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 | ||
=Agenda= | =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'=== | ==='process has causal agent' o 'in taxon' -> 'in taxon'=== | ||
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https://github.com/geneontology/go-ontology/issues/20419 | https://github.com/geneontology/go-ontology/issues/20419 | ||
=== Cellular Component, ShEx, and GO-CAMs === | |||
=== 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 | |||
*** [http://noctua.geneontology.org/editor/graph/gomodel:5fb9cc0600000424 RNA helicase (not DEAD-box, they seem to be different)] | |||
** Receptors | |||
*** [http://noctua.geneontology.org/editor/graph/gomodel:5fce9b7300000287 Different ways of modeling ire-1, an unfolded protein receptor with two other activities] | |||
*** [http://noctua.geneontology.org/editor/graph/gomodel:5fb9cc0600000424 BMP receptor activity] | |||
*** [http://noctua.geneontology.org/editor/graph/gomodel:5df932e000002940 G protein-coupled receptors (coupled to inhibitory G proteins (Gi))] | |||
** Signaling adaptors and sequestering activities | |||
*** [http://noctua.geneontology.org/editor/graph/gomodel:584b49fa00000436 ced-4 activity in core apoptotic program] | |||
** DNA-binding transcription factors | |||
*** [http://noctua.geneontology.org/editor/graph/gomodel:5fa76ad400000000 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. | * 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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** Change root Cellular Component annotations to Cellular Anatomical Entity (throughout GO) | ** 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 | ** Change ShEx value to an OR statement, for example: MF occurs_in AnatomicalEntity OR CellularComponent | ||
** Move Protein-Containing Complex out of Cellular Component into its own GO aspect and make Cellular Component a | ** Work on RO to see if there is a relation that could be used as a parent for all children of Cellular Component relations - [https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002131&viewMode=All&siblings=true 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 == | == 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.
- 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