17:08:13 <RRSAgent> RRSAgent has joined #hcls2
17:08:13 <RRSAgent> logging to http://www.w3.org/2010/11/18-hcls2-irc
17:08:24 <michel> zakim, this is tmo
17:08:24 <Zakim> ok, michel; that matches SW_HCLS(TMO)11:00AM
17:08:44 <michel> scribenick Bob
17:08:52 <michel> zakim, who is here?
17:08:52 <Zakim> On the phone I see Bob_Powers, ??P32, +1.518.276.aaaa, +1.302.598.aabb, mscottm
17:08:57 <Zakim> On IRC I see RRSAgent, Zakim, Bob, Joanne, michel, trish_whetzel, ericP
17:09:03 <michel> zakim ??P32 is michel
17:09:12 <michel> zakim, ??P32 is michel
17:09:12 <Zakim> +michel; got it
17:10:21 <Bob> Michel: Post-mortem on the paper
17:11:05 <Bob> Joanne: Grateful to take it on; challenging w. group this size
17:11:44 <Bob> ... Jim McCusker really helped
17:12:10 <Bob> ... could bring in provenance considerations too
17:12:44 <Bob> ... late nite w. EricP and Jim
17:13:05 <Bob> ... Thanks to Michel for re-proofing
17:14:00 <Bob> ... working on section on queries, working with table
17:14:46 <Bob> ... Most of text is wrangled to the ground.
17:15:30 <Bob> ... what level of detail on the query descriptions
17:16:12 <Bob> ... second question: what to say re significance of queries
17:16:51 <Bob> Michel: No need to discuss syntax;
17:17:11 <Bob> ... but can query with broader terms than those in the data
17:17:43 <Bob> ... describe in terms of data sources, add any discussion of real inferencing
17:18:07 <Bob> Scott: Point out significance of being able to make general queries
17:18:34 <Bob> ... hospitals, each department having own IT dept
17:18:48 <Zakim> +EricP
17:18:59 <Bob> ... point out advantages of having all patient data in one place
17:19:19 <Bob> ... plus clinical trials, plus drug and other scientific information
17:19:47 <Bob> ... tone for queries: It's about the fact that can combine info in ways not possible before
17:20:30 <Bob> ... important to remember that added value is ability to query across data sources
17:22:32 <Bob> Joanne: Deadline has a little bit of play; reviewers get full version a little later
17:23:31 <Bob> EricP: "It's not going to be us, is it?" :)
17:24:06 <Bob> Michel: Great job, significant expansion of BioOnt paper
17:24:30 <Bob> ... broadness from both Joanne and Deborah, placed in context of what's important
17:24:55 <Bob> ... paper is nicely well rounded; EricP unit testing, XML to RDF
17:25:15 <Bob> ... will get some interesting feedback from reviewers
17:26:08 <Bob> EricP: Need more co-ordination. (Giving several different views on data0
17:26:41 <Joanne> I sent the email to Larissa (and the other organizers) that we plan to send it later today.
17:26:44 <Bob> ... representation of some of the more complex tests
17:27:05 <Bob> ... generic, vs simple pattern for units
17:27:21 <Bob> ... have not got all original XML data into Indivo
17:29:14 <Bob> Michel: EricP and I will try to figure out the coverage and what needs to be translated
17:29:46 <Bob> ... think re how the knowledge needs to be represented, SNPs(?) etc
17:30:47 <Bob> Joanne: Wrap up all the paper to-dos
17:31:11 <Bob> Michel: Patient records in TMKB come from the original XML
17:31:41 <Bob> EricP: doc files had angle brackets for XML, blue sky view of patient record
17:32:02 <Bob> ... tailor that against somebody else's blue sky, started mapping into Indivo
17:32:17 <Bob> ... pieces of these data have not made it thru the pipe
17:32:52 <Bob> ... also grddl, test data are not quite done
17:33:10 <Bob> (would have to hear this w/o typing to grok :)
17:33:43 <Bob> EricP: Will take back to Indivo, negotiate and address how the XML schema looks
17:34:02 <Bob> Michel: How to involve Indivo spec to handle what we expect
17:34:23 <Bob> ... plus work with then to standarize path to RDF
17:34:58 <Bob> Joanne: This is valuable to get Indivo on board in RDF
17:35:13 <Bob> ... important contribution from HCLS
17:35:43 <mscottm> mscottm has joined #hcls2
17:35:55 <Bob> Joanne: More than best practices, it's a requirement
17:35:56 <mscottm> Joanne: It's a requirement that hasn't been met.
17:36:12 <mscottm> +1
17:36:58 <Bob> EricP: caMatch(?) for tracking EHR system
17:37:19 <Bob> ... for clinical trial protocol requirements
17:37:36 <Bob> Joanne: ICD-11, any contact?
17:37:57 <Bob> can't hear you!
17:38:04 <trish_whetzel> WHO is using WebProtege ->iCat to develop ICD-11
17:38:47 <Bob> EricP: WHO contracted w Stanford for software, build ontologies
17:38:59 <trish_whetzel> @eric, how do you see TMO to be normative for i2b2?
17:39:49 <Bob> Trish: Project has been iterative over that last year plus.
17:40:21 <Bob> Scott: Nice part of pushing semweb forward
17:40:36 <trish_whetzel> iCat development has been an iterative process to include new features as requested by WHO
17:40:56 <Bob> ... IMI got $2B, there are 3 IMIs, w Open Pharma Space
17:41:32 <Bob> ... will use semweb. Plus math modeling, plus EHR stuff, all supposed to co-ordinate
17:41:51 <Bob> ... large pressure to move in the direction of our paper
17:42:25 <Bob> ... people talking, throwing money. But we did it.
17:43:27 <Bob> Scott: Leaking over to us; room to hire possibly W3C folks
17:44:01 <Bob> ... nice piece of news: Cannot get around RDF to manage resources
17:44:18 <Bob> ... and there are 3 IMIs that all need to co-ordinate.
17:44:51 <trish_whetzel> Thoughts on submitting to Spring AMIA TBI or CRI 
17:44:58 <Zakim> -michel
17:44:59 <trish_whetzel> AMIA Deadline is Dec. 15
17:46:25 <Zakim> -EricP
17:48:12 <Bob> Joanne: query 12, how to tell whether using inferencing
17:48:40 <Joanne> http://esw.w3.org/HCLSIG/PharmaOntology/Queries
17:49:05 <Joanne>  Are there any AD patients without the APOE4 allele as these would be good candidates for the clinical trial involving Bapineuzumab?
17:49:20 <Joanne>  Which existing marketed drugs might potentially be re-purposed for AD because they are known to modulate genes that are implicated in the disease?
17:50:09 <Bob> Query 6: Are there any AD patients...
17:52:25 <Bob> Query 12: pharmgkb manually curated
17:52:47 <Bob> Scott: reasoning has already been done in pharmgkb
17:53:00 <Bob> ... relates genes and drugs to diseases
17:53:35 <Bob> ... a bit like diseaseome. Win here is that the interesting relations are already there.
17:58:47 <trish_whetzel> Need to move to next call. Bye
17:58:58 <Zakim> - +1.302.598.aabb
18:01:35 <Zakim> - +1.518.276.aaaa
18:01:40 <Zakim> -mscottm
18:01:42 <Zakim> SW_HCLS(TMO)11:00AM has ended
18:01:46 <Zakim> Attendees were Bob_Powers, +1.518.276.aaaa, +1.302.598.aabb, mscottm, michel, EricP
19:24:48 <Zakim> Zakim has left #hcls2
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20:06:20 <michel> rrsagent, draft minutes
20:06:20 <RRSAgent> I have made the request to generate http://www.w3.org/2010/11/18-hcls2-minutes.html michel
20:06:28 <michel> rrsagent, make log world-visible