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15:01:16 <Zakim> + +1.248.957.aacc
15:01:35 <Zakim> +michel
15:03:05 <Zakim> +Tony
15:04:05 <Zakim> +EricP
15:05:40 <michel> zakim, who is here?
15:05:40 <Zakim> On the phone I see +1.510.705.aaaa, +1.248.957.aacc, michel, Tony, EricP
15:05:42 <Zakim> On IRC I see RRSAgent, michel, egombocz, BobF, achille_zappa, MacTed, Zakim, egonw__, ericP
15:05:43 <ericP> Zakim, Tony is temporarily BobF
15:05:47 <Zakim> +BobF; got it
15:06:26 <Zakim> +??P0
15:06:49 <ericP> ??P0 is dlrubin
15:07:05 <ericP> zakim, ??P0 is dlrubin
15:07:08 <Zakim> +dlrubin; got it
15:08:58 <ericP> http://www.w3.org/2012/06/14-hcls-minutes
15:09:53 <michel> michel asks for a summary of last meeting
15:10:07 <ericP> topic: last CDS call
15:10:08 <michel> bobF matthias talked about his medical code project
15:10:21 <ericP> -> http://www.w3.org/2012/06/14-hcls-minutes minutes
15:10:52 <ericP> -> http://safety-code.org/ safety code interface
15:13:13 <michel> http://bio2rdf.semanticscience.org:8006/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fpharmgkb_resource%3Aassociation_PA451906_PA27829&sid=100
15:14:47 <michel> topic: snps
15:15:42 <ericP> michel: DBSNP contains >12M SNPS. we're focusing on those in PharmGKB (about 4400)
15:16:08 <ericP> ... that's more than the 400 matthias is using, but only a subset are interesting
15:16:21 <ericP> ... i will recieve certain info from DBSNP
15:16:23 <michel> http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2032582
15:16:32 <ericP> ... issue is which info...
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15:17:37 <ericP> ... info includes the species, build from which it was derived, 
15:18:12 <ericP> BobF: overlap with previous DBSNP extract?
15:18:23 <ericP> michel: i don't know how to keep that resource up to date
15:18:45 <ericP> ... wanted to have a lightweight approach to focus on SNPs of interest
15:19:06 <ericP> ... parsing all of DBSNP has been problematic
15:19:24 <BobF> eutils from NCBI
15:19:32 <bharath> bharath has left #hcls
15:19:33 <ericP> ... using EUtils to retrived records from NCBI
15:20:16 <ericP> BobF: that project was a snapshot to do prototype dev
15:20:37 <ericP> ... i made a high-level pass through the relevent attributes in DBSNP
15:20:57 <ericP> ... worth reviewing for re-application here
15:24:31 <ericP> ... attributes of interest:
15:25:48 <michel> rsid, chromosome file, snp class, validated?, alleles, symbol, locus_id, mma_aac, fxn-class, allele, prot_acc, frame, residue
15:26:01 <michel> 4 tables - rs, val, snp, loc
15:26:20 <ericP> s/mma_aac/mrna_aac/
15:28:32 <Zakim> -dlrubin
15:28:35 <ericP> val - current validation of a SNP
15:36:00 <ericP> michel: what attributes do we prioritize?
15:36:29 <ericP> BobF: not the volatile attributes, just IDs and higher-level annotations
15:37:02 <ericP> ... base location on a genomic contig or all SSIDs for a SNP are in the realm of DBSNP
15:39:16 <ericP> ... those won't have many motivating use cases
15:41:26 <michel> http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2032582
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15:45:47 <ericP> http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2032582
15:46:05 <michel> eutils url - http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=2032582&retmode=xml
15:46:46 <michel> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=2032582&retmode=xml
15:53:57 <egombocz> apologies to all of you - I need to leave early due to another upcoming meeting
15:54:09 <Zakim> - +1.510.705.aaaa
15:59:34 <Zakim> -EricP
16:05:02 <Zakim> -BobF
16:05:04 <Zakim> -michel
16:05:12 <Zakim> - +1.248.957.aacc
16:05:14 <Zakim> SW_HCLS()11:00AM has ended
16:05:16 <Zakim> Attendees were +1.510.705.aaaa, +1.248.957.aabb, +1.248.957.aacc, michel, EricP, BobF, dlrubin
16:06:42 <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)
16:07:24 <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
16:07:58 <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
16:08:34 <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
16:08:53 <bavya> how can we get those 4400 snps present in pharmgkb
16:09:21 <michel> michel to write parser to obtained selected fields from eutils service for 4400 annotated snps in pharmgkb
16:10:14 <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
16:10:21 <bavya> can i know which fields were used to select these SNPA
16:10:25 <bavya> *SNPs
16:10:38 <michel> this is a sparql query on our endpoint containing pharmgkb snp annotations
16:10:47 <michel> http://bio2rdf.semanticscience.org:8006/sparql/
16:10:55 <michel> SELECT distinct ?v WHERE {   ?x a <http://bio2rdf.org/pharmgkb_vocabulary:Association> .  ?x <http://bio2rdf.org/pharmgkb_vocabulary:variant> ?v } 
16:11:19 <bavya> I got it . thank you 
16:11:23 <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
16:12:48 <michel> Meeting: W3C HCLS – Pharmacogenomics
16:12:52 <michel> Chair: Michel Dumontier
16:18:54 <michel> rrsagent, draft minutes
16:18:54 <RRSAgent> I have made the request to generate http://www.w3.org/2012/06/21-hcls-minutes.html michel
16:19:00 <michel> rrsagent, make log world-visible
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