W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > October 2011

RE: ensembl SPARQL endpoint

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Thu, 20 Oct 2011 08:20:35 -0700
Message-ID: <e0fff663d1e15e270bfd3e1cbce72ef9@mail.gmail.com>
To: Helena Deus <helenadeus@gmail.com>
Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>, philip.cotter@ucd.ie, Philippe <proccaserra@gmail.com>, Joachim Baran <Joachim.Baran@oicr.on.ca>
hi lena,



also, if you find a sparql end point for other sequence
databases/repositories often they will have a one-to-one reference into
ensemble.



cheers,

michael



Michael Miller

Software Engineer

Institute for Systems Biology





*From:* public-semweb-lifesci-request@w3.org [mailto:
public-semweb-lifesci-request@w3.org] *On Behalf Of *Joachim Baran
*Sent:* Wednesday, October 19, 2011 7:31 AM
*To:* Philippe; Helena Deus
*Cc:* W3C HCLSIG hcls; philip.cotter@ucd.ie
*Subject:* Re: ensembl SPARQL endpoint



Hello,



On 19/10/2011 10:53, Helena Deus wrote:

I am working with agilent probe_ids and it seems only ensembl has the
correspondence to the correct gene. Does anyone know of any plans for
RDF-izing or adding a SPARQL endpoint to ensembl?

  A subset of SPARQL is supported in the release candidate 7 of BioMart
0.8:
https://code.oicr.on.ca/svn/biomart/biomart-java/branches/release-0_8-candidate_7



  Output is either provided in form of SPARQL-XML or RDF N3. The processors
for formatting are selected in the query URL, which are "SPARQLXML" and
"RDFN3" respectively. In the documentation, only "SPARQLXML" is given as an
example, but you can replace it with "RDFN3"*.



Joachim



* in most cases





*Joachim Baran, PhD**
*Database Programmer/Technical Analyst, Informatics and Bio-computing

*Ontario Institute for Cancer Research*
MaRS Centre, South Tower

101 College Street, Suite 800

Toronto, Ontario, Canada M5G 0A3



Tel: 647-258-4319

Toll-free: 1-866-678-6427

www.oicr.on.ca



This message and any attachments may contain confidential and/or privileged
information for the sole use of the intended recipient. Any review or
distribution by anyone other than the person for whom it was originally
intended is strictly prohibited. If you have received this message in error,
please contact the sender and delete all copies. Opinions, conclusions or
other information contained in this message may not be that of the
organization.
Received on Thursday, 20 October 2011 15:21:11 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:01:04 GMT