Difference between revisions of "Ontology meeting 2021-03-22"

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


Revisit RHEA policy: we should not put known dead links into the ontology just so the ticket can be closed.


=Revisit RHEA policy: we should not put known dead links into the ontology just so the ticket can be closed.=


===Any blocking issues for ontology editors?===
===Any blocking issues for ontology editors?===

Revision as of 10:15, 22 March 2021

Attendees

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



Agenda

Announcements

Discussion

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?


Revisit RHEA policy: we should not put known dead links into the ontology just so the ticket can be closed.

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