Ontology meeting 2020-12-14: Difference between revisions
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===Sequence Ontology in go-lego (for Noctua)=== | ===Sequence Ontology in go-lego (for Noctua)=== | ||
https://github.com/geneontology/go-ontology/issues/20419 | https://github.com/geneontology/go-ontology/issues/20419 | ||
=== 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 | |||
** Move Protein-Containing Complex out of Cellular Component into its own GO aspect and make Cellular Component a sublclass of Anatomical Entity | |||
== Other Business == | == Other Business == |
Revision as of 11:26, 9 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
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
- Move Protein-Containing Complex out of Cellular Component into its own GO aspect and make Cellular Component a sublclass of Anatomical Entity
Other Business
https://github.com/geneontology/go-ontology/projects/1