See also: IRC log
??P0 is dlrubin
http://www.w3.org/2012/06/14-hcls-minutes
<michel> michel asks for a summary of last meeting
<michel> bobF matthias talked about his medical code project
-> http://www.w3.org/2012/06/14-hcls-minutes minutes
-> http://safety-code.org/ safety code interface
michel: DBSNP contains >12M
SNPS. we're focusing on those in PharmGKB (about 4400)
... that's more than the 400 matthias is using, but only a
subset are interesting
... i will recieve certain info from DBSNP
<michel> http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2032582
michel: issue is which
info...
... info includes the species, build from which it was
derived,
BobF: overlap with previous DBSNP extract?
michel: i don't know how to keep
that resource up to date
... wanted to have a lightweight approach to focus on SNPs of
interest
... parsing all of DBSNP has been problematic
<BobF> eutils from NCBI
michel: using EUtils to retrived records from NCBI
BobF: that project was a snapshot
to do prototype dev
... i made a high-level pass through the relevent attributes in
DBSNP
... worth reviewing for re-application here
... attributes of interest:
<michel> rsid, chromosome file, snp class, validated?, alleles, symbol, locus_id, mrna_aac, fxn-class, allele, prot_acc, frame, residue
<michel> 4 tables - rs, val, snp, loc
val - current validation of a SNP
michel: what attributes do we prioritize?
BobF: not the volatile
attributes, just IDs and higher-level annotations
... base location on a genomic contig or all SSIDs for a SNP
are in the realm of DBSNP
... those won't have many motivating use cases
<michel> http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2032582
http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2032582
<michel> eutils url - http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=2032582&retmode=xml
<michel> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=2032582&retmode=xml
<egombocz> apologies to all of you - I need to leave early due to another upcoming meeting
<michel> on examining the dbsnp record, bobF suggests : rsid, build, validation status, variation class, alleles, chromosome #, associated genes (geneid + symbol), mRNA + proteins + their (functional) changes, linked ncbi resources (unigene, omim, pdb)
<michel> we examined the population genetics - an initial summary of the allelic frequency is discounted due to the highly variable populations from which they were drawn
<michel> bobF suggests that we examine and limit population studies to those that are well regarded (hapmap, pharmgkb, others) with good numbers and good descriptions of the populations
<michel> bobF notes that (and michel confirms) that population information is not directly linked to the dbsnp entry; will have to get at it another way - perhaps there is another eutils service for it
<bavya> how can we get those 4400 snps present in pharmgkb
<michel> michel to write parser to obtained selected fields from eutils service for 4400 annotated snps in pharmgkb
<michel> that list is available here: http://bio2rdf.semanticscience.org:8006/sparql/?default-graph-uri=&query=SELECT+distinct+%3Fv%0D%0AWHERE+%7B+%0D%0A+%3Fx+a+%3Chttp%3A%2F%2Fbio2rdf.org%2Fpharmgkb_vocabulary%3AAssociation%3E+.%0D%0A+%3Fx+%3Chttp%3A%2F%2Fbio2rdf.org%2Fpharmgkb_vocabulary%3Avariant%3E+%3Fv%0D%0A%7D%0D%0A&format=text%2Fhtml&timeout=0&debug=on
<bavya> can i know which fields were used to select these SNPA
<bavya> *SNPs
<michel> this is a sparql query on our endpoint containing pharmgkb snp annotations
<michel> http://bio2rdf.semanticscience.org:8006/sparql/
<michel> SELECT distinct ?v WHERE { ?x a <http://bio2rdf.org/pharmgkb_vocabulary:Association> . ?x <http://bio2rdf.org/pharmgkb_vocabulary:variant> ?v }
<bavya> I got it . thank you
<michel> the eutils service, then with one example snp: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=2032582&retmode=xml
This is scribe.perl Revision: 1.136 of Date: 2011/05/12 12:01:43 Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ Guessing input format: RRSAgent_Text_Format (score 1.00) Succeeded: s/mma_aac/mrna_aac/ No ScribeNick specified. Guessing ScribeNick: ericP Inferring Scribes: ericP Default Present: +1.510.705.aaaa, +1.248.957.aabb, +1.248.957.aacc, michel, EricP, BobF, dlrubin Present: +1.510.705.aaaa +1.248.957.aabb +1.248.957.aacc michel EricP BobF dlrubin Got date from IRC log name: 21 Jun 2012 Guessing minutes URL: http://www.w3.org/2012/06/21-hcls-minutes.html People with action items:[End of scribe.perl diagnostic output]