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

Chris Mungall cjmungall at lbl.gov
Tue Apr 10 15:54:43 PDT 2012


oboInOwl:obsolete should be declared obsolete, I don't recommend reverting to this.

You should use the owl:deprecated annotation property. This is the standard way to translate obsolete classes in the obo2owl translation. Tim added support for this in Protege.


On Apr 10, 2012, at 3:27 PM, Jie Zheng wrote:

> 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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