Ontology meeting 2023-03-20

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

OntoBot change agent demo

  • Chris to demo [5-10 mins]

Script to download annotations

Editors discussion items

Obsolete versus merge

Are there situations where we can merge? see

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

CARO vs UBERON

GO, RHEA, EC aligment

Tickets by ontology editors