The metpo-proposal skill (.claude/skills/metpo-proposal/SKILL.md) lists, under acceptable definition_source (IAO:0000119) forms:
Reused PATO/GO definition → the source CURIE itself → PATO:0000052
definition_source means "where the definition text came from" (PMID, DOI, BacDive, ISBN). A reused ontology term is a cross-ontology mapping, not provenance. Emitting those CURIEs into definition_source conflates the two: no exact/close/narrow distinction, no mapping justification or confidence, and invisible to SSSOM tooling. This is the same conflation tracked in berkeleybop/metpo#344 (124 such rows already in the METPO sheet).
Proposal: when a proposed term reuses or aligns to an existing ontology class, emit it as a mapping annotation with an IRI (skos:exactMatch / skos:closeMatch / skos:narrowMatch, or oboInOwl:hasDbXref) in a dedicated column, and reserve definition_source for real citations. Update the SKILL guidance and scripts/extract_metpo_proposals.py accordingly.
Cross-repo cleanup hub: berkeleybop/metpo#344.
🤖 Generated with Claude Code
The
metpo-proposalskill (.claude/skills/metpo-proposal/SKILL.md) lists, under acceptabledefinition_source(IAO:0000119) forms:definition_sourcemeans "where the definition text came from" (PMID, DOI, BacDive, ISBN). A reused ontology term is a cross-ontology mapping, not provenance. Emitting those CURIEs intodefinition_sourceconflates the two: no exact/close/narrow distinction, no mapping justification or confidence, and invisible to SSSOM tooling. This is the same conflation tracked in berkeleybop/metpo#344 (124 such rows already in the METPO sheet).Proposal: when a proposed term reuses or aligns to an existing ontology class, emit it as a mapping annotation with an IRI (
skos:exactMatch/skos:closeMatch/skos:narrowMatch, oroboInOwl:hasDbXref) in a dedicated column, and reservedefinition_sourcefor real citations. Update the SKILL guidance andscripts/extract_metpo_proposals.pyaccordingly.Cross-repo cleanup hub: berkeleybop/metpo#344.
🤖 Generated with Claude Code