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






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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