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HCLS Task Force Chairs meeting record

From: Eric Prud'hommeaux <eric@w3.org>
Date: Mon, 6 Jul 2009 10:27:20 -0400
To: public-semweb-lifesci@w3.org
Message-ID: <20090706142720.GA6387@w3.org>

                             HCLS Task Force Chairs

06 Jul 2009

   See also: [2]IRC log


          Scott_Marshall, Susie Stephens, Tim Clark, Vipul, John_Madden,
          EricP, Kei_Cheung, Kei





     * [3]Topics
         1. [4]COI [Vipul]
         2. [5]Terminology [JohnM]
         3. [6]BioRDF [kei]
         4. [7]LODD
         5. [8]translational medicine ont
         6. [9]scientific discourse
         7. [10]TPAC
     * [11]Summary of Action Items

   <scribe> scribenick: ericP

COI [Vipul]

   vipul: Rachel gave talk at AMIA -- big success
   ... also submitted for anual symposium and @@1
   ... Helen is sketching out patient privacy
   ... need to coord with John Madden
   ... patient privacy crosses task forces

   ericP: we were supposed to have sent an abstract a month before

   Susie: and other tracks, like in-use?

   ericP: in-use seemed to be (according to the chair) more deployed stuff

   vipul: i expect security/policy will get a life of its own
   ... (just by the size of it)
   ... i would be participating from the payer perspective
   ... key issue is rallying the momentum

   susie: so ericP's techy presentation during the main call was related

   vipul: like with COI, we need to give ericP real use cases to give them
   more impact

   susie: CIO of lilly is interested, but timing was off for the call
   ... he was meant to be writing use cases, worth prodding him

   mscottm: COI has a great demo for pharma

   vipul: it would be great to make sure everyone can use the demo

   mscottm: i've been focusing my 1.5min demo on AIDA, but should demo COI
   ... any chance of getting an intrest group note out?

   vipul: good point, with feedback, questions from the audience...

   <scribe> ACTION: Susie to forward relevent invites to adrian sechum
   [recorded in

Terminology [JohnM]

   John: SKOS on a bit of a haietus (SP?)
   ... but progress with mscottm which i haven't seen
   ... interest and progress on privacy front
   ... we have permission to reveal some of our patient pathology data via
   d2r if we have appropriate protection
   ... have to install ericP's software and hook it up to our database
   ... did a poster at AMIA spring meeting in Orlando
   ... big emphasis on GRDDL and transforms
   ... attendance was thin -- only got attention from Peter Elkin
   ... Rachel said that kent spackman and ohter ihdo folks are releasing
   an OWL-ized version of SNOMED

   ericP: would be good to connect Peter @@2 (Kaiser) with IHDO initiative

   Susie: a paper with pro's (above) and con's (from JohnM) would be good

   JohnM: HHS secretary asked a bunch of us to write a use cases in
   pathology white paper
   ... Mary Kennedy and I wrote up the paper. in editing cycle now
   ... tried to emphasize the benefits of common identifiers in health
   care field, specifically IRIs
   ... + chapter on SNOMED and OWL
   ... + chapter on higher levels of interop
   ... can consider it a contribution of W3C

   mscottm: at f2f, harold solbrig showed interest

   JohnM: expect he's really busy, need to chase him down

   mscottm: randy raymond right called once

   <mscottm> [13]http://ii4sm.com/

   <mscottm> [14]http://hcls.deri.org/coi/demo/

   mscottm: if folks remember other folks like these, let's put them in a

BioRDF [kei]

   <mscottm> DILS

   kei: Data Integration in Life Science paper submitted

   <mscottm> Data Integration in the Life Sciences

   kei: collab between LODD and BioRDF task forces
   ... submitted a poster
   ... ania, june, matthias have been working on this poster
   ... converted the @@3 database into RDF
   ... june will release it when it's clean
   ... couple weeks before the deadline arrives

   <mscottm> huajun chen

   kei: hujun chen's keen to integrate western med data and easter herbal
   ... hard for him to participate (time zone) - may need to accomodate
   ... </update on TCM>
   ... considering extension of Query Federation
   ... have a paper BioInformatics - editor is working on it
   ... don't have final pub date
   ... could continue with more data
   ... discussed image data, microarray data...
   ... can also consider upper-level meta-data to guide query federation
   ... in our last attempted, we hard-coded the query plan
   ... so extensions could use meta-data to generate that plan
   ... can extend AIDA or FeDeRate to use this meta-data

   mscottm: do you see opportunites for an interest group note?

   kei: perhaps in terms of query federation

   ericP: i expet that most fora don't want papers to have dual-submission
   so may have to choose between IG note vs. peer-reviewed paper

   mscottm: hclskb note is a counter-example


   Susie: workign with jun and anya to add TCM data source
   ... also working on Slider
   ... have the joint poster with BioRDF at DILS
   ... working on a paper for iTriplify challenge
   ... Bosse and I [Susie] working on the use case
   ... e.g. what drug targets do these herbs work against vs. conventional
   ... e.g. comparing side-effects

translational medicine ont

   UNKNOWN_SPEAKER: goal was to create this high-level domain which one
   could plug data into so we could ask questions
   ... based upon the questions, we have 113 entities that could be in the
   ont -- weeding out duplications and subtle overlaps (e.g. compound vs.
   entire drug)
   ... we're defining used cases in Xgenomics
   ... once we select a use case, we'll roll out a demo based on those use
   ... so we're likely to want to include some pharma data

scientific discourse

   timC: lots of side collaborations
   ... paolo and alex will be posting IG notes for SWAN/SIOC integration
   ... expect to talk with peter buckingham about it
   ... now discussing the semantics of annotation
   ... e.g. asserted links to terminology
   ... need to be open and available in RDF as well
   ... working with mary ann martone on aligning with the model

   mscottm: touches with matthias's work on aTags
   ... other tasks where annotation is the next step
   ... want to create different provenance models when you create the
   ... e.g. who said it when

   timC: would be interested to work on this as a joint task
   ... depends on where matthias wants to work on aTags
   ... i think matthias is cautious about getting to theoretical

   mscottm: need to find out if matthias is intersted in the non-manual
   annotations (or stuff supplied by wikiprofessional)

   kei: can we integrate this with federation

   timC: our core job is to get the model right
   ... then folks can apply what ever processing they want
   ... my interest is semi-automatic annotation of web content

   mscottm: one unifying app would be:
   ... .. create an aTag
   ... .. federate that with the SWAN data so you can view it as an
   assertion by the asserter

   timC: i think there a few intersting apps
   ... would like to create an uber-task around september


   Susie: 2-6 Nov in Santa Clara
   ... we meet 2-3 Nov
   ... need agendas from the task force leads
   ... captured the main ideas for future work on the wiki (6 bullets)

Summary of Action Items

   [NEW] ACTION: Susie to forward relevent invites to adrian sechum
   [recorded in

   [End of minutes]

    Minutes formatted by David Booth's [16]scribe.perl version 1.135
    ([17]CVS log)
    $Date: 2009/07/06 14:20:42 $


   1. http://www.w3.org/
   2. http://www.w3.org/2009/07/06-hclschairs-irc
   3. http://www.w3.org/2009/07/06-hclschairs-minutes#agenda
   4. http://www.w3.org/2009/07/06-hclschairs-minutes#item00
   5. http://www.w3.org/2009/07/06-hclschairs-minutes#item01
   6. http://www.w3.org/2009/07/06-hclschairs-minutes#item02
   7. http://www.w3.org/2009/07/06-hclschairs-minutes#item03
   8. http://www.w3.org/2009/07/06-hclschairs-minutes#item04
   9. http://www.w3.org/2009/07/06-hclschairs-minutes#item05
  10. http://www.w3.org/2009/07/06-hclschairs-minutes#item06
  11. http://www.w3.org/2009/07/06-hclschairs-minutes#ActionSummary
  12. http://www.w3.org/2009/07/06-hclschairs-minutes.html#action01
  13. http://ii4sm.com/
  14. http://hcls.deri.org/coi/demo/
  15. http://www.w3.org/2009/07/06-hclschairs-minutes.html#action01
  16. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
  17. http://dev.w3.org/cvsweb/2002/scribe/


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