- From: Remzi Celebi <remzicelebi@gmail.com>
- Date: Fri, 6 Sep 2013 11:32:10 +0300
- To: Michel Dumontier <michel.dumontier@gmail.com>
- Cc: Matthias Samwald <matthias.samwald@meduniwien.ac.at>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
- Message-ID: <CAKg-rDP7LPr77d+_5TFf1F_LzgZK-1ix_Nx=WJFAUZcjphL7QQ@mail.gmail.com>
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