Ontology meeting 2021-02-01
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Attendees
- Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Eric
- Present:
- Regrets:
Agenda
Announcement
Next week: ontology tickets jamboree
(Compound) Molecular Functions -- BLOCKING FOR GO-CAM
(Review):
- Examples:
- Molecules with ATPase activity
- RNA helicase (not DEAD-box, they seem to be different)
- => Resolved: is_a ATPase, being implemented, including for transporters (ABC and P-types)
- OK
- RNA helicase (not DEAD-box, they seem to be different)
- DNA-binding transcription factors
- p53/p21
- => Resolved: has_part 'transcription regulatory region sequence-specific DNA binding', DONE, see Ticket 16214
- OK
- p53/p21
- Signaling adaptors and sequestering activities
- ced-4 activity in core apoptotic program
- => Sequestering activity: Resolved: protein sequestering activity: is_a 'molecular sequestering activity' and ('has part' some 'protein binding')'
- => Signaling adaptor activity: Proposed: is_a 'protein-macromolecule adaptor activity' and (has_part some 'protein binding' REDUNDANT) and part of' some 'BP signaling (not yet implemented)
- OK
- ced-4 activity in core apoptotic program
- Receptors
- TM receptor S/T-PK activity, example: BMP receptor activity
- => Proposal: transmembrane receptor protein serine/threonine kinase activity: is_a 'signaling receptor activity' and has part some 'protein serine-threonine kinase activity' and has_part receptor ligand binding)
- TO DO: Check with Ruth
- G protein-coupled receptors (coupled to inhibitory G proteins (Gi))
- => Proposal: 'G protein-coupled receptor activity' is_a 'signaling receptor activity' and other MF = has_part
- Different ways of modeling ire-1, an unfolded protein receptor with two other activities
- => To complete - Kimberly: sorted on GO-CAM call: we would create a new term with all 3 activities
- TM receptor S/T-PK activity, example: BMP receptor activity
- Molecules with ATPase activity
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.
xref types
- https://github.com/geneontology/go-ontology/issues/20620
- Documentation: http://wiki.geneontology.org/index.php/Guidelines_for_%27database_cross_references%27_and_%27definition_database_cross_references%27#General_cross-reference_types
Other Business
https://github.com/geneontology/go-ontology/projects/1