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

Jie Zheng jiezheng at pcbi.upenn.edu
Tue Apr 10 15:27:28 PDT 2012


Hi Ray,

Thanks for identified the bug. We have tried to open OBI in both Protege 
3 and Protege 4. Both worked fine. The issue cause by replacing 
oboInOwl:obsolete root terms by Owl:deprecate. Same should define the 
deprecated term as <owl:DeprecatedClass rdf:ID="OBSOLETE_TERM" />. For 
making sure everything worked well, I reverted to oboInOwl:obsolete root 
terms. Hope parsing go through this time.

Thanks,

Jie


On 4/10/2012 4:33 PM, Ray Fergerson wrote:
>
> Jie,
>
> 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.
>
> Ray
>
> ----------------------------
>
> 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
>
> ways:
>
>     *: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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