Ontology meeting 2022-05-23
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- Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
- Present:
- Regrets:
Announcement
No call next week - Memorial Day
Review documentation
- defxref:
- Guidelines_for_GO_textual_definitions#Database_cross-references_for_definitions
- To clarify:
- "abbreviation for the database being cross-referenced (see the list of database cross-references used in GO users.yaml) " ====> how do we know which are 'valid' databases to cross reference to?
- "For definitions created at meetings, the dbxref has 'mtg_' followed by the meeting start date; e.g. definitions written at the June 2006 content meeting on CNS development have the dbxref GOC:mtg_15jun06.)" ===> I (Pascale) propose that we dont do this anymore - but how could we reference meetings? Many time we also have a GO_REF. Ideally we should have
- the list of people that attended the meeting
- A summary of the discussion and the recommendations
- ideally ideally we should just link to PMIDs that the experts and curators at the meeting used to create/edit the terms
- To clarify:
- Guidelines_for_'database_cross_references'_and_'definition_database_cross_references'#Adding_database_cross-reference_types
Relation: is small molecule regulator
- Is 'is small molecule regulator' OK under 'participates in'? https://github.com/oborel/obo-relations/issues/369
- Should 'participates in' be disjoint from 'has participant'? https://github.com/oborel/obo-relations/issues/609
Editors discussion tickets
- User requests:
- proteinogenic amino acid biosynthesis and non-proteinogenic amino acid biosynthesis
- Bring back co-factor biosynthetic process https://github.com/geneontology/go-ontology/issues/23267
- peptide alpha-N-acetyltransferase activity children cause true path violation (Harold)
- UDP-beta-L-arabinofuranose transport & transporter
- Pascale: subclasses calculated by Protégé not the same as those requested by user