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14:54:02 <RRSAgent> logging to http://www.w3.org/2012/05/17-HCLS-irc
14:54:11 <michel> zakim, this is pharmagenomics
14:54:11 <Zakim> sorry, michel, I do not see a conference named 'pharmagenomics' in progress or scheduled at this time
14:54:19 <michel> zakim, list conferences
14:54:19 <Zakim> I see T&S_GLDWG()10:00AM active
14:54:20 <Zakim> also scheduled at this time are WAI_PFWG(HTML TF)10:00AM, MM_MMI(EMMA)10:00AM, SW_HCLS()11:00AM, I18N_WG(MLW)11:00AM, SW_(PROV)11:00AM, Team_Global(review)8:00AM,
14:54:22 <Zakim> ... VB_VBWG(CCXML)11:00AM, Team_(CLOUD)10:00AM, SW_RDFa()10:00AM, XML_PMWG()10:00AM, WAI_ERTWG(Eval TF)10:00AM, Styl_XSL-FO-()11:00AM, SYMM_TTWG()10:00AM, UW_WebTVIG()11:00AM,
14:54:25 <Zakim> ... WF_TF()9:00AM, SW_HCLS(TMO)11:00AM, Team_Comm()10:30AM, Math_IG()10:00AM, XML_QueryWG(XSLT)11:00AM, INC_(DecisionXG)10:00AM
14:54:40 <michel> zakim, this is sw_hcls
14:54:40 <Zakim> "sw_hcls" matches SW_HCLS()11:00AM, and SW_HCLS(TMO)11:00AM, michel
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14:54:55 <michel> zakim, this is SW_HCLS(TMO)
14:54:55 <Zakim> michel, I see SW_HCLS(TMO)11:00AM in the schedule but not yet started.  Perhaps you mean "this will be SW_HCLS(TMO)".
14:55:04 <michel> zakim, this will be SW_HCLS(TMO)
14:55:04 <Zakim> ok, michel; I see SW_HCLS(TMO)11:00AM scheduled to start in 5 minutes
14:55:12 <michel> chair: Michel
14:55:36 <michel> Meeting: W3C HCLS – Pharmacogenomics 
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15:00:27 <michel> zakim, who is here?
15:00:27 <Zakim> SW_HCLS(TMO)11:00AM has not yet started, michel
15:00:28 <Zakim> On IRC I see kalpana, matthias_samwald, egombocz, RRSAgent, Zakim, michel, achille_z, MacTed, egonw, ericP
15:00:35 <michel> zakim, this is hcls
15:00:35 <Zakim> ok, michel; that matches SW_HCLS()11:00AM
15:00:41 <michel> zakim, who is here?
15:00:41 <Zakim> On the phone I see +1.510.705.aaaa, michel
15:00:43 <Zakim> On IRC I see kalpana, matthias_samwald, egombocz, RRSAgent, Zakim, michel, achille_z, MacTed, egonw, ericP
15:01:10 <HarryH> HarryH has joined #hcls
15:01:11 <Zakim> +??P28
15:01:11 <michel> zakim, aaaa is egombocz
15:01:11 <Zakim> +egombocz; got it
15:01:32 <michel> zakim, ??P28 is matthias_samwald
15:01:40 <Zakim> +matthias_samwald; got it
15:02:36 <Zakim> + +1.412.623.aabb
15:03:23 <Zakim> + +20416aacc
15:03:32 <Zakim> +??P38
15:03:44 <HarryH> +1.412.623.aabb  would be me - Harry Hochheiser, University of Pittsburgh
15:04:37 <michel> zakim, ??P38 is kalpana
15:04:38 <Zakim> +kalpana; got it
15:05:09 <mscottm> mscottm has joined #hcls
15:05:37 <mscottm> Zakim, who is here?
15:05:37 <Zakim> On the phone I see egombocz, michel, matthias_samwald, +1.412.623.aabb, +20416aacc, kalpana
15:05:40 <Zakim> On IRC I see mscottm, HarryH, kalpana, matthias_samwald, egombocz, RRSAgent, Zakim, michel, achille_z, MacTed, egonw, ericP
15:09:08 <michel> Erich - building a big kb, selecting certain datasets - interested in pharmgkb, etc
15:09:34 <michel> Harry - biomedical informatics - interested in how to present clinically useful information
15:09:40 <mscottm> Kalpana: We (Metaome) have a product http://www.distilbio.com/ , gave a webinar for M. Scott Marshall to BioRDF/LODD a month or so ago. We are interested in providing some features interesting in the clinical setting, for clinical decision support, etc.
15:10:32 <michel> matthias: PGx in clinical setting - medical doctors & patients with IP tools to make sense of it
15:10:33 <mscottm> Kalpana is an Invited Expert to HCLS.
15:10:51 <Zakim> +EricP
15:11:42 <michel> mscottm: applying PGx in the clinical setting; CDS and generic information retrieval; link in gene variants into pathology, radiology, etc
15:13:07 <michel> ericP: W3C staff contact for HCLS; initially on life sciences now more on health care
15:13:41 <mscottm> Michel: interested in PGx in the clinical setting, also from Bio2RDF perspective, furthering pharmacogenomics for drug development
15:13:48 <michel> pharmgkb: http://www.pharmgkb.org/downloads.jsp
15:15:31 <mscottm> I should mention that Joanne sent her regrets (conflict with meeting).
15:18:23 <mscottm> Michel: Some RDFization was done by Joanne Luciano and Jim McCusker, and I did some RDFization focused on (OWL) modeling.
15:20:15 <mscottm> Michel: A couple datasets of interest: 1) side effects not on the label (off-label side effects)
15:20:59 <mscottm> ..2) Drug-drug interactions
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15:22:41 <mscottm> Michel: We are especially interested in side effects that can be related to a genetic variation
15:22:54 <michel> github for bio2rdf scripts: https://github.com/bio2rdf/bio2rdf-scripts
15:24:49 <michel> pharmgkb: https://github.com/bio2rdf/bio2rdf-scripts/blob/master/pharmgkb/pharmgkb.php
15:26:11 <mscottm> variants and clinical annotations - need license to access, can't redistribute.
15:26:48 <Zakim> + +1.650.427.aadd
15:27:20 <mscottm> Zakim, +1.650.427.aadd is Daniel_Rubin
15:27:20 <Zakim> +Daniel_Rubin; got it
15:27:30 <Daniel> Daniel has joined #hcls
15:27:46 <mscottm> Zakim, Daniel_Rubin is Daniel
15:27:46 <Zakim> +Daniel; got it
15:27:58 <michel> pharmgkb sparql endpoint: http://bio2rdf.semanticscience.org:8006/sparql/
15:28:15 <michel> pharmgkb sparql endpoint : http://bio2rdf.semanticscience.org:8006/fct/
15:29:13 <mscottm> +1
15:32:20 <Zakim> -Daniel
15:33:11 <egombocz> http://bio2rdf.semanticscience.org:8006/fct/facet.vsp?cmd=text&sid=35
15:35:29 <michel> warfarin as text search with drug-drug-interaction type : http://bio2rdf.semanticscience.org:8006/fct/facet.vsp?cmd=set_class&iri=http%3A%2F%2Fbio2rdf.org%2Fpharmgkb_vocabulary%3Adrug-drug-interaction&lang=&datatype=uri&sid=28
15:37:37 <mscottm> Michel: <demo> Start with http://bio2rdf.semanticscience.org:8006/fct/ , enter warfarin
15:38:22 <mscottm> ..Go to bottom of page, click on Type
15:38:52 <mscottm> ..Click on drug-drug-interaction (top of list)
15:39:34 <michel> http://bio2rdf.semanticscience.org:8006/fct/facet.vsp?cmd=set_view&sid=41&type=list-count&limit=20&offset=0
15:39:52 <mscottm> ..Go to bottom of page, right side: click on Referencing Attributes
15:41:31 <mscottm> ..Click on event in attribute list
15:42:43 <egombocz> http://bio2rdf.semanticscience.org:8006/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fumls%3AC0013404&sid=41
15:43:23 <michel> http://bio2rdf.semanticscience.org:8006/fct/facet.vsp?cmd=open_property&iri=http%3A%2F%2Fbio2rdf.org%2Fpharmgkb_vocabulary%3Achemical&lang=&datatype=uri&sid=41
15:45:33 <michel> facet permalink: http://bio2rdf.semanticscience.org:8006/fct/facet.vsp?qxml=%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%20%3F%3E%3Cquery%20inference%3D%22%22%20same-as%3D%22%22%20view3%3D%22%22%20s-term%3D%22%22%20c-term%3D%22%22%3E%3Ctext%3Ewarfarin%3C%2Ftext%3E%3Cclass%20iri%3D%22http%3A%2F%2Fbio2rdf.org%2Fpharmgkb_vocabulary%3Adrug-drug-intera
15:48:32 <mscottm> Select "choking sensation".
15:48:58 <michel> warfarin - variant drug annotation - http://goo.gl/66M2g
15:49:37 <mscottm> Michel notes that he needs to load labels for PubChem Ids so that we don't see id numbers for the list of Entities
15:55:27 <matthias_samwald> Could we have a link again? 
15:56:16 <michel> warfarin-linked clinical phenotype annotation -  http://bio2rdf.semanticscience.org:8006/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fpharmgkb%3A769146159&sid=50
15:56:37 <matthias_samwald> yes
15:56:53 <michel> warfarin entry: http://bio2rdf.semanticscience.org:8006/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fpharmgkb%3APA451906&sid=50
16:01:34 <michel> warfarin-linked clinical annotation :http://bio2rdf.semanticscience.org:8006/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fpharmgkb%3A655384758&sid=50
16:03:18 <michel> http://goo.gl/tTORx
16:08:08 <matthias_samwald> need to leave -- bye!
16:08:13 <Zakim> -matthias_samwald
16:12:39 <mscottm> Michel proposes to write a script to select clinically relevant validated SNPs and query the NCBI service and convert a selection of the XML records for inclusion in the KB
16:13:02 <michel> i'll convert only some fields - we can talk about exactly which ones when we get there
16:14:49 <HarryH> Thanks! This is fascinating.
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16:16:43 <michel> sparql javascript - http://www.thefigtrees.net/lee/sw/sparql.js
16:16:55 <michel> http://www.thefigtrees.net/lee/blog/2006/04/sparql_calendar_demo_a_sparql.html
16:17:00 <mscottm> Michel mentioned screen sharing with a Google Hangout earlier in the call. Something to think about for next demo.
16:18:52 <mscottm> Michel: PharmGKB has restructured their web pages to present clinical relevant information *first*.
16:23:03 <mscottm> s/clinical relevant/clinically relevant/
16:24:30 <mscottm> scribenick: mscottm
16:24:41 <Zakim> - +1.412.623.aabb
16:24:50 <Zakim> -michel
16:24:50 <michel> rrsagent, draft minutes
16:24:50 <RRSAgent> I have made the request to generate http://www.w3.org/2012/05/17-HCLS-minutes.html michel
16:25:00 <michel> rrsagent, make log world-visible
16:25:05 <kalpana> thank you
16:25:21 <mscottm> thank you for coming Kalpana
16:27:04 <Zakim> -kalpana
16:33:23 <egombocz> thank you all
16:33:30 <Zakim> -egombocz
16:41:25 <Zakim> -EricP
16:41:27 <Zakim> - +20416aacc
16:41:28 <Zakim> SW_HCLS()11:00AM has ended
16:41:28 <Zakim> Attendees were +1.510.705.aaaa, michel, egombocz, matthias_samwald, +1.412.623.aabb, +20416aacc, kalpana, EricP, Daniel
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18:26:29 <ericP> et voila!
18:30:29 <ericP> http://www.w3.org/2012/04/FHIR/
18:30:42 <michel> https://docs.google.com/a/jerven.eu/viewer?a=v&pid=sites&srcid=amVydmVuLmV1fGplcnZlbnxneDo0MTBmMTQ1M2I2N2M2M2Uw
19:08:37 <ericP> http://okfnpad.org/jrRBSEb6CI
19:09:06 <michel> rdf/owl : http://okfnpad.org/rLGeo0dMk9
19:15:22 <michel> http://idi.fundacionctic.org/muo/muo-vocab.html
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