Ontology meeting 2020-12-14: Difference between revisions

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=Present=
=Present=
 
Peter, Harold, Jim, Paul, Tanya, Kimberly, Pascale


Regrets:
Regrets:
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=Group members=  
=Group members=  


Pascale, Karen, Harold, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
Pascale, Karen, Harold, Peter, Jim, Tanya, Kimberly, David, Chris, Paul, David




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===Call next week? ===
===Call next week? ===
=Discusssion topics=
===xrefs on obsolete/merged terms===
See e.g. https://github.com/geneontology/go-ontology/issues/20135


==='process has causal agent' o 'in taxon' -> 'in taxon'===
==='process has causal agent' o 'in taxon' -> 'in taxon'===
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=== (Compound) Molecular Functions ===
=== (Compound) Molecular Functions -- BLOCKING FOR GO-CAM ===
Will continue after the holidays.  
Will continue after the holidays.  


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*** [http://noctua.geneontology.org/editor/graph/gomodel:5fa76ad400000000 p53/p21]
*** [http://noctua.geneontology.org/editor/graph/gomodel:5fa76ad400000000 p53/p21]


=== Cellular Component, ShEx, and GO-CAMs ===
=== 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.
* 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.
* Most non-protein-containing complex GO CC terms are a child of Cellular Anatomical Entity which is a subclass of Anatomical Entity.
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*** Take this issue to the RO call(s)?
*** 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
** Move Protein-Containing Complex out of Cellular Component into its own GO aspect and make Cellular Component a subclass of Anatomical Entity


== Other Business ==
== Other Business ==

Latest revision as of 14:09, 14 December 2020

Present

Peter, Harold, Jim, Paul, Tanya, Kimberly, Pascale

Regrets:

Group members

Pascale, Karen, Harold, Peter, Jim, Tanya, Kimberly, David, Chris, Paul, David


Agenda

Call next week?

Discusssion topics

xrefs on obsolete/merged terms

See e.g. https://github.com/geneontology/go-ontology/issues/20135

'process has causal agent' o 'in taxon' -> 'in taxon'

Proposed RO change https://github.com/oborel/obo-relations/pull/413

for GO issue https://github.com/geneontology/go-ontology/issues/17613

-> may not be acceptable

Sequence Ontology in go-lego (for Noctua)

https://github.com/geneontology/go-ontology/issues/20419


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.

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


Minutes should be recorded on individual tickets and in individual projects