Ontology meeting 2020-01-27: Difference between revisions
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See calendar for details | See calendar for details | ||
On call: | On call: David, Harold, Karen, Peter, Kimberly, Jim, Tanya, Chris, Barbara, Pascale, Bill | ||
= Agenda = | = Agenda = | ||
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*[https://github.com/oborel/obo-relations/issues/344 'acts on population of'] | *[https://github.com/oborel/obo-relations/issues/344 'acts on population of'] | ||
====GOREL relations that could be retired and replaced with existing RO relations==== | ====GOREL relations that could potentially be retired and replaced with existing RO relations==== | ||
====='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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**Review these terms? What process(es) do they define? | **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' | *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 | *In ropending.owl | ||
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<rdfs:label>results_in_maintenance_of</rdfs:label> | <rdfs:label>results_in_maintenance_of</rdfs:label> | ||
</owl:ObjectProperty> | </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 | |||
**In the ontology, logical definitions (8): | |||
***nuclear division = organelle fission and 'results in fission of' some nucleus | |||
**http://wiki.geneontology.org/index.php/XP:biological_process_xp_cellular_component | |||
**No design pattern (that I could find) | |||
**Is there another way to define these terms similarly to how we might re-define terms that use 'results in division of', i.e. using 'occurs in' or 'has input'? | |||
*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 | |||
<!-- http://purl.obolibrary.org/obo/GOREL_0002004 --> | |||
<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 | |||
<!-- http://purl.obolibrary.org/obo/GOREL_0002005 --> | |||
<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== | ==Other Business== |
Latest revision as of 13:14, 27 January 2020
Conference Line
See calendar for details
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)
- 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
'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?
- In the ontology, logical definitions (16):
- 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
- In the ontology, logical definitions (8):
- nuclear division = organelle fission and 'results in fission of' some nucleus
- http://wiki.geneontology.org/index.php/XP:biological_process_xp_cellular_component
- No design pattern (that I could find)
- Is there another way to define these terms similarly to how we might re-define terms that use 'results in division of', i.e. using 'occurs in' or 'has input'?
- In the ontology, logical definitions (8):
- 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.
- In the ontology, logical definitions (26):
- 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?
- In the ontology, logical definitions (7):
- 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