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[protege-owl] OBO to OWL

Nick Drummond nick.drummond at cs.manchester.ac.uk
Tue May 13 05:17:18 PDT 2008


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
>>>
>>>
>>>
>>>
>>>
>>>
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