Ontology meeting 2022-11-28
- Group members: Pascale, Harold, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul
- Present:
- Regrets:
Announcements
This is the second-to-last call of the year. Next week (Dec 5th) we will talk about cell differentiation & children term definitions, Dec 12th is the no GO calls week, and Dec 19th Pascale (and others?) is on vacation.
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
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
Projects
unnecessary grouping terms in the chemical homeostasis branch
https://github.com/geneontology/go-ontology/issues/24455
and more generally, the correct biological level of classification for chemicals:
- ion (ie , monoatomic ions)
- amino acid
- carbohydrate
- lipid
- nucleic acid
- other molecules that dont fall in these classes:
- water
- ammonium
- phosphate
- sulfate
- ascorbate
- possibly others
Obsolete BPs "regulation MF"
https://github.com/geneontology/go-ontology/projects/34?add_cards_query=is%3Aopen
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?