Ontology meeting 2021-03-22

Attendees

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

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Agenda

Discussion

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?

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

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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?

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xref types

• https://github.com/geneontology/go-ontology/issues/20620
• Documentation: Guidelines_for_'database_cross_references'_and_'definition_database_cross_references'#Adding_cross-reference_types

Other Business

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

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

• Merge 'host cell' into 'host cellular component' - see https://github.com/geneontology/go-ontology/issues/19800