We should also aim for compliance with OBO Foundry principles; e.g., 
although not completed one can see summary notes from OBO meeting in 
Cambridge last week:
http://obofoundry.org/wiki/index.php/OBO_Foundry_Workshop_2010/outcomes/tuesday#Review_of_principles_and_criteria_.28Barry.29

and take into account existing accepted reference, neighbouring and 
candidate OBO Foundry ontologies:
http://obofoundry.org/

Barry

Am 24.02.2010 16:13, schrieb Nina Jeliazkova:
> Sylvia.Escher at item.fraunhofer.de wrote:
>    
>> Dear Nina, dear Christoph,
>>
>> this not really clear for me, probably because I'm not an expert in file
>> formats/porgramming. The owl file from protege can be stored as XML.
>> However, this can not be read by ACCESS although ACCESS can read normal
>> XML-files.Therefore we would like to do an XML file first.
>>
>> The ontology is the defintion of an hierachical relationship between
>> organs/descriptors etc. Why do we need to do this with the owl format and
>> could not do it in  XML format?
>>
>>      
> Besides hierarchical relationships, there is more for an ontology
> definitions - relationships between objects, specified by RDF
> properties.  This is not possible to introduce in XML files.
>
> We decided to work with RDF triples, because it is a W3C standard for
> describing data and can allow reasoning , querying and merging data from
> different sources.
>
> BTW, are there any plans to expose RepDose as an OpenTox service and
> allow to use in OpenTox models?
>
> Best regards,
> Nina
>
>
>    
>> As long as none can explain this to me, I would prefer the XML file.
>> Christoph, can you probably give me an explanation? Perhaps it easier in
>> german than in english.
>>
>> Kind regards, Sylvia
>>
>>
>>
>> -------------------------------------------------------------------------
>> Dr. Sylvia Escher
>> Group Manager Structure Activity Relationships
>> Chemical Risk Assessment
>> Fraunhofer Institute of Toxicology and Experimental Medicine (ITEM)
>> Nikolai-Fuchs-Strasse 1, 30625 Hannover, Germany
>> Tel: +49 511 5350-330, Fax: +49 511 5350-335
>> mailto:Sylvia.Escher at item.fraunhofer.de
>> www.item.fraunhofer.de
>>
>>
>>
>>
>> Nina Jeliazkova<nina at acad.bg>
>> Gesendet von: development-bounces at opentox.org
>> 24.02.2010 15:06
>> Bitte antworten an
>> jeliazkova.nina at gmail.com; Bitte antworten an
>> opentox development mailing list<development at opentox.org>
>>
>>
>> An
>> iva at lml.bas.bg, opentox development mailing list<development at opentox.org>
>> Kopie
>> Sylvia.Escher at item.fraunhofer.de, olga.tcheremenskaia at iss.it
>> Thema
>> Re: [OTDev] Protege - XML file from other sources
>>
>>
>>
>>
>>
>>
>> Dear Sylvia,
>>
>> RDF and OWL purpose is not to be directly imported into a relational
>> database, like MS Access,  there are different systems for RDF triple
>> storage.  It is completely normal and expected you can't import it into
>> MS Access.
>> If you develop it into another format, it will not be an ontology and
>> not possible to use in OpenTox services.
>>
>> Best regards,
>> Nina
>>
>> Ivelina Nikolova wrote:
>>
>>      
>>> Dear Sylvia,
>>>
>>> may you send me the problematic file, so that I can try
>>> elaborating on where  the problem comes from.
>>>
>>> Ivelina
>>>
>>>
>>>
>>> Sylvia.Escher at item.fraunhofer.de wrote:
>>>
>>>
>>>        
>>>> Dear Ivelina,
>>>>
>>>> thank you for your help. I think in one OPENTOX telco, we decided to
>>>>
>>>>          
>> use
>>
>>      
>>>> Protege and the owl file format/RD files format to describe an ontology
>>>>
>>>>          
>>
>>      
>>>> like the organ ontology that we are developing.
>>>>
>>>> so we are currently working with that programme and I do not see that
>>>>
>>>>          
>> it
>>
>>      
>>>> is already a ready to use application. We would e.g. like to load the
>>>> Protege file in XML.format  into the ACCESS database RepDose as well.
>>>> Normally ACCESS can read XML format but fails to read the Protege file.
>>>>
>>>> Thus, I would like to know whether it would be a problem, if we simply
>>>> create an XML file for the ontology, for which we do not use Protege?
>>>>
>>>>          
>> If
>>
>>      
>>>> you do not have any constraints against the  XML file, then we will go
>>>>
>>>>          
>> on
>>
>>      
>>>> with this format for OPENTOX. Olga, Nina what do you think about it?
>>>> Perhaps someelse cold then convert the XML file into an Protege
>>>>
>>>>          
>> readable
>>
>>      
>>>> format.
>>>>
>>>> Kind regards, Sylvia
>>>>
>>>>
>>>>
>>>>
>>>>          
>> -------------------------------------------------------------------------
>>
>>      
>>>> Dr. Sylvia Escher
>>>> Group Manager Structure Activity Relationships
>>>> Chemical Risk Assessment
>>>> Fraunhofer Institute of Toxicology and Experimental Medicine (ITEM)
>>>> Nikolai-Fuchs-Strasse 1, 30625 Hannover, Germany
>>>> Tel: +49 511 5350-330, Fax: +49 511 5350-335
>>>> mailto:Sylvia.Escher at item.fraunhofer.de
>>>> www.item.fraunhofer.de
>>>>
>>>>
>>>>
>>>>
>>>> Ivelina Nikolova<iva at lml.bas.bg>
>>>> Gesendet von: development-bounces at opentox.org
>>>> 24.02.2010 13:46
>>>> Bitte antworten an
>>>> iva at lml.bas.bg; Bitte antworten an
>>>> opentox development mailing list<development at opentox.org>
>>>>
>>>>
>>>> An
>>>> opentox development mailing list<development at opentox.org>
>>>> Kopie
>>>>
>>>> Thema
>>>> Re: [OTDev] Protege help
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Dear Helvi,
>>>>
>>>> May you specify better what would like to use the ontology for?
>>>> The OWL file is a valid XML file as well, so there shouldn't be a
>>>>
>>>>          
>> problem
>>
>>      
>>>> if the mark-up structure is accepted by the application.
>>>> If you want to upload compounds or features and calculate
>>>> something out of them you need to upload a file with individuals
>>>> not the ontology itself.
>>>>
>>>> As for visualisation within Protege you can try Jambalaya plug-in.
>>>> Go to Project/Configure menu and check the Jambalaya tab. Then a
>>>> new tab will appear in the main frame. There you can drag&drop
>>>> from the left sideobjects which need to be visualised.
>>>>
>>>> I hope this helps.
>>>>
>>>> Best,
>>>> Iva
>>>>
>>>> helvi.grimm at item.fraunhofer.de wrote:
>>>>
>>>>
>>>>
>>>>          
>>>>> Dear Nina, dear Ivelina,
>>>>>
>>>>> i have a little problem with Protege. How can I convert the owl  to
>>>>>
>>>>>            
>> xml
>>
>>      
>>>>> files to use these in Repdose? I tried to use the convert- function in
>>>>>
>>>>>            
>>
>>      
>>>>> Protege, but i couldn't read the converted file in access. Have you
>>>>>
>>>>>            
>> any
>>
>>      
>>>>> idea how can i do this? The second problem is a little bit smaller, do
>>>>>
>>>>>            
>>
>>      
>>>>>
>>>>>            
>>>> you
>>>>
>>>>
>>>>
>>>>          
>>>>> know a programme or tool how can i extract the picture from Protege
>>>>>
>>>>>            
>> (in
>>
>>      
>>>>> addition to screenshot) ?
>>>>> It would be nice, if you could help me.
>>>>>
>>>>> with kindly regards
>>>>> Helvi
>>>>> _______________________________________________
>>>>> Development mailing list
>>>>> Development at opentox.org
>>>>> http://www.opentox.org/mailman/listinfo/development
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>            
>>>> _______________________________________________
>>>> Development mailing list
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>>>>
>>>>
>>>>
>>>>
>>>>
>>>>          
>>> _______________________________________________
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>>>
>>>
>>>        
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>>
>>      
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