Ontology meeting 2023-03-20: Difference between revisions
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* '''Group members:''' Pascale, Raymond, Val, Edith | * '''Group members:''' Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, David, Chris, Paul | ||
* '''Present:''' | * '''Present:''' Pascale, Raymond, Edith, Jim, Tanya, Kimberly, David, Chris, Paul | ||
* '''Regrets:''' | * '''Regrets:''' Val, Peter | ||
=Announcements= | |||
==GOC consortium== | ==GOC consortium== | ||
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* Any suggestions for working group sessions? | * Any suggestions for working group sessions? | ||
=New Protege version= | =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 | * New Instruction page [[Protege5_6_setup_for_GO_Eds]] in progress | ||
* | * Did everyone have a chance to test? | ||
=OntoBot change agent demo= | ==OntoBot change agent demo== | ||
* Chris to demo [5-10 mins] | * Chris to demo [5-10 mins] | ||
* AI mention at GOC meeting | |||
* | |||
== Pharynx terms in GO == | == Pharynx terms in GO == | ||
Line 62: | Line 56: | ||
=Tickets by ontology editors= | =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''' | |||
[[Category:Meetings]] | [[Category:Meetings]] | ||
[[Category:Ontology]] | [[Category:Ontology]] |
Latest revision as of 12:05, 22 March 2023
- 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