Ontology meeting 2021-01-04
Present
Regrets
Group members
Pascale, Karen, Harold, Peter, Jim, Tanya, Kimberly, David, Chris, Paul, David
Agenda
Call next week?
Technically next week is the 'no meeting' week
Sequence Ontology in go-lego (for Noctua)
https://github.com/geneontology/go-ontology/issues/20419 Pascale working with Colin - right now we will use SO terms to create logical definitions for GO terms; maybe this will avoid the need to use SO in Noctua
GitHub Discussions feature
https://docs.github.com/en/free-pro-team@latest/discussions
(Compound) Molecular Functions -- BLOCKING FOR GO-CAM
Will continue after the holidays.
- Examples:
- Molecules with ATPase activity
- Receptors
- 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
Other Business
https://github.com/geneontology/go-ontology/projects/1