Ontology meeting 2024-01-22

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


Discussion points

Blocking issues on Ongoing tickets

Regulation closure for taxon constraints

See https://github.com/geneontology/go-ontology/issues/26271 We can now use the relation 'regulates in other organism', so we need to

  1. Add this relation in the ontology: see https://github.com/geneontology/go-ontology/issues/26840
  2.  Remove redundant TC between terms and their regulation

alpha-ketoglutarate (aka 2-oxoglutarate) dehydrogenase complex terms

  • Steven, Raymond

https://github.com/geneontology/go-ontology/issues/26122

  • No question so far

Stress-activated MAPK cascade

Poorly defined; seems to overlap with other terms: https://github.com/geneontology/go-ontology/issues/26810 Are we agreeing that :

  • define by members
  • use the label preferred by the community
  • if the label mismatches the definition, include a systemaitic_synonym, and a curator note that they should *not* annotate to the label
  • obsolete the stress-activated grouping as it’s not defined by members, reannotate the ~40 direct annotations (to a pair of terms)

Objectives & Priorities for 2024

New term requests

Remain high priority

BP refactor

Pascale & Paul

Review design patterns (continued from last week)

Repo: https://github.com/geneontology/go-ontology/tree/master/docs/patterns

transport

signaling receptor activity by input

ligand incorrectly identified as the input (GH ticket)

      • Broader question: do we want all ligands as MF? Or should these move to x signal transduction, and keep a single activity, 'signaling receptor activity'?
        • Noting that most 'signal transduction' (BP) children have no logical definition. How about, for example:
 GO:0038027 apolipoprotein A-I-mediated signaling pathway
 'cell surface receptor signaling pathway'
  and ('starts with' some 'signaling receptor activity')
  and ('has small molecule activator' some 'apolipoprotein A-I')
  • Noting also that there is no 'small molecule' in ChEBI; so any PRO is a ChEBI:chemical entity
  • Discussion and AI
    • We do want to keep the receptor activities and use these to logically defined the signaling pathways
    • Remove relationship: signal transduction part of cell communication; this is not always true, since there are intracellular signaling pathways
    • Add new DP for signal transduction

involved_in_x_y

Other tickets/projects

  • Obsoletion single-step processes & regulation of MF
  • Obsoletion of MF/BP involved in BP
  • Signaling cassettes
  • Multi-organisms processes:
    • remove 'viral terms'
    • keep 'symbiont-mediated' and 'venom-mediated' xxx
    • finish alignment with PathGO (~ 75% done)