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[protege-owl] OBO to OWL

Paria Kashfi hajar.kashfi at chalmers.se
Tue May 6 05:12:59 PDT 2008


Thank you for your response,
by "that the structure of ontology has changed somehow" I mean that 
,actually, I can't see any of those classes like disease, Xerostomia( 
one of its child) and etc at all
what I can see is a hierarchy of numbers and codes that seems 
meaningless to me

Regards
paria

Timothy Redmond wrote:
> I suspect that I know the answer to the first question.  I will  
> investigate and get help with the others.
>
>   
>> I could see the converted ontology in my classes view but I realized  
>> that the structure of ontology has changed somehow- I 'd browsed  
>> this ontology in OBOEdit so I knew how should it look like-
>>     
>
> I have heard that OBO edit does not show the class hierarchy.  It  
> shows some sort of combined class hierarchy plus partonomy view.  I am  
> guessing that the reason that the structure looks different is because  
> protege does not have a tab for this combined class hierarchy and  
> partonomy.  It is clear that we need to make some such thing.
>
>   
>> the first question raised in my mind was " is OBOConverted plugin  
>> reliable?"
>>     
>
>
> There are several mechanisms out there for converting OBO to OWL (the  
> owl api - and hence Protege 4 - has one for example).  But generally  
> these translations do not conform with the informal definition given  
> by the OBO developers.  So in some sense part of the OBO edit tab's  
> claim to fame is that its translation has been accepted by the OBO  
> developers as a correct approach.  Not a full answer to your question  
> but this is why the OBO converter is useful.
>
> -Timothy
>
> On May 3, 2008, at 11:43 PM, Paria Kashfi wrote:
>
>   
>> Hi all,
>> During my researches, I found Human Disease Ontology bu in OBO format
>> I tried o use OBOConverter tab in Protege 3.3 to convert it to OWL.  
>> I faced some problems:
>> I couldn't convert this ontology and add it to my own ontology- I  
>> found that there are some duplicate class names in these two  
>> ontologies - hence I tried to create a new project and do the same  
>> task. this time, I could see the converted ontology in my classes  
>> view but I realized that the structure of ontology has changed  
>> somehow- I 'd browsed this ontology in OBOEdit so I knew how should  
>> it look like-
>> the first question raised in my mind was " is OBOConverted plugin  
>> reliable?"
>> for the third try I downloaded OBOEdiPlugin to convert OBO to OWL  
>> using OBOEdit
>> this time, the problem was that I could not run OBOEdit when this  
>> plugin is added in extensions folder as mentioned here
>> http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page
>>
>> I also tried to use this OWL version of Human Disease ontology
>> http://www.obofoundry.org/cgi-bin/detail.cgi?id=disease_ontology
>> but I couldn't open this ontology in Protege, there's a problem in  
>> OWL file as protege says!
>> I hope someone can help me to find a correct version of Human  
>> Disease ontology in OWL or at least solve converting problems!
>>
>> Thank you in advance
>> Paria
>>
>>
>>
>>
>>
>>
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