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?

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
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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
>>>
>>> 
>>> 
>> _______________________________________________
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>>
>>
>> 
>> 
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