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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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