Comments (6)
dustine32
commented on June 22, 2024
Correction: Previous rule 3 above still holds for -involved_in->BP GPAD lines. Translate this to GP<-enabled_by-(GO:0003674)-part_of->BP
Also, when enables in GPAD relation col, change relation to enabled_by and reverse subject-object.
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dustine32
commented on June 22, 2024
Still need to handle NOT qualifiers.
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dustine32
commented on June 22, 2024
An example of a NOT qualifier in OWL:
<http://model.geneontology.org/8b70d37c-dbc7-49bd-87e5-58356afe0923/5c52a4bb00000003> rdf:type owl:NamedIndividual ,
[ rdf:type owl:Class ;
owl:complementOf <http://purl.obolibrary.org/obo/GO_0003674>
]
As it appears in graph editor:
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dougli1sqrd
commented on June 22, 2024
Do we have an example of a full gpad/gaf line with a NOT into Turtle? I'm a little confused by what this TTL is and how it relates to the image shown above.
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goodb
commented on June 22, 2024
@dougli1sqrd See http://noctua-dev.berkeleybop.org/editor/graph/gomodel:5c533d1100000051
e.g. gpad:
FB FBgn0015926 enables|NOT GO:0019003 pmid:17 ECO:0007651 20190201 GO_Central contributor=http://orcid.org/0000-0002-7334-7852|noctua-model-id=gomodel:5c533d1100000051|model-state=development
OWL:
@prefix : <http://model.geneontology.org/5c533d1100000051#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@base <http://model.geneontology.org/5c533d1100000051> .
<http://model.geneontology.org/5c533d1100000051> rdf:type owl:Ontology ;
owl:versionIRI <http://model.geneontology.org/5c533d1100000051> ;
owl:imports <http://purl.obolibrary.org/obo/go/extensions/go-lego.owl> ;
<http://geneontology.org/lego/modelstate> "development"^^xsd:string ;
<http://purl.org/dc/elements/1.1/title> "demo for NOT"^^xsd:string ;
<http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-7334-7852"^^xsd:string ;
<http://purl.org/pav/providedBy> "http://geneontology.org"^^xsd:string ;
<http://purl.org/dc/elements/1.1/date> "2019-02-01"^^xsd:string .
#################################################################
# Annotation properties
#################################################################
### http://geneontology.org/lego/evidence
<http://geneontology.org/lego/evidence> rdf:type owl:AnnotationProperty .
### http://geneontology.org/lego/hint/layout/x
<http://geneontology.org/lego/hint/layout/x> rdf:type owl:AnnotationProperty .
### http://geneontology.org/lego/hint/layout/y
<http://geneontology.org/lego/hint/layout/y> rdf:type owl:AnnotationProperty .
### http://purl.org/pav/providedBy
<http://purl.org/pav/providedBy> rdf:type owl:AnnotationProperty .
#################################################################
# Classes
#################################################################
### http://flybase.org/reports/FBgn0015926
<http://flybase.org/reports/FBgn0015926> rdf:type owl:Class .
#################################################################
# Individuals
#################################################################
### http://model.geneontology.org/5c533d1100000051/5c533d1100000052
<http://model.geneontology.org/5c533d1100000051/5c533d1100000052> rdf:type owl:NamedIndividual ,
<http://flybase.org/reports/FBgn0015926> ;
<http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-7334-7852"^^xsd:string ;
<http://purl.org/dc/elements/1.1/date> "2019-02-01"^^xsd:string ;
<http://purl.org/pav/providedBy> "http://geneontology.org"^^xsd:string .
### http://model.geneontology.org/5c533d1100000051/5c533d1100000053
<http://model.geneontology.org/5c533d1100000051/5c533d1100000053> rdf:type owl:NamedIndividual ,
[ rdf:type owl:Class ;
owl:complementOf <http://purl.obolibrary.org/obo/GO_0019003>
] ;
<http://purl.obolibrary.org/obo/RO_0002333> <http://model.geneontology.org/5c533d1100000051/5c533d1100000052> ;
<http://geneontology.org/lego/hint/layout/x> "75"^^xsd:string ;
<http://geneontology.org/lego/hint/layout/y> "75"^^xsd:string ;
<http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-7334-7852"^^xsd:string ;
<http://purl.org/dc/elements/1.1/date> "2019-02-01"^^xsd:string ;
<http://purl.org/pav/providedBy> "http://geneontology.org"^^xsd:string .
[ rdf:type owl:Axiom ;
owl:annotatedSource <http://model.geneontology.org/5c533d1100000051/5c533d1100000053> ;
owl:annotatedProperty <http://purl.obolibrary.org/obo/RO_0002333> ;
owl:annotatedTarget <http://model.geneontology.org/5c533d1100000051/5c533d1100000052> ;
<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5c533d1100000051/5c533d1100000054> ;
<http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-7334-7852"^^xsd:string ;
<http://purl.org/dc/elements/1.1/date> "2019-02-01"^^xsd:string ;
<http://purl.org/pav/providedBy> "http://geneontology.org"^^xsd:string
] .
### http://model.geneontology.org/5c533d1100000051/5c533d1100000054
<http://model.geneontology.org/5c533d1100000051/5c533d1100000054> rdf:type owl:NamedIndividual ,
<http://purl.obolibrary.org/obo/ECO_0007652> ;
<http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-7334-7852"^^xsd:string ;
<http://purl.org/dc/elements/1.1/date> "2019-02-01"^^xsd:string ;
<http://purl.org/dc/elements/1.1/source> "pmid:17"^^xsd:string ;
<http://purl.org/pav/providedBy> "http://geneontology.org"^^xsd:string .
### Generated by the OWL API (version 4.2.8) https://github.com/owlcs/owlapi
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dustine32
commented on June 22, 2024
Closing this since it's pretty much done. In general, the qualifiers are being used in the models. If not verbatim, they are translated to some other form. The only remaining issue is handling the NOT qualifier and this has a separate ticket #10 open for it.
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Related Issues (20)
- Update extension validation rules TSV
- Update extension validation rules for acts_o_population_of HOT 3
- Create test files for additional annotation metadata HOT 31
- No extension is an island HOT 4
- Resolve Shex failures in MGI annotations due to invalid identifiers for binding input HOT 38
- add taxon metadata for each model HOT 5
- Create test files for WB import HOT 12
- Write translated models out in N-Quads format HOT 1
- Proteoforms shouldn't be split into separate models HOT 14
- Handle pipe-separation in translation of with/from field HOT 1
- Handling interacting taxon data
- Add date and contributor to ALL annotation individuals? Not just evidence and Axiom? HOT 4
- Emit comment in annotation properties HOT 1
- Collapse comma-delimited objects of chain relations
- Add providedBy to all individuals HOT 2
- Add gene symbol to model title HOT 14
- Param to set modelstate HOT 1
- Comment missing some text from the GPAD HOT 1
- Set import model states to production so annotations are in GPAD outputs from dev HOT 5
- Processing annotation contributors for multiple GPAD lines with single annotation id HOT 5
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