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16:04:59 <RRSAgent> logging to http://www.w3.org/2011/01/06-hcls-irc
16:05:04 <matthias_samwald> zakim, this is hcls
16:05:04 <Zakim> ok, matthias_samwald; that matches SW_HCLS()11:00AM
16:05:12 <matthias_samwald> high five!
16:05:16 <Susie> Susie has joined #hcls
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16:06:08 <Zakim> + +1.781.431.aadd
16:06:40 <ericP> Zakim, please dial ericP-office
16:06:40 <Zakim> ok, ericP; the call is being made
16:06:42 <Zakim> +EricP
16:07:13 <Zakim> +??P8
16:07:21 <michel> Zakim, ??P8 is michel
16:07:21 <Zakim> +michel; got it
16:07:38 <Bob> scribe Bob
16:07:54 <mscottm> scribenick Bob
16:09:11 <Bob> Automate radiologists and pathologists communication
16:09:58 <Bob> Formulate appropiate queries, whether reports are consonant or dissonant
16:10:36 <Bob> Scott: Been involved in DERI project, we have put that use case front and center
16:11:07 <Bob> ... can use that as a use case to leverage w. Terminology
16:11:28 <Bob> ... Pink Ribbon project in Netherlands
16:11:57 <Bob> ... might look for connection w. Pink Ribbon on breast cance
16:12:26 <Bob> ... breast cancer is a familiar area for radiologists, paths
16:12:53 <Bob> Some RDF infrastructure is already in place for this use case
16:13:07 <Bob> ... also have some XML data
16:14:04 <Bob> Scott: Last HCLS call, agenda re i2b2, relevance, demos etc.
16:14:07 <Zakim> +??P27
16:14:28 <Tim> Tim has joined #HCLS
16:14:34 <Bob> ... also talking about EPRs
16:15:05 <Bob> ... Indivo has been sorted out by ericP
16:15:56 <Bob> EricP: i2b2 is in triple format, combo of concept code, value, unit
16:16:13 <Bob> ... a bit of structure for describing events, facts
16:16:29 <Zakim> + +31.62.427.aaee
16:16:35 <Zakim> - +20416aabb
16:16:46 <mscottm> Sorry - that was me I solved it
16:16:58 <Bob> ... working w. Dave Connally(?) to take RDBS
16:17:04 <ericP> connolly
16:17:36 <Bob> ... Question: go to i2b2, Indivo datastores
16:18:39 <mscottm> KUMC = Kansas University Medical Center
16:18:44 <Bob> ... Work is happening KUMC
16:19:25 <Bob> Scott: Looking for connections w. particular task forces
16:20:04 <Bob> EricP: Working w. proposals for funding
16:20:23 <Bob> Scott: Productive fun, get that going
16:20:47 <Bob> Tim: Sci Discourse, last call Dec 20
16:21:17 <Bob> ... Working on a number of related threads:
16:21:50 <Bob> ... rhetorical document structure; There are a number of efforts in the group to bring one model together
16:22:19 <Bob> ... working to put a spec together: ORB Ontology of rhetorical blocks
16:23:02 <Bob> ... similarities and differences; Want semweb representation independent of order of entities
16:23:32 <Bob> ... Also bibliographic references and citations
16:23:45 <Bob> ... want to satisfy library requirements
16:24:09 <Bob> ... FRBR Functional requirements for biblographic records
16:24:24 <Bob> ... want to satisfy FRBR, SWAN and others
16:24:40 <Bob> ... paper coming in J. BioMed. Sem.
16:25:09 <Bob> ... Also Data interpretations: OBI, myExperiment and SWAN
16:25:44 <Bob> ... no paper yet; we have a first cut OWL model
16:26:13 <Bob> ... Annotation ontology, now being extended(?)
16:26:44 <Bob> ... Scientific article of the future: Status is that nobody has done anything yet :-)
16:27:00 <Bob> ... interesting workshop: Beyond PDF
16:28:05 <Bob> ... this workshop is very relevant to our group
16:28:33 <Bob> ... We started several different threads at the beginning of last year
16:28:50 <Bob> ... code is coming around some of these threads
16:29:43 <Bob> Scott: BioRDF last couple of months submitted to Problems workshop
16:30:05 <Bob> ... microarray studies; also text mining
16:30:42 <Bob> ... most recent call, started looking at how to build on microarray work
16:31:25 <Bob> ... important: re-using existing microarray analyses
16:31:42 <Bob> ... RDF analogue of what Gene Atlas already does
16:32:16 <Bob> ... hoping by creating another pub, show how to issue sparql requests
16:33:06 <Bob> Q: How far away from having stack for GeneLib?
16:33:27 <Bob> Scott: Number of people think that it's fairly trivial
16:33:39 <Bob> ... it's already tabular
16:34:08 <Bob> ... another step is to take it to publishers; important to upload data
16:34:41 <Bob> ... see if we can get this moving.  It is an inevitability.
16:35:14 <Bob> ... trying to create infrastructure
16:35:39 <Bob> ... much of the data is already in json
16:35:55 <Bob> Tim: Would really like to see a spec on this!
16:37:06 <Bob> Scott: OBI reps of experimental conditions; but our scope is somewhat larger
16:37:34 <Bob> EricP: Would a simple spec be sufficient?
16:37:46 <Bob> ... trying not to volunteer :-)
16:38:08 <Bob> Tim: Would like to see a capstone, b/c other people could use the representation
16:38:38 <Bob> ... carve out a subset of OBI
16:38:55 <Bob> ... we could integrate experimental conditions from OBI, no problem
16:39:16 <Bob> Sounding here like a big agreement on a push for this.
16:39:53 <Bob> Scott: Capturing results of text mining --> RDF, can go full circle
16:40:33 <Bob> ... creating a M&M section; perform microarray in Traverna, store in triple store
16:41:31 <Bob> Scott: Tim really important angle, to plan the conclusion on this
16:43:10 <Bob> Tim: There will be a doodle poll on how to close the gap
16:43:33 <Bob> Scott: Article, note or practices; these are all possibilities
16:46:03 <Bob> Scott: COI
16:46:41 <Bob> EricP: i2b2 stuff.  The other side is Mark Wilkinson project to make web services w. graph pattern
16:47:10 <mscottm> re: Mark Wilkinson (and Chris Baker and Michel Dumontier) SADI project
16:47:44 <Bob> Scott: LODD
16:48:08 <Bob> Susie: LODD taking minimalistic approach w aggressive time frame
16:48:23 <Bob> ... document that outlines best practices for generating linked data
16:48:46 <Bob> ... people w. experiences encountering roadblock after roadblock
16:49:11 <Bob> ... need realist view of the world, or can one take shortcuts
16:49:28 <Bob> ... have identified a number of different issues
16:49:56 <michel> q+ vis-a-vis linkeddata.org
16:49:57 <Bob> ... Feb 1 deadline for a paper
16:50:27 <Bob> ... Scott is also driving the effort in describing best practices
16:50:31 <michel> http://linkeddata.org/guides-and-tutorials
16:50:36 <johnM> guys, I've got to go. Talk soon, Scott.
16:50:43 <Zakim> -John_Madden
16:50:44 <mscottm> Thanks for coming John.
16:51:09 <Bob> Michel: Important that any document also goes to the link above
16:52:07 <Bob> Scott: Michel on TM
16:52:29 <Bob> Michel: Demo, still a few issues on patient records, EricP, Joanne, Tim
16:52:48 <Bob> ... a bit akin to what we were talking about with Tim above
16:53:21 <Bob> ... keen to know about overlaps in healthcare. EricP is bridging groups
16:53:40 <Bob> ... would make sense for COI to be brought into TMO?
16:54:26 <Bob> EricP: COI happening independent of calls.
16:55:04 <Bob> Michel: EHR stuff is happening in TM.  Records, datasets
16:55:27 <Bob> EricP: COI is acting as clients of TM, no modeling suggestions
16:55:51 <Bob> Michel: Wonder if we should consider to revive COI?
16:56:17 <Bob> EricP: Indivo and i2b2 integrated w. workflow will add momentum
16:56:44 <Bob> Scott: 1) COI coming back?
16:56:55 <Zakim> -??P27
16:57:11 <Bob> ... 2) TM is going inevitably into patient records
16:57:32 <Bob> ... should make it clear outside that TM is doing this work, more prominent
16:57:50 <Bob> EricP: All for it.
16:58:51 <Bob> Scott: Re-frame the work of TM, make patient records more front and center?
16:59:12 <Bob> Michel: Have an opportunity to showcase; want a revived, active group.
16:59:43 <Bob> ... brother is at McMaster, work going on there about Indivo.
16:59:51 <Zakim> - +1.610.651.aacc
17:00:37 <Bob> Scott: Good to be transparent from main web page; TM doing stuff w. patient records, COI in sleep mode.
17:01:43 <Bob> Michel: Planning F2F before EO charter??
17:02:00 <Bob> Scott: F2F has been un-planned.
17:02:15 <bbalsa> bbalsa has joined #HCLS
17:03:02 <Bob> ... has been judged not be important.  But worth considering again; it is getting late.
17:03:40 <Bob> Michel: Have been discussing HCLS re-chartering with some people.
17:04:01 <Zakim> -michel
17:04:02 <Zakim> -Bob_Powers
17:04:04 <Zakim> -EricP
17:04:06 <Zakim> -??P41
17:04:08 <Zakim> - +1.781.431.aadd
17:04:12 <Zakim> SW_HCLS()11:00AM has ended
17:04:14 <Zakim> Attendees were +1.610.651.aaaa, +20416aabb, Bob_Powers, +1.610.651.aacc, John_Madden, +1.781.431.aadd, EricP, michel, +31.62.427.aaee
17:34:52 <mscottm>   RRSAgent, please draft minutes
17:34:52 <RRSAgent> I have made the request to generate http://www.w3.org/2011/01/06-hcls-minutes.html mscottm
17:34:59 <mscottm>   RRSAgent, please make log world-visible
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