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

[jie zheng]

Thanks,

Jie

On 4/10/2012 8:32 PM, Chris Mungall wrote:
>
> 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 the legacy oboInOwl mapping and has now been superseded.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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