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

Jie Zheng jiezheng at pcbi.upenn.edu
Tue Apr 10 16:04:49 PDT 2012


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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