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[protege-owl] OBO to OWL

Paria Kashfi hajar.kashfi at chalmers.se
Tue May 13 13:10:34 PDT 2008


Hi
actually I couldn't solve this problem yet
have you tried the web service link Juan sent to me? not me, but maybe 
it helps
Good luck

Nick Drummond wrote:
> Paria, Tim,
>
> When I used the P3.4 OBO converter tab (!) to convert the gene  
> ontology I also ended up with a flat hierarchy with no structure.
> There should be a few roots such as biological process that have got a  
> lot of subclasses. Is the converter being maintained? Is this a bug?
> Actually, trying this again now with the current OBO1.2 version of the  
> gene ontology the plugin fails with an error  
> "java.lang.RuntimeException: Undefined Property in Relationship." and  
> no stacktrace.
>
> The only issue I currently know about with the translation[1] done  
> when an OBO ontology is loaded by P4 is the representation of synonyms  
> etc.
> They are implemented as straight annotations - whereas the P3  
> converter reifies them into annotations containing anonymous  
> individuals.
>
> If anyone could shed light on any other issues that would be great.
>
> Nick
>
> [1] http://www.med.univ-rennes1.fr/lim/doc_175.pdf
>
> On 6 May 2008, at 13:12, Paria Kashfi wrote:
>
>   
>> 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
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> <hajar_kashfi.vcf>_______________________________________________
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