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RE: Is there an NCBI taxonomy in OWL ?

From: andrea splendiani \(RRes-Roth\) <andrea.splendiani@bbsrc.ac.uk>
Date: Thu, 26 Feb 2009 00:13:20 -0000
Message-ID: <C20D81024E1CAE4893D45B58FA0FFF6401101053@rothe2ksrv1.rothamsted.bbsrc.ac.uk>
To: "Erick Antezana" <erant@psb.ugent.be>
Cc: "public-semweb-lifesci hcls" <public-semweb-lifesci@w3.org>, "Vladimir Mironov" <vladimir.mironov@bio.ntnu.no>, "Martin Kuiper" <martin.kuiper@bio.ntnu.no>
Hi,
Yes, I already had downloaded you files ;)
>From a first inspection, they seemed to contain a reduction of the NCBI
Taxonomy (in terms of properties).

I was playing as well with your system, actually at:
http://biogw-db.hpc.ntnu.no:8892/sparql

but the query:

select ?x where {
	ssb:NCBI_4530 rdfs:label ?x .

}
Gets in timeout all the time. Shouldn't be such a pretentious query, I
guess, even if you compute transitiveness.

I used to be familiar with biotop, 'till about one year ago. But I don't
aware of the fact that there is a off-the-shelf taxonomy there.

Ciao,
Andrea



-----Original Message-----
From: Erick Antezana [mailto:erant@psb.ugent.be] 
Sent: 25 February 2009 20:51
To: andrea splendiani (RRes-Roth)
Cc: public-semweb-lifesci hcls; Vladimir Mironov; Martin Kuiper
Subject: Re: Is there an NCBI taxonomy in OWL ?

Hi Andrea,
 
  you can find an RDF at

http://www.semantic-systems-biology.org/biogateway/resources#ncbi

and play with it from:

http://www.semantic-systems-biology.org/biogateway/querying

I would also recommend taking a look at the work of Schulz et al:

http://bioinformatics.oxfordjournals.org/cgi/content/full/24/13/i313
http://www.imbi.uni-freiburg.de/biotop/

cheers,
Erick

Andrea Splendiani wrote:
> Hi,
>
> I was looking for an NCBI Taxnomoy in OWL, but I didn't find it (or 
> better, could find fragment from other projects...)
>
> What is strange though, is that on the obo foundry website 
> (berkeleybop.org/ontologies) there are notes on the ncbi taxonomy 
> representation in owl... but not the representation itself.
>
> Does anybody have some hint about where I can fin an OWL version ? Or 
> even an RDF version ? Even better would a sparql endpoint containing 
> it...
>
> best,
> Andrea Splendiani
>
>
Received on Thursday, 26 February 2009 00:14:08 GMT

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