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


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

OntoBot change agent demo

  • Chris to demo [5-10 mins]
  • AI mention at GOC meeting

Pharynx terms in GO

Phagocytosis versus endocytsosis

Asserted classes versus logical definitions

Example: mRNA phosphatase activity is_a pyrophosphatase, not a phosphatase

not sure this is the easiest example Cjm (talk) 22:07, 19 March 2023 (EDT)

 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


GO, RHEA, EC aligment

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