HCLSIG/Meetings/2010-05-06 Conference Call
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- 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
- 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
06 May 2010
Scribe Joshua, ericP
* Topics 1. BioRDF update [Kei] 2. LODD 3. COI update 4. Scientific Discourse 5. Scientific Discourse update 6. TMO update 7. Terminology 8. SPARQL * Summary of Action Items __________________________________________________________________
<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: 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.
<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> https://wiki.nci.nih.gov/display/VCDE/Protocol+Eligibility+Criteria +Proof-of-Concept+-+Notes
-> 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)
<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> 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 update
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: 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?
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.
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
<johnM> Hi guys, I had to step away for a few minutes...
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 scribe.perl version 1.135 (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/