14:01:31 <RRSAgent> RRSAgent has joined #hcls2
14:01:31 <RRSAgent> logging to http://www.w3.org/2009/10/29-hcls2-irc
14:01:38 <johnM> zakim, this is term
14:01:38 <Zakim> johnM, I see SW_HCLS(Term)10:00AM in the schedule but not yet started.  Perhaps you mean "this will be term".
14:01:45 <johnM> zakim, this will be term
14:01:45 <Zakim> ok, johnM; I see SW_HCLS(Term)10:00AM scheduled to start now
14:03:15 <nalbarr> nalbarr has joined #hcls2
14:04:02 <Zakim> SW_HCLS(Term)10:00AM has now started
14:04:10 <Zakim> +John_Madden
14:04:11 <Zakim> + +1.847.832.aaaa
14:04:14 <Zakim> - +1.847.832.aaaa
14:04:36 <johnM> zakim, +1.847.832.aaaa is nalbarr
14:04:36 <Zakim> sorry, johnM, I do not recognize a party named '+1.847.832.aaaa'
14:04:52 <Zakim> + +1.847.832.aabb
14:04:59 <johnM> zakim, 1.847.832.aaaa is nalbarr
14:04:59 <Zakim> sorry, johnM, I do not recognize a party named '1.847.832.aaaa'
14:05:39 <johnM> zakim, +1.847.832.aabb is nalbarr
14:05:39 <Zakim> +nalbarr; got it
14:06:04 <Zakim> -nalbarr
14:06:05 <Zakim> -John_Madden
14:06:06 <Zakim> SW_HCLS(Term)10:00AM has ended
14:06:07 <Zakim> Attendees were John_Madden, +1.847.832.aaaa, nalbarr
15:02:21 <michel> michel has joined #HCLS2
15:24:13 <bbalsa> bbalsa has joined #HCLS2
15:55:13 <Susie> Susie has joined #hcls2
16:02:20 <ElgarPichler> ElgarPichler has joined #hcls2
16:02:55 <ericP> Zakim, please dial ericP-office
16:02:55 <Zakim> sorry, ericP, I don't know what conference this is
16:03:01 <ericP> Zakim, this is hcls2
16:03:01 <Zakim> ok, ericP; that matches SW_HCLS(TransMed)11:00AM
16:03:03 <ericP> Zakim, please dial ericP-office
16:03:03 <Zakim> ok, ericP; the call is being made
16:03:04 <Zakim> +EricP
16:03:15 <Zakim> +ElgarPichler
16:03:18 <Zakim> + +1.410.706.aaee
16:03:19 <Zakim> + +1.414.491.aaff
16:03:26 <Zakim> + +049308385aagg
16:03:44 <Zakim> +??P24
16:04:09 <Zakim> + +0122342aahh
16:04:31 <ericP> q+ to ask if TMO folks need a bridge (or can find another) during the f2f
16:04:34 <Zakim> +Joanne_Luciano
16:05:43 <matthias_samwald> matthias_samwald has joined #hcls2
16:05:47 <ericP> yes
16:06:10 <ericP> meeting: TMO
16:06:12 <Joanne> Joanne has joined #hcls2
16:06:26 <ericP> chair: Susie
16:06:30 <ericP> scribenic: ericP 
16:06:38 <ericP> topic: the paper
16:06:45 <ericP> Susie: paper deadline extended
16:07:01 <cdenney> cdenney has joined #HCLS2
16:07:05 <ericP> ... (perhaps for everybody?)
16:07:17 <cdenney> I can't get on the phone line - it says it is full.
16:08:00 <cdenney> yes
16:08:16 <matthias_samwald> i also get a "this conference is full".
16:08:55 <cdenney> Glad to hear it wasn't personal. (blocking me)  :-)
16:09:46 <ericP> Susie: despite our extension to 30Nov, Barry would like an abstract tomorrow
16:10:20 <ericP> ... propose to start one this evening and get feedback from folks over tomorrow
16:10:34 <ericP> colin: trying to write one now in the google doc
16:10:47 <ericP> Susie: cool, will use that this evening
16:10:59 <AnjaJentzsch> AnjaJentzsch has joined #hcls2
16:11:16 <ericP> colin: like the idea of putting philosophy into another paper
16:12:07 <ericP> ... currently lack a description of how the paitent data was generated
16:12:15 <ericP> Susie: should have more this weekend
16:12:33 <ericP> colin: also need a short desc of the toy interface (pubby)
16:13:04 <ericP> cdenney, matthias_samwald, i've asked for the limit to be bumped up, but seen no live bodies to respond
16:13:20 <ericP> colin: [something about indivo ont]
16:13:33 <ericP> Susie: need to work out paper authors and order
16:14:01 <ericP> ... like to be inclusive, i.e. two calls or more in last two months, plus offline contributions
16:14:11 <ericP> ... for abstract tomorrow, alphabetical order
16:14:27 <ericP> ... chose paper order nearer [real] deadline
16:14:59 <ericP> topic: ontology updates
16:15:08 <ericP> Susie: recent updates?
16:15:26 <ericP> colon: haven't touched it myself. elgar has added MeSH
16:15:45 <ericP> ... expect criticisms when folks pour it into the triple store
16:16:08 <ericP> Zakim, who is speaking?
16:16:19 <Zakim> ericP, listening for 10 seconds I heard sound from the following: ElgarPichler (84%), Joanne_Luciano (4%)
16:16:29 <ericP> elgar: edded all of the xref that i could find
16:16:44 <ericP> ... used best judgement selecting reasonable sources
16:16:45 <AnjaJentzsch> can someone invite me to the google doc? anjeve@gmail.com - thanks
16:16:57 <ericP> ... folks might want SNOMED
16:17:30 <ericP> ... have added comments to the overall structure into google project /doc directory
16:18:03 <ericP> [ericP and peter interested in reviewing and helping the ontology]
16:18:23 <ericP> i suspect matthias_samwald would be interested as well
16:18:44 <ericP> [elgar unable to connect via Mibbit]
16:19:03 <ericP> Zakim, who is speaking?
16:19:08 <matthias_samwald> (i am still unable to connect via audio, giving up now. will read the irc though)
16:19:15 <Zakim> ericP, listening for 11 seconds I heard sound from the following: +1.610.651.aadd (85%)
16:19:33 <ericP> matthias_samwald, you could try *0
16:19:44 <ericP> topic: imports into triple store
16:19:54 <ericP> AnjaJentzsch: converted to RDF
16:20:12 <ericP> ... unsure about Medicare Plan D over-the-counter drugs
16:20:21 <ericP> ... asking for help from d2r folks
16:20:42 <Joanne> what's *0 ?  ( I was muted myself -- i sent Elgar and Peter Kos an email with each other's email address)
16:20:42 <ericP> ... end point is up, folks can query the server
16:20:47 <AnjaJentzsch> http://www4.wiwiss.fu-berlin.de/medicare/
16:21:13 <ericP> Susie: you can pick up @@1's comments from last week's minutes
16:21:40 <ericP> ... my interpreation: folks are sometimes covered by both BCBS and Medicare
16:22:00 <ericP> AnjaJentzsch: @@2 and Jun submitted a demo to linked data
16:22:02 <AnjaJentzsch> http://tinyurl.com/yzdc9a5
16:22:13 <ericP> ... can query for alternative medicines
16:22:22 <ericP> ... might be busy for the next hours/days
16:22:41 <ericP> Susie: would be nice if Michel could get access to Medicare data ASAP
16:22:57 <ericP> AnjaJentzsch: can't fix d2r [myself], but will try
16:23:06 <ericP> Susie: alternative plans?
16:23:33 <ericP> AnjaJentzsch: any tool which queries the...
16:24:00 <ericP> Susie: we want to extract data from panel 2 from a DuBois paper
16:24:09 <ericP> ... has DSM codes
16:24:31 <ericP> ... Trish was going to look at correspondance
16:24:38 <ericP> ... also asked Joanne and Michel
16:24:54 <ericP> Trish: gone through part
16:25:10 <ericP> ... for diagnostics, finding MRI, ...
16:25:41 <ericP> ... was feading panel 2 text to NCBI's tagging tool
16:26:07 <ericP> ... matches found for e.g. memory recall issues
16:26:18 <ericP> Susie: good coverage from one ontology?
16:26:36 <ericP> Trish: hitting SNOMED NCIT, BirnLex
16:26:51 <ericP> ... not sure all that has gone into the neuroinformatics framework
16:26:59 <ericP> Susie: unsure of intersection of those
16:27:16 <ericP> ... Mary Anne Martone might have the answer
16:27:27 <ericP> Trish: spoked with Birn folks yesterday
16:27:46 <ericP> Susie: carry on with lead; let me know if you hit a dead end
16:28:38 <ericP> Joanne: think Trish has gotten more out of Panel 2
16:28:55 <ericP> ... met with Michel, who i expect is working on querying it
16:29:17 <ericP> Michel: you can stick in some text, and get some markup
16:29:37 <ericP> ... but you don't get ontology matches through the web interface
16:29:44 <ericP> ... have to fall back to the web service
16:30:00 <ericP> Trish: also having trouble with the web interface
16:30:38 <ericP> Joanne: you get back a cloud of terms, e.g. memory, referenced many times
16:30:48 <ericP> ... don't see the ontologies
16:31:15 <ericP> ... terminizer draws on fewer ontologies, but has more useful interface
16:31:39 <ericP> ... had exactly what i needed for the influenza ontology
16:32:00 <ericP> Trish: have time to continue on this
16:32:26 <ericP> Susie: one we see the best fit ontologies, need to choose
16:32:40 <ericP> ... seems like SNOMED and NCI were the best
16:33:21 <ericP> Lynn: am a PI on the @@3 ontology
16:33:37 <ericP> ... can't distribute SNOMED on the web
16:33:54 <ericP> s/@@3/Disease Ontology/
16:34:44 <ericP> Susie: are there other criteria (besides liscencing) we should look for?
16:35:04 <ericP> Lynn: BFO ontology is very new
16:35:14 <ericP> Colin: propose OBO foundry
16:36:01 <ericP> Peter: some of the electronic medical records ontologies are based on their implementation system
16:36:21 <ericP> ... seen a bunch of source datasets
16:36:41 <ericP> ... is it exceptable to code towards ICD9 or LOINC?
16:37:03 <ericP> Susie: final focus is to develop TMO and develop an app to use it
16:37:14 <ericP> ... we've id'd a bunch of sources
16:37:38 <ericP> ... prolly best to map the data sources we're using to terminilogies already applied there
16:37:51 <ericP> ... for EMR, we've been using Indivo where possible
16:38:08 <ericP> ... asked Ben Adida and Ken Mandel to make the rest available
16:38:24 <ericP> ... doesn't look like it will happen in time, so we're rolling our own
16:38:34 <ericP> ... makes sense to make it as like an EMR as possible
16:39:02 <ericP> ... we wouldn't seen LOINC or ICD9 in pharmas
16:39:15 <ericP> Lynn: we've mapped ICD9 to Disease Ontology
16:39:33 <cdenney> wondering about the last comment... wouldn't see icd-9 in pharma?
16:39:41 <cdenney> we are using icd-9
16:40:16 <ericP> peter: would like to look at the EMR data to see how it fits [oops, forgot]
16:40:50 <ericP> Colin: terms of use of LOINC are alarming, rules like "don't dillute"
16:41:14 <cdenney> is anyone using MedDRA terms?
16:41:29 <ericP> Elgar: test for no liscencing by seeing if the ontology has level 0 restriction in UMLS
16:41:50 <ericP> Lynn: also if it's in OBO foundry
16:42:15 <ericP> Susie: Trish, you're taking the lead on panel 2 of DuBois
16:42:27 <ericP> ... can you get us some mappings by next week?
16:42:54 <ericP> Trish: mostly seeing [matches on] terms related to cognitian rather than diagnsotic tests
16:43:13 <ericP> Susie: i've been generating fake patient data in Indivo where possible
16:43:23 <ericP> ... Peter has be reviewing and enhancing
16:43:28 <ericP> ... three sections:
16:43:40 <ericP> ... .. demographitcs, contact
16:43:48 <ericP> ... .. genetics profile
16:44:04 <ericP> ... .. encounters
16:44:39 <ericP> ... Peter has improvied demo and contact info, as well as static info
16:45:00 <ericP> ... put together some hemo data, cholestoral, ... in encounters
16:45:34 <ericP> ... hoping peter can help with realistic data for other encounters, e.g. patient presents symptoms
16:45:50 <ericP> ... would like to complete one patient and develop 5 more in a google doc
16:46:05 <ericP> ... have discussed the intended distribution of patient data
16:46:13 <ericP> ... Indivo is capturing XML data
16:46:33 <ericP> ... expect ericP to GRDDL it
16:47:12 <ericP> Peter: will try, have other high-priority projects
16:47:30 <ericP> ... can look at the first patient set this week, the other patient sets in the next two weeks
16:47:35 <ericP> ... hemotology was 2 hours
16:47:43 <ericP> ... another 2 hours for the other aspects
16:47:58 <ericP> ... quite a lot of evening time, maybe 6 hours?
16:48:12 <ericP> Joanne: what can you turf to others?
16:48:17 <ericP> Peter: two aspects:
16:48:31 <ericP> ... .. examine Indivo and look at expression therein
16:48:48 <ericP> ... .. translating coding terminology
16:49:15 <ericP> ... finding the codes which match the use case example data
16:49:37 <ericP> ... would help if the use case data were already input
16:50:06 <ericP> Susie: would like Peter to finish patient1 so others can contribute more patients
16:50:24 <ericP> Peter: will work on this patient this week, hope to have a template next week
16:50:39 <ericP> [XML template]
16:51:26 <ericP> Susie: already have list of patients (.doc), exchanged with Peter
16:51:31 <ericP> ... will make available
16:51:59 <ericP> Chris: intrested in the display of the pharmacogenomics section
16:52:19 <ericP> s/pharmacogenomics/pharmacogenetics
16:52:55 <ericP> Chris: sent you an exmaple of the bedside data needed to tailor substance adminstration
16:53:35 <ericP> Susie: that's the next step, would be nice to have an offline call to start
16:53:40 <ericP> topic: data loading
16:54:01 <ericP> Susie: user interface
16:54:06 <ericP> topic: user interface
16:54:29 <ericP> Bosse: looked into Openvista which Chris proposed
16:54:37 <ericP> ... is already a good user interface
16:54:57 <ericP> ... enhancing for tailored medicine or treatment
16:55:13 <ericP> ... propose Emanual P of Novartis's approach
16:55:25 <ericP> ... menu of options
16:55:45 <ericP> ... e.g. point to a word
16:55:52 <ericP> ... link to a faceted browser
16:56:12 <ericP> ... have good answer from Chris, will extend
16:56:38 <ericP> ... i have not gotten OpenVista running
16:56:49 <ericP> ... saw video presentation
16:57:02 <ericP> ... is a structure/organized interface
16:57:16 <ericP> ... am not an expert developer any more
16:58:02 <ericP> ... need a developer
16:58:29 <ericP> Andreas: OpenVista is based on TCRS (the VA system)
16:58:49 <ericP> ... sent Chris a sample of TCRS
16:59:06 <ericP> ... i recommend adding a tab to OpenVista
16:59:11 <ericP> ... code is in C#
16:59:16 <ericP> ... adding a tab is easy
17:00:01 <ericP> ACTION: Andreas to send said link to Susie to incorporate into minutes
17:00:30 <ericP> Andreas: would expect physicians faced with new problems would go to this tab
17:01:02 <ericP> Susie: we don't need a strong interface for the paper
17:01:31 <ericP> ... need to decide if the tool allows the physician enter symptoms and the tool does some inferencing
17:01:42 <ericP> ... or a tool for researchers
17:02:06 <ericP> ... need to decide what interface we want to demo and where to start
17:02:26 <ericP> Andreas: pretty sure that CTRS is available
17:02:35 <ericP> ... not sure if it's open source
17:02:44 <ericP> ... it's avail from Delphi
17:03:43 <ericP> topic: f2f logistics
17:03:57 <ericP> Susie: task break-out time allocated
17:04:58 <ericP> RRSAgent, please draft minutes
17:04:58 <RRSAgent> I have made the request to generate http://www.w3.org/2009/10/29-hcls2-minutes.html ericP
17:05:11 <ericP> RRSAgent, please make log world-visible
17:06:19 <Zakim> - +1.610.651.aadd
17:06:22 <Zakim> -??P12
17:06:23 <Zakim> - +1.414.491.aaff
17:06:23 <Zakim> - +1.302.598.aabb
17:06:24 <Zakim> - +049308385aagg
17:06:24 <Zakim> -??P24
17:06:24 <Zakim> -EricP
17:06:25 <Zakim> - +0122342aahh
17:06:26 <Zakim> -ElgarPichler
17:06:29 <Zakim> - +1.410.706.aaee
17:06:31 <Zakim> -Bosse
17:06:32 <Zakim> - +0151709aaaa
17:06:35 <Zakim> -Joanne_Luciano
17:06:37 <Zakim> - +1.518.542.aacc
17:06:39 <Zakim> -Julia
17:06:41 <Zakim> SW_HCLS(TransMed)11:00AM has ended
17:06:44 <Zakim> Attendees were +0151709aaaa, +1.302.598.aabb, +1.518.542.aacc, Julia, +1.610.651.aadd, Bosse, EricP, ElgarPichler, +1.410.706.aaee, +1.414.491.aaff, +049308385aagg, +0122342aahh,
17:06:46 <Zakim> ... Joanne_Luciano
17:07:20 <ericP> Susie: will re-send f2f agenda, hilighting break-out session, and including dial-in logistics for TMO call
17:07:29 <ericP> RRSAgent, please draft minutes
17:07:29 <RRSAgent> I have made the request to generate http://www.w3.org/2009/10/29-hcls2-minutes.html ericP
18:29:29 <Zakim> Zakim has left #hcls2