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:
  • 'acts on population of'
• GOREL relations that could be retired and replaced with an existing RO relation:
  • '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 OR '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)
    • For annotation, it looks like curators primarily 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 primarily 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: 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

Other Business

https://github.com/geneontology/go-ontology/projects/1