HCLSIG/Meetings/2010-05-06 Conference Call

Conference Details

• Date of Call: Thursday May 6, 2010
• Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 British Summer Time (BST), 17:00 Central European Time (CET)
• Dial-In #: +1.617.761.6200 (Cambridge, MA)
• Dial-In #: +33.4.89.06.34.99 (Nice, France)
• Dial-In #: +44.117.370.6152 (Bristol, UK)
• Participant Access Code: 4257 ("HCLS").
• IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Click on mibbit for instant IRC access.
• Duration: ~1h
• Convener: Scott
• Scribe: EricP

Agenda

• Updates by BioRDF, Terminology, COI, LODD, Translational Medicine Ontology, Scientific Discourse - All
• Followup discussion HCLS Gatherings Boston & Raleigh - All
• Grant opportunities - All
• W3C Standards update: SPARQL, OWL2, RDB2RDF, Provenance - Eric
• AOB

Minutes

See also http://www.w3.org/2010/05/06-hcls-minutes

                                    HCLS

06 May 2010

Attendees

 Present

 Regrets

 Chair
        mscottm

 Scribe
        Joshua, ericP

Contents

   * [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>
 [12]http://ibl.mdanderson.org/~mhdeus/sparql_federation/endpoint.php

 <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.

LODD

 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
 others?
 ... 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
 RDF
 ... specifically, for expression and evaluation of clinical trial
 criteria
 ... expression, debugging, and knowledge management to assist in
 authoring
 ... 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)

 <Joshua>
 [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 notes on above work

 Joshua: working on refactoring caMatch codebase (currently based on
 JSF)

 weak!

 <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

 <mscottm>
 [16]http://wiki.cvrgrid.org/index.php/CVRG_iGoogle_Federated_Query_Gadg
 et

 <scribe> scribenick: Joshua

 mscottm: Stephen Granite working on Cardio project - relates to query
 federation
 ... 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
 myGrid/myExperiment/BioCatalogue
 ... 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
 cases
 ... 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

 [20]http://sourceforge.net/projects/omv2/

 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

Terminology

 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

SPARQL

 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 $

References

 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/