Ontology meeting 2020-12-14
- 1 Present
- 2 Group members
- 3 Agenda
- 4 Discusssion topics
- 4.1 xrefs on obsolete/merged terms
- 4.2 'process has causal agent' o 'in taxon' -> 'in taxon'
- 4.3 Sequence Ontology in go-lego (for Noctua)
- 4.4 GitHub Discussions feature
- 4.5 (Compound) Molecular Functions -- BLOCKING FOR GO-CAM
- 4.6 Cellular Component, ShEx, and GO-CAMs -- BLOCKING FOR GO-CAM
- 4.7 Other Business
Peter, Harold, Jim, Paul, Tanya, Kimberly, Pascale
Pascale, Karen, Harold, Peter, Jim, Tanya, Kimberly, David, Chris, Paul, David
Call next week?
xrefs on obsolete/merged terms
'process has causal agent' o 'in taxon' -> 'in taxon'
Proposed RO change https://github.com/oborel/obo-relations/pull/413
-> 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.
- Molecules with ATPase activity
- Signaling adaptors and sequestering activities
- DNA-binding transcription factors
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