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[protege-owl] OBO to OWL

Timothy Redmond tredmond at stanford.edu
Mon May 5 08:55:36 PDT 2008


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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