Ontology meeting 2020-01-27
Conference Line
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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
GOREL relations that could be retired and replaced with existing RO relations
'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 used '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 used '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
- 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'?
Other Business
https://github.com/geneontology/go-ontology/projects/1