Ontology meeting 2020-02-03: Difference between revisions
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====GOREL relations that could potentially be retired and replaced with existing RO relations==== | ====GOREL relations that could potentially be retired and replaced with existing RO relations==== | ||
*ACTION: As a pilot, David and Kimberly replaced 'occurs in' in cell division logical definitions with 'has input' for specific cell types | |||
*https://github.com/geneontology/go-ontology/pull/18690 | |||
*Also removed some asserted parents for cell division terms - this changed some parentage wrt neuroblasts and somatic stem cell parentage (but is now consistent with CL) | |||
*Overall, this wasn't too difficult and we could continue along these lines for the other relations in question (results in fission of, results in fusion of, results in maintenance of, results in distribution of) | |||
From 2020-01-27 call: | |||
====='results in division of' (GOREL:0001019)===== | ====='results in division of' (GOREL:0001019)===== | ||
*Not used in the ontology | *Not used in the ontology | ||
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**PROPOSAL 3: some hybrid of the above 'occurs in' and 'has input' and 'has output'? | **PROPOSAL 3: some hybrid of the above 'occurs in' and 'has input' and 'has output'? | ||
*PROPOSED ACTION: create a design pattern | *PROPOSED ACTION: create a design pattern | ||
==Other Business== | ==Other Business== |
Revision as of 15:43, 30 January 2020
Conference Line
See calendar for details
On call:
Agenda
Discussion topics
Aligning Ontology, Annotation, ShEx
- We are creating ontology term-specific shapes in the ShEx schema
- The goal is to align what is used for annotation with the equivalent expression in logical definitions of the ontology
- We are also moving towards only using RO relations in GO, i.e. retiring, or incorporating into RO, GOREL relations or RO-pending relations
GOREL relations proposed to RO
- 'acts on population of'
- no comments or action on this ticket - who can help with this?
GOREL relations that could potentially be retired and replaced with existing RO relations
- ACTION: As a pilot, David and Kimberly replaced 'occurs in' in cell division logical definitions with 'has input' for specific cell types
- https://github.com/geneontology/go-ontology/pull/18690
- Also removed some asserted parents for cell division terms - this changed some parentage wrt neuroblasts and somatic stem cell parentage (but is now consistent with CL)
- Overall, this wasn't too difficult and we could continue along these lines for the other relations in question (results in fission of, results in fusion of, results in maintenance of, results in distribution of)
From 2020-01-27 call:
'results in division of' (GOREL:0001019)
- Not used in the ontology
- In the ontology, logical definitions use:
- 'occurs in', e.g. cystoblast division = cell division and 'occurs in' some cystoblast
- 'has input', e.g. germ-line stem cell division = cell division and 'has input' some germ-line stem cell
- loosely, but not exclusively, along somatic vs stem cell lines
- No design pattern (that I could find)
- In the ontology, logical definitions use:
- For annotation, it looks like curators use 'occurs in', 'has participant, 'results in division of' although there aren't many annotation extensions at all for 'cell division' and children
- GO
[Typedef] id: results_in_division_of name: results_in_division_of namespace: external comment: use occurs_in xref: GOREL:0001019 is_a: has_participant ! has participant
- GOREL
[Typedef] id: results_in_division_of name: results_in_division_of namespace: go/extensions/gorel def: "The relationship linking a entity and its participation in a process that results in the division of the entity into two entities of the same type." [GOC:mtg_berkeley_2013] comment: Example of use: an annotation of gene X to cell division with results_in_division_of CL:0000057 (fibroblast) means that at the end of the process a single fibroblast has divided into two fibroblasts. subset: AE_cell_or_anatomical subset: display_for_curators subset: valid_for_annotation_extension xref: GOREL:0001019 property_value: local_domain BFO:0000015 xsd:string property_value: local_range "CL:0000000 WBbt:0004017" xsd:string property_value: usage "The relationship linking a entity and its participation in a process that results in the division of the entity into two entities of the same type." xsd:string domain: BFO:0000015 range: CL:0000000 is_a: go_annotation_extension_relation ! go annotation extension relation is_a: has_participant ! has participant
- regulates_o_results_in_division_of
- Not used in the ontology
- For annotation, it looks like curators use 'regulates o has participant', 'regulates o results in division of' although there are very few of these annotations
[Typedef] id: regulates_o_results_in_division_of name: regulates division of namespace: go/extensions/gorel def: "This is the combination of the regulates relation with the results_in_division_of relation." [GOC:mtg_berkeley_2013] subset: display_for_curators subset: valid_for_annotation_extension xref: GOREL:0001024 property_value: local_domain GO:0008150 xsd:string property_value: local_range "CL:0000000 WBbt:0004017" xsd:string property_value: usage "This is the combination of the regulates relation with the results_in_division_of relation." xsd:string domain: BFO:0000015 is_a: go_annotation_extension_relation ! go annotation extension relation is_a: regulates_o_has_participant ! regulates_o_has_participant equivalent_to_chain: regulates results_in_division_of ! results_in_division_of
- PROPOSED ACTION: obsolete 'results in division of' and 'regulates o results in division of'
- Replacement:
- PROPOSAL 1: use 'occurs in' for logical definitions and to provide context in annotation for what cell is dividing and 'regulates o occurs in' for standard regulation annotations
- PROPOSAL 2: use 'has input' and 'has output' for logical definitions and to provide context in annotation for what cell is dividing and what cells that division produces and 'regulates o has input', 'regulates o has output' for standard regulation annotations
- PROPOSAL 3: some hybrid of the above 'occurs in' and 'has input' and 'has output'?
- PROPOSED ACTION: create a design pattern
Other Business
https://github.com/geneontology/go-ontology/projects/1