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Re: Is there an NCBI taxonomy in OWL ?

From: Ward Blonde <ward.blonde@psb.vib-ugent.be>
Date: Thu, 26 Feb 2009 10:30:46 +0100
Message-ID: <49A66146.1040200@psb.vib-ugent.be>
To: "andrea splendiani (RRes-Roth)" <andrea.splendiani@bbsrc.ac.uk>
CC: Erick Antezana <erant@psb.ugent.be>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>, Vladimir Mironov <vladimir.mironov@bio.ntnu.no>, Martin Kuiper <martin.kuiper@bio.ntnu.no>
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: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 Friday, 27 February 2009 17:35:48 GMT

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