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[bioontology-support] [BioPortal] Ontology for Biomedical Investigations Parsing Failed

Ray Fergerson ray.fergerson at
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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