Ontology meeting 2017-07-21

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How will we distribute ontology editing tasks for the signaling work? Shall an editor join each group. Kimberly and DavidH can't do it all.


August Meeting Agenda


  • On call: Chris, David H., Eric, Jim, Karen, Kimberly, Pascale, Tanya

Signaling Pathways

  • Distributing ontology editing tasks
    • Ca2+ Signaling - ?
      • Annotation possibly claimed by Penelope?
    • GPCR - Pascale
      • No one has formally claimed the annotation part of this, yet
    • MAPK - David H.
    • Wnt - Kimberly (with Giulia and Helen)
  • Review of github organization for this project

Import Pipeline

  • Chris has taken care of this

Vitamins vs Co-Factors

  • Will need to work with ChEBI to request appropriate role curation
  • Curators who filed the go-ontology ticket should work with ChEBI to get roles they need
  • What will ontology editors then need to do?
    • Right now, manual maintenance is required, i.e. manually decide what chemical roles get added
    • Discuss this at the August meeting

Autophagy and CVT Pathway

  • These two processes share some gene products
  • CVT pathway relation to autophagy in the ontology has been examined several times in the past
  • What's the correct relation?
  • Molecular definitions of autophagy and related processes.
  • How about grouping terms like autophagy-like process or autophagic machinery-dependent process?
  • Curators should know what more specific process is being studied in the papers they're reading and use the more specific terms for annotations
  • David H will add proposals for re-naming the grouping term in the corresponding ticket

GO Inferences Report

  • Chris has fixed this

GO Slims

  • We need someone to own each of the GO slims
  • Set up a yaml metadata file for each GO slim
    • Would include who is responsible for it
  • Also document what the GO slim is used for
  • Document practice for how each GO slim is generated
  • Groups may be balancing, differently, number of terms in slim vs how many gps map to nothing
  • Maybe periodically find list of genes that map to nothing and create a new grouping term in the ontology or not in the ontology, but useful for categorization?