Ontology meeting 2023-03-13

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  • Group members: Pascale, Raymond, Val, Edith, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
  • Present: Pascale, Raymond, Val, Edith, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
  • Regrets:

GOC consortium

  • April 27th-29th, Padua, Italy
  • Any suggestions for working group sessions?

New Protege version

  • New Instruction page Protege5_6_setup_for_GO_Eds in progress
  • Jim testing ontology build: [1] 
  • Noting issue with ID ranges : Jim renamed our ID range file because this feature is broken. ID ranges will keep on working the same way they were before
  • Today: Will get everyone started
  • Review unmerged pull requests - will need to have conflicts resolved or redone after new Protege save

Reviewing pending PRs

  • AI: Review GOCHE documentation (confusion about ChEBI roles and GOCHE roles)
  • AI: Check with terms use GOCHE terms
  • AI: Close open PRs

Script to download annotations

Editors discussion items

Obsolete versus merge

Are there situations where we can merge? see

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

GO, RHEA, EC aligment

Tickets by ontology editors