Re: Is there an NCBI taxonomy in OWL ?

[Ward Blonde]

Hi Andrea,
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.
  
From
http://www.semantic-systems-biology.org/biogateway/querying
you can use the prepared 'template' to come to such a query:

BASE   <http://www.semantic-systems-biology.org/>
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
PREFIX ssb:<http://www.semantic-systems-biology.org/SSB#>
SELECT *
WHERE {
GRAPH <SSB> {
  ssb:NCBI_4530 rdfs:label ?x .
}
}

returning: x Oryza sativa
You could also replace SSB by ncbi if you are only interested in that graph.
It is strange though if you got a time-out instead of an error for the 
query you mention.

cheers,
Ward

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:er...@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