Ontology meeting 2024-01-08

From GO Wiki
Jump to navigation Jump to search
  • Group members: Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul
  • Present: Pascale, Raymond, Chris, Jim, Steven, Edith, Peter, Paul T.
  • Regrets:

Announcements

No call next week - MLK day

Discussion points

Objectives & Priorities for 2024

Review design patterns

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

transport

  • easiest? Can we aim to add a LD to all terms, that matches the DP of its superclass?
  • Discussion
    • Axes of classification:
      • mechanism
      • substrate (should be a secondary axis)
      • target location
    • Action points:

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

many terms should be obsoleted; which terms should remain?


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)

New term requests