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Re: Our paper won the distinguished paper/talk award at Medinfo2013

From: Michel Dumontier <michel.dumontier@gmail.com>
Date: Wed, 4 Sep 2013 20:49:52 -0700
Message-ID: <CALcEXf5ojHss_M397_kJ3uRY2xOnCU3jkEAbaDrz8rdzaPafVA@mail.gmail.com>
To: Matthias Samwald <matthias.samwald@meduniwien.ac.at>
Cc: Remzi Celebi <remzicelebi@gmail.com>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
Hi,
  I've finally committed my dbsnp converter [1]. it's currently just in a
branch of my fork of bio2rdf-scripts, but eventually we'll get it into
bio2rdf.  it works by calling eutils and converting selected elements into
RDF. it works with a comma-separated list of rs ids, or by processing the
set of omim-related clinically relevant snps. i'm planning to add support
to process the pharmgkb variants, and maybe all of dbsnp, once i figure out
how to get the big list of them.

you can browse an example entry [2] on my *temporary* endpoint, or do a
search using the facet browser [3]. suggestions welcome

m.

[1]
https://github.com/micheldumontier/bio2rdf-scripts/blob/dbsnp/dbsnp/dbsnp.php
[2] http://goo.gl/5D85t8
[3] http://goo.gl/nvjD4V <http://s3.semanticscience.org:12068/fct/>




On Mon, Sep 2, 2013 at 12:42 AM, Matthias Samwald <
matthias.samwald@meduniwien.ac.at> wrote:

> **
> Dear Remzi,
>
> Sorry if this was a bit misleading: In our work we just did a conversion
> of a very selective subset of dbSNP entries (those we identified as
> essential pharmacogenetic markers), and for those we only converted basic
> information (variants for each SNP/indel).
>
> Bio2RDF also does not have dbSNP in its entirety (Michel can correct me if
> this has changed recently). However, some dbSNP entries are represented in
> a very rudimentary way, such as those mentioned in PharmGKB. An example is:
> http://bio2rdf.org/dbsnp:rs1042713
>
> These entities do not contain much information from dbSNP, but at least
> they serve as an entry point to other datasets in Bio2RDF (such as
> PharmGKB). We mapped to these identifiers.
>
> Cheers,
> Matthias
>
>
>  *From:* Remzi Celebi <remzicelebi@gmail.com>
> *Sent:* Sunday, September 01, 2013 1:05 PM
> *To:* Matthias Samwald <matthias.samwald@meduniwien.ac.at>
> *Cc:* Tom Morris <tfmorris@gmail.com> ; Joanne Luciano<jluciano@gmail.com>; Robert,
> Ph.D. Freimuth <Freimuth.Robert@mayo.edu> ; Joanne Luciano<jluciano@cs.rpi.edu>; Simon
> Lin MD <LINMD.SIMON@mcrf.mfldclin.edu> ; Robert Powers<rpowers@predmed.com>; M.
> Scott Marshall <mscottmarshall@gmail.com> ; michel.dumontier@gmail.com ; Richard
> Boyce <rdb20@pitt.edu> ; public-semweb-lifesci hcls<public-semweb-lifesci@w3.org>
>  *Subject:* Re: Our paper won the distinguished paper/talk award at
> Medinfo2013
>
>  Hi Matthias,
> Congratulation. Good work.
> In the paper,  you have mentioned about the conversion of dbSNP to RDF. I
> haven't seen dbSNP on the list of the converted datasets under Bio2RDF
> project. I am also struggling to convert dbSNP to RDF. Could you tell me
> where can I find the RDF verison of dbSNP or Can I access to the script
> written for conversion if there is any?
> Thanks in advance,
>
> Remzi
>
>
> 2013/8/26 Matthias Samwald <matthias.samwald@meduniwien.ac.at>
>
>> **
>>
>> I have to correct myself. The link on rpi.edu (probably uploaded by
>> Joanne) points to a draft of the paper. I uploaded the final version of the
>> paper to
>> http://samwald.info/res/samwald_medinfo2013_final.pdf
>>
>> Sorry,
>> Matthias
>>
>>
>>
>> Tom Morris wrote:
>>
>> > Any links to the paper/presentation?  Are these them?
>> > http://tw.rpi.edu/media/2013/03/14/2b0f/Medinfo2013_JSL.pdf
>>
>>
>
>
>
> --
> Remzi Çelebi
>



-- 
Michel Dumontier
Associate Professor of Medicine (Biomedical Informatics), Stanford
University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com
Received on Thursday, 5 September 2013 03:50:41 UTC

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