Ontology meeting 2021-03-22

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Attendees

  • Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul, Eric
  • Present:
  • Regrets:



Agenda

Announcements

Discussion

Revisit Rhea policy

  • New Rheas: Pascale & Harold propose NOT to wait for the Rhea to be public to add it to a GO term. Too much waiting and going back. We need to close tickets.
  • ACTION: Filter out Rhea xrefs that are not valid (Jim)

What kinds of MF terms would be appropriate for the multi-drug resistance transporters.

Karen I’ve followed the line of thought that you and Paul suggested at the Jamboree, and would like to see what you guys think before I go any further.

The two relevant tickets are:


Can protein complexes be is_a cellular anatomical entity?

See ribosome question, https://github.com/geneontology/go-ontology/issues/21143

Also, if we allow that, how does that impact ShEx? Do we already have cases like this? What default relationship gets added?



Any blocking issues for ontology editors?

New relationships after using equivalent Rhea reaction

https://github.com/geneontology/go-ontology/issues/20839

Jim generated a ttl file.

*Discussion:

  • Created Logical definition
  • Plan: going forward, creating new terms:
    • add Rhea description in textual definition
    • bring EC mapping from Rhea
    • pull EC name automatically
    • retrospectively  ??''
  • Next step:
    • check if those logical definitions cause problems in inferences
    • Jim to check if some subsumptions are missing

id ranges file

https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/go-idranges.txt

  • do we need "The Original Set (OS) of GO terms"
  • do we need both the text and owl files?



xref types

Other Business

https://github.com/geneontology/go-ontology/projects/1


Minutes should be recorded on individual tickets and in individual projects

To do from previous calls

Cellular Component, ShEx, and GO-CAMs

Pascale spoke to Patrick Masson Proposal is to have 3 branches:

  • cellular anatomical entity
    • move 'other organism part' here (if we don't obsolete that term)
  • virion compoment (merge of 'virion' and 'virion part' (no annotations))
  • protein-containing complex