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Re: GXA triples

From: Helena Deus <helenadeus@gmail.com>
Date: Sun, 10 Jul 2011 19:55:23 +0100
Message-ID: <CAPkJ_9nXPu=4qSK_mwu3qSEzkRRTNBYonD_ijxGQ5JdBbVamfA@mail.gmail.com>
To: tomasz.adamusiak@ebi.ac.uk
Cc: Jun Zhao <jun.zhao@zoo.ox.ac.uk>, Tomasz Adamusiak <tomasz@ebi.ac.uk>, James Malone <malone@ebi.ac.uk>, expressionrdf@googlegroups.com, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Hi,

I am trying to find where the description of the genes in the GXA sparql
endpoint can be found (in RDF to that it can be pulled into the query):

SPARQLing GXA, I get a list of genes from an experiment; each gene looks
something like this: "
http://www.ensembl.org/Gene/Summary?g=ENSMUSG00000058207"
There does not seem to be more info about each of the genes in the
endpoint.

I can follow the link and find out that this is the same as
http://www.ncbi.nlm.nih.gov/gene/20714 , with linked data equivalent
http://bio2rdf.org/geneid:20714

Is this information anywhere in a machine processable format?
I am looking got a SPARQL endpoint/RDF doc (or even other format conversible
to RDF) where I can discover that :

ENSMUSG00000058207 == geneid:20714

Thanks
(sorry about the blunteness, trying to see if such mappings can be included
in the methods for the paper);

Best
Lena


On Wed, Jul 6, 2011 at 11:42 AM, Tomasz Adamusiak <tomasz@ebi.ac.uk> wrote:

> Hi All,
>
> Jun has kindly reloaded a new batch of Atlas triples that James and I
> generated. In this release there are up to 500 top differentially expressed
> genes per experiment available and a total number of triples increased from
> ~37 to ~170 million.
>
> More information is available at:
> http://www.ebi.ac.uk/efo/**semanticweb/atlas<http://www.ebi.ac.uk/efo/semanticweb/atlas>
>
> SPARQL examples are collated at:
> http://code.google.com/p/open-**biomed/wiki/**GeneExpressionAtlas<http://code.google.com/p/open-biomed/wiki/GeneExpressionAtlas>
>
> We've also deployed a secondary endpoint that mirrors the data:
> http://wwwdev.ebi.ac.uk/**microarray-srv/openrdf-sesame/**repositories/gxa<http://wwwdev.ebi.ac.uk/microarray-srv/openrdf-sesame/repositories/gxa>
>
> Feedback very much welcome.
>
> Cheers
> Tomasz
>
>
> --
> Tomasz Adamusiak, MD, PhD
> European Bioinformatics Institute
> +44 (0) 1223 492 562
> tomasz.adamusiak@ebi.ac.uk
>
>
>


-- 
Helena F. Deus
Post-Doctoral Researcher at DERI/NUIG
http://lenadeus.info/
Received on Sunday, 10 July 2011 18:56:12 GMT

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