HCLSIG/Meetings/2013-05-07 Conference Call

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Meeting:       HCLS General Forum
Convener:      Michel Dumontier
Date:          May 7, 2013 @ 11am EDT
Frequency:     1st Tuesday of the month
Past Meetings: http://goo.gl/NFqPx
Dial-In #:     +1.617.761.6200 (Cambridge, MA)
VoIP address:  sip:zakim@voip.w3.org
Participant    Access Code: 4257 ("HCLS")
IRC Channel:   irc.w3.org port 6665 channel #HCLS
IRC Web:       http://irc.w3.org



[11:03] <@ericP> Topic: pharmacogenomics

[11:04] <@ericP> scribenick: bobP

[11:04] <michel> http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-05-01_Conference_Call

[11:04] <bobP> Michel: PGx, we are taking inventory of priorties, planning

[11:05] <bobP> ... Bob Friemuth also has objectives, not yet posted here

[11:05] <bobP> ... next week we talk about which agendas w interdependencies

[11:06] <bobP> ... this is part of re-organization; not waiting for people, but sharing

[11:06] <bobP> ... conversations about what everybody wants to do and how to get there

[11:07] <bobP> ericP: You got objectives and plan

[11:08] <bobP> Michel: Yes; more fitting projects than having just one big project

[11:08] <bobP> ... synergy among projects

[11:08] <bobP> ... to complement each others priorities

[11:11] <bobP> CDISC from Roche

[11:12] <michel> kerstin: working on CDISC

[11:13] <michel> ... proposal from Roche to move emerging technologies working group; semantic web

[11:13] <michel> ... 40 people engaged in this

[11:14] <michel> ... formation of specific teams over the next few weeks. includes documentation and use cases

[11:14] <michel> charlie: representation of existing standards. participation by FDA is positive

[11:15] <dbooth> Topic: SemTech workshop on "RDF as a Universal Healthcare Exchange Language"

[11:16] <dbooth> There will be a free workshop on "RDF as a Universal Healthcare Exchange Language" at the SemTech Conference in San Francisco on Monday June 3: http://semtechbizsf2013.semanticweb.com/sessionPop.cfm?confid=70&proposalid=5296

[11:16] <dbooth> There will also be an associated panel discussion as part of the SemTech conference, on Wednesday June 5:

[11:16] <dbooth> http://semtechbizsf2013.semanticweb.com/sessionPop.cfm?confid=70&proposalid=5226

[11:16] <dbooth> The workshop is "by invitation only", but the main reason is just to ensure that we do not exceed the room capacity. There is a form (linked from the workshop page) that allows you to apply to attend, and we expect most to be accepted. I would encourage all in the HCLS to come and participate if you can. Participants in the workshop (which is free) will also receive a 15% conference discount if they choose to also attend the rest of the conference. Let me

[11:16] <dbooth> know if you have questions: david@dbooth.org

[11:17] <dbooth> topic: clinical informatics

[11:17] <dbooth> http://www.w3.org/2013/Talks/0507-HCLS-egp/

[11:20] <michel> slide 3 - typical clinical data - encounter, allergies, immunizations, history, demographics, vitals, labs, diagnosis, prescription, etc

[11:20] <michel> slide 4 - example procedure

[11:23] <michel> slide 5 - simple RDF graph; encounter, location, patient, physician, clinic

[11:24] <michel> slide 6 - enable coding systems; replace "codeine" with "influenza vaccination"

[11:26] <michel> http://codingsystems.org/2.16.840.1.113883.6.88/2670

[11:28] <michel> ont:substance <http://codingsystems.org/2.16.840.1.113883.6.88/2670>

[11:29] <Kerstin> More info on URIs for SNOMED: http://informatics.mayo.edu/cts2/index.php/ExternalURI

[11:29] <michel> michel: are we heading to URIs?

[11:29] <michel> eric: that's the idea :)

[11:31] <michel> slide 7 - rdf description

[11:33] <michel> eric: measure what they observe against medical knowledge, in coded terms.

[11:34] <michel> ... where is the most energy being put in these systems?

[11:34] <michel> ... patient encounter, procedures performed.

[11:35] <michel> ... 23andme, patientlikeme - people putting in their data; bulk of data will be in CDA as part of meaningful use act

[11:36] <michel> ... hl7 v3 has not had the expected uptake; very complex in v3 messaging; little motivation to upgrade

[11:36] <michel> ... between CDA and BRIDG (clinical trials), defined in terms of the RIM. bulk of data is in the RIM.

[11:37] <rafael> http://ccda-scorecard.smartplatforms.org/static/ccdaScorecard/#/

[11:37] <michel> slide 8 - immunization record in CCDA; complex

[11:37] <michel> ... xml structure; who performed it, responsible organization

[11:38] <michel> slide 10 - a reflection of that complexity into RDF.

[11:40] <michel> slide 11 - e.g. manufactured material acted in the consumption role of a substance administration

[11:41] <dbooth> q+ To ask why not turn those codes into RDF properties?

[11:42] <michel> michel: easy simplification is turning those code references into URIs, and provide human readable descriptions for them

[11:44] <michel> eric: ids are provided for the type; some are specific instances

[11:44] <michel> ... some rules to infer the identity of an instance

[11:44] <michel> ... so that all the statements use that id as the subject

[11:45] <michel> ... so that records can be transferred

[11:46] <michel> time is usually fairly distinguishing... temporal tagging

[11:47] <michel> charlie: data is being distributed; things can get separated. microbiology test - issues around incompleteness, uncertainty

[11:47] <dbooth> The work of de-duping is pushed into the heuristic rules that generate URIs from a collection of (presumably) uniquely identify that thing, whether it is an event or whatever.

[11:49] <dbooth> s/collection of/collection of properties that/

[11:49] <michel> eric: timing information will provide heuristics to debug issues. when did an id fail to merge?

[11:50] <dbooth> eric: want to lean on institutions to mint new UUIDs for new events.

[11:51] <dbooth> But for de-duping, you want them also NOT mint UUIDs for non-new events.

[11:51] <michel> eric: uuids should be made for events under their jurisdication

[11:51] * michel thanks david, your help is invaluable here :)

[11:52] <michel> eric: having it in RDF not only means we can query effectively, but easier to integrate

[11:54] <michel> rafael: problem with all our systems is that we don't have a good method to cross-validate other assertions. provenance is key.

[11:56] <michel> eric: adding PROV to assertions would be the way forward; can figure out what information was present at that time

[11:56] <Kerstin> Beside the identifiers/de-duplificatation of the health records/documents we also have the identifiers of what they document. Check out: "Referent tracking" http://www.referent-tracking.com/RTU/?page=index

[11:56] <bobP> Prov Ontology http://www.w3.org/TR/prov-o/

[11:57] <michel> eric: this sparql at this time, we got these results; doing it later, gives different results, and compare

[11:57] <michel> cool :)

[11:58] <michel> rich: working on de-duplication; transfer of information for supportive care. use cases for supporting clinical research?

[11:59] <michel> eric: CDISC semantic web representation of clinical trials. If used BRIDG (based on RIM), reasonable to transform/merge data with some html document (?)

[12:00] <michel> eric: lot of information in a clinical trial; merging clinical care/clinical trial data offers much opportunities

[12:01] <michel> charlie: are there standards? yes for human subjects. problem is educating clinical trial community. increasing amount of effort into semantically interoperate between trials and research

[12:02] <michel> charlie: IMI funded EHR4CR ...

[12:02] <rafael> http://ccda-scorecard.smartplatforms.org/static/ccdaScorecard/#/

[12:02] <michel> eric: worth the time for all this work

[12:25] <Zakim> SW_HCLS()11:00AM has ended

[12:25] <Zakim> Attendees were +1.412.624.aaaa, Bob_Powers, +1.650.804.aabb, michel, Kerstin_Forsberg, ericP, DBooth, +, +1.410.905.aadd, +1.510.421.aaee, Tony, +1.919.681.aaff