Ontology meeting 2022-11-28: Difference between revisions

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* other molecules that dont fall in these classes:  
* other molecules that dont fall in these classes:  
** water
** water
** ammonium
** phosphate
** phosphate
** sulfate
** sulfate
** ascorbate  
** ascorbate  
** possibly others  
** possibly others
 


==Obsolete BPs "regulation MF"==
==Obsolete BPs "regulation MF"==

Revision as of 06:02, 28 November 2022

  • 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


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?

regulation of biological quality

Add axioms for regulation of biological quality