15:01:30 RRSAgent has joined #hcls 15:01:30 logging to http://www.w3.org/2012/10/02-hcls-irc 15:01:39 Meeting: W3C HCLS – General Meeting 15:01:50 Chair: Michel Dumontier 15:02:02 zakim, this is hcls 15:02:02 ok, michel; that matches SW_HCLS()11:00AM 15:02:08 Zakim, please dial ericP-office 15:02:08 ok, ericP; the call is being made 15:02:09 +EricP 15:02:16 -Bob_Powers 15:02:37 + +1.613.293.aabb 15:02:40 Zakim, who is here? 15:02:40 On the phone I see +1.510.705.aaaa, EricP, +1.613.293.aabb 15:02:42 On IRC I see RRSAgent, Zakim, egombocz, michel, bobP, MacTed, ericP 15:02:44 +Bob_Powers 15:02:55 Zakim, aaaa is erich 15:02:58 +erich; got it 15:03:09 Zakim, aabb is michel 15:03:09 +michel; got it 15:03:13 Zakim, who is here? 15:03:13 On the phone I see erich, EricP, michel, Bob_Powers 15:03:14 On IRC I see RRSAgent, Zakim, egombocz, michel, bobP, MacTed, ericP 15:04:33 + +33.1.73.71.aacc 15:04:49 Zakim, aacc is charlie 15:04:49 +charlie; got it 15:05:30 +Kerstin_Forsberg 15:06:29 scribenick: bobP 15:06:35 kerfors has joined #hcls 15:07:01 Michel: Roundup of the task forces 15:08:02 ... Linked Life Data. working on two W3C notes 15:08:38 ... 2nd note is Expression RDF; sparql to query multiple endpoints w data in different forms 15:09:06 ... trying to write W3C note for conceptual framework for expression data, standard representation 15:09:29 ... working w Gene Expression Atlas 15:09:45 ... have a nice diagram. Next meeting is Tues 15:11:01 ... Groups that have pathways etc, we would be drafting notes 15:12:13 Michel: Next is Helena to link life data, figure out transformations to complexes, relationships to diseases etc 15:12:28 ... work is in progress, busy at DERI. 15:13:08 ... I will visit DERI at end of Nov. Another group has released new sparql editor 15:13:30 ... also working on a cloud platform 15:14:07 Michel: Systems Biology. Working closely w Matthias in clincial decision support 15:14:23 ... trying to overcome the problem of alleles and genotypes 15:14:59 ... people categorized as *1 or *2; but as more SNPs discovered, allele definitions are renewed 15:15:30 ... Bob Freimuth has come up w OWL reasoning solution, even if the nomenclature changes in the future 15:15:41 ... working on an AMIA presentation 15:16:27 Michel: Mattias also has Medical Microdata Compendium; should explore w linked open data sets 15:16:39 ... using sparql and PGx 15:17:07 Michel: This is a quick run-through. 15:17:21 ... Want to talk about Charlie and ericP are working on. 15:17:32 -> http://www.w3.org/wiki/HCLS/ClinicalObservationsInteroperability TF page 15:17:38 ericP: Current COI task force page 15:17:45 :) 15:17:47 topic: reviving COI 15:19:04 ... Goal of COI was to address: given a lot of standards, and need interop, then if standards were based on RDF interop would be easier 15:19:17 ... notion was to come up w a demonstrator 15:20:18 ... I created what HL7 would look like in RDF, (straw man who stood up :) 15:20:44 ... demonstrator did have the cool effect that, given RDF, here's how we can get interop 15:21:17 ... to take a clinical trial, express as query in language familiar like CDISC-y 15:21:40 ... CRO people can write these kinds of queries 15:22:00 ... But language of hospitals is HL7 15:22:47 ... n clinics in HL7-like; write a Xform from pattern -> pattern, pushes query into CDISC-like 15:23:30 ... Xform through three different materializations to do this pipeline 15:24:07 ... shorter: use queries within sparql construct rules (?) 15:24:11 +[IPcaller] 15:24:45 ... This worked over one corpus of clincial records; success w inclusion and exclusion criteria 15:24:51 Lena has joined #hcls 15:25:25 ... queries can get large, but they are quite effect b/c they go directly to the RDB 15:26:04 ... This was the initial project at COI. Perform recruitment queries for trials 15:26:31 ... Working now w Lloyd McKenzie(?) to turn HL7 into OWL 15:26:52 ... he is xforming UML into OWL(?) 15:27:08 ... we get for free an RDF representation of RIM 15:27:23 ... used also to define the wire format FHIR 15:27:43 ... data can be either true RDF or grrdl-able into RDF 15:28:38 apologies to all - need to leave for another meeting 15:28:47 ... Another feature is Charlie's use case: snomed here, hl7 there, still a big space in how clinicians write things down 15:28:49 -erich 15:29:30 ... need to establish equivalences through longitudinal records 15:31:07 http://www.amia.org/jointsummits2013/proposals-types 15:31:59 podium presentation due oct 11 15:32:47 Q: There is a goup in HL7 Clinical Interop Consortium 15:33:17 Charlie(?): One of the goals is to decide RIM/ SNOMED/ etc 15:33:49 ... would like to get CIC and COI talking together; working on the same problems 15:34:59 Kersten: FDA has an interest in next-gen exchange formats 15:35:27 ... talk about HL7 v3 format and others 15:36:09 ... FDA asking for inputs on other options; I am following along on a series of interesting discussions 15:36:36 ... ericP should be in their coming meeting, like w the FHIR work 15:36:47 Turning CDISC standards into RDF/OWL & SKOS and also using ISO11179. Joint presentation AstraZeneca and Roche at the CDISC Europe conference earlier this year http://kerfors.blogspot.se/2012/05/semantic-models-for-cdisc-based.html 15:36:53 Kersten: Also I work in the CDISC community 15:37:25 ... Roche has all CDISC and internal, all in RDF 15:37:46 ... time to review that work. Would be good if we had all different standards in RDF 15:38:04 ... CDISC conference late Oct Baltimore 15:38:49 ... we have put together an open discussion w Roche and we are going to do what we say 15:39:46 ... also looking for way to publish this in the short term 15:40:12 ... then push RDF work back to CDISC 15:40:37 Kersten: News that there is a new pre-competitive org Transcelerate 15:41:06 ... pharma thinks cdisc too slow, maybe Transcelerate can push faster 15:41:19 ... Roche work meeting next week 15:42:13 Scott: Interesting that Transcelerate has emerged; to push important work 15:42:24 Kersten: Frank H. will review 15:43:11 ericP: Keep our eye on: Work w Roche CDISC, and they have their own defs of observations etc 15:43:23 ... those are based on HL7 v3 observations 15:43:45 ... we should make sure that defs are dropped-in pieces 15:44:06 Also, an interesting presentation from CDISC SHARE and GSK on the problems with today's data standards and the idea of using "mind maps" for the next generation of "concept based" standards http://kerfors.blogspot.se/2012/09/mind-maps-just-begging-for-rdf-triples.html 15:44:15 Charlie: Then we are sitting right in the middle of the anaphylaxis AE problem. 15:44:36 ericP: Work for normalizing forms will be relevant to both trials and care 15:45:07 Charlie: IMI(?) has been building solution? 15:45:28 Kersten: Pushing, but it's not easy. 15:46:01 ...ehr4cr is more hl7/rim type of model as opposed to semantic web oriented... 15:47:13 ericP: Anaphylaxis use case, any successes will have immediate applicability 15:47:59 ... with the RDF representation, we can turn the crank; CRO observations/hospitial observations 15:48:25 Charlie(?): BRIDG is subset of RIM 15:48:44 ericP: Lloyd mailed an OWL representation of BRIDG 15:49:16 Charlie: Lloyd will re-do the BRIDG-RIM map in OWL 15:49:22 ericP: Cool. 15:51:46 Michel: Will do two AMIA submissions 15:53:24 Michel: This meeting is adjourned. 15:53:25 -[IPcaller] 15:54:25 rrsagen, draft minutes 15:54:35 rrsagent, draft minutes 15:54:35 I have made the request to generate http://www.w3.org/2012/10/02-hcls-minutes.html bobP 15:54:49 action item: revive COI task force, select chair 15:56:12 -michel 15:58:00 FDA meeting https://www.federalregister.gov/articles/2012/08/14/2012-19748/regulatory-new-drug-review-solutions-for-study-data-exchange-standards-notice-of-meeting-request-for 16:06:39 -charlie 16:08:27 -EricP 16:08:29 -Kerstin_Forsberg 16:08:45 rrsagent, make logs public 16:09:04 -Bob_Powers 16:09:05 SW_HCLS()11:00AM has ended 16:09:05 Attendees were +1.510.705.aaaa, Bob_Powers, EricP, +1.613.293.aabb, erich, michel, +33.1.73.71.aacc, charlie, Kerstin_Forsberg, [IPcaller] 16:58:18 egonw has joined #HCLS 17:16:05 egonw has joined #HCLS 17:26:20 Zakim has left #hcls 17:26:42 MacTed has joined #hcls