Ontology meeting 2022-11-28

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

Improving workflow for obsoletions

Obsoletion Ticket templates

• Improved obsoletion templates & provided a checklist for the GO editor in the go-ontology repo obsoletion template
  • go-ontology obsoletion ticket template: https://github.com/geneontology/go-ontology/issues/new?assignees=&labels=obsoletion&template=term-obsoletion.md&title=Obsoletion+request%3A+%5BGO+ID%3ATerm+label%5D
  • go-annotation review for obsoletion ticket template: https://github.com/geneontology/go-annotation/issues/new?assignees=&labels=annotation+review&template=annotation-review-for-obsoletion.md&title=Review+annotations+to+%5BINSERT+GO+TERM%5D
  • go-announcements obsoletion ticket template: https://github.com/geneontology/go-announcements/issues/new?assignees=&labels=obsoletion&template=obsoletion-notice.md&title=Obsoletion+notice%3A+%5BGO+ID%3A+term+label%5D

Improvements for getting lists annotations to review

• we need to get EXP (+TAS NAS?) in a single command
• we need to get the mappings
  • internal: 'easy' to get with grep -r "GOID" in the /ontology/external2go folder
  • external:
    1. should be cleaned up: http://release.geneontology.org/2022-11-03/ontology/external2go/index.html

Following up on prevous items

Design patterns

NAD, NADH, NADPH processes logical definitions inconsistencies

Jim https://github.com/geneontology/go-ontology/issues/24279

regulation of pH

Jim https://github.com/geneontology/go-ontology/pull/24256/files

cell morphogenesis

Causing DP issues: https://github.com/geneontology/go-ontology/issues/24299

Could we say that for cells, morphogenesis is the same as differentiation?

regulation of biological quality

Add axioms for regulation of biological quality