMC (PMID:33432106). PMC7801662 full text, Fig. 5 and supplement Figs. S1-S3 were inspected. Wild-type Chlamydomonas reinhardtii showed net redistribution toward lower viscosity in some tested conditions but not others. Short-flagella results are not substituted for the wild type. Measurements followed pump stoppage; optical filtering limited phototactic bias. Interface reorientation, speed and angular diffusion jointly affect transport; a uniform profile is not positive evidence of net migration. The confined sharp-interface experiment does not directly validate an unconfined slowly varying gradient model. Strain accession provenance remains unresolved.

    +

    Abstract, exact-matched at Europe PMC (PMID:33432106). PMC7801662 full text, Fig. 5 and supplement Figs. S1-S3 were inspected. Wild-type Chlamydomonas reinhardtii showed net redistribution toward lower viscosity in some tested conditions but not others. Short-flagella results are not substituted for the wild type. Measurements followed pump stoppage; optical filtering limited phototactic bias. Interface reorientation, speed and angular diffusion jointly affect transport; a uniform profile is not positive evidence of net migration. The confined sharp-interface experiment does not directly validate an unconfined slowly varying gradient model. Strain accession provenance remains unresolved.

  • DOI:10.1103/physrevlett.120.208002
    suitable body shapes create viscotaxis based on a systematic asymmetry of viscous forces acting on a microswimmer.
    -

    Abstract, exact-matched at Europe PMC (PMID:29864289); full text not inspected. This is a theoretical framework for self-propelled swimmers in slowly varying viscosity fields, not a new biological migration assay or receptor discovery. It supports a possible hydrodynamic contribution without requiring a universal sensory pathway. Suggested functions of microbial body-shape changes are not treated as experimentally established molecular mechanisms.

    +

    Abstract, exact-matched at Europe PMC (PMID:29864289); full text not inspected. This is a theoretical framework for self-propelled swimmers in slowly varying viscosity fields, not a new biological migration assay or receptor discovery. It supports a possible hydrodynamic contribution without requiring a universal sensory pathway. Suggested functions of microbial body-shape changes are not treated as experimentally established molecular mechanisms.

    • @@ -119,7 +120,7 @@

    kg-microbe context

    via parent_proxy.

      -
    • METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]
      • +
    • motile METPO:1000702 [+24.397, -70.567, +20.807, -80.811, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -277,7 +278,7 @@

    Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed viscotaxis -

      Created traitmech:000593 under motile METPO:1000702 with three primary DOI sources: 10.1099/00221287-109-1-113 (PMID:731206), 10.1038/s41598-020-79887-7 (PMID:33432106; PMCID:PMC7801662), and 10.1103/physrevlett.120.208002 (PMID:29864289). Three abstract snippets exactly matched authoritative Europe PMC metadata. Inspected the algae full text, Fig. 5 and supplementary Figs. S1-S3 to retain conditional redistribution and distinguish wild-type from short-flagella results, uniform-speed responses, and hydrodynamic models. Fresh seed: 399 IDs, 344 present and 55 absent in the pre-change 987-record corpus. Whole-repository ignored-and-hidden searches and structured OWL review found no exact record or term; broader research mentions concern viscosity-dependent swimming speed. Reserved METPO:1054700 in v470. Deferred historical strain taxonomy, natural strain accessions, canonical examples, external equivalents and molecular graphs in two discussions. Validated dry run and seven focused tests passed. Existing add-trait guidance covers the evidence boundaries without further edits.

    +

    Created traitmech:000593 under motile METPO:1000702 with three primary DOI sources: 10.1099/00221287-109-1-113 (PMID:731206), 10.1038/s41598-020-79887-7 (PMID:33432106; PMCID:PMC7801662), and 10.1103/physrevlett.120.208002 (PMID:29864289). Three abstract snippets exactly matched authoritative Europe PMC metadata. Inspected the algae full text, Fig. 5 and supplementary Figs. S1-S3 to retain conditional redistribution and distinguish wild-type from short-flagella results, uniform-speed responses, and hydrodynamic models. Fresh seed: 399 IDs, 344 present and 55 absent in the pre-change 987-record corpus. Whole-repository ignored-and-hidden searches and structured OWL review found no exact record or term; broader research mentions concern viscosity-dependent swimming speed. Reserved METPO:1054700 in v470. Deferred historical strain taxonomy, natural strain accessions, canonical examples, external equivalents and molecular graphs in two discussions. Validated dry run and seven focused tests passed. Existing add-trait guidance covers the evidence boundaries without further edits.

    • Read this curation session @@ -309,7 +310,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    PROPOSED
    +
    PROPOSED + + +
    + What this status means +

    Candidate trait proposed from literature research to fill a coverage gap; not yet curator-reviewed. Must carry at least two distinct literature citations (across definition_source and evidence) — this is enforced by scripts/audit_proposals.py in the `qc` target.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -338,12 +348,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-10-04 09:36 UTC diff --git a/pages/traits/quantitative_property/has_maximum_observed_value.html b/pages/traits/quantitative_property/has_maximum_observed_value.html index d8ed27ee3ff..f841a75cdba 100644 --- a/pages/traits/quantitative_property/has_maximum_observed_value.html +++ b/pages/traits/quantitative_property/has_maximum_observed_value.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    DATATYPE_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/quantitative_property/has_minimum_observed_value.html b/pages/traits/quantitative_property/has_minimum_observed_value.html index a484d02a338..0c68821a36d 100644 --- a/pages/traits/quantitative_property/has_minimum_observed_value.html +++ b/pages/traits/quantitative_property/has_minimum_observed_value.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    DATATYPE_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/quantitative_property/has_observed_spot_value.html b/pages/traits/quantitative_property/has_observed_spot_value.html index c0cd0367635..45dacf1ea9c 100644 --- a/pages/traits/quantitative_property/has_observed_spot_value.html +++ b/pages/traits/quantitative_property/has_observed_spot_value.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    DATATYPE_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/quantitative_property/has_value.html b/pages/traits/quantitative_property/has_value.html index ced41f71025..fb6eeea5caf 100644 --- a/pages/traits/quantitative_property/has_value.html +++ b/pages/traits/quantitative_property/has_value.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -85,7 +86,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:2000071 [-0.023, -0.016, -0.102, +0.094, …]
      • +
    • has value METPO:2000071 [-0.023, -0.016, -0.102, +0.094, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -217,7 +218,16 @@

    Identifier

    Term kind
    DATATYPE_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -246,12 +256,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/quantitative_property/has_value_comments.html b/pages/traits/quantitative_property/has_value_comments.html index d914904a891..2dd00f7197c 100644 --- a/pages/traits/quantitative_property/has_value_comments.html +++ b/pages/traits/quantitative_property/has_value_comments.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    DATATYPE_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/quantitative_property/is_negative_data.html b/pages/traits/quantitative_property/is_negative_data.html index 0f333de350e..ff9af733874 100644 --- a/pages/traits/quantitative_property/is_negative_data.html +++ b/pages/traits/quantitative_property/is_negative_data.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -94,7 +95,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -226,7 +227,16 @@

    Identifier

    Term kind
    DATATYPE_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -255,12 +265,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/quantitative_property/observation_data_property.html b/pages/traits/quantitative_property/observation_data_property.html index e837033fddb..953f28a0f4e 100644 --- a/pages/traits/quantitative_property/observation_data_property.html +++ b/pages/traits/quantitative_property/observation_data_property.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -100,7 +101,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -232,7 +233,16 @@

    Identifier

    Term kind
    DATATYPE_PROPERTY
    Status
    -
    DEPRECATED
    +
    DEPRECATED + + +
    + What this status means +

    Superseded by another TraitRecord.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -261,12 +271,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-17 22:30 UTC diff --git a/pages/traits/upper/biological_process.html b/pages/traits/upper/biological_process.html index 093ef6d0fd9..a677fdf6c7b 100644 --- a/pages/traits/upper/biological_process.html +++ b/pages/traits/upper/biological_process.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -115,11 +116,11 @@

    Edge evidence

  • metabolism - METPO:1000060 + METPO:1000060 specializes biological process METPO:1000630 - rdfs:subClassOf + rdfs:subClassOf

    In TraitMech, metabolism is the non-environmental child class under biological process.

    • @@ -298,7 +299,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -549,7 +550,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -913,12 +923,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 06:15 UTC diff --git a/pages/traits/upper/chemical_entity.html b/pages/traits/upper/chemical_entity.html index 380648685be..f3a28e43223 100644 --- a/pages/traits/upper/chemical_entity.html +++ b/pages/traits/upper/chemical_entity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -120,7 +121,7 @@

    kg-microbe context

    via direct_metpo.

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -233,7 +234,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -262,12 +272,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 16:30 UTC diff --git a/pages/traits/upper/enzyme.html b/pages/traits/upper/enzyme.html index 2fbc05c3fff..fe756ca0743 100644 --- a/pages/traits/upper/enzyme.html +++ b/pages/traits/upper/enzyme.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000527 [+0.167, -0.909, -0.249, +1.095, …]
      • +
    • enzyme METPO:1000527 [+0.167, -0.909, -0.249, +1.095, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -232,7 +233,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    @@ -261,12 +271,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 16:45 UTC diff --git a/pages/traits/upper/material_entity.html b/pages/traits/upper/material_entity.html index 505bdc4fe2a..bdfb07e900e 100644 --- a/pages/traits/upper/material_entity.html +++ b/pages/traits/upper/material_entity.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    METPO:1000186 can bear quality - METPO:1000188 + METPO:1000188

    Material entities provide bearers for qualities used in trait descriptions.

      @@ -115,7 +116,7 @@

      Edge evidence

    • observation - METPO:1001000 + METPO:1001000 can be about material entity METPO:1000186 @@ -137,7 +138,7 @@

      Edge evidence

      METPO:1000186 can participate in biological process - METPO:1000630 + METPO:1000630 biolink:participates_in

      Material entities can participate in biological processes, but this upper record has no direct TraitMech children.

        @@ -208,7 +209,7 @@

        kg-microbe context

        via direct_metpo.

        512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

        @@ -417,7 +418,16 @@

        Identifier

        Term kind
        CLASS
        Status
        -
        REVIEWED
        +
        REVIEWED + + +
        + What this status means +

        Curator has signed off on label / definition / parents.

        +

        Quoted from the schema's status definitions.

        +
        + +
    @@ -781,12 +791,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/upper/microbe.html b/pages/traits/upper/microbe.html index bf6c8df9ee5..4a65dcbf0d7 100644 --- a/pages/traits/upper/microbe.html +++ b/pages/traits/upper/microbe.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -113,7 +114,7 @@

    kg-microbe context

    via direct_metpo.

      -
    • METPO:1000525 [+0.029, -0.773, +0.243, +1.218, …]
      • +
    • microbe METPO:1000525 [+0.029, -0.773, +0.243, +1.218, …]

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

    @@ -193,7 +194,7 @@

    Curation history

  • · CREATED_UPPER_CLASS_RECORD · claude -

    Created upper-ontology CLASS record for METPO:1000525 (microbe) so that the domain of un-deprecated metabolism OBJECT_PROPERTYs (which all declare domain https://w3id.org/metpo/1000525) resolves to a curated TraitMech record.

    +

    Created upper-ontology CLASS record for METPO:1000525 (microbe) so that the domain of un-deprecated metabolism OBJECT_PROPERTYs (which all declare domain https://w3id.org/metpo/1000525) resolves to a curated TraitMech record.

  • @@ -232,7 +233,16 @@

    Identifier

    Term kind
    CLASS
    Status
    -
    REVIEWED
    +
    REVIEWED + + +
    + What this status means +

    Curator has signed off on label / definition / parents.

    +

    Quoted from the schema's status definitions.

    +
    + +
    • @@ -261,12 +271,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-05-16 16:45 UTC diff --git a/pages/traits/upper/observation.html b/pages/traits/upper/observation.html index d6de4098f52..40d84ff2cc1 100644 --- a/pages/traits/upper/observation.html +++ b/pages/traits/upper/observation.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -118,7 +119,7 @@

    Edge evidence

    records measured quality - METPO:1000188 + METPO:1000188

    Observation data record a measured quality.

      @@ -137,7 +138,7 @@

      Edge evidence

      METPO:1001000 is about material entity - METPO:1000186 + METPO:1000186

      Observation records are about material entities or samples and their qualities.

        @@ -356,7 +357,7 @@

        kg-microbe context

        via direct_metpo.

        512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

        @@ -589,7 +590,16 @@

        Identifier

        Term kind
        CLASS
        Status
        -
        REVIEWED
        +
        REVIEWED + + +
        + What this status means +

        Curator has signed off on label / definition / parents.

        +

        Quoted from the schema's status definitions.

        +
        + +
    @@ -953,12 +963,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/upper/phenotype.html b/pages/traits/upper/phenotype.html index 0213dba3ecb..b69d9490548 100644 --- a/pages/traits/upper/phenotype.html +++ b/pages/traits/upper/phenotype.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,8 +100,8 @@

    Edge evidence

    METPO:1000059 is a quality - METPO:1000188 - rdfs:subClassOf + METPO:1000188 + rdfs:subClassOf

    Phenotypes are modeled as qualities or quality-bearing descriptions of entities.

      @@ -119,7 +120,7 @@

      Edge evidence

      specializes phenotype METPO:1000059 - rdfs:subClassOf + rdfs:subClassOf

      Morphology classes are non-environmental child phenotypes in TraitMech.

        @@ -134,11 +135,11 @@

        Edge evidence

      • trophic type - METPO:1000631 + METPO:1000631 specializes phenotype METPO:1000059 - rdfs:subClassOf + rdfs:subClassOf

        Trophic type is retained as a non-environmental physiology child under phenotype.

          @@ -153,11 +154,11 @@

          Edge evidence

        • pathogenic to host - METPO:1004000 + METPO:1004000 specializes phenotype METPO:1000059 - rdfs:subClassOf + rdfs:subClassOf

          Pathogenic-to-host is retained as a non-environmental ecology child under phenotype.

            @@ -646,7 +647,7 @@

            kg-microbe context

            via direct_metpo.

              -
            • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]
              • +
            • phenotype METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

            512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

            @@ -861,7 +862,16 @@

            Identifier

            Term kind
            CLASS
            Status
            -
            REVIEWED
            +
            REVIEWED + + +
            + What this status means +

            Curator has signed off on label / definition / parents.

            +

            Quoted from the schema's status definitions.

            +
            + +
    @@ -1225,12 +1235,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 03:23 UTC diff --git a/pages/traits/upper/quality.html b/pages/traits/upper/quality.html index 17a2e2f446f..281cb4634ae 100644 --- a/pages/traits/upper/quality.html +++ b/pages/traits/upper/quality.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +
    @@ -99,7 +100,7 @@

    Edge evidence

    METPO:1000188 characterizes material entity - METPO:1000186 + METPO:1000186

    Qualities characterize or inhere in entities.

      @@ -115,11 +116,11 @@

      Edge evidence

    • phenotype - METPO:1000059 + METPO:1000059 is a quality METPO:1000188 - rdfs:subClassOf + rdfs:subClassOf

      Phenotype is a quality-derived child class in TraitMech.

        @@ -134,11 +135,11 @@

        Edge evidence

      • biosafety level - METPO:1001101 + METPO:1001101 is a quality METPO:1000188 - rdfs:subClassOf + rdfs:subClassOf

        Biosafety level is a reviewed non-genomic child quality in TraitMech's ecology category.

          @@ -239,7 +240,7 @@

          kg-microbe context

          via direct_metpo.

            -
          • METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]
            • +
          • quality METPO:1000188 [-0.956, -1.962, -3.148, +1.274, …]

          512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

          @@ -454,7 +455,16 @@

          Identifier

          Term kind
          CLASS
          Status
          -
          REVIEWED
          +
          REVIEWED + + +
          + What this status means +

          Curator has signed off on label / definition / parents.

          +

          Quoted from the schema's status definitions.

          +
          + +
    @@ -818,12 +828,14 @@

    kg-microbe

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML)
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Record as of 2026-08-26 06:15 UTC diff --git a/pages/umap.html b/pages/umap.html index 009becc7083..cc41c280088 100644 --- a/pages/umap.html +++ b/pages/umap.html @@ -7,6 +7,7 @@ +
    TraitMech @@ -18,13 +19,13 @@ Embedding space Graph layout Data JSON - Schema + Schema GitHub METPO
    -
    +

    TraitMech › Embedding space

    @@ -52,7 +53,7 @@

    Trait embedding space

    View data as table
    -
    +
    @@ -262,12 +263,14 @@

    Trait embedding space

    kg-microbe · METPO · traits.json · - LinkML schema + LinkML schema + (YAML) -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    Corpus as of 2026-10-25 21:40 UTC diff --git a/scripts/render_discussions_shell.py b/scripts/render_discussions_shell.py index 6e466d53e48..dfb5935edd5 100644 --- a/scripts/render_discussions_shell.py +++ b/scripts/render_discussions_shell.py @@ -13,21 +13,31 @@ REPO_ROOT = Path(__file__).resolve().parents[1] START = "" END = "" +LICENSE_BASE = "https://github.com/CultureBotAI/TraitMech/blob/main" def render_shell(text: str) -> str: text = re.sub(re.escape(START) + r".*?" + re.escape(END) + r"\n?", "", text, flags=re.S) - if text.count("") != 1 or text.count('
    -
    +
    {% block content %}{% endblock %}
    -
    - Project data: CC BY 4.0 · - code: BSD-3-Clause · - third-party source terms apply +
    + Project data: CC BY 4.0. + Code: BSD-3-Clause. + Third-party source material keeps its own terms + (licence scope).
    + {% block provenance -%}
    {% if generated_at %}{{ stamp_scope | default('Corpus') }} as of {{ generated_at }}{% else %}TraitMech{% endif %} · Ontology baseline: METPO {{ metpo_version }} @@ -54,6 +58,7 @@ · embedding coverage {{ embedding_coverage_pct }}% (kg-microbe deepwalk 512-D, 2026-04-25)
    + {%- endblock %}

    All Mech projects

    diff --git a/src/traitmech/templates/discussions.css b/src/traitmech/templates/discussions.css index d729b10300b..18aef2caea8 100644 --- a/src/traitmech/templates/discussions.css +++ b/src/traitmech/templates/discussions.css @@ -15,3 +15,5 @@ .badge { background:var(--badge); color:var(--badge-fg); } .badge.gap { background:var(--gap); color:var(--gap-fg); } a:focus-visible, button:focus-visible, input:focus-visible { outline-color:var(--accent); } +.shell-footer { max-width:1200px; margin:1.5rem auto 2rem; padding:1rem 1.25rem; + border-top:1px solid var(--line); color:var(--muted); font-size:.85rem; } diff --git a/src/traitmech/templates/graph.html b/src/traitmech/templates/graph.html index 95ee86e8398..2e893a302f1 100644 --- a/src/traitmech/templates/graph.html +++ b/src/traitmech/templates/graph.html @@ -28,7 +28,7 @@

    Trait graph layout (sfdp)

    View data as table
    -
    +
    LabelCURIECategoryPaCMAP xPaCMAP y
    diff --git a/src/traitmech/templates/index.html b/src/traitmech/templates/index.html index aeb78732a54..137fb2a5e5c 100644 --- a/src/traitmech/templates/index.html +++ b/src/traitmech/templates/index.html @@ -50,6 +50,18 @@ .btn{display:inline-block;background:var(--accent);color:#fff;padding:.5em 1.15em; border-radius:999px;font-size:.9rem;font-weight:600} .btn:hover{filter:brightness(.93);text-decoration:none} + .skip-link{position:absolute;left:1rem;top:-4rem;z-index:2100;padding:.5rem .75rem; + background:var(--card);color:var(--accent);border:2px solid var(--accent);border-radius:6px} + .skip-link:focus{top:.5rem} + main:focus{outline:none} + .notice{margin-top:28px;background:var(--card);border:1px solid var(--line);border-radius:16px;padding:22px 28px} + .notice h2{margin:0 0 .4em;font-size:1.15rem} + .notice p{margin:.4em 0;color:var(--muted);font-size:.95rem} + .notice dl{margin:.6em 0 0;display:grid;grid-template-columns:max-content 1fr;gap:.45em 1em} + .notice dt{font-weight:600} + .notice dt span{display:block;font-weight:400;color:var(--muted);font-size:.85rem} + .notice dd{margin:0;color:var(--muted);font-size:.95rem;overflow-wrap:anywhere} + @media (max-width:560px){.notice dl{grid-template-columns:1fr}.notice dd{margin-bottom:.4em}} footer{border-top:1px solid var(--line);background:rgba(255,255,255,.45); padding:30px 24px;text-align:center;font-size:.9rem;color:var(--muted)} footer .fam{margin:.2em 0} @@ -113,6 +125,7 @@ +

    TraitMech

    @@ -136,7 +149,7 @@

    TraitMech

    {{ embedding_coverage_pct }}%embedded
    -
    +
    🔎
    @@ -152,23 +165,38 @@

    Embedding browser

    💻
    -
    View on GitHub →Download traits.json →LinkML schema →
    +
    View on GitHub →Download traits.json →Schema reference →

    Data, Schema & GitHub

    -

    Source code, bulk corpus JSON export, LinkML schema, and the curation workflow.

    +

    Source code, bulk corpus JSON export, LinkML schema documentation generated from the schema, and the curation workflow.

    + {% if statuses %} +
    +

    Curation status

    +

    Records carry one of these statuses. Each definition is quoted from the + schema; a record page explains its own + status beside it and lists every recorded curation event with its curator.

    +
    + {% for status in statuses %} +
    {{ status.text }} {{ status_counts.get(status.text, 0) }} records
    +
    {{ status.description }}
    + {% endfor %} +
    +
    + {% endif %}
    LabelCURIECategoryLayout xLayout y
    @@ -59,7 +59,9 @@

    Full-corpus text embedding map (BGE-large + PaCMAP)

    const margin = { top: 20, right: 20, bottom: 30, left: 30 }; const svg = d3.select("#umap-plot").append("svg") - .attr("width", W).attr("height", H); + .attr("width", W).attr("height", H) + .attr("viewBox", "0 0 " + W + " " + H) + .style("width", "100%").style("height", "auto"); const g = svg.append("g") .attr("transform", `translate(${margin.left},${margin.top})`); diff --git a/src/traitmech/templates/schema.html b/src/traitmech/templates/schema.html new file mode 100644 index 00000000000..34359e48900 --- /dev/null +++ b/src/traitmech/templates/schema.html @@ -0,0 +1,69 @@ +{% extends "base.html" %} +{% block content %} +
    +

    TraitMech › Schema

    +

    {{ schema.title }}

    + {% if schema.description %}

    {{ schema.description }}

    {% endif %} +

    Generated by just gen-pages from the LinkML schema + {% for module in schema.modules %}{{ module }}{% if not loop.last %}, {% endif %}{% endfor %}. + Slots are listed as LinkML resolves them for each class, with imports and slot usage applied. + Descriptions are shown as written in the schema, without links: the identifiers in them are often format examples. + {% if schema.license %}Schema licence: {{ schema.license }}.{% endif %}

    +
    + + + +
    +

    Classes ({{ schema.classes|length }})

    + {% for cls in schema.classes %} +
    +

    {{ cls.name }}{% if cls.is_a %} is a {{ cls.is_a }}{% endif %}

    + {% if cls.description %}

    {{ cls.description }}

    {% endif %} + {% if cls.source and cls.source != schema.source %}

    Defined in the shared module {{ cls.source }}.

    {% endif %} + {% if cls.slots %} +
    +
    LabelCURIECategoryTerm kindPaCMAP xPaCMAP y
    + + + + {% for slot in cls.slots %} + + + + + + + {% endfor %} + +
    {{ cls.name }} slots ({{ cls.slots|length }})
    SlotRangeCardinalityDescription
    {{ slot.name }}{% if slot.identifier %} (identifier){% endif %}{% for r in slot.ranges %}{% if r.kind == 'type' %}{{ r.name }}{% else %}{{ r.name }}{% endif %}{% if not loop.last %} or {% endif %}{% endfor %}{{ 'Required' if slot.required else 'Optional' }}{% if slot.multivalued %}, multivalued{% endif %}{{ slot.description }}{% if slot.pattern %}
    Pattern {{ slot.pattern }}{% endif %}
    +
    + {% else %} +

    This class declares no slots.

    + {% endif %} + + {% endfor %} + + +
    +

    Enumerations ({{ schema.enums|length }})

    + {% for enum in schema.enums %} +
    +

    {{ enum.name }}

    + {% if enum.description %}

    {{ enum.description }}

    {% endif %} + {% if enum.source and enum.source != schema.source %}

    Defined in the shared module {{ enum.source }}.

    {% endif %} +
    + {% for value in enum.permissible %} +
    {{ value.text }}{% if value.meaning %} {{ value.meaning | term_link }}{% endif %}
    +
    {% if value.description %}{{ value.description }}{% else %}No description.{% endif %}
    + {% endfor %} +
    +
    + {% endfor %} +
    +{% endblock %} diff --git a/src/traitmech/templates/sequence-map.html b/src/traitmech/templates/sequence-map.html index 155c5e3f27f..a9f68c7b33c 100644 --- a/src/traitmech/templates/sequence-map.html +++ b/src/traitmech/templates/sequence-map.html @@ -27,7 +27,7 @@

    Protein sequence embedding map (ESM-2 pLM + PaCMAP)

    View protein embeddings as table
    -
    +
    @@ -60,7 +60,9 @@

    Protein sequence embedding map (ESM-2 pLM + PaCMAP)

    const margin = { top: 24, right: 24, bottom: 32, left: 32 }; const svg = d3.select("#umap-plot").append("svg") - .attr("width", W).attr("height", H); + .attr("width", W).attr("height", H) + .attr("viewBox", "0 0 " + W + " " + H) + .style("width", "100%").style("height", "auto"); const g = svg.append("g") .attr("transform", `translate(${margin.left},${margin.top})`); diff --git a/src/traitmech/templates/style.css b/src/traitmech/templates/style.css index 41b18f7f31b..97b82107110 100644 --- a/src/traitmech/templates/style.css +++ b/src/traitmech/templates/style.css @@ -361,7 +361,8 @@ table.trait-list tr:hover { background: var(--accent-soft); } .protein-example-table-wrap, .detail-table-scroll { max-width: 100%; overflow-x: auto; overflow-wrap: normal; } .protein-example-table-wrap:focus-visible, -.detail-table-scroll:focus-visible { outline: 3px solid var(--accent); outline-offset: 2px; } +.detail-table-scroll:focus-visible, +.data-table-scroll:focus-visible { outline: 3px solid var(--accent); outline-offset: 2px; } .protein-example-table { border-collapse: collapse; font-size: 0.8rem; @@ -610,6 +611,11 @@ label.facet-opt .cnt { padding: 1rem; margin: 0; } +/* Stacked above the content on a narrow screen, a sticky sidebar stayed pinned + over the catalogue table or map plot it filters while the reader scrolled. */ +@media (max-width: 860px) { + .facet-sidebar { position: static; max-height: none; } +} .facet-sidebar h2, .facet-sidebar h3 { font-size: 0.78rem; text-transform: uppercase; @@ -685,3 +691,35 @@ label.facet-opt .cnt { /* Category names and provenance remain readable on narrow screens. */ h1 { overflow-wrap: anywhere; } .pathograph-status { padding: .75rem; color: var(--muted); } + +/* Generated schema reference (pages/schema.html). Built from existing tokens so + both themes are inherited; the slot tables keep their columns and scroll + inside their own region on a narrow screen. */ +.schema-contents, .schema-class, .schema-enum { margin: 1rem 0; overflow-wrap: anywhere; } +.schema-class h3, .schema-enum h3 { margin: 0 0 0.4rem; } +.schema-table { min-width: 720px; } +.schema-table td:last-child { min-width: 20rem; } +.schema-table caption { text-align: left; padding: 0 0 0.4rem; } +/* Slot names are case-sensitive identifiers: undo the uppercase column-header + treatment table.trait-list gives every th. */ +.schema-table th[scope="row"] { font-weight: 400; white-space: nowrap; text-transform: none; + letter-spacing: normal; background: none; color: var(--fg); font-size: inherit; } +.schema-table th[scope="row"], .schema-table td { vertical-align: top; } +.schema-values dt { margin-top: 0.5rem; } +.schema-values dd { margin-left: 1rem; color: var(--muted); } + +/* Skip link: the first tab stop on every page, shown only while focused. */ +.skip-link { position: absolute; left: 1rem; top: -4rem; z-index: 2100; padding: 0.5rem 0.75rem; + background: var(--card-bg); color: var(--accent); border: 2px solid var(--accent); border-radius: 4px; } +.skip-link:focus { top: 0.5rem; } +main:focus { outline: none; } + +/* Curation status explained beside the status on record pages. */ +.status-meaning { margin-top: 0.35rem; } +.status-meaning summary { cursor: pointer; color: var(--accent); font-size: 0.85rem; } +.status-meaning p { margin: 0.35rem 0 0; } + +/* Not-found page (404.html at the publishing root). */ +.not-found-search { margin: 1.25rem 0; flex-wrap: wrap; } +.not-found-search label { flex-basis: 100%; font-weight: 600; } +.not-found-links { line-height: 1.9; } diff --git a/src/traitmech/templates/trait.html b/src/traitmech/templates/trait.html index addb605cded..8a2ed1d9c63 100644 --- a/src/traitmech/templates/trait.html +++ b/src/traitmech/templates/trait.html @@ -32,8 +32,8 @@

    Trait evidence ({{ trait.evid {% for ev in trait.evidence %}
  • {{ citation(ev.reference) }} - {% if ev.snippet %}
    {{ ev.snippet }}
    {% endif %} - {% if ev.notes %}

    {{ ev.notes }}

    {% endif %} + {% if ev.snippet %}
    {{ ev.snippet | autolink }}
    {% endif %} + {% if ev.notes %}

    {{ ev.notes | autolink }}

    {% endif %}
    • {% endfor %} @@ -46,9 +46,9 @@

    Trait evidence ({{ trait.evid {% set graph_dom_id = "pathograph-" ~ loop.index %}

    {{ graph.title }}

    - {% if graph.description %}

    {{ graph.description }}

    {% endif %} + {% if graph.description %}

    {{ graph.description | autolink }}

    {% endif %} {% if graph.scope_status %} -

    {{ graph.scope_status }}{% if graph.scope_notes %} · {{ graph.scope_notes }}{% endif %}

    +

    {{ graph.scope_status }}{% if graph.scope_notes %} · {{ graph.scope_notes | autolink }}{% endif %}

    {% endif %} {% if graph.issues %}
    @@ -77,18 +77,18 @@

    Edge evidence

    {% for edge in graph.evidence_rows %}
  • {{ edge.source }} - {% if edge.source_grounding %}{% set sg_url = edge.source_grounding | curie_url %}{% if sg_url %}{{ edge.source_grounding }}{% else %}{{ edge.source_grounding }}{% endif %}{% endif %} + {% if edge.source_grounding %}{{ edge.source_grounding | term_link }}{% endif %} {{ edge.predicate }} {{ edge.target }} - {% if edge.target_grounding %}{% set tg_url = edge.target_grounding | curie_url %}{% if tg_url %}{{ edge.target_grounding }}{% else %}{{ edge.target_grounding }}{% endif %}{% endif %} - {% if edge.predicate_id %}{% set pid_url = edge.predicate_id | curie_url %}{% if pid_url %}{{ edge.predicate_id }}{% else %}{{ edge.predicate_id }}{% endif %}{% endif %} - {% if edge.description %}

    {{ edge.description }}

    {% endif %} + {% if edge.target_grounding %}{{ edge.target_grounding | term_link }}{% endif %} + {% if edge.predicate_id %}{{ edge.predicate_id | term_link }}{% endif %} + {% if edge.description %}

    {{ edge.description | autolink }}

    {% endif %}
      {% for ev in edge.evidence %}
    • {{ citation(ev.reference) }} - {% if ev.snippet %}{{ ev.snippet }}{% endif %} - {% if ev.notes %}{{ ev.notes }}{% endif %} + {% if ev.snippet %}{{ ev.snippet | autolink }}{% endif %} + {% if ev.notes %}{{ ev.notes | autolink }}{% endif %}
      • {% endfor %}
    @@ -106,7 +106,7 @@

    Pathway context

  • {{ link.node_label }}: {{ link.identifier }} {{ link.relation }} -

    {{ link.basis }}

    +

    {{ link.basis | autolink }}

    PathwayMech source version {{ link.source_version }}
    • {% endfor %} @@ -132,21 +132,21 @@

    Protein and taxon examples

    {% for ds in trait.datasets %} - + @@ -233,7 +233,7 @@

    Children ({{ children|length }})

    Synonyms ({{ trait.synonyms|length }})

      {% for s in trait.synonyms %} -
    • {{ s.synonym_text }} {{ s.synonym_type }}{% if s.source %} · {{ s.source }}{% endif %}
      • +
    • {{ s.synonym_text }} {{ s.synonym_type }}{% if s.source %} · {{ citation(s.source) }}{% endif %}
      • {% endfor %}
    @@ -243,7 +243,7 @@

    Synonyms ({{ trait.synonyms|length }})

    Cross-references

      - {% for x in trait.xrefs %}{% set x_url = x | curie_url %}
    • {% if x_url %}{{ x }}{% else %}{{ x }}{% endif %}
      • {% endfor %} + {% for x in trait.xrefs %}
    • {{ x | term_link }}
      • {% endfor %}
    {% endif %} @@ -256,7 +256,7 @@

    kg-microbe context

    via {{ kgm_match.match_method }}.

      {% for node in kgm_match.kgm_nodes %} -
    • {{ node }}{% if node in node_dim_preview %} {{ node_dim_preview[node] }}{% endif %}
      • +
    • {{ node | term_link(parent_labels.get(node)) }}{% if node in node_dim_preview %} {{ node_dim_preview[node] }}{% endif %}
      • {% endfor %}

    512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe ({{ embedding_release }}).

    @@ -294,7 +294,7 @@

    Deep research

    ontologies, and some are known to be wrong. Check any CURIE against the source before using it. - 
    {{ research_md }}
    + 
    {{ research_md | autolink }}
    {% if research_total_lines > research_shown_lines %}

    Showing the first {{ research_shown_lines }} of {{ research_total_lines }} lines of findings; the linked file also carries the @@ -329,7 +329,7 @@

    Canonical examples {% if ex.reference %} {{ citation(ex.reference) }} {% endif %} - {% if ex.note %}{{ ex.note }}{% endif %} + {% if ex.note %}{{ ex.note | autolink }}{% endif %} {% endfor %} @@ -367,7 +367,7 @@

    Discussions and Knowledge Gaps ({{ trait.discussions|leng mechanism it concerns.

    {% endif %} - {% if d.rationale %}

    {{ d.rationale }}

    {% endif %} + {% if d.rationale %}

    {{ d.rationale | autolink }}

    {% endif %} {% if d.proposed_experiments %}

    Proposed experiments

    @@ -376,7 +376,7 @@

    Proposed experiments

  • {% if x.name %}{{ x.name }}{% endif %} {% if x.approach %}{{ x.approach }}{% endif %} - {% if x.description %}{{ x.description }}{% endif %} + {% if x.description %}{{ x.description | autolink }}{% endif %} {% if x.model_systems %}Model systems: {{ x.model_systems|join(', ') }}{% endif %} {% if x.perturbations %}Perturbations: @@ -403,15 +403,15 @@

    Evidence

  • {{ citation(e.reference) }} {% if e.supports %}{{ e.supports|replace('_', ' ') }}{% endif %} - {% if e.snippet %}
    {{ e.snippet }}
    {% endif %} - {% if e.explanation %}{{ e.explanation }}{% endif %} + {% if e.snippet %}
    {{ e.snippet | autolink }}
    {% endif %} + {% if e.explanation %}{{ e.explanation | autolink }}{% endif %}
    • {% endfor %} {% endif %} {% if d.resolution_note %} -

    Resolution: {{ d.resolution_note }}

    +

    Resolution: {{ d.resolution_note | autolink }}

    {% endif %} {# Provenance for a discussion that was raised one way and curated @@ -421,7 +421,7 @@

    Evidence

    {% if d.notes %}
    Provenance -

    {{ d.notes }}

    +

    {{ d.notes | autolink }}

    {% endif %} @@ -436,7 +436,7 @@

    Curation history

  • · {{ ev.action }}{% if ev.curator %} · {{ ev.curator }}{% endif %} - {% if ev.changes %}

    {{ ev.changes }}

    {% endif %} + {% if ev.changes %}

    {{ ev.changes | autolink }}

    {% endif %}
    • {% endfor %} {% endif %} @@ -445,8 +445,8 @@

    Recorded curation sessions

      {% for item in curation_sessions %}
    • {% for actor in item.session.actors %} · {{ actor.name }}{% endfor %} -
        {% for ev in item.events %}
      • {{ ev.type }} — {{ ev.summary }} - {% if ev.details %}

        {{ ev.details }}

        {% endif %}
        • {% endfor %}
      +
        {% for ev in item.events %}
      • {{ ev.type }} — {{ ev.summary | autolink }} + {% if ev.details %}

        {{ ev.details | autolink }}

        {% endif %}
        • {% endfor %}
      Read this curation session
      • {% endfor %}
    {% endif %} @@ -485,7 +485,16 @@

    Identifier

    Term kind
    {{ trait.term_kind }}
    Status
    -
    {{ trait.mapping_status }}
    +
    {{ trait.mapping_status }} + {% set status_meaning = (status_meanings or {}).get(trait.mapping_status) %} + {% if status_meaning %} +
    + What this status means +

    {{ status_meaning }}

    +

    Quoted from the schema's status definitions.

    +
    + {% endif %} +
    diff --git a/src/traitmech/templates/umap.html b/src/traitmech/templates/umap.html index d3d2007870b..435a83fbb17 100644 --- a/src/traitmech/templates/umap.html +++ b/src/traitmech/templates/umap.html @@ -26,7 +26,7 @@

    Trait embedding space

    View data as table
    -
    +

    ProteinUniProtGeneTaxonTraitLength (aa)PaCMAP xPaCMAP y
    {% set tid = ex.taxon_id|replace('NCBITaxon:','') %} - {{ ex.taxon_label }} -
    {{ ex.taxon_id }} + {{ ex.taxon_label }} +
    {{ ex.taxon_id }}         		{{ ex.entry_status }}
    retrieved {{ ex.retrieved_on }}{% if ex.entry_version %} · entry v{{ ex.entry_version }}{% endif %}{% if ex.sequence_version %} · sequence v{{ ex.sequence_version }}{% endif %}     		- {% if ex.role %}

    {{ ex.role }}

    {% endif %} + {% if ex.role %}

    {{ ex.role | autolink }}

    {% endif %}
      {% for ev in ex.evidence %}
    • {{ citation(ev.reference) }} - {% if ev.snippet %}{{ ev.snippet }}{% endif %} - {% if ev.notes %}{{ ev.notes }}{% endif %} + {% if ev.snippet %}{{ ev.snippet | autolink }}{% endif %} + {% if ev.notes %}{{ ev.notes | autolink }}{% endif %}
      • {% endfor %}
    @@ -173,7 +173,7 @@

    Datasets ({{ trait.datasets|length }})

    {{ ds.title or ds.accession }}{% if ds.description %}
    {{ ds.description }}{% endif %}    		{{ ds.title or ds.accession }}{% if ds.description %}
    {{ ds.description | autolink }}{% endif %}    		 {% if ds.dataset_type %}{{ ds.dataset_type }}{% endif %} {{ ds.repository or '' }} {% if ds.url %}{{ ds.accession or ds.url }}{% else %}{{ ds.accession or '' }}{% endif %}
    diff --git a/tests/test_unified_site_features.py b/tests/test_unified_site_features.py new file mode 100644 index 00000000000..a49dbe6c5cd --- /dev/null +++ b/tests/test_unified_site_features.py @@ -0,0 +1,699 @@ +"""X-Mech unified website features on the TraitMech site (wave 1, 2026-10-25). + +Covers the five features the 2026-10-25 review left partial: references in free +text are followable (evidence), displayed CURIEs resolve and own-record CURIEs +open their record page (term_links), readable schema documentation generated +from the schema (schema_docs), the licence footer on every page type (license), +and map plots that fit a phone (responsive). Each test is driven by an input on +which the old rendering and the new one differ. +""" + +from __future__ import annotations + +import re +import sys +from html.parser import HTMLParser +from pathlib import Path + +import pytest +import yaml + +ROOT = Path(__file__).resolve().parents[1] +sys.path.insert(0, str(ROOT / "scripts")) + +from render_discussions_shell import render_shell # noqa: E402 +from render_trait_pages import ( # noqa: E402 + RESEARCH_PREVIEW_LINES, + SITE_ROOT, + TRAITS_DIR, + autolink, + curie_url, + mapping_statuses, + render_not_found, + research_answer, + research_report, + schema_reference, + template_environment, + write_html, +) + +TEMPLATES = ROOT / "src" / "traitmech" / "templates" +GH = "https://github.com/CultureBotAI/TraitMech/blob/main" +LICENSE_LINKS = {f"{GH}/LICENSE-DATA", f"{GH}/LICENSE-CODE", f"{GH}/LICENSE"} +YAML_URL = f"{GH}/data/traits/ecology/example.yaml" + + +class Page(HTMLParser): + """Anchors with their text, footer text and anchors, and visible text.""" + + def __init__(self, html: str): + super().__init__(convert_charrefs=True) + self.anchors: list[tuple[dict, str]] = [] + self.footer_links: list[str] = [] + self.footer_text: list[str] = [] + self.text: list[str] = [] + self.ids: set[str] = set() + self.tags: list[str] = [] + self._open: list[tuple[dict, list[str]]] = [] + self._footer = 0 + self.feed(html) + + def handle_starttag(self, tag, attrs): + attrs = dict(attrs) + self.tags.append(tag) + if attrs.get("id"): + self.ids.add(attrs["id"]) + if tag == "footer": + self._footer += 1 + if tag == "a": + self._open.append((attrs, [])) + if self._footer: + self.footer_links.append(attrs.get("href", "")) + + def handle_endtag(self, tag): + if tag == "a" and self._open: + attrs, text = self._open.pop() + self.anchors.append((attrs, " ".join("".join(text).split()))) + if tag == "footer": + self._footer -= 1 + + def handle_data(self, data): + self.text.append(data) + for _, text in self._open: + text.append(data) + if self._footer: + self.footer_text.append(data) + + def hrefs(self) -> list[str]: + return [attrs.get("href", "") for attrs, _ in self.anchors] + + def anchor(self, href: str) -> tuple[dict, str]: + matches = [(attrs, text) for attrs, text in self.anchors if attrs.get("href") == href] + assert matches, f"no anchor to {href}" + return matches[0] + + def plain_text(self) -> str: + return " ".join("".join(self.text).split()) + + def footer(self) -> str: + return " ".join("".join(self.footer_text).split()) + + +def render_trait(trait: dict, graphs=None, **context) -> Page: + values = { + "causal_graphs": graphs or [], "kgm_match": {"n_kgm_nodes": 0}, + "parent_pages": {}, "parent_labels": {}, "root": "../../", + "yaml_blob_url": YAML_URL, **context, + } + return Page(template_environment().get_template("trait.html").render( + trait={"label": "Example", "trait_category": "ECOLOGY", **trait}, **values, + )) + + +# ---------------------------------------------------------------- evidence -- + +LINKED_TOKENS = [ + ("See PMID:40891913.", "https://pubmed.ncbi.nlm.nih.gov/40891913/", "PMID:40891913"), + ("from PMID 12345;", "https://pubmed.ncbi.nlm.nih.gov/12345/", "PMID 12345"), + ("full text PMC2983100.", "https://pmc.ncbi.nlm.nih.gov/articles/PMC2983100/", "PMC2983100"), + ("(DOI:10.1128/mBio.00390-21).", "https://doi.org/10.1128/mBio.00390-21", + "DOI:10.1128/mBio.00390-21"), + ("cited as doi 10.3389/fmicb.2021.705326, here", "https://doi.org/10.3389/fmicb.2021.705326", + "doi 10.3389/fmicb.2021.705326"), + ("quote :ref{doi=10.1101/2023.03.28.534373} end", "https://doi.org/10.1101/2023.03.28.534373", + "doi=10.1101/2023.03.28.534373"), + ("bare 10.1371/journal.pbio.3002726.s002) here", "https://doi.org/10.1371/journal.pbio.3002726.s002", + "10.1371/journal.pbio.3002726.s002"), + ("pdf at https://example.org/a/Leveau2008.pdf.", "https://example.org/a/Leveau2008.pdf", + "https://example.org/a/Leveau2008.pdf"), + ("(https://en.wikipedia.org/wiki/Foo_(bar))", "https://en.wikipedia.org/wiki/Foo_(bar)", + "https://en.wikipedia.org/wiki/Foo_(bar)"), + ("q https://example.org/?a=1&b=2 end", "https://example.org/?a=1&b=2", "https://example.org/?a=1&b=2"), +] + + +@pytest.mark.parametrize("text,href,label", LINKED_TOKENS) +def test_autolink_links_reference_tokens_and_keeps_surrounding_text(text, href, label): + page = Page(str(autolink(text))) + attrs, anchor_text = page.anchor(href) + assert anchor_text == label + assert attrs["rel"] == "nofollow noreferrer" + # The text a reader sees is unchanged: only the token became an anchor. + assert page.plain_text() == " ".join(text.split()) + + +UNLINKED_TEXT = [ + "javascript:alert(1)", "data:text/html,x", "https://user:pw@evil.example/", + "https://", "version v10.1234/abc", "PMID:not-a-number", "see doi.org/10.1038/x", + "ftp://example.org/file", "PMC12 is too short", +] + + +@pytest.mark.parametrize("text", UNLINKED_TEXT) +def test_autolink_leaves_unsafe_or_non_reference_text_unlinked(text): + page = Page(str(autolink(text))) + assert page.anchors == [] + assert page.plain_text() == " ".join(text.split()) + + +def test_autolink_escapes_markup_and_cannot_break_out_of_the_attribute(): + html = str(autolink(' https://example.org/x" onclick="alert(2) &')) + page = Page(html) + assert "script" not in page.tags + assert page.hrefs() == ["https://example.org/x"] + assert not any(key.startswith("on") for attrs, _ in page.anchors for key in attrs) + assert "" in page.plain_text() + assert autolink(None) == "" and str(autolink(42)) == "42" + + +MARKDOWN_TOKENS = [ + # Link syntax: the text and the target are each linked, and neither takes "](". + ("[10.1038/nrmicro2166](https://doi.org/10.1038/nrmicro2166)", + ["https://doi.org/10.1038/nrmicro2166", "https://doi.org/10.1038/nrmicro2166"]), + ("[https://example.org/x](https://example.org/x)", + ["https://example.org/x", "https://example.org/x"]), + # Bold and inline code close the token; the marks stay visible text. + ("**10.1099/ijs.0.003251-0**", ["https://doi.org/10.1099/ijs.0.003251-0"]), + ("`10.1146/annurev-cellbio-101011-155745`", + ["https://doi.org/10.1146/annurev-cellbio-101011-155745"]), + ("see **https://example.org/y**, and `https://example.org/z`", + ["https://example.org/y", "https://example.org/z"]), +] + + +PARENTHESISED_TOKENS = [ + # A ")" that closes no "(" opened inside the token ends it, and scanning + # resumes there, so a second URL joined without whitespace is its own (#2033). + ("(https://a.example/x)-(https://b.example/y)", + ["https://a.example/x", "https://b.example/y"]), + ("see (https://a/x), (https://b/y)", ["https://a/x", "https://b/y"]), + # Parentheses opened inside the token are part of it. + ("see https://en.wikipedia.org/wiki/Foo_(bar) for more", + ["https://en.wikipedia.org/wiki/Foo_(bar)"]), + ("(see 10.1016/0005-2744(70)90044-4)", ["https://doi.org/10.1016/0005-2744(70)90044-4"]), +] + + +@pytest.mark.parametrize("text,hrefs", PARENTHESISED_TOKENS) +def test_autolink_ends_a_token_at_a_parenthesis_it_never_opened(text, hrefs): + page = Page(str(autolink(text))) + assert page.hrefs() == hrefs + assert page.plain_text() == text + + +@pytest.mark.parametrize("text,hrefs", MARKDOWN_TOKENS) +def test_autolink_stops_at_markdown_syntax(text, hrefs): + """Research previews are Markdown, and its marks are not part of a DOI or URL (#2022).""" + page = Page(str(autolink(text))) + assert page.hrefs() == hrefs + assert page.plain_text() == text + + +def test_research_preview_links_carry_no_markdown_debris(): + """Every rendered preview, including the four whose DOI links were broken (#2022).""" + debris = re.compile(r"%5D|%5B|%2A|%60|\]\(|[*`\]]$") + hrefs: list[str] = [] + previews = 0 + for path in sorted(TRAITS_DIR.glob("*/*.yaml")): + report = research_report(path.parent.name, path.stem) + if report is None: + continue + preview = "\n".join(research_answer(report.read_text())[:RESEARCH_PREVIEW_LINES]) + hrefs += Page(str(autolink(preview))).hrefs() + previews += 1 + assert previews > 300 + assert [href for href in hrefs if debris.search(href)] == [] + for doi in ("10.1038/nrmicro2166", "10.1099/ijs.0.003251-0", "10.3390/biom10040550", + "10.1146/annurev-cellbio-101011-155745"): + assert f"https://doi.org/{doi}" in hrefs + + +def test_free_text_references_link_in_every_record_context(): + """Each surface the 2026-10-25 review found carrying plain-text references.""" + trait = { + "synonyms": [{"synonym_text": "biofilm-forming", "synonym_type": "RELATED_SYNONYM", + "source": "DOI:10.1038/nrmicro.2016.94"}], + "evidence": [{"reference": "PMID:1", "snippet": "verbatim https://example.org/snippet", + "notes": "Full text PMC2983100."}], + "curation_history": [{"timestamp": "2026-10-01T00:00:00Z", "action": "UPDATE", + "changes": "Added PMID:40891913 as support."}], + "canonical_examples": [{"taxon_label": "Bacillus subtilis", "taxon_id": "NCBITaxon:1423", + "note": "See DOI:10.1128/AEM.02483-09."}], + "discussions": [{"discussion_id": "gap-1", "prompt": "Why?", + "rationale": "Raised by doi:10.1093/ismejo/wrag201", + "notes": "Scan sentence from PMID:42039744."}], + } + graphs = [{"title": "Mechanism", "description": "After :ref{doi=10.1101/2023.03.28.534373}", + "evidence_rows": [{"edge_id": "edge-1", "source": "a", "target": "b", + "description": "See https://example.org/edge", + "evidence": [{"reference": "PMID:2", + "notes": "PMID 777 discusses it"}]}]}] + page = render_trait(trait, graphs, curation_sessions=[{ + "session": {"timestamp": "2026-10-02T00:00:00Z", "actors": [{"name": "codex"}]}, + "events": [{"type": "UPDATE", "summary": "Checked https://example.org/session", + "details": "Compared with PMID:31"}], + "source_url": f"{GH}/history/records/x/y.yaml"}]) + hrefs = set(page.hrefs()) + for expected in [ + "https://doi.org/10.1038/nrmicro.2016.94", # synonym source + "https://example.org/snippet", # evidence snippet + "https://pmc.ncbi.nlm.nih.gov/articles/PMC2983100/", # evidence notes + "https://pubmed.ncbi.nlm.nih.gov/40891913/", # curation history + "https://doi.org/10.1128/AEM.02483-09", # canonical example note + "https://doi.org/10.1093/ismejo/wrag201", # discussion rationale + "https://pubmed.ncbi.nlm.nih.gov/42039744/", # discussion provenance + "https://doi.org/10.1101/2023.03.28.534373", # graph description directive + "https://example.org/edge", # edge description + "https://pubmed.ncbi.nlm.nih.gov/777/", # edge evidence notes + "https://example.org/session", # session summary + "https://pubmed.ncbi.nlm.nih.gov/31/", # session details + ]: + assert expected in hrefs, expected + + +def test_real_synonym_source_from_the_review_is_linked(): + trait = yaml.safe_load((ROOT / "data/traits/ecology/biofilm_formation.yaml").read_text()) + sources = [s["source"] for s in trait["synonyms"] if str(s.get("source", "")).startswith("DOI:")] + assert "DOI:10.1038/nrmicro.2016.94" in sources + html = template_environment().get_template("trait.html").render( + trait=trait, causal_graphs=[], kgm_match={"n_kgm_nodes": 0}, + parent_pages={}, parent_labels={}, root="../../") + # The same DOI is also cited elsewhere on this page, so look inside the card. + synonyms = Page(re.search(r'
      .*?
    ', html, re.S).group(0)) + assert synonyms.anchor("https://doi.org/10.1038/nrmicro.2016.94")[1] == "DOI:10.1038/nrmicro.2016.94" + + +# -------------------------------------------------------------- term_links -- + +@pytest.mark.parametrize("curie,expected", [ + ("MICRO:0000001", "http://purl.obolibrary.org/obo/MICRO_0000001"), + ("rdfs:subClassOf", "http://www.w3.org/2000/01/rdf-schema#subClassOf"), + ("GO:0008150", "https://amigo.geneontology.org/amigo/term/GO:0008150"), + ("NCIT:C12345", "https://bioregistry.io/NCIT:C12345"), + ("traitmech:000123", None), + ("not a curie", None), + ("X:", None), + ("", None), +]) +def test_curie_resolver_map_with_registry_fallback(curie, expected): + assert curie_url(curie) == expected + + +def graph_with_groundings(*groundings): + rows = [{"edge_id": f"edge-{i}", "source": f"node {i}", "source_grounding": grounding, + "target": "trait", "target_grounding": None, "predicate": "affects", + "predicate_id": "rdfs:subClassOf", "evidence": []} + for i, grounding in enumerate(groundings, start=1)] + return [{"title": "Mechanism", "evidence_rows": rows}] + + +def test_own_record_groundings_open_their_record_page(): + page_path = {"traitmech:000700": "traits/metabolism/other.html", + "METPO:1000059": "traits/upper/phenotype.html", + "traitmech:000001": "traits/ecology/example.html"} + page = render_trait( + {"identifier": "traitmech:000001"}, + graph_with_groundings("traitmech:000700", "METPO:1000059", "traitmech:000001", + "CHEBI:15377", "traitmech:999999", "NCIT:C1"), + page_path=page_path) + hrefs = page.hrefs() + assert "../../traits/metabolism/other.html" in hrefs + assert "../../traits/upper/phenotype.html" in hrefs + # The page's own identifier resolves like its Identifier card, not to itself. + assert "../../traits/ecology/example.html" not in hrefs + assert YAML_URL in hrefs + assert "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15377" in hrefs + assert "https://bioregistry.io/NCIT:C1" in hrefs + assert "http://www.w3.org/2000/01/rdf-schema#subClassOf" in hrefs + # A local id with no record page stays visible but is not linked anywhere. + assert "traitmech:999999" in page.plain_text() + assert not any("999999" in href for href in hrefs) + assert "#" not in hrefs + + +def test_kg_microbe_nodes_show_the_label_and_link_the_record(): + page = render_trait( + {"identifier": "traitmech:000626"}, + kgm_match={"n_kgm_nodes": 1, "kgm_nodes": ["METPO:1000059"], "match_method": "parent_proxy"}, + parent_labels={"METPO:1000059": "phenotype"}, + page_path={"METPO:1000059": "traits/upper/phenotype.html"}, + node_dim_preview={}) + assert page.anchor("../../traits/upper/phenotype.html")[1] == "phenotype METPO:1000059" + + +def test_direct_metpo_node_resolves_to_the_authority_not_a_self_link(): + page = render_trait( + {"identifier": "METPO:1004002"}, + kgm_match={"n_kgm_nodes": 1, "kgm_nodes": ["METPO:1004002"], "match_method": "direct_metpo"}, + parent_labels={"METPO:1004002": "animal pathogen"}, + page_path={"METPO:1004002": "traits/ecology/example.html"}, node_dim_preview={}) + assert page.anchor("https://w3id.org/metpo/1004002")[1] == "animal pathogen METPO:1004002" + assert "../../traits/ecology/example.html" not in page.hrefs() + + +def test_cross_references_use_the_resolver_map(): + page = render_trait({"xrefs": ["MICRO:0000123", "GO:0009060"]}) + assert "http://purl.obolibrary.org/obo/MICRO_0000123" in page.hrefs() + assert "https://amigo.geneontology.org/amigo/term/GO:0009060" in page.hrefs() + + +# ------------------------------------------------------------- schema_docs -- + +def test_schema_reference_documents_every_class_slot_and_enum(): + from linkml_runtime.utils.schemaview import SchemaView + + view = SchemaView(str(ROOT / "src/traitmech/schema/traitmech.yaml")) + reference = schema_reference() + assert [c["name"] for c in reference["classes"]][0] == "TraitRecord" + assert {c["name"] for c in reference["classes"]} == set(view.all_classes()) + assert {e["name"] for e in reference["enums"]} == set(view.all_enums()) + record = next(c for c in reference["classes"] if c["name"] == "TraitRecord") + induced = [slot.name for slot in view.class_induced_slots("TraitRecord")] + assert [slot["name"] for slot in record["slots"]] == induced + # Slots docs/SCHEMA.md never listed, so a hand-written page would be stale. + for name in ("causal_graphs", "canonical_examples", "discussions", "datasets"): + assert name in induced + slots = {slot["name"]: slot for slot in record["slots"]} + assert slots["identifier"]["required"] and slots["identifier"]["identifier"] + assert slots["causal_graphs"]["multivalued"] + assert slots["causal_graphs"]["ranges"] == [{"name": "CausalGraph", "kind": "class"}] + status = next(e for e in reference["enums"] if e["name"] == "MappingStatusEnum") + assert {"SEEDED", "PROPOSED", "REVIEWED", "DEPRECATED"} <= {v["text"] for v in status["permissible"]} + + +def render_schema_page() -> str: + return template_environment().get_template("schema.html").render( + title="LinkML schema", root="", schema=schema_reference(), gh_blob_base=GH, + metpo_version="2026-06-12", generated_at="2026-10-25 00:00 UTC", total_traits=1, + embedding_coverage_pct="100.0") + + +def test_schema_page_matches_the_committed_render_and_anchors_resolve(tmp_path): + """pages/schema.html was written by a separate `just gen-pages` process, so equality + above the footer (which carries the corpus stamp) is a cross-process check.""" + write_html(tmp_path / "schema.html", render_schema_page()) + html = (tmp_path / "schema.html").read_text() + committed = (ROOT / "pages" / "schema.html").read_text() + assert html.split("", html, re.S).group(0)) + assert nav.anchor(f"{root}schema.html")[1] == "Schema" + assert f"{root}schema.html" in Page(html).footer_links + + +# ----------------------------------------------------------------- license -- + +def page_context(template: str, root: str) -> dict: + context = {"root": root, "title": "T", "total_traits": 1, "metpo_version": "2026-06-12", + "generated_at": "2026-10-25 00:00 UTC", "embedding_coverage_pct": "100.0", + "category_counts": {"ECOLOGY": 1}, "embedding_per_category": {}, "traits": [], + "category": "ECOLOGY", "n_points": 0, "data_url": "data/x.json", + "href_by_id": "{}", "graph_edges": "[]", "n_edges": 0} + if template == "trait.html": + context.update(trait={"label": "Example", "trait_category": "ECOLOGY"}, causal_graphs=[], + kgm_match={"n_kgm_nodes": 0}, parent_pages={}, parent_labels={}) + if template == "schema.html": + context.update(schema=schema_reference(), gh_blob_base=GH) + return context + + +PAGE_TYPES = [("index.html", ""), ("browse.html", ""), ("category.html", "../"), + ("trait.html", "../../"), ("map.html", ""), ("sequence-map.html", ""), + ("umap.html", ""), ("graph.html", ""), ("schema.html", "")] + + +@pytest.mark.parametrize("template,root", PAGE_TYPES) +def test_every_page_type_footer_states_the_repository_licences(template, root): + page = Page(template_environment().get_template(template).render(**page_context(template, root))) + assert LICENSE_LINKS <= set(page.footer_links) + footer = page.footer() + assert "Project data: CC BY 4.0." in footer + assert "Code: BSD-3-Clause." in footer + assert "Third-party source material keeps its own terms (licence scope)." in footer + + +def licence_terms() -> dict[str, str]: + """The data and code licences as LICENSE names them, in the form a footer prints.""" + scope = (ROOT / "LICENSE").read_text() + data = re.search(r"Project-authored data,.*?licensed under .*?\((CC-BY-(\d+\.\d+))\)\.\s+" + r"See LICENSE-DATA", scope, re.S) + code = re.search(r"Project-authored code,.*?licensed under (\S+)\.\s+See LICENSE-CODE", + scope, re.S) + assert data and code and "retain their own licenses" in scope + # The scope file and the legal texts it points to must name the same licences. + assert (ROOT / "LICENSE-DATA").read_text().startswith(f"Attribution {data.group(2)} International") + assert (ROOT / "LICENSE-CODE").read_text().startswith( + code.group(1).replace("-", " ", 1) + " License") + return {"data": data.group(1).replace("-", " "), "code": code.group(1)} + + +@pytest.mark.parametrize("footer_source", ["base.html", "index.html", "discussions shell"]) +def test_footer_licences_match_the_licence_files(footer_source): + """The footer words are derived from the licence files, then read from a rendered footer.""" + terms = licence_terms() + if footer_source == "discussions shell": + html = render_shell(RAW_DISCUSSIONS) + else: + template, root = ("category.html", "../") if footer_source == "base.html" else (footer_source, "") + html = template_environment().get_template(template).render(**page_context(template, root)) + page = Page(html) + assert page.anchor(f"{GH}/LICENSE-DATA")[1] == terms["data"] + assert page.anchor(f"{GH}/LICENSE-CODE")[1] == terms["code"] + assert f"Project data: {terms['data']}." in page.footer() + assert f"Code: {terms['code']}." in page.footer() + + +RAW_DISCUSSIONS = ('
    Content
    ' + '') + + +def test_discussions_index_carries_the_licence_footer_once(): + result = render_shell(RAW_DISCUSSIONS) + assert render_shell(result) == result + page = Page(result) + assert LICENSE_LINKS <= set(page.footer_links) + assert result.count('class="shell-footer"') == 1 + assert "Third-party source material keeps its own terms" in page.footer() + with pytest.raises(ValueError, match="template changed"): + render_shell(RAW_DISCUSSIONS.replace("", "")) + + +def test_committed_discussions_index_is_current_with_the_shell(): + index = (ROOT / "app/discussions/index.html").read_text() + assert render_shell(index) == index + assert LICENSE_LINKS <= set(Page(index).footer_links) + + +# -------------------------------------------------------------- responsive -- + +MAP_TEMPLATES = ["map.html", "sequence-map.html", "umap.html", "graph.html"] + + +@pytest.mark.parametrize("template", MAP_TEMPLATES) +def test_map_plot_scales_to_its_container(template): + """A fixed-width SVG overflowed a 390 px viewport to 553 px (2026-10-25 review).""" + source = (TEMPLATES / template).read_text() + chain = re.search(r'append\("svg"\)(.*?);', source, re.S) + assert chain, "plot SVG creation not found" + assert '.attr("viewBox", "0 0 " + W + " " + H)' in chain.group(1) + assert '.style("width", "100%")' in chain.group(1) + assert '.style("height", "auto")' in chain.group(1) + + +def test_facet_sidebar_is_not_pinned_over_content_on_narrow_screens(): + """Stacked above the table or plot at 390 px, a sticky sidebar covered it while scrolling.""" + css = (TEMPLATES / "style.css").read_text() + base = css.index(".facet-sidebar {\n position: sticky;") + override = re.search(r"@media \(max-width: 860px\) \{\s*\.facet-sidebar \{ position: static;", css) + # Equal specificity, so the override only wins if it comes after the base rule. + assert override and override.start() > base + + +@pytest.mark.parametrize("template", MAP_TEMPLATES) +def test_map_data_table_scrolls_in_a_named_focusable_region(template): + html = template_environment().get_template(template).render(**page_context(template, "")) + match = re.search(r'
    ]*)>', html) + assert match + attrs = match.group(1) + assert 'role="region"' in attrs and 'tabindex="0"' in attrs and 'aria-label="' in attrs + + +# --------------------------------------------- catalogue candidate features -- + +class FirstTabStop(HTMLParser): + """The first keyboard-focusable element in , and every
    .""" + + def __init__(self, html: str): + super().__init__(convert_charrefs=True) + self.first: tuple[str, dict] | None = None + self.mains: list[dict] = [] + self._body = False + self.feed(html) + + def handle_starttag(self, tag, attrs): + attrs = dict(attrs) + self._body = self._body or tag == "body" + if tag == "main": + self.mains.append(attrs) + focusable = ((tag == "a" and "href" in attrs) + or tag in {"button", "input", "select", "textarea", "summary"} + or attrs.get("tabindex") not in (None, "-1")) + if self._body and self.first is None and focusable: + self.first = (tag, attrs) + + +@pytest.mark.parametrize("template,root", PAGE_TYPES + [("404.html", SITE_ROOT + "pages/")]) +def test_first_tab_stop_skips_to_main(template, root): + page = FirstTabStop(template_environment().get_template(template).render( + **page_context(template, root))) + tag, attrs = page.first + assert (tag, attrs.get("href"), attrs.get("class")) == ("a", "#main-content", "skip-link") + assert [main.get("id") for main in page.mains] == ["main-content"] + + +def test_not_found_page_is_current_and_every_site_link_is_root_absolute(tmp_path): + """GitHub Pages serves /404.html for a missing URL at any depth (#2021).""" + write_html(tmp_path / "404.html", render_not_found(template_environment())) + committed = (ROOT / "404.html").read_text() + assert (tmp_path / "404.html").read_text() == committed + targets = re.findall(r'(?:href|src|action)="([^"]+)"', committed) + site = [target for target in targets if not target.startswith(("https://", "#"))] + assert len(site) >= 10 + for target in site: + # A relative link would resolve against whatever missing path was asked for. + assert target.startswith(SITE_ROOT), target + assert (ROOT / target[len(SITE_ROOT):]).is_file(), target + page = Page(committed) + assert {SITE_ROOT + "pages/index.html", SITE_ROOT + "pages/browse.html"} <= set(page.hrefs()) + assert f'action="{SITE_ROOT}pages/browse.html"' in committed + assert "Page not found" in page.plain_text() + # Independent of corpus state, so a curation PR never rewrites it. + assert "Corpus as of" not in committed and "TraitRecords" not in committed + + +def schema_status_meanings() -> dict[str, str]: + from linkml_runtime.utils.schemaview import SchemaView + + enum = SchemaView(str(ROOT / "src/traitmech/schema/traitmech.yaml")).get_enum("MappingStatusEnum") + return {text: " ".join(value.description.split()) + for text, value in enum.permissible_values.items()} + + +@pytest.mark.parametrize("status", ["SEEDED", "PROPOSED", "REVIEWED", "DEPRECATED"]) +def test_record_page_explains_its_status_in_the_schemas_words(status): + statuses = mapping_statuses(schema_reference()) + html = template_environment().get_template("trait.html").render( + trait={"label": "Example", "trait_category": "ECOLOGY", "mapping_status": status}, + causal_graphs=[], kgm_match={"n_kgm_nodes": 0}, parent_pages={}, parent_labels={}, + root="../../", status_meanings={s["text"]: s["description"] for s in statuses}) + card = Page(re.search(r'
    .*?
    ', html, re.S).group(0)) + assert "What this status means" in card.plain_text() + assert schema_status_meanings()[status] in card.plain_text() + assert "../../schema.html#enum-MappingStatusEnum" in card.hrefs() + + +def test_landing_states_what_each_status_means_with_its_count(): + statuses = mapping_statuses(schema_reference()) + context = page_context("index.html", "") + context.update(statuses=statuses, status_counts={"REVIEWED": 2, "PROPOSED": 1}) + html = template_environment().get_template("index.html").render(**context) + notice = Page(re.search(r'
    ', html, re.S).group(0)) + text = notice.plain_text() + counts = {"SEEDED": 0, "PROPOSED": 1, "REVIEWED": 2, "DEPRECATED": 0} + for status, meaning in schema_status_meanings().items(): + assert f"{status} {counts[status]} records {meaning}" in text + assert "schema.html#enum-MappingStatusEnum" in notice.hrefs() + + +def test_committed_pages_carry_the_curation_notice(): + landing = (ROOT / "pages" / "index.html").read_text() + assert '
    ' in landing + record = (ROOT / "pages/traits/ecology/animal_pathogen.html").read_text() + status = yaml.safe_load((ROOT / "data/traits/ecology/animal_pathogen.yaml").read_text())["mapping_status"] + disclosure = Page(re.search(r'
    .*?
    ', record, re.S).group(0)) + assert schema_status_meanings()[status] in disclosure.plain_text() + + + +# ------------------------------------------------------- sibling Mech links -- + +# The fleet's verified sibling routes: each Mech's search route and the two +# specific-record routes from the X-Mech unified standard's route table, every +# one loaded live with HTTP 200 on 2026-10-25. A link elsewhere on a sibling +# site is a guess that nothing here can check. +VERIFIED_SIBLING_ROUTES = ( + "https://culturebotai.github.io/CultureMech/app/browser.html?q=", + "https://culturebotai.github.io/MediaIngredientMech/browser.html?q=", + "https://culturebotai.github.io/CommunityMech/browser.html?q=", + "https://culturebotai.github.io/proteintraitsmech/browse.html?q=", + "https://culturebotai.github.io/AntibioticMech/pages/browse.html?q=", + "https://culturebotai.github.io/CellStructureMech/pages/browse.html?q=", + "https://culturebotai.github.io/HabitatMech/pages/browse.html?q=", + "https://culturebotai.github.io/NaturalProductMech/pages/browse.html?q=", + "https://culturebotai.github.io/TaxonMech/pages/browse.html?q=", + "https://culturebotai.github.io/TaxonMech/pages/taxon.html?id=NCBITaxon:", + "https://culturebotai.github.io/PathwayMech/pages/browse.html?q=", + "https://culturebotai.github.io/PathwayMech/pages/records/", + "https://culturebotai.github.io/DUFMech/index.html?q=", + "https://culturebotai.github.io/CMMMech/pages/browse.html?q=", + "https://culturebotai.github.io/AIMech/pages/browse.html?q=", +) +# The footer's sibling-site links carry no query: each must be exactly a site +# root (all four answered HTTP 200 on 2026-10-25), as must the suite directory. +SIBLING_SITE_ROOTS = { + "https://culturebotai.github.io/CultureMech/", + "https://culturebotai.github.io/MediaIngredientMech/", + "https://culturebotai.github.io/CommunityMech/", + "https://culturebotai.github.io/proteintraitsmech/", + "https://culturebotai.github.io/mechs/", +} +FLEET_URL = re.compile(r"https?://culturebotai\.github\.io/[^\s\"'<>)]*") + + +def unverified_sibling_urls(text: str) -> set[str]: + return {url for url in FLEET_URL.findall(text) + if not url.startswith("https://culturebotai.github.io/TraitMech/") + and url not in SIBLING_SITE_ROOTS and not url.startswith(VERIFIED_SIBLING_ROUTES)} + + +def test_sibling_links_in_renderer_sources_use_verified_routes(): + sources = [*sorted(TEMPLATES.glob("*.html")), + *(ROOT / "scripts" / name for name in ( + "render_trait_pages.py", "trait_causal_graph.py", "render_discussions_shell.py"))] + found = {str(path.relative_to(ROOT)): unverified_sibling_urls(path.read_text()) for path in sources} + assert {path: urls for path, urls in found.items() if urls} == {} + + +def test_every_sibling_link_in_the_built_site_uses_a_verified_route(): + built = [*sorted((ROOT / "pages").rglob("*.html")), ROOT / "404.html", + ROOT / "app" / "discussions" / "index.html"] + assert len(built) > 1100 + emitted: set[str] = set() + bad: dict[str, set[str]] = {} + for path in built: + text = path.read_text() + emitted |= set(FLEET_URL.findall(text)) + if urls := unverified_sibling_urls(text): + bad[str(path.relative_to(ROOT))] = urls + assert bad == {} + # Not vacuous: the corpus does link sibling records, not only site roots. + assert any(url.startswith("https://culturebotai.github.io/PathwayMech/pages/records/") + for url in emitted)
    LabelCURIECategoryPaCMAP xPaCMAP y