Ontology meeting 2021-03-15
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- Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul, Eric
- New Rheas: Pascale & Harold propose NOT to wait for the Rhea to be public to add it to a GO term. Too much waiting and going back. We need to close tickets.
- Obsoletions: For terms that are clearly wrong & with no annotations, no mappings, no xrefs, not in subsets: announce + obsolete immediately. We can always restore the term in the unlikely event that there is an objection
- New helpdesk ticket from Paul Pavlidis about releases: https://github.com/geneontology/helpdesk/issues/302
Follow up: Cellular Component, ShEx, and GO-CAMs -- BLOCKING FOR GO-CAM
Pascale spoke to Patrick Masson Proposal is to have 3 branches:
- cellular anatomical entity
- move 'other organism part' here (if we don't obsolete that term)
- virion compoment (merge of 'virion' and 'virion part' (no annotations))
- protein-containing complex
- On a related note, 'host cell' and 'host cell part' can probably merge into 'host cellular component' - see https://github.com/geneontology/go-ontology/issues/19800
New relationships after using equivalent Rhea reaction
Jim generated a ttl file.
- Created Logical definition
- Plan: going forward, creating new terms:
- add Rhea description in textual definition
- bring EC mapping from Rhea
- pull EC name automatically
- retrospectively ??''
- Next step:
- check if those logical definitions cause problems in inferences
- Jim to check if some subsumptions are missing
id ranges file
- do we need "The Original Set (OS) of GO terms"
- do we need both the text and owl files?
- Documentation: Guidelines_for_'database_cross_references'_and_'definition_database_cross_references'#Adding_cross-reference_types