Use relation in GPAD col 3 (qualifiers) for predicate

[dustine32]

We had initially decided to infer this GO-CAM structure from an annotation's aspect:

1. A molecular function annotation is just GP <-enabled_by- MF.
2. A cellular component annotation is just GP -part_of-> CC.
3. A biological process annotation is just GP <-enabled_by- (GO:0003674) -part_of-> BP. In the latter case, both the enabled_by and part_of edge have the same evidence from the original BP annotation.

Since we're now using GPAD, where the relation is explicitly stated, we can just create triples using this instead (after converting to RO of course). So, for this example line (where involved_in translates to RO:0002331):

WB	WBGene00000001	involved_in	GO:0008286	PMID:12393910|WB_REF:WBPaper00005614	ECO:0000316	WB:WBGene00000898		20151214	WB

Triple will be WB:WBGene00000001-RO:0002331->GO:0008286.

[dustine32]

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.

[dustine32]

Still need to handle NOT qualifiers.

[dustine32]

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:

[dougli1sqrd]

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.

[goodb]

@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

[dustine32]

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.