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HCLS meeting record: 2008-06-12

From: Eric Prud'hommeaux <eric@w3.org>
Date: Thu, 12 Jun 2008 14:55:02 -0400
To: public-semweb-lifesci@w3.org
Message-ID: <20080612185502.GT5591@w3.org>
http://www.w3.org/2008/06/12-hcls-minutes

                                      HCLS

12 Jun 2008

   See also: [2]IRC log

Attendees

   Present
          Chime, Susie, Scott, EricP, +~25 folks

   Regrets
   Chair
          Susie Stephends

   Scribe
          ericP

Contents

     * [3]Topics
         1. [4]Introduction to Co-chairs and Team contact - Chime, Scott,
            Susie
         2. [5]Group Structure - Scott
         3. [6]Participation Expectations - Susie
         4. [7]roll call
         5. [8]Charter Overview - Chime
         6. [9]Proposed Projects - Chime, Scott, Susie
         7. [10]Q&A
     * [11]Summary of Action Items
     __________________________________________________________________

Introduction to Co-chairs and Team contact - Chime, Scott, Susie

     * [12]HCLSIG Wiki Home Page
     * [13]Introductions Wiki Page

   Susie: principal research scientist at Eli Lilly
   ... involved in RDF since 2002
   ... chaired BioRDF

   chimezie: lead architect on SemanticDB at Cleveland Clinic

   mscottm: postdoc researcher at Univ AMS

   mscottm: work with lab for E-Science on knowledge management/capture
   ... involted with semweb
   ... compsci background, who has worked with biologists for a while

   <Susie> Eric Prud'hommeaux sem web since 98, and team contact at W3C

   <Susie> Happy to help with questions

   Susie: encourage folks to post their intros on the wiki

Group Structure - Scott

     * [14]integration of many data sources to answer scientific queries
     * [15]TPAC Schedule
     * [16]Main HCLS Mailing List
     * [17]these minutes

   mscottm: in 2002 there was a big meeting where people aired what they
   wanted out of the SemWeb in the areas of health care and life sciences

   mscottm: an ambitious group, focused on data integration in health
   care, life science, biological modeling, tranlsational medicine

   mscottm: crosses many databases

   mscottm: first incarnation of the group started several task forces
   around areas of work
   ... in this incarnation, we expect to have several projects with weekly
   calls
   ... continuing from last charter, we have BioRDF task force and
   Clinical Observations Interoperability
   ... would like to gather project descriptions
   ... face to face meeting: 20-21Oct during the W3C Technical Plenary

   mscottm: meeting is in Mandelieu

   ericP: How do you manage a phone call with 40 or 50 people? We use IRC
   and some derivative of Robert's Rules of Order.
   ... we have a web-based IRC client which is available to Members and
   Invited Experts (more later)

   <eneumann> Anyone except Susie from pharma on this call?

   <mscottm> Therese Vachon from Novartis might show up when another TC is
   done.

   <Zakim> ericP, you wanted to say something clever

   ericP: there are some other tricks for managing agenda and that sort of
   thing.

   <AdrianP> Hi, just joined

   <mscottm> Hi Adrian

   ericP: The W3C site is backed by a revision control system called CVS.
   ... A lot of these documents are edited by elected editors, responding
   to comments in publc mailing lists.
   ... Wiki's have their own form of concensus (most prolific wins).
   ... So W3C also has wiki space for things which invite that group
   dynamic.
   ... W3C is a member-based industry consortium
   ... that is, we invite participation from folks appointed by
   representatives of the various members.
   ... for this group, we'll have lots of invited experts

   susie: note the email alias team-hcls-chairs

   <mscottm> team-hcls-chairs@w3.org

Participation Expectations - Susie

   susie: work expectations:
   ... .. participation is public, but we expect the majority will be
   members of W3C
   ... .. non-members can explore the IE path

   <mscottm> IE = "Invited Expert"

   susie: .. better to be a member, access to more resources
   ... .. we'll be pruning the mail list shortly to include members and
   IEs
   ... .. would recommend assigning a minimum of 10% time to the group
   ... .. appreciate that work preempts
   ... .. there will be less exploration than the first HCLS group; we
   expect the participants to be able to work on deliverabless
   ... .. deliverables will include conferences and papers
   ... .. meeting records will document action items, decisions, ...
   ... commitments:
   ... .. it's important to be clear when you can do something
   ... .. also important to respect other participants at all levels
   ... .. [ref Postel's Law]

   -> [18]http://en.wikipedia.org/wiki/Postel's_law Postel's Law

   susie: i expect that following these guidelines will make a productive
   group

Charter Overview - Chime

     * [19]Health care and Life Sciences Interest Group (New) Charter

   chimezie: Charter defines the mandiate and scope of an interest group
   ... scope, goals, deliverables, liasons
   ... goals:
   ... .. 1st: advocate, develop tools, and suporting documents for SemWeb
   in health care, life science
   ... .. document use cases
   ... use cases useful for defining what we need to do and when we've
   succeeded
   ... will develop implementations that meet these use cases
   ... develop high-level vocabularies
   ... diseminate this info to govornments, other bodies...
   ... charter lays out separation of the primary domains of this group:
   biology, health care, trans therap
   ... primary value proposition is in integrating diverse databases
   ... Trans Therapeutics: working on "bench to bedside": preclinical
   trial data to affect patient medication
   ... health care
   ... coordiation with other groups:
   ... .. many of the standards in this area are sill develping

   <AdrianP> would propose a liaison with W3C RIF

   chimezie: another group to liase with is RIF

   [20]RIF WG

   <AdrianP> yes, we are working on such use cases

   <AdrianP> e.g.
   [21]http://www.w3.org/2005/rules/wiki/UCR#Ruleset_Integration_for_Medic
   al_Decision_Support

   chimezie: relevent recently closed groups: SPARQL, GRDDL
   ... this IG is charterd for 3 years (starting 1 June)
   ... want to work with HL7, CDISC, those managing SNOMED -GT

   eneumann: lots of nearby activities that aren't SemWeb-based
   ... the folks working BRIDG wanted to get more involved
   ... BRIDG working with CDISC, HL7, National Cancer Instituted
   ... they are now aware that there is an OWL version of BRIDG

   chimezie: how does these liasons work
   ... we often invite them to speak to tasks forces

   marco: how open are you to new use cases?
   ... if you work 10% of your time, it needs to be in sync with your
   interests

Proposed Projects - Chime, Scott, Susie

   susie: acknoweldging the need for synergy beteen HCLS participation and
   day jobs, we've selected some tasks

   <chimezie> [22]Project Ideas

   susie: we ask your advice on these tasks and invite new proposals
   ... if there projects that you are working on, you may enter it in the
   wiki page (Project Ideas)

   <AdrianP> I already started to add to this projects

   susie: alternatively, you can send email to the
   public-semweb-lifesci@w3.org list, or to the team-hcls-chairs@w3.org if
   you just want input from the chairs

   tx AdrianP

   <mscottm>
   [23]http://esw.w3.org/topic/HCLS/ClinicalObservationsInteroperability

   chimezie: Clinical Osbervations Interoperability task force (ongoing)
   lead by Vipul
   ... re-purposing existing clinical models and developing new ones
   ... lots of recent activity

   susie: Vipul will give us a 20 minute overview during the next HCLS
   call (2 weeks from today)

   chimezie: we encourage SNOMED to distribute in OWL

   <mscottm>
   [24]http://esw.w3.org/topic/HCLSIG/Project_Ideas/DecisionSupportRuleLan
   guages

   <mscottm> oops - this one:
   [25]http://esw.w3.org/topic/HCLSIG/Project_Ideas/DecisionSupportRuleLan
   guages

   chimezie: ISTC is now planning to distribute as a secondary deployment
   ... RIF is a language for exchanging rules
   ... we can give them use cases in the area of Clinical Decision Support
   ... we can see how well these rules can support these use cases
   ... [task] identify archetypal data that comes up a lot in health care
   scenarios to push for standards in those small areas of KR

   AdrianP: [editor of the RIF UC&R document] I can easily add your use
   cases to the UC&R doc

   susie: CDISC creates clinical interchange standards approved by the FDA

   <mscottm> [26]http://esw.w3.org/topic/HCLSIG/Project_Ideas/CDISC

   susie: [task] work with CDISC to create ontology of data elements
   withing the SDTM
   ... [task] (similar to drug safety and efficacy) labeling and modeling
   biomarkers

   <mscottm>
   [27]http://esw.w3.org/topic/HCLSIG/Project_Ideas/ClinicalTrials

   <AdrianP> I'm also working on several use cases which exploit rules in
   HCLS

   susie: [task] clinicaltrials.gov documents clinical trials around the
   world
   ... lillytrials.com includes lilly trials
   ... FDA publishes the Orange Book
   ... sometimes the data is available in HTML
   ... sometimes it's all trapped in PDFs
   ... project would involve picking a therapeutic area to mining the data
   in those papers
   ... [task] diseasome written up in nature, new england journal of
   medicine
   ... barabassy interested in working with us to publish diseasome in
   RDF/OWL
   ... [task] how can SIOC benifit the scientific/medical communities?

   <mscottm> [28]http://esw.w3.org/topic/HCLSIG/Project_Ideas/Diseasome

   susie: this has become a big focus area for lots of folks

   <mscottm> [29]http://esw.w3.org/topic/HCLSIG/Project_Ideas/SIOC

   susie: harvard just won a large grant for this
   ... create a graph of who's publishing with whom

   <mscottm> [30]http://esw.w3.org/topic/HCLSIG/Project_Ideas/PCMR

   susie: [task] (less certain how to persue this just now) personally
   managed health care records
   ... clinical trials subjects get their genome scanned, but don't keep
   that information
   ... both google and microsoft are working on storage for this area
   ... we can be ahead of the curve (or leading edge) on this

   mscottm: [covering life science/bio projects]
   ... some of these could form basis of projects that have already be
   defined

   <mscottm> [31]http://esw.w3.org/topic/HCLSIG/Project_Ideas/KB

   mscottm: my top interest is enchancing the HCLS Knowledge Base
   ... could include adding diseasome data from barabassy
   ... would this find genetic reasons for diseases that are related to
   each other'
   ... [project] add chemical structures (KB currently biased towards
   neurology)
   ... can add other things like anatomy and physiology
   ... [task] distribution of the KB across multiple locations
   ... fairly challenging, people ask "can it be distributed?"

   <AdrianP> we could probably host another triple store here at the
   Biotec Center in Dresden

   mscottm: require nitty gritty work on query engines

   <AdrianP> or a verbalized language, a controlled english interface

   mscottm: [task] enhance the query interface to make it easier to
   compose queries without having to know all the namespaces

   mscottm: similarly to getting to know the contents of a KB requires the
   same work

   <mscottm> [32]http://www.w3.org/TR/2008/NOTE-hcls-senselab-20080604/

   <kidehen_> ericP: Does a query interface exist?

   <ericP> kidehen_, only have SPARQL endpoints so far

   <kidehen_> ericP: is the a link to something I can see?

   <kidehen_> ericP: s/the/there

   <mscottm> [33]http://esw.w3.org/topic/HCLSIG/Project_Ideas/eScience

   <matthiassamwald> kidehen_, some of us have built UIs that access parts
   of the Knowledge Base, such as Entrez Neuron:
   [34]http://neuroweb3.med.yale.edu:8090/

   <ericP> kidehen_, i think it's in the hcls-kb doc

   mscottm: [task] add e-science to our work, including grid computing

   mscottm: web services are a way for us to collaborate
   ... you can use Taverna (SP?) to compose workflows out of multiple web
   services

   <mscottm> [35]http://myexperiment.org/

   mscottm: sharing workflows is getting easier
   ... you can trigger web services by clicking on something on a web page
   ... should look for synergy between these projects and other HCLS
   projects

   <AdrianP> there is a synergy with the Rule Responder project, which
   allows to describe rule-based workflows

   mscottm: e.g. exporting diseasome in RDF would be usefully shared
   ... e-science allows you to, e.g. export text-mined medline in RDF --
   surprisingly in-reach

   <matthiassamwald> shameless self-promotion of a prototype RDF/OWL
   wrapper for a text mining service:
   [36]http://whatizit.neurocommons.org/

   mscottm: main questions are "how do you wnat to represent the info, and
   how would you clean it up"

   <mscottm>
   [37]http://esw.w3.org/topic/HCLSIG/Project_Ideas/SemanticWikis

   mscottm: also want to explore the use of semantic wikis

   <dingl> we may look at some work on semantic media wiki at RPI

   <dingl> [38]http://tw.rpi.edu/wiki/index.php/Main_Page

Q&A

   AdrianP: how do we get folks to work on a project?

   susie: document the project, and if there's sufficient interest, off
   you go
   ... the lead person will pick task force meeting times, and report
   during the HCLS calls
   ... these projects will have indepencence and their own lifespan
   ... expect most to be done within a year

   mscottm: if you have project ideas, try to keep in mind that synergy
   with other projects helps your goal
   ... helps to aim for a particlar demo/implementation

   kei: could expand the KB with, e.g. herbal medicine
   ... china has dbs about these herbs

   ericP: I expect that Huajun will be spearheading something like that

   <Huajun> yes, I am working with kei together on this project actually

   susie: western pharmaceuticals are interested in easter meds

   <matthiassamwald> [39]http://richard.cyganiak.de/2007/10/lod/

   matthiassamwald: would be great aim to turn our projects into something
   that creates a coherent datastructure
   ... many independent participants in linked open data follow some rules
   to create an aggregated project

   susie: reminds me that we'd like projects with common threads through
   the different silos
   ... don't want isolated projects; want to bridge them all together
   ... don't expect they'll all link together right from the start, but if
   you use e.g. the same compound as an example, we can link them together

   Next call: two weeks June 26

   susie: tx to all participants, tx for your participation

Summary of Action Items

   [End of minutes]
     __________________________________________________________________


    Minutes formatted by David Booth's [40]scribe.perl version 1.133
    ([41]CVS log)
    $Date: 2008/06/12 18:53:34 $

References

   1. http://www.w3.org/
   2. http://www.w3.org/2008/06/12-hcls-irc
   3. http://www.w3.org/2008/06/12-hcls-minutes#agenda
   4. http://www.w3.org/2008/06/12-hcls-minutes#item01
   5. http://www.w3.org/2008/06/12-hcls-minutes#item02
   6. http://www.w3.org/2008/06/12-hcls-minutes#item03
   7. http://www.w3.org/2008/06/12-hcls-minutes#item04
   8. http://www.w3.org/2008/06/12-hcls-minutes#item05
   9. http://www.w3.org/2008/06/12-hcls-minutes#item06
  10. http://www.w3.org/2008/06/12-hcls-minutes#item07
  11. http://www.w3.org/2008/06/12-hcls-minutes#ActionSummary
  12. http://esw.w3.org/topic/HCLSIG
  13. http://esw.w3.org/topic/Introductions
  14. http://www.w3.org/TR/hcls-kb/
  15. http://www.w3.org/2008/10/TPAC/Schedule
  16. http://lists.w3.org/Archives/Public/public-semweb-lifesci/
  17. http://www.w3.org/2008/06/12-hcls-minutes
  18. http://en.wikipedia.org/wiki/Postel's_law
  19. http://www.w3.org/2008/05/HCLSIGCharter
  20. http://www.w3.org/2005/rules/wiki/RIF_Working_Group
  21. http://www.w3.org/2005/rules/wiki/UCR#Ruleset_Integration_for_Medical_Decision_Support
  22. http://esw.w3.org/topic/HCLSIG/Project_Ideas
  23. http://esw.w3.org/topic/HCLS/ClinicalObservationsInteroperability
  24. http://esw.w3.org/topic/HCLSIG/Project_Ideas/DecisionSupportRuleLanguages
  25. http://esw.w3.org/topic/HCLSIG/Project_Ideas/DecisionSupportRuleLanguages
  26. http://esw.w3.org/topic/HCLSIG/Project_Ideas/CDISC
  27. http://esw.w3.org/topic/HCLSIG/Project_Ideas/ClinicalTrials
  28. http://esw.w3.org/topic/HCLSIG/Project_Ideas/Diseasome
  29. http://esw.w3.org/topic/HCLSIG/Project_Ideas/SIOC
  30. http://esw.w3.org/topic/HCLSIG/Project_Ideas/PCMR
  31. http://esw.w3.org/topic/HCLSIG/Project_Ideas/KB
  32. http://www.w3.org/TR/2008/NOTE-hcls-senselab-20080604/
  33. http://esw.w3.org/topic/HCLSIG/Project_Ideas/eScience
  34. http://neuroweb3.med.yale.edu:8090/
  35. http://myexperiment.org/
  36. http://whatizit.neurocommons.org/
  37. http://esw.w3.org/topic/HCLSIG/Project_Ideas/SemanticWikis
  38. http://tw.rpi.edu/wiki/index.php/Main_Page
  39. http://richard.cyganiak.de/2007/10/lod/
  40. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
  41. http://dev.w3.org/cvsweb/2002/scribe/
-- 
-eric

office: +1.617.258.5741 32-G528, MIT, Cambridge, MA 02144 USA
mobile: +1.617.599.3509

(eric@w3.org)
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Received on Thursday, 12 June 2008 18:55:42 GMT

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