Ontology meeting 2024-01-29

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


Discussion points

Proposal to switch to 'has primary input'

  • Relations have been changed in the ontology months ago
  • Proposal (Kimberly):
    • update existing annotations in Noctua and Protein2GO
    • Get the list of currency chemicals (Reactome?) - added to Pathways2GO agend for 2024-01-25
    • Curator call: discuss usage and guideline
    • Double-check Noctua behavior
    • Double-check Protein2GO behavior

Blocking issues on ongoing tickets

Guidelines for protein-containing complexes

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