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

Chris Mungall cjmungall at lbl.gov
Tue Apr 10 17:32:10 PDT 2012


Yes, this is equivalent to what I suggested - see table 16.
http://www.w3.org/TR/owl2-mapping-to-rdf/

The main point is to avoid oboInOwl:Obsolete. This was introduced in the legacy oboInOwl mapping and has now been superseded.

On Apr 10, 2012, at 4:04 PM, Jie Zheng wrote:

> Hi Chris,
> 
> I defined the obsolete property or class as the subProperty or subClass of "http://www.w3.org/2002/07/owl#DeprecatedProperty" or "http://www.w3.org/2002/07/owl#DeprecatedClass". 
> 
> This is how I did:
>     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000222">
>         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_describes</rdfs:label>
>           <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#DeprecatedProperty"/>
>         <obo:IAO_0000231 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
>     </owl:ObjectProperty>
> 
> As Bioportal developers pointed out, I misused it. Should I use it as:
> <owl:DeprecatedProperty rdf:ID="http://purl.obolibrary.org/obo/IAO_0000222">
>         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_describes</rdfs:label>
>         <obo:IAO_0000231 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
>  </owl:DeprecatedProperty>
> 
> Thanks,
> 
> Jie
> 
> 
> 
> On 4/10/2012 6:54 PM, Chris Mungall wrote:
>> 
>> 
>> 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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>> 
> 

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