W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > February 2008

Re: BioRDF Brainstorming

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Tue, 12 Feb 2008 23:41:08 -0500
Message-Id: <20E3212B-E94C-4227-8DAD-14A4569A8F1E@gmail.com>
Cc: Kei Cheung <kei.cheung@yale.edu>, 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>, Luis Marenco <luis.marenco@yale.edu>
To: ernest.lim@yale.edu


On Feb 12, 2008, at 11:07 PM, Ernest wrote:

> Sorry this is probably obvious to everyone but for the query below,  
> where can we run it? or what can we run it against? I think Kei and  
> I are unclear if there is a sparql endpoint that we can use or is  
> there an owl file containing all this data that we can download?

You can both download it and/or run it.

Sparql endpoints:
* http://hcls.deri.ie/sparql
* http://sw.neurocommons.org:8890/sparql

Download:
http://sw.neurocommons.org/2007/kb-sources/ (I expect there will be a  
durable version on the w3c site soon)
gene-owl.tgz is the entrez gene info.
The other files are there too - let me know if it isn't clear which  
you need to do some query.

Note the dates of the files - they are not current. We're working on  
putting in to place a system that keeps our endpoint up to date.

Regards,
Alan

>
> Thanks
>
> Ernie
>
> Alan Ruttenberg <alanruttenberg@gmail.com> wrote:
>
> 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:
> prefix dc:
> prefix sc:
> prefix rdfs:
> select ?g ?taxon ?title
> from
> where
> { graph
> { ?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 04:41:20 GMT

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