14:15:47 <RRSAgent> RRSAgent has joined #HCLS
14:15:47 <RRSAgent> logging to http://www.w3.org/2013/05/01-HCLS-irc
14:15:51 <matthias_samwald> zakim, this is hcls
14:15:51 <Zakim> ok, matthias_samwald; that matches SW_HCLS(LODD)10:15AM
14:15:56 <matthias_samwald> zakim, who is here?
14:15:57 <Zakim> On the phone I see +1.206.371.aaaa, ??P1, Bob_Powers
14:15:58 <Zakim> On IRC I see RRSAgent, Zakim, michel, matthias_samwald, bobP, TallTed, egonw_, ericP
14:15:58 <Zakim> +michel
14:16:00 <Zakim> -Bob_Powers
14:16:32 <Zakim> +Bob_Powers
14:16:57 <michel> michel has changed the topic to: #hcls  W3C HCLS – Clinical Pharmacogenomics
14:17:07 <michel> Meeting: W3C HCLS – Clinical Pharmacogenomics
14:17:36 <matthias_samwald> http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-05-01_Conference_Call
14:17:44 <boycer> boycer has joined #HCLS
14:18:10 <matthias_samwald> hi rich, can I post your 3-6-12 months goals to the wiki page on http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-05-01_Conference_Call
14:18:14 <matthias_samwald> ???
14:19:22 <boycer> sure
14:19:32 <matthias_samwald> okay, i will do that right away.
14:19:44 <boycer> phone is quite, is anyone speaking
14:20:02 <boycer> quiet (i meant)
14:22:51 <michel> matthias: reasoner workshop submission
14:23:09 <michel>  ... good opportunity to put our ontology in front of the ontology developers
14:25:54 <michel> michel: met with ian horrock's group; they are developing many reasoners; need datasets
14:27:02 <Zakim> +[GVoice]
14:27:12 <ericP> Zakim, [GVoice] is me
14:27:12 <Zakim> +ericP; got it
14:30:17 <michel> http://ore2013.cs.manchester.ac.uk/
14:31:30 <Zakim> + +1.507.269.aabb
14:34:00 <michel> http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-05-01_Conference_Call
14:35:04 <Zakim> +Tony
14:35:06 <Zakim> - +1.507.269.aabb
14:35:19 <michel> matthias: building the ontology-backed framework for clinical decision support. better, bigger, faster; how to put this all into clinical practice
14:36:03 <michel>  ... medical safety codes to give personalized drug/drug dosing recommendations based on a small but highly relevant set of biomarkers, as cheaply as posible
14:36:23 <michel>  ... make clinical decision support equally available; genomic CDS ontology + OWL reasoning
14:37:04 <michel>  ... in the next year, we'll continue to develop this so to have a working system and in 3+years time to have in clinical practice
14:38:58 <michel>  ... in the next 3 months: submit CDS to owl reasoner workshop; finalize decision support rules - need to collaborate with Jeff Pan (TrOWL); submit a paper to a journal on the ontology work
14:39:53 <michel> eric: have interest in TrOWL; closed world, una, other reasoning tasks
14:40:38 <ericP> -> http://www.w3.org/2012/12/rdf-val/ W3C RDF Validation Workshop
14:40:44 <BobF> BobF has joined #HCLS
14:41:03 <BobF> zakim, who is here?
14:41:03 <Zakim> On the phone I see +1.206.371.aaaa, ??P1, michel, Bob_Powers, ericP, Tony
14:41:05 <Zakim> On IRC I see BobF, boycer, RRSAgent, Zakim, michel, matthias_samwald, bobP, TallTed, egonw_, ericP
14:41:07 <michel> matthias: update w3c wiki and associated web sites
14:41:34 <ericP> (it would be nice to get some TrOWL examples into http://www.w3.org/2012/12/rdf-val/SOTA#CWA_UNA)
14:43:24 <michel> bobF: lots of potential to collaborate
14:43:35 <michel>  ... tremendous potential for medical safety codes
14:44:45 <michel>  ... pharmgkb interest in bioinformatics; aware of scope creep; limiting to their own priorities; willing to collaborate, but resourced elsewhere / no new maintenance requirements
14:45:11 <michel>  ... what would that relationship look like
14:46:30 <michel>  ... at mayo - set of priorities have been identified; anything beyond that can be pursued on their own time.
14:46:37 <michel>  ... standardized coding of genetic results
14:46:45 <michel>  ... evaluation of genetics-based ontologies
14:48:01 <bobP> PGRN chip for 84 genes
14:48:04 <matthias_samwald> PGRNseq
14:48:04 <michel>  ... pgrn chip - 84 pgx genes, will be adopted by many sites including EMERGE network; for a large number of patients
14:48:30 <michel>  ... near term: think of how we can facilitate the interpretation of that data
14:48:38 <michel>  ... medical safety code
14:49:56 <michel> matthias: ontology based on a set of genes and markers created last year. pgrnseq came up with their own genes; should be put into the ontology and medical safety code project
14:50:16 <michel>  ... different profiles for different projects/countries
14:50:28 <michel>  ... still need to select the most important markers is essential
14:50:41 <bobP> (Foundation Medicine also has a list of 200+ genes, in an important selection)
14:51:42 <michel> bobF: if we can come up with an ontology that can be extended at will, then any arbitrary set of variants could be selected, encoded  and sent to server for ui display
14:51:56 <michel>  ... if you have 84 gene panel, then that's what you encode and resolve
14:52:00 <michel> +1
14:52:29 <boycer> +1
14:53:16 <michel> michel: how feasible is this customization?
14:53:30 <michel> matthias: concern about proliferation of codes / systems
14:54:18 <michel>  ... best solution would be to curated and selected collection based on the work done by others
14:55:16 <michel>  ... advertising post-doc position to work on all this. would speed it up. if you know somebody, let matthias know!
14:56:54 <michel> rich: collab with school of pharmacy; optimize use of information in product labelling; feedback to regulatory agency
14:58:03 <michel>  ... using semantic model to annotate large number of drugs that have biomarkers; represent that using open annotation standard; more provenance and linking; demonstrate the value with useability studies
14:58:50 <michel>  ... have phd student working on the project; proof of concept to provide recommendations in different care settings
14:59:38 <michel>  ... have server to serve up demonstration with lab data to trigger rules in genomic CDS ontology; then expand PoC - make this as clinically useful as possible
15:00:39 <michel>  ... 3 month - finish annotations. new group will start in the fall.
15:01:24 <michel>  ... 6 months - quality; task-oriented usability study.
15:01:31 <michel>  ... get funding and write papers !
15:05:40 <michel> michel: want to have access to product label annotation platform : drug effects, drug indications, drug-drug interactions
15:06:40 <matthias_samwald> scribenick: matthias_samwald
15:07:08 <matthias_samwald> michel: our work focused on phenotypes a lot
15:07:44 <matthias_samwald> ... using phenotype ontology (drug effects in animal models)
15:09:18 <boycer> +1
15:09:22 <matthias_samwald> ... cross-species analysis
15:09:40 <matthias_samwald> ... elucidate drug effects, relation to pathways, mechanistic basis of drug effects
15:10:28 <matthias_samwald> ... in 10-15 years: understandig how genetic variant affect system as a whole
15:11:45 <matthias_samwald> michel: in next 6 months i hope to integrate data from Bio2RDF to help drive some more ontology-based research
15:11:55 <matthias_samwald> ... how do we formalize data in RDF as OWL ontologies?
15:12:10 <matthias_samwald> ... can we find contradictions in animal models?
15:18:29 <matthias_samwald> michel: we will continue the discussion in the next meeting and hear about the plans of people who could not talk about them today
15:18:47 <boycer> +1 for additional discussion, especially on how to support mutual research interests
15:18:50 <Zakim> -Tony
15:18:56 <Zakim> - +1.206.371.aaaa
15:19:02 <Zakim> -Bob_Powers
15:19:03 <Zakim> -michel
15:19:04 <Zakim> -??P1
15:19:04 <Zakim> -ericP
15:19:05 <Zakim> SW_HCLS(LODD)10:15AM has ended
15:19:05 <Zakim> Attendees were +1.206.371.aaaa, michel, Bob_Powers, ericP, +1.507.269.aabb, Tony
15:19:21 <michel> rrsagent, draft minutes
15:19:21 <RRSAgent> I have made the request to generate http://www.w3.org/2013/05/01-HCLS-minutes.html michel
15:19:30 <michel> rrsagent, make log world-visible
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