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Re: BioRDF Brainstorming

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Tue, 12 Feb 2008 22:56:27 -0500
Message-Id: <29E89268-3DF9-4F66-BB8C-6FD10FCD797A@gmail.com>
Cc: olivier@nlm.nih.gov, eric neumann <ekneumann@gmail.com>, Matthias Samwald <samwald@gmx.at>, Susie M Stephens <STEPHENS_SUSIE_M@lilly.com>, public-semweb-lifesci@w3.org, Holger Stenzhorn <holger.stenzhorn@deri.org>, Ernest.Lim@Yale.edu, Luis Marenco <luis.marenco@yale.edu>
To: Kei Cheung <kei.cheung@yale.edu>


On Feb 12, 2008, at 3:58 PM, Kei Cheung wrote:

> Also, I have a question regarding retrieval of entez gene  
> information including gene ids, symbols, and snyonyms. Is such  
> information available from the HCLS KB and/or RDF entrez gene  
> dataset that Olivier's group had created?

Here is a query that returns the uri, species, and name (we don't  
distinguish between name, symbol, or synonym currently)

prefix xsd: <http://www.w3.org/2001/XMLSchema#>
prefix dc: <http://purl.org/dc/elements/1.1/>
prefix sc: <http://purl.org/science/owl/sciencecommons/>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
select  ?g ?taxon ?title
from <http://purl.org/commons/hcls/gene>
where
{  graph <http://purl.org/commons/hcls/gene>
    { ?g sc:describes_gene_type ?type.
      ?g dc:title ?title.
      ?g dc:identifier "6780"^^xsd:string.
      ?g sc:from_species_described_by ?taxon
     }
}
http://purl.org/commons/record/ncbi_gene/6780 http://purl.org/commons/ 
record/taxon/9606 FLJ25010
http://purl.org/commons/record/ncbi_gene/6780 http://purl.org/commons/ 
record/taxon/9606 STAU
http://purl.org/commons/record/ncbi_gene/6780 http://purl.org/commons/ 
record/taxon/9606 STAU1
http://purl.org/commons/record/ncbi_gene/6780 http://purl.org/commons/ 
record/taxon/9606 staufen, RNA binding protein, homolog 1 (Drosophila)

There are some more queries at http://tinyurl.com/yq7xyo
Received on Wednesday, 13 February 2008 04:54:48 GMT

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