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[bioontology-support] [BioPortal] Ontology for Biomedical Investigations Parsing Failed
ray.fergerson at stanford.edu
Tue Apr 10 13:33:45 PDT 2012
It took a while to track this down; the cause was quite obscure.
Unfortunately the ontology has bugs in it that unfortunately neither
Protégé 4 nor the OWL api catch. The errors result in incorrect query-time
behavior on Protégé.
The message below is from Tim Redmond (resident Protégé & OWL expert) that
should explain how to fix the ontology.
Message for obi folk:
The provided ontologies were not in OWL 2 because of their use of
reserved names. While the deviation is not serious, it turns out -
unfortunately - that Protege 3 is sensitive to this deviation.
The reserved names in question are owl:DeprecatedClass and
owl:DeprecatedProperty. These two terms can be used in the RDF/XML
serialization but should not appear in the OWL ontology itself. These
terms can appear in the RDF/XML serialization in the following two
*:x rdf:type owl:DeprecatedClass .
*:x rdf:type owl:DeprecatedProperty .
In the provided ontlogies this usage pattern does not appear. However
these names appear in disjoint classes axioms, SubClassOf axioms,
declaration axioms, SubObjectPropertyOf axioms and ObjectProperty
domain and range axioms.
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