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

From: Remzi Celebi <remzicelebi@gmail.com>
Date: Fri, 6 Sep 2013 11:32:10 +0300
Message-ID: <CAKg-rDP7LPr77d+_5TFf1F_LzgZK-1ix_Nx=WJFAUZcjphL7QQ@mail.gmail.com>
To: Michel Dumontier <michel.dumontier@gmail.com>
Cc: Matthias Samwald <matthias.samwald@meduniwien.ac.at>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
Thanks for your comments.
For conversion of big list of SNPs, the BioQ
<http://bioq.saclab.net/>creates a tool utilizing a set of database
including dbsnp. You can access
the tables as MySQL dumps. By looking what you have converted, you only
need to process
_loc_snp_summary<http://bioq.saclab.net/query/download_table.php?db=bioq_dbsnp_human_137&table=_loc_snp_summary&format=mysql>table.





2013/9/5 Michel Dumontier <michel.dumontier@gmail.com>

> 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
>



-- 
Remzi Çelebi
Received on Friday, 6 September 2013 08:33:17 UTC

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