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
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> Re: [OTDev] Protege help
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>
> 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
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>>     
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