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 <[EMAIL PROTECTED]> 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
