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16:56:27 <RRSAgent> logging to http://www.w3.org/2011/01/20-hcls2-irc
16:59:52 <Bob> Bob has joined #hcls2
17:01:19 <matthias_samwald> matthias_samwald has joined #hcls2
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17:03:09 <michel> zakim, this is tmo
17:03:09 <Zakim> ok, michel; that matches SW_HCLS(TMO)11:00AM
17:03:19 <michel> zakim, who is here?
17:03:19 <Zakim> On the phone I see Bob_Powers, +1.570.724.aaaa, Joanne_Luciano, [IPcaller]
17:03:22 <Zakim> On IRC I see matthias_samwald, Bob, RRSAgent, Zakim, michel, ericP
17:03:27 <Zakim> +??P32
17:03:36 <michel> zakim, [IPcaller] is michel
17:03:36 <Zakim> +michel; got it
17:03:50 <matthias_samwald> zakim, ??P32 is matthias_samwald
17:03:51 <Zakim> +matthias_samwald; got it
17:04:23 <michel> scribenick bob
17:05:01 <bbalsa> bbalsa has joined #HCLS2
17:05:46 <Zakim> +Bosse
17:05:48 <Zakim> +danielR
17:06:08 <michel> zakim, +1.570.724.aaaa is bosse
17:06:09 <Zakim> +bosse; got it
17:07:17 <Bob> Michel: Review for the special issue
17:07:28 <Zakim> + +1.781.431.aabb
17:08:18 <Bob> ... deadline will be Feb 7, must include revised version and replies to reviewers
17:08:22 <michel> http://esw.w3.org/HCLSIG/PharmaOntology/Publications/JBMS-reviews
17:09:04 <Bob> ... Review #1 How do patient records reflect...
17:10:18 <michel> action item: chris to address "realism" of the synthetic patient records
17:10:18 <Bob> Chris: Want to tackle this; Michel's point about patient records being a bridge is good
17:10:41 <Bob> ... Albany Med has various different medical records
17:10:59 <Bob> ... each version has an abridged version 
17:11:38 <Bob> Michel: We should deal w. issue, but thought we already addressed it
17:12:10 <epichler> epichler has joined #HCLS2
17:12:17 <Bob> Joanne: Write up separate sections before integrating into google doc?
17:12:29 <Zakim> +mscottm
17:12:40 <mscottm> mscottm has joined #hcls2
17:12:58 <Bob> Michel: Making action items for people in irc
17:14:17 <Bob> Michel: Next point is security and patient confidentiality
17:14:39 <Bob> ... how do we deal w, in semweb approach and our approach?
17:14:57 <Bob> ... add a section wrt privacy/security
17:15:19 <Bob> ... there has been some work on triple store security
17:15:47 <Bob> Joanne: Will ask ericP plus RPI
17:16:03 <michel> action item: add section detailing security/privacy of patient records using SW technologies -> Joanne + ericP
17:16:30 <Bob> Some kind of anonymization, will that be covered in the paper?
17:16:53 <Bob> Joanne: We do not discuss anonymization in paper.
17:17:18 <Bob> Michel: Next, longitudinal data does not seem to be addressed
17:17:35 <mscottm> Zakim, who is here?
17:17:35 <Zakim> On the phone I see Bob_Powers, bosse, Joanne_Luciano, michel, matthias_samwald, Bosse, danielR, +1.781.431.aabb, mscottm
17:17:37 <Zakim> On IRC I see mscottm, epichler, bbalsa, matthias_samwald, Bob, RRSAgent, Zakim, michel, ericP
17:18:00 <Bob> Scott: Ex BP, checked at each visit.
17:18:24 <Bob> (sorry!)
17:19:07 <Bob> Joanne: Longitudinal connections are being done at the app level
17:19:41 <Bob> Chris: These connections are best left to the clear objective data
17:19:46 <michel> how do we address the representation of longitudinal data
17:20:11 <Zakim> -danielR
17:20:28 <Bob> Michel: Collection of events ordered by time, we deal w. simply
17:21:02 <Bob> ... sparql over events thru time would connect things longitudinally
17:21:38 <Bob> Elgar: (some subtle objection here)
17:22:09 <Bob> Michel: This is a domain of information artifacts w. time stamps
17:22:29 <Bob> ... we are not formally treating the timestamping of events
17:23:57 <Bob> Michel: Will work w. ericP to look at time stamps
17:24:15 <Bob> ... then there's ordering as an important value add
17:24:39 <michel> action item: longitudinal data - michel, chris and ericP ; find interesting longitudinal query to ask using SPARQL
17:24:40 <Bob> Chris: Trying to keep it very simple
17:25:05 <Bob> ... send Chris example queries re medical or clinical
17:25:52 <Bob> Michel: Next, assigned to Joanne, Tim and ericP
17:26:14 <michel> action item:  sparql example that identifies AD patients "without the apoe4 allele" seems to only performs a string match against the value of the apoe4 property.
17:26:35 <Bob> Michel: Review #2 w 8 points
17:27:26 <Bob> ... Do we have enough characteristics to make it clinically interesting
17:28:56 <Bob> ... move AD stuff from footnote in methods up into text
17:30:34 <michel> action item: move AD use case details from methods to use case section - bosse
17:31:39 <Zakim> -Joanne_Luciano
17:31:45 <michel> action item: Ontology Design section points to “research questions” but wrong table is listed - elgar
17:32:16 <Zakim> +Joanne_Luciano
17:33:07 <michel> action item: remove reference to "real world entities", as this is not of interest to us - michel
17:34:18 <michel> action item: cite the relation ontology paper - http://genomebiology.com/2005/6/5/R46 - joanne
17:35:31 <michel> action item:  Figure 3 in the current version of the manuscript seems to have nothing to do with mappings. This looks like the wrong figure was uploaded ?? - Joanne
17:36:26 <mscottm> I don't understand what it means - which questions are being referred to? 
17:39:31 <michel> action item: bring unit testing and data mapping into the use case - elgar + others working on use case
17:40:54 <michel> action item: queries were included as supplementary data - elgar
17:41:23 <michel> elgar - add 'queries operational as of XXXX'
17:42:18 <michel> add the answers to the supplementary data document
17:43:06 <michel> action item: fix first sentence of the SPARQL queries section to 14 listed questions: joanne
17:43:48 <Bob> Michel: What else should we do for this paper?
17:44:19 <Bob> Joanne: AMIA asks for a demo, address this later
17:45:22 <michel> action item: prepare response to reviewers - michel
17:46:45 <Bob> Michel: Will create a response-to-reviewers doc
17:47:04 <Bob> ... also need dedicated reviewers
17:47:58 <Bob> ... Scott and Elgar will give the first big read
17:48:03 <michel> action item: review the paper - matthias, scott
17:49:06 <Bob> Joanne: Will put in a fresh google doc
17:51:49 <michel> response to reviewers - https://docs.google.com/document/d/1XoRj-Ysxa0xOX2n3MBNcG7_dT7cEA4C3ITKn3z1rCPc/edit?hl=en&authkey=CJXJhtsP
17:53:09 <Bob> Michel: Trying to schedule a meeting w. EHR Oscar(?)
17:56:15 <matthias_samwald> i will probably not be available on Tuesday evening.
17:56:34 <matthias_samwald> yeah :)
17:57:04 <Bob> Michel: Poster presentations for AMIA
17:57:13 <Bob> Joanne: We are podium too
17:57:13 <mscottm> Congrats!
17:57:46 <Bob> ... AZ is interesting for AMIA and would make a good demo
17:58:17 <Bob> ... CSHALS meeting, RPI/W3C doing demo, will show mash-ups, sparql etc
17:59:10 <Zakim> - +1.781.431.aabb
17:59:11 <Zakim> -Bob_Powers
17:59:11 <Zakim> -Joanne_Luciano
17:59:12 <Zakim> -mscottm
17:59:12 <Zakim> -Bosse
17:59:13 <Zakim> -michel
17:59:14 <Zakim> -bosse
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17:59:22 <michel> rrsagent, draft minutes
17:59:22 <RRSAgent> I have made the request to generate http://www.w3.org/2011/01/20-hcls2-minutes.html michel
17:59:29 <michel> rrsagent, make log world-visible
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17:59:42 <Zakim> -matthias_samwald
17:59:44 <Zakim> SW_HCLS(TMO)11:00AM has ended
17:59:46 <Zakim> Attendees were Bob_Powers, Joanne_Luciano, michel, matthias_samwald, Bosse, danielR, +1.781.431.aabb, mscottm
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