Ontology meeting 2020-12-14

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Peter, Harold, Jim, Paul, Tanya, Kimberly, Pascale


Group members

Pascale, Karen, Harold, Peter, Jim, Tanya, Kimberly, David, Chris, Paul, David


Call next week?

Discusssion topics

xrefs on obsolete/merged terms

See e.g. https://github.com/geneontology/go-ontology/issues/20135

'process has causal agent' o 'in taxon' -> 'in taxon'

Proposed RO change https://github.com/oborel/obo-relations/pull/413

for GO issue https://github.com/geneontology/go-ontology/issues/17613

-> may not be acceptable

Sequence Ontology in go-lego (for Noctua)


GitHub Discussions feature


(Compound) Molecular Functions -- BLOCKING FOR GO-CAM

Will continue after the holidays.

Cellular Component, ShEx, and GO-CAMs -- BLOCKING FOR GO-CAM

  • The ShEx specifications state that MFs can occur in an Anatomical Entity and that GPs or Protein-Containing Complexes can be located in an Anatomical Entity.
  • Most non-protein-containing complex GO CC terms are a child of Cellular Anatomical Entity which is a subclass of Anatomical Entity.
  • However, annotations to root Cellular Component result in ShEx violations because root Cellular Component is NOT a subclass of Anatomical Entity.
  • How do we fix this?
    • Change root Cellular Component annotations to Cellular Anatomical Entity (throughout GO)
    • Change ShEx value to an OR statement, for example: MF occurs_in AnatomicalEntity OR CellularComponent
    • Work on RO to see if there is a relation that could be used as a parent for all children of Cellular Component relations - overlaps?
      • Take this issue to the RO call(s)?
    • Move Protein-Containing Complex out of Cellular Component into its own GO aspect and make Cellular Component a subclass of Anatomical Entity

Other Business


Minutes should be recorded on individual tickets and in individual projects