Ontology meeting 2021-01-04
- Group members: Pascale, Karen, Harold, Peter, Jim, Tanya, Kimberly, David, Chris, Paul, Eric
- Present: Pascale, Karen, Harold, Tanya, Peter, Kimberly, Chris, Jim, Eric
- Regrets: David
Call next week?
Technically next week is the 'no meeting' week. However the week after, Jan 18th, is the Martin Luther King Jr. Day; who is off on Jan 18th?
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 (which terms we can instantiate versus which we need to use as extensions is still under discussion) - to be revisited
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
- Documentation: http://wiki.geneontology.org/index.php/Guidelines_for_%27database_cross_references%27_and_%27definition_database_cross_references%27#General_cross-reference_types