Ontology meeting 2021-02-22

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Attendees

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


Agenda

Announcements

Discussion

Guidelines_for_using_ChEBI_terms

http://wiki.geneontology.org/index.php/Guidelines_for_using_ChEBI_terms This is linked from the main ontology documentation page: Ontology_Development

ShEx vs ontology relations

Should they align ? See this ticket: https://github.com/geneontology/go-ontology/issues/12349

Not all children of GO:0015318 (inorganic molecular entity transmembrane transporter activity) are inorganic

Should we merge this ticket and get rid of some grouping classes ? https://github.com/geneontology/go-ontology/issues/20872#issuecomment-780882533

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
    • Another option (pascale) would be to use 'Cellular Anatomical Entity' and the PMID you are curating; and filter that from the exports. Only Cellular_component and ND and the GOREF for ND do get exported; otherwise ND annotations get filtered out.

Discussion

  • Chris: suggests keeping the current practice and use root Cellular Component and ND.
  • Action would be to change the ShEX to allow a direct annotation to occurs_is/is active in root Cellular Component

xref types

Other Business

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


Minutes should be recorded on individual tickets and in individual projects

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