Open mcodescu opened 8 years ago
Now I notice that the prefix is declared in the ontologies imported by bonedysplasia.
The imported ontology http://purl.org/obo/owl/PATO.owl seems to have been converted from OBO to RDF/XML, and it contains:
<!--oboInOwl meta-model - we must declare this here, otherwise the ontology will be OWL-Full unless we import http://www.geneontology.org/formats/oboInOwl#-->
https://ontohub.org/sandbox/testGenIndividuals.owl is a minimal file for the problem of generated anonymous individuals. With hets: v0.99, 1458196355
, I get
logic OWL.RL-ALC
Prefix: : <http://purl.org/obo/owl/>
Prefix: oban: <http://purl.org/obo/oban/>
Prefix: obo: <http://purl.org/obo/owl/obo#>
Prefix: oboContent: <http://purl.org/obo/owl/>
Prefix: oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
Prefix: owl: <http://www.w3.org/2002/07/owl#>
Prefix: owl11: <http://www.w3.org/2006/12/owl11#onClass>
Prefix: owl2: <http://www.w3.org/2006/12/owl2#onClass>
Prefix: rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
Prefix: rdfs: <http://www.w3.org/2000/01/rdf-schema#>
Prefix: xsd: <http://www.w3.org/2001/XMLSchema#>
Class: oboInOwl:DbXref
Class: oboInOwl:Definition
AnnotationProperty: oboInOwl:hasDbXref
AnnotationProperty: oboInOwl:hasDefinition
AnnotationProperty: oboInOwl:hasOBONamespace
AnnotationProperty: oboInOwl:hasURI
AnnotationProperty: label
Individual: _:genid1
Annotations: oboInOwl:hasDbXref _:genid2
Individual: _:genid1
Annotations: label
"An inability to completely empty the `urinary bladder` (FMA:15900) during the process of `urination` (GO:0060073) owing to a neurological condition."@en
Individual: _:genid2
Annotations: oboInOwl:hasURI
"http://purl.org/obo/owl/HPO#HPO_probinson"^^xsd:anyURI
Individual: _:genid2
Annotations: label "HPO:probinson"
Individual: _:genid3
Annotations: oboInOwl:hasURI
"http://purl.org/obo/owl/UMLS#UMLS_C0005697"^^xsd:anyURI
Individual: _:genid3
Annotations: label "UMLS:C0005697"
Class: HP#HP_0000002
Annotations: oboInOwl:hasOBONamespace "human_phenotype"
Annotations: label "Abnormality of body height"@en
Class: HP#HP_0000011
Annotations: oboInOwl:hasDbXref _:genid3
Annotations: oboInOwl:hasDefinition _:genid1
Annotations: oboInOwl:hasOBONamespace "human_phenotype"
Annotations: label "Neurogenic bladder"@en
Individual: _:genid1
Types: oboInOwl:Definition
Individual: _:genid2
Types: oboInOwl:DbXref
Individual: _:genid3
Types: oboInOwl:DbXref
Opening the file in Protege and saving it in Manchester syntax has a similar result:
Prefix: : <http://purl.org/obo/owl/>
Prefix: oban: <http://purl.org/obo/oban/>
Prefix: obo: <http://purl.org/obo/owl/obo#>
Prefix: oboContent: <http://purl.org/obo/owl/>
Prefix: oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
Prefix: owl11: <http://www.w3.org/2006/12/owl11#onClass>
Prefix: owl2: <http://www.w3.org/2006/12/owl2#onClass>
Prefix: owl: <http://www.w3.org/2002/07/owl#>
Prefix: rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
Prefix: rdfs: <http://www.w3.org/2000/01/rdf-schema#>
Prefix: xml: <http://www.w3.org/XML/1998/namespace>
Prefix: xsd: <http://www.w3.org/2001/XMLSchema#>
Ontology: <http://www.semanticweb.org/test/ontologies/2016/3/untitled-ontology-24>
AnnotationProperty: oboInOwl:hasDbXref
AnnotationProperty: oboInOwl:hasDefinition
AnnotationProperty: oboInOwl:hasOBONamespace
AnnotationProperty: oboInOwl:hasURI
AnnotationProperty: rdfs:label
Datatype: rdf:PlainLiteral
Datatype: xsd:anyURI
Class: <http://purl.org/obo/owl/HP#HP_0000002>
Annotations:
oboInOwl:hasOBONamespace "human_phenotype",
rdfs:label "Abnormality of body height"@en
Class: <http://purl.org/obo/owl/HP#HP_0000011>
Annotations:
oboInOwl:hasDbXref _:genid6,
oboInOwl:hasOBONamespace "human_phenotype",
oboInOwl:hasDefinition _:genid2,
rdfs:label "Neurogenic bladder"@en
Class: oboInOwl:DbXref
Individuals:
_:genid4,
_:genid6
Class: oboInOwl:Definition
Individuals:
_:genid2
Individual: _:genid1
Annotations:
oboInOwl:hasDbXref _:genid4
Individual: _:genid2
Annotations:
rdfs:label "An inability to completely empty the `urinary bladder` (FMA:15900) during the process of `urination` (GO:0060073) owing to a neurological condition."@en
Types:
oboInOwl:Definition
Individual: _:genid4
Annotations:
rdfs:label "HPO:probinson",
oboInOwl:hasURI "http://purl.org/obo/owl/HPO#HPO_probinson"^^xsd:anyURI
Types:
oboInOwl:DbXref
Individual: _:genid6
Annotations:
rdfs:label "UMLS:C0005697",
oboInOwl:hasURI "http://purl.org/obo/owl/UMLS#UMLS_C0005697"^^xsd:anyURI
Types:
oboInOwl:DbXref
With the ontology https://ontohub.org/bioportal_mappings/BDO.owl, I save the theory of the node BDO_http%3A%2F%2Fpurl.org%2Fskeletome%2Fbonedysplasia as an owl file, with a random URL for the name of the ontology and the empty prefix. When I try to analyze the resulting file again, the parser complains about the prefix oboInOwl:
The prefix appears in the ontology, e.g. in
Class: oboInOwl:Definition
but not in the prefix declarations part of the ontology.