Ontology meeting 2022-11-28: Difference between revisions
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*** should be cleaned up: http://release.geneontology.org/2022-11-03/ontology/external2go/index.html | *** should be cleaned up: http://release.geneontology.org/2022-11-03/ontology/external2go/index.html | ||
* one option would be at add all mappings (internal + external) in AmiGO: for eg GO:0018024 has a UniRule mapping but that is not showing up in AmiGO. It would be easy to copy from AmiGO, and then we'd get both internal and external on one go. | * one option would be at add all mappings (internal + external) in AmiGO: for eg GO:0018024 has a UniRule mapping but that is not showing up in AmiGO. It would be easy to copy from AmiGO, and then we'd get both internal and external on one go. | ||
=GO update paper 2023= | |||
https://docs.google.com/document/d/1jaGHywr2_DrflIDUqs0iebmfSRssTcOpcNtIsfFg-Dw/edit# | |||
See section on ontology; we explained many reasons of changes, so users better know what to expect | |||
=Tickets by ontology editors= | =Tickets by ontology editors= |
Revision as of 06:45, 24 November 2022
- 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:
- should be cleaned up: http://release.geneontology.org/2022-11-03/ontology/external2go/index.html
- one option would be at add all mappings (internal + external) in AmiGO: for eg GO:0018024 has a UniRule mapping but that is not showing up in AmiGO. It would be easy to copy from AmiGO, and then we'd get both internal and external on one go.
GO update paper 2023
https://docs.google.com/document/d/1jaGHywr2_DrflIDUqs0iebmfSRssTcOpcNtIsfFg-Dw/edit# See section on ontology; we explained many reasons of changes, so users better know what to expect
Tickets by ontology editors
Following up on prevous items
Design patterns
Discussions arising from BP refactoring
homeostasis at the organism level in multicellular organisms
- 'Circulating levels' used in animals; does that make sense in pants? Tanya -> no
- suggestions (by email):
- intra organismal x homeostasis
- intra multicellular organismal x homeostasis
- organismal x homeostasis (+ restriction of do not annotate single celled organisms)
Cellular component Assembly
- AI: query genes annotated to both assembly of a complex and part of the same complex.
- AI: improve definition to clarify that the annotated genes must mediate the process, not just be a structural constituent
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?