Ontology meeting 2020-12-14: Difference between revisions

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** Change ShEx value to an OR statement, for example: MF occurs_in AnatomicalEntity OR CellularComponent
** 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 - [https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002131&viewMode=All&siblings=true overlaps]?
** Work on RO to see if there is a relation that could be used as a parent for all children of Cellular Component relations - [https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002131&viewMode=All&siblings=true overlaps]?
** Take this issue to the RO call(s)?
*** 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 sublclass of Anatomical Entity
** Move Protein-Containing Complex out of Cellular Component into its own GO aspect and make Cellular Component a sublclass of Anatomical Entity



Revision as of 11:42, 10 December 2020

Present

Regrets:

Group members

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


Agenda

'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)

https://github.com/geneontology/go-ontology/issues/20419

Compound Molecular Functions

Cellular Component, ShEx, and GO-CAMs

  • 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 sublclass of Anatomical Entity

GitHub Discussions feature

https://docs.github.com/en/free-pro-team@latest/discussions

Other Business

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


Minutes should be recorded on individual tickets and in individual projects