Ontology meeting 2020-01-27

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On call: David, Harold, Karen, Peter, Kimberly, Jim, Tanya, Chris, Barbara, Pascale, Bill

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 potentially 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)
  • 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
'results in maintenance of' (GOREL:0012006)
  • Used in the ontology
    • In the ontology, logical definitions (16):
      • chromatin maintenance = cellular process and 'results in maintenance of' some chromatin
      • adherens junction maintenance = cell-cell junction maintenance and 'results in maintenance of' some adherens junction
    • No design pattern (that I could find)
    • Review these terms? What process(es) do they define?
  • For annotation, it doesn't appear to be used (nor does there appear to be a 'regulates o results in maintenance of')
  • In ropending.owl
   <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GOREL_0012006">
       <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002592"/>
       <oboInOwl:hasDbXref>GOREL:0012006</oboInOwl:hasDbXref>
       <oboInOwl:id>results_in_maintenance_of</oboInOwl:id>
       <oboInOwl:shorthand>results_in_maintenance_of</oboInOwl:shorthand>
       <rdfs:label>results_in_maintenance_of</rdfs:label>
   </owl:ObjectProperty>
  • PROPOSED ACTION: review annotations (starting from leaf nodes)?
    • Some annotated entities may actually be components of the 'maintained' cellular component
    • Determine what 'maintenance' terms correspond to defined processes and should be kept in the ontology
    • Leave out of ShEx for now
'results in fission of' (GOREL:0002004)
  • Used in the ontology
  • For annotation, it doesn't appear to be used? (nor does there appear to be a 'regulates o results in fission of')
  • In ropending.owl
   <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GOREL_0002004">
       <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOREL:0002004</oboInOwl:hasDbXref>
       <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">results_in_fission_of</oboInOwl:id>
       <oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">results_in_fission_of</oboInOwl:shorthand>
       <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">results_in_fission_of</rdfs:label>
   </owl:ObjectProperty>
  • PROPOSED ACTION: review logical definitions?
    • Leave out of ShEx for now
'results in fusion of' (GOREL:0012006)
  • Used in the ontology
    • In the ontology, logical definitions (26):
      • mitochondrial fusion = cellular process and 'results in fusion of' some mitochondrial
      • plasma membrane = cellular process and 'results in fusion of' some plasma membrane
    • No design pattern (that I could find)
    • Is there another way to define these terms? This might be tricky.
      • Some organelles and membrane could fuse to multiple other organelles and membranes, so it might be necessary to specify inputs and outputs.
  • For annotation, it doesn't appear to be used (nor does there appear to be a 'regulates o results in fusion of')
  • In ropending.owl
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GOREL_0002005">
       <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOREL:0002005</oboInOwl:hasDbXref>
       <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">results_in_fusion_of</oboInOwl:id>
       <oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">results_in_fusion_of</oboInOwl:shorthand>
       <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">results_in_fusion_of</rdfs:label>
   </owl:ObjectProperty>
  • PROPOSED ACTION: review logical definitions?
    • Leave out of ShEx for now
'results in distribution of' (GOREL:0002003)
  • Used in the ontology
    • In the ontology, logical definitions (7):
      • endoplasmic reticulum inheritance = organelle inheritance and 'results in distribution of' some endoplasmic reticulum
    • No design pattern (that I could find)
    • Is there another way to define these terms?
  • For annotation, it doesn't appear to be used (nor does there appear to be a 'regulates o results in distribution of')
  • In ropending.owl
 <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GOREL_0002003">
       <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOREL:0002003</oboInOwl:hasDbXref>
       <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">results_in_distribution_of</oboInOwl:id>
       <oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">results_in_distribution_of</oboInOwl:shorthand>
       <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">results_in_distribution_of</rdfs:label>
   </owl:ObjectProperty>
  • PROPOSED ACTION: review logical definitions?
    • Leave out of ShEx for now

Other Business

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

Minutes should be recorded on individual tickets and in individual projects