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Meeting Record Clinical Decision Support for Personalized Medicine Task Force 8 March 2012

From: Eric Prud'hommeaux <eric@w3.org>
Date: Thu, 8 Mar 2012 12:15:18 -0500
To: Matthias Samwald <matthias.samwald@meduniwien.ac.at>, public-semweb-lifesci@w3.org
Cc: Russ Altman <russ.altman@stanford.edu>, Nigam Shah <nigam@stanford.edu>, Allan Hanbury <hanbury@ifs.tuwien.ac.at>, Peter Tonellato <peter_tonellato@hms.harvard.edu>, Holger Stenzhorn <holger.stenzhorn@uks.eu>, Benjamin Good <ben.mcgee.good@gmail.com>, Michael Cariaso <cariaso@gmail.com>, Kensaku Kawamoto <kensaku.kawamoto@utah.edu>, Dirk Colaert <dirk.colaert@agfa.com>, Peter Robinson <peter.robinson@charite.de>, Vassil Momtchev <vassil.momtchev@ontotext.com>, Holger Knublauch <holger@knublauch.com>, Markus Bundschus <markus.bundschus@roche.com>, Gökhan Karakülah <gokhanism@gmail.com>, Michel_Dumontier <Michel_Dumontier@carleton.ca>, Charlie Mead <meadch@mail.nih.gov>, "M. Scott Marshall" <mscottmarshall@gmail.com>
Message-ID: <20120308171516.GC7403@w3.org>


                      W3C HCLS - Clinical Decision Support

08 Mar 2012




          Matthias Samwald



     * [2]Topics
     * [3]Summary of Action Items

   <egombocz> works - (I'm the 510-705...)

   <Khan> [IPcaller.a], +1.954.633.aacc might be me

   Khan: intro from [4]Atif Khan

   alan hanburry

   <scribe> scribenick: ericP

   alanH: colleague of matthias in vienna

   <matthias_samwald> mcariaso: are you on the call now?

   <cariaso_SNPedia> no, my local DNS is ailing

   peterRobinson: geneticist and informaticist in Berlin, modelling human
   phenotypes in disease

   <mscottm2> Hi Michael Cariaso! (Michael wasn't it?) We met at BioIT
   World Hannover 2009.

   matthias_samwald: welcome to the new CDS task force
   ... this is part of the W3C Semantic Web for Health Care and Life
   Sciences Interest Group
   ... this is the 3rd iteration of the IG

   <Joanne_Luciano> Intro: [5]http://tw.rpi.edu/web/person/JoanneLuciano -
   Research Assoc Prof at Tetherless World Constellation, Rensselaer
   Polytechnic Institute, Troy NY USA, multidisciplinary (math, comp sci,
   neurosci, molecular bio, web science) multiple disease areas

   matthias_samwald: we've explored how semantic technologies can be used
   to drive progress in basic biological research, applied pharmaceutical
   R&D and health care
   ... driving motivation is to bridge the gap between bilological
   research and clinical application
   ... in 2007, the group created one of the first large-scale RDF repo,
   with several hundred million triples
   ... we've seen uptake of these technologies in large scale systems in
   ... Translational Medicine Ontology Task Force bridged pharma research
   and therapies
   ... we made progress in mapping research to drug development leads
   ... the way drugs are developed is changing as it's becoming harder to
   bring drugs to market

   <michel> Intro: Michel Dumontier - W3C HCLS Chair, Associate Professor
   @ Carleton University; Interest in increased understanding of medical
   biochemistry through biomedical knowledge representation and reasoning.

   matthias_samwald: the drugs on the market are helping only a fraction
   of the people, and are harming a fraction as well

   <mscottm2> if you don't have mute on your phone (or know how to use
   it), try these touchtone sequences: Mute: 61# , Unmute: 60#

   matthias_samwald: "Translational Medicine" is a trendy word which is
   about using genetic markets to tailor therapies
   ... e.g. predicting adverse events to a particular compound in a
   particular individual
   ... TM hasn't been widely adopted because it's hard to juggle the
   hundreds of markers
   ... the CDS Task Force's hypothesis is that computing infrastructure
   will be important to helping doctors response to markers
   ... we are taking a step from building drug development KBs to KBs to
   help with drug selection or treatment choice
   ... we'll create prototypical implementations
   ... there are several ways to create decision support apps, e.g. HL7's
   OpenCDS which uses rules engines, it's valuable to explore how the
   Semantic Web stack can be more flexible and connect to large KBs

   <matthias_samwald> [6]http://www.w3.org/wiki/HCLSIG/CDS

   matthias_samwald: this is summarized in the CDS wiki page
   ... we have 3 listed use cases which are suggestions for task force
   ... UC1 has uses LODD and patient data to propose medications
   ... UC2 connects SemWeb stuff to OpenCDS to provide a standard
   interface for CDS
   ... UC3 connects and enhances cancer data to create a "living review"
   ... that was an overview of the proposals. would like to hear how this
   can be connected to your projects
   ... we'd like a demo and a bioinformatics paper for each of the use

   Atif Khan: at U Waterloo

   <Khan> Atif Khan

   scribe: constructing a CDS system which incorporates SemWeb and
   machine-learning techniques
   ... most CDS systems don't have access to all the available knowledge
   ... when you remove some of the information, the performance of CDS
   systems degrades rapidly
   ... just came back from IHI where we compared SemWeb and
   machine-learning systems

   <Khan> CDC BRFSS

   ericP: it sounds like you have some investment in what we want to do:
   DB, rules

   Khan: CDC BRFSS has around 450K individuals with 450+ features
   ... we were looking for info which have holes in them [incomplete]
   ... medical records are multi-dimensional, with reports on different
   ... we worked on the 2010 edition of CDC BRFSS
   ... you can download it
   ... we needed to RDF-ize it ourselves
   ... we worked with a local physician to help us model a prescription
   protocol (e.g. if you're pregnant, don't take X) from Mayo clinic

   Michael K: work on SNPpedia, incorporating 23andMe etc. to allow people
   to dig deaper into their genome

   scribe: thanks to upstream data sources
   ... we're not trying to be the source or validator, just integrator

   matthias_samwald: SNPedia uses semantic media wiki

   <Lena> (long live the linked data geeks :D )

   matthias_samwald: exposing some of the data in RDF

   Michael K: it was a recognized plus, but it wasn't our decision feature

   scribe: we used to have a SPARQL back end which wasn't getting much use
   but was doubling the memory footprint so i turned it off
   ... i'm on the board of semantic mediawiki foundation
   ... also wikidata

   <cariaso_SNPedia> [8]http://meta.wikimedia.org/wiki/Wikidata

   matthias_samwald: interested in extending the RDF available?
   ... the goal being to integrate that data with the cloud of e.g. drug

   Michael C: afraid of a snapshot because our data is dynamic

   scribe: i presume what you want is already there, unless you want extra

   matthias_samwald: some is in RDF but some isn't
   ... not sure this requires changes to SMW vs. just adding markup to the

   Michael C: may be opaque to us

   scribe: for each paper, what's the key gene, what are the pathways,
   etc, that's not avail
   ... we need folks to write [[pathway foo]]...
   ... happy to help with feature reqs, suspect that we just need more
   ... so this is a call to the community
   ... happy to improve templates

   peterRobinson: we've developed the human phenotype ontology
   ... OBO ontology with about 10K isa terms
   ... being used by databases at NCBI and Sanger
   ... we've used the OWL representation
   ... we have a "phenomizer" product
   ... would love to have access to more data

   <cariaso_SNPedia> minor clarifications, now that I can read the
   transcript (I'm on the foundation for Semantic Mediawiki . which is
   more correctly known as OSDA
   [9]http://semantic-mediawiki.org/wiki/Open_Semantic_Data_Association )

   <cariaso_SNPedia> I'm also (probably) part of the wikidata project, but
   there is no foundation. Its purely in the to-be-coded stage.

   peterRobinson: in human genetics there are about 10 features
   ... mostly people type these into Google
   ... we've used semantic similarity searches on the ontology graph
   ... as a physician, it's hard to find resources for rare diseases on
   ... would like to say "patient with disease X, complication Y and
   genotype Z"
   ... would like to predict drug side-effects
   ... as genomics data increases, what's the best combo of drugs

   matthias_samwald: would be great to find common ground in terms of
   representation and format
   ... michel's group is using the same technologies, with mappable

   <Lena> ericP: "all standards are a popularity contest"

   <Lena> ericP: irc.w3.org

   matthias_samwald: the work we do here should be goal-oriented

   <Khan> Two quick questions:

   matthias_samwald: the goal isn't so much to have chats as to produce
   prototypes and document them in scientific journals

   <Khan> 1. Clinical decision support target users?

   <Khan> 2. What are some of the desired features of a CDS from an end
   user's prospective?

   Khan, the COI use case was mostly patient recruitment

   <Khan> ok- thanks

   Khan, re: desired features of a CDS, my non-authoritative perspective
   is that we need to have actionable information gathered from
   integrative queries and inferences

   matthias_samwald: CDS task force is connected to pharmacogenomics TF,
   both in intent and data

   next telecon: 2 weeks

Summary of Action Items

   [End of minutes]

    Minutes formatted by David Booth's [10]scribe.perl version 1.136
    ([11]CVS log)
    $Date: 2012/03/08 17:12:40 $


   1. http://www.w3.org/
   2. http://www.w3.org/2012/03/08-hcls-minutes#agenda
   3. http://www.w3.org/2012/03/08-hcls-minutes#ActionSummary
   4. http://cs.uwaterloo.ca/~a78khan
   5. http://tw.rpi.edu/web/person/JoanneLuciano
   6. http://www.w3.org/wiki/HCLSIG/CDS
   7. http://www.w3.org/wiki/HCLSIG/CDS>
   8. http://meta.wikimedia.org/wiki/Wikidata
   9. http://semantic-mediawiki.org/wiki/Open_Semantic_Data_Association
  10. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
  11. http://dev.w3.org/cvsweb/2002/scribe/
Received on Thursday, 8 March 2012 17:15:53 UTC

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