Ontology meeting 2023-03-20
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- Group members: Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, David, Chris, Paul
- Present: Pascale, Raymond, Edith, Jim, Tanya, Kimberly, David, Chris, Paul
- Regrets: Val, Peter
Announcements
GOC consortium
- April 27th-29th, Padua, Italy
- Any suggestions for working group sessions?
No call next week
Alliance all hands meeting, some people will be traveling; Pascale out next week
Editors discussion items
New Protege version
- New Instruction page Protege5_6_setup_for_GO_Eds in progress
- Did everyone have a chance to test?
OntoBot change agent demo
- Chris to demo [5-10 mins]
- AI mention at GOC meeting
Pharynx terms in GO
- Pharynx terms used for C. elegans annotations get flagged if the GO term uses the UBERON pharynx (or child) term in the logical definition
- We might be stalled here by UBERON work: https://github.com/obophenotype/uberon/issues/2728
Phagocytosis versus endocytsosis
Asserted classes versus logical definitions
Example: mRNA phosphatase activity is_a pyrophosphatase, not a phosphatase
Logical definitions should do most of the work for us
Procedure to mark terms to be obsoleted
- This would give curators and editors of ontologies using GO a way to know which terms are scheduled for obsoletion
- There is a property that we can use
Test new process to when obsoleting terms with taxon constraints
- Use GH actions ? Pascale to test
https://github.com/geneontology/go-ontology/issues/24489 https://github.com/geneontology/go-ontology/issues/24490
CARO vs UBERON
- https://github.com/oborel/obo-relations/issues/695
- Implications for ontology development and ShEx
GO, RHEA, EC aligment
- Created a project in the go-ontology repo
- Will update guidelines
- Question: Do we need to keep comments about obsolete/transferred ECs, such as GO:0047091 , has comment "Note that EC:1.13.12.10 was merged into this term."
Tickets by ontology editors
Pending Action items
GOCHE documentation
From 2023-03-13 call
- AI: Review GOCHE documentation (confusion about ChEBI roles and GOCHE roles)
- AI: Check with terms use GOCHE terms
- AI: Close open PRs