Ontology meeting 2021-03-22: Difference between revisions
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Also, if we allow that, how does that impact ShEx? Do we already have cases like this? What default relationship gets added? | Also, if we allow that, how does that impact ShEx? Do we already have cases like this? What default relationship gets added? | ||
Revisit RHEA policy: we should not put known dead links into the ontology just so the ticket can be closed. | |||
Revision as of 10:07, 22 March 2021
Attendees
- Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul, Eric
- Present:
- Regrets:
Agenda
Announcements
Discussion
What kinds of MF terms would be appropriate for the multi-drug resistance transporters.
Karen I’ve followed the line of thought that you and Paul suggested at the Jamboree, and would like to see what you guys think before I go any further.
The two relevant tickets are:
- obsolete: drug binding: https://github.com/geneontology/go-ontology/issues/19480
- NTRs: pyridinium ion transport: https://github.com/geneontology/go-ontology/issues/19642
Can protein complexes be is_a cellular anatomical entity?
See ribosome question, https://github.com/geneontology/go-ontology/issues/21143
Also, if we allow that, how does that impact ShEx? Do we already have cases like this? What default relationship gets added?
Revisit RHEA policy: we should not put known dead links into the ontology just so the ticket can be closed.
Any blocking issues for ontology editors?
New relationships after using equivalent Rhea reaction
https://github.com/geneontology/go-ontology/issues/20839
Jim generated a ttl file.
*Discussion:
- 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
https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/go-idranges.txt
- do we need "The Original Set (OS) of GO terms"
- do we need both the text and owl files?
xref types
- https://github.com/geneontology/go-ontology/issues/20620
- Documentation: Guidelines_for_'database_cross_references'_and_'definition_database_cross_references'#Adding_cross-reference_types
Other Business
https://github.com/geneontology/go-ontology/projects/1
Minutes should be recorded on individual tickets and in individual projects
To do from previous calls
Cellular Component, ShEx, and GO-CAMs
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
- Merge 'host cell' into 'host cellular component' - see https://github.com/geneontology/go-ontology/issues/19800