Ontology meeting 2021-01-04

Attendees

• 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

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Agenda

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

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
    • RNA helicase (not DEAD-box, they seem to be different)
  • Receptors
    • Different ways of modeling ire-1, an unfolded protein receptor with two other activities
    • BMP receptor activity
    • G protein-coupled receptors (coupled to inhibitory G proteins (Gi))
  • Signaling adaptors and sequestering activities
    • ced-4 activity in core apoptotic program
  • DNA-binding transcription factors
    • p53/p21

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

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