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
>>> Development at opentox.org
>>> http://www.opentox.org/mailman/listinfo/development
>>>
>>>
>>>
>>>
>>>       
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