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meeting record: 6 May HCLS telecon

From: Eric Prud'hommeaux <eric@w3.org>
Date: Thu, 6 May 2010 10:53:28 -0700
To: public-semweb-lifesci@w3.org
Message-ID: <20100506175327.GA28886@w3.org>


06 May 2010





          Joshua, ericP


     * [2]Topics
         1. [3]BioRDF update [Kei]
         2. [4]LODD
         3. [5]COI update
         4. [6]Scientific Discourse
         5. [7]Scientific Discourse update
         6. [8]TMO update
         7. [9]Terminology
         8. [10]SPARQL
     * [11]Summary of Action Items

   <Joshua> ok

   <ericP> scribenick: Joshua

BioRDF update [Kei]

   Kei: [giving BioRDF update]
   ... Focusing on RDF representaiton of GeneList
   ... Doing multiple iterations... Created first version by hand...
   producing OWL ontology and RDF serialization.
   ... Getting feedback and refining.

   <jluciano> nick Joanne

   Kei: Goal: Produce several queries to validate design; will drive the
   query federation use case.
   ... Trying to identify other existing ontologies that are relevant to
   this ontology? -> Should use to enable federated query.

   <ericP> kei: we're creating a demo for this sort of query

   got it, thanks

   <ericP> ... it's an i-phone app like Don's

   kei: investigating feasibility of creating I-Phone app.
   ... looking for broader collaboration with scientific discourse with
   task force
   ... any other BioRDF updates?


   <mscottm> Susie: LODD created the RDF version of Diseasome in linked
   data, Matthias has probably added it to the HCLS KB

   susie: how does RDF representation of Diseaseome relate to this.

   kei: Questions if federated query would work on linked data sets.


   susie: new adverse events data set available
   ... RxNorm dataset available on LODD
   ... future datasets - brain atlas, ...
   ... exploring tidying update connections among early data sources -
   using semantic mappings rather than syntactic
   ... upcoming work - mapping complex datasets over to RDF

   <Susie> [13]http://esw.w3.org/HCLSIG/LODD/Mapping_Experimental_Data

   susie: straightforward to convert catalog datasets to RDF - goal is to
   provide recommendations for more complicating mappings
   ... should enable federation and linking to existing LODD sources
   ... starting with Alzheimer data set
   ... are there relational schemas that are harder than mapping than
   ... what are best tools for mapping, what kind of simplification is
   appropriate, mapping to global ontologies, etc.
   ... this should inform/enable federated query use cases

   <johnM> sorry i'm late

   susie: opportunity for this group to get involved in federated query
   ... wants to produce a note about this

   kei: mapping of gene list is not complicated... more interested in
   linking with other data sets.

COI update

   <ericP> scribenick: ericP

   Joshua: working on a proof-of-concept to inform caBIG community about
   ... specifically, for expression and evaluation of clinical trial
   ... expression, debugging, and knowledge management to assist in
   ... using SWObjects to translate from Bridge (OWL) to existing patient
   recruitment models
   ... working with Helen Chen to generate proofs to validate (and help
   authoring) eligibility criteria
   ... using ERGO (samson tu)


   +Proof-of-Concept+-+Notes notes on above work

   Joshua: working on refactoring caMatch codebase (currently based on


   <mscottm> EricP: working on adding SPARQL 1.1 to SWObjects

   <mscottm> ..JNI interface to SWObjects from MIT student (for his access
   from python)

   <Joshua> scott: following up one OWL version of BRIDG

   mscottm: per COI, i'll contact cecil lynch and david ibersen hearst to
   see if they plan to release RDF version of BRIDG


   <scribe> scribenick: Joshua

   mscottm: Stephen Granite working on Cardio project - relates to query
   ... interested in EHRs and incorporating cardio charts into EHRs.
   ... could be sources of realistic data.

Scientific Discourse

Scientific Discourse update

   <mscottm> [17]http://esw.w3.org/File:SWAN-myExp-v4.jpg

   mscottm: SWAN/myExperiment ontology -> using BioRDF and OBI to link up
   with SWAN/myExperiment.
   ... looking for comments
   ... need for semantic annotation of services
   ... David Newmann - described the landscape of
   ... Taverna folks working on semantic annotation tools
   ... need approach to identifiers that will work with there Taverna code

   <mscottm> [18]http://wiki.knoesis.org/index.php/Provenir_Ontology

   mscottm: Manchester folks have some links to this work.
   ... need data source metadata in order to enable federated query use
   ... NCBO about to expose SPARQL endpoint to all content - need metadata
   to describe named graphs

   susie: We've used SMW as catalog of data sources.
   ... provides SPARQL endpoint

   mscottm: would J&J be interested to provide access/sandbox?

   susie: this was discussed workshop - don't know how sharing would work
   - could describe how it works

   mscottm: maybe this relates to vOID?

   <mscottm> [19]http://semanticweb.org/wiki/VoiD

   what about OMV?

   OMV = ontology metadata vocabulary


   ericp: Laurant might be able to help out

   kei: Any use of SMW Halo extension?

   susie: no - looks good - but not our focus

   kei: asking about expressivity of mapping supported by Halo

   susie: J&J paper provides initial investigation into mapping strategies
   ... discovered difficulties mapping to ontologies with different scope
   ... replacing the Common Resource Ontology with TMO

   mscottm: Any NCBO ontologies that could be used?

   susie: TMO seems best.. J&J will likely use this.

TMO update

   susie: evaluations at early stages
   ... health care org as payor
   ... enhancing work around representing patient info
   ... using URIs and RxNorm and ICD9 rather than xsd:string
   ... investigating VistA as UI
   ... Stonebrook assembling test data in June
   ... submission to BioOntology SIG - next paper at IHI conference
   ... patient records - Harvard has made PHR system open source
   ... Samson Tu will be presenting drug ontology
   ... Obujie presenting ont about patient records


   mscottm: Madden has provided data from Duke
   ... Jason S. from SmartHealthData, data sharing effort may give us
   access to test data - Carolina Data Warehouse for Health

   <mscottm> [21]http://www.dbmi.pitt.edu/faculty/crowley.html

   <johnM> Hi guys, I had to step away for a few minutes...

   <mscottm> [22]http://caties.cabig.upmc.edu/

   mscottm: Rebecca Crowley has data sharing effort with anonymized
   clinical data, may be good source for demo data.

   ericp: RIF has gone to Proposed Recommendation


   ericp: SPARQL Federation will be auxilliary to Query 1.1?
   ... query federation docs done by Eric may be included as auxilliary
   doc to SPARQL Query 1.1 spec

Summary of Action Items

   [End of minutes]

    Minutes formatted by David Booth's [23]scribe.perl version 1.135
    ([24]CVS log)
    $Date: 2010/05/06 17:50:20 $


   1. http://www.w3.org/
   2. http://www.w3.org/2010/05/06-hcls-minutes#agenda
   3. http://www.w3.org/2010/05/06-hcls-minutes#item01
   4. http://www.w3.org/2010/05/06-hcls-minutes#item02
   5. http://www.w3.org/2010/05/06-hcls-minutes#item03
   6. http://www.w3.org/2010/05/06-hcls-minutes#item04
   7. http://www.w3.org/2010/05/06-hcls-minutes#item05
   8. http://www.w3.org/2010/05/06-hcls-minutes#item06
   9. http://www.w3.org/2010/05/06-hcls-minutes#item07
  10. http://www.w3.org/2010/05/06-hcls-minutes#item08
  11. http://www.w3.org/2010/05/06-hcls-minutes#ActionSummary
  12. http://ibl.mdanderson.org/~mhdeus/sparql_federation/endpoint.php
  13. http://esw.w3.org/HCLSIG/LODD/Mapping_Experimental_Data
  14. https://wiki.nci.nih.gov/display/VCDE/Protocol+Eligibility+Criteria+Proof-of-Concept+-+Notes
  15. https://wiki.nci.nih.gov/display/VCDE/Protocol+Eligibility+Criteria+Proof-of-Concept+-+Notes
  16. http://wiki.cvrgrid.org/index.php/CVRG_iGoogle_Federated_Query_Gadget
  17. http://esw.w3.org/File:SWAN-myExp-v4.jpg
  18. http://wiki.knoesis.org/index.php/Provenir_Ontology
  19. http://semanticweb.org/wiki/VoiD
  20. http://sourceforge.net/projects/omv2/
  21. http://www.dbmi.pitt.edu/faculty/crowley.html
  22. http://caties.cabig.upmc.edu/
  23. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
  24. http://dev.w3.org/cvsweb/2002/scribe/

Received on Thursday, 6 May 2010 17:54:13 UTC

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