HCLSIG/Meetings/2009-02-19 Conference Call

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Conference Details

  • Date of Call: Thursday February 19, 2009
  • Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 Greenwich Mean Time (GMT), 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)
  • Duration: ~1h
  • Convener: Scott, Susie

Agenda

Minutes

Attendees: Oliver, Scott, Vipul, John, EricP, Kei, Matthias, Jun, Helen, Marco

Apologies: Bosse

  • <kei> susie: new sparql working group started -- new sparql features can be requested
  • <ericP> -> http://lists.w3.org/Archives/Public/public-rdf-dawg/2009JanMar/0000 SPARQL2 intro mail
  • <kei> susie: Lilly started getting involved in this new group
  • <kei> susie: eric, when the first call starts on Feb 24
  • <kei> scott: what are the general things looked for by the group?
  • <kei> eric: accept proposals that represent community interest -- not sparql DL for now, but it could happen even though it's a little bit controversial ...
  • <kei> eric: update, dealing with list, aggregate, etc
  • <kei> susie: the sparql group will have a f2f meeting -- maybe on May 4
  • <kei> susie: task update and input to C-SHALS and F2F
  • <kei> vipul: update on COI -- helen, holger and eric worked hard on getting the demo to be ready
  • <kei> vipul: set up goals, demonstrate key value proposition with a use case, Helen sent out slides.
  • <kei> vipul: AMIA submission was accepted
  • <kei> vipul: patient related use case -- need an interoperability layer and use the pharma ontology use case
  • <kei> susie: ready for the C-SHALS meeting
  • <kei> vipul: yes
  • <kei> vipul: focus on the value proposition aspect and eric will focus on the technical aspect of the demo ...
  • <kei> eric: give a coi overview or vipul give it?
  • <kei> vipul: technical aspect covered in the coi and eric will do the broader stuff ...
  • <kei> susie: f2f meeting?
  • <kei> vipul: helen, rachael, eric, holger are key players of coi
  • <kei> susie: use case can create opportunity for collaboration between coi and pharma ontology
  • <kei> susie: terminology update -- John
  • <kei> john: need some advice for the presentation
  • <kei> john: scott got snomed mapping to work -- browse snomed with skos relationships ...
  • <mscottm> http://aida.science.uva.nl:9999/search/
  • <kei> john: fancier interface can be shown ...
  • <mscottm> http://tarski.duhs.org:8080/openrdf-sesame
  • <kei> susie: why skos approach is chosen over owl ...
  • <kei> john: want to talk about coordination structured medical documents -- using grddl to extract semantics
  • <kei> john: relationship between med doc. and sw standards ...
  • <kei> susie: grddl is an interesting technology
  • <kei> susie: cdisc -- why pharma should be interested in snomed?
  • <kei> john: may be able to address it ...
  • <kei> john: not useful for largescale inferencing, but useful for other purposes ...
  • <kei> john: can a live demo be supported?
  • <kei> susie: wireless connection should be available, but backup screenshots should be made just in case ...
  • <kei> john: some of the queries are slow and live demo can take up time for a short presentation ...
  • <kei> john: scott -- nice interface to show the stuff?
  • <kei> susie: f2f meeting? any thoughts?
  • <kei> john: need some input ...
  • <kei> susie: technical things, hands on
  • <kei> john: skos representation transits to owl representation
  • <kei> john: how to make skos more expressive ...
  • <kei> john: rdfs or owl -- next steps ...
  • <kei> scott: terminology -- umls should be discussed ...
  • <kei> scott: what are terms I can use starting with the terms (e.g., MeSH) one knows ...
  • <kei> john: chime proposed a light-weight patient-physician ontology -- this can serve as a good example/model
  • <kei> susie: potential overlap between pharma ontology and terminology -- lightweight ontology
  • <kei> john: chime got something going and would be nice to build on that ...
  • <kei> susie: chime will participate as an advisor in the pharma ontology ...
  • <ericP> susie already persuing CPR. rock!
  • <mscottm> 1+
  • <kei> john: supportive of the collaboration
  • <kei> susie: signs and symptoms overlaps with diseases ...
  • <kei> susie: john -- send announcements to the hcls group about the terminology meeting.
  • <ericP> -> http://www.cambridgesemantics.com/2008/09/sem-web-introduction/ LeeF's C-SHALS slides
  • <kei> eric: biordf coordination -- hcls kb ...
  • <Susie> kei: BioRDF group has been active
  • <Susie> kei: 2 main activities
  • <Susie> Kei: most active is query federation
  • <Susie> Kei: multiple HCLS KBs in different locations
  • <Susie> Kei: want to query those and other data sources
  • <Susie> Kei: exploring SPARQL endpoint to linked data
  • <Susie> Kei: looking to create a linked data interface
  • <Susie> Kei: Virtuosos has a built in interface for linked daat
  • <Susie> Kei: Need to use 3rd party software with Allegrograph
  • <mscottm> http://www4.wiwiss.fu-berlin.de/pubby/
  • <Susie> Kei: currently using pubby, but there are issues
  • <Susie> Kei: want metadata that describes linked data
  • <Susie> Kei: Jun has been helping to explian voiD
  • <Jun> vocabulary of interlinked datasets: http://rdfs.org/ns/void-guide
  • <Susie> Kei: Created some voiD descriptions for Senselab
  • <matthias_samwald> http://sw.deri.org/2007/07/sitemapextension/
  • <Susie> Kei: Jun has also created a site map for more intelligent resource discovery
  • <Susie> Kei: exploring Eric's federated approach for querying databases
  • <Jun> our void descriptions can be found at: http://code.google.com/p/junsbriefcase/source/browse/#svn/trunk/biordf2009_query_federation_case
  • <Susie> Kei: EricP is working on enhancing his code
  • <Susie> Kei: nice to try before C-SHALS
  • <Susie> EricP: have 2 COI items ahead of it in the queue, but will try to get it done in time
  • <Susie> Kei: query federation will be a major component of C-SHALS talk
  • <Susie> Kei: will also introduce the group, cover Matthias's atag work, and discuss future directions
  • <Susie> Kei: future work could involve working more closely with LODD
  • <Susie> Kei: could put LODD into the HCLS KB
  • <Susie> Kei: asking BioRDF for input regarding the F2F
  • <Susie> Kei: collaboration across the F2F would be interesting
  • <Susie> Kei: also an opportunity to interact with people who are interested in URIs
  • <Susie> Scott: URI workshop is on April 29
  • <Susie> Scott: URI workshop expectations have been reduced
  • <Susie> Scott: will be a geeking opportunity
  • <Susie> Scott: URI workshop is open to all interested parties
  • <Susie> Susie: HCLS IG is open to members of the group, invited presenters, or people who would like to get more involved going forwards
  • <mscottm> Some of the requirements are on these and related pages http://neurocommons.org/page/Shared_names , more info will follow
  • <kei> susie: update on lodd
  • <kei> susie: converted 4 datasets into linked data representation -- diseasome, drugbank, clinical trials.gov and DailyMed.
  • <kei> susie: a paper was submitted to the LOD workshop at W3 conference
  • <kei> susie: make sure the mappings are optimal
  • <kei> susie: marble data browswer was explored, but performance and stability could be issue
  • <kei> susie: the datasets were indexed and viewed through a faceted browswer developed at DERI
  • <kei> susie: Lilly is interested in linking data internally
  • <kei> susie: going forwards: extending it to physician, patient view point -- Kei, Bosse, Don, Jun, Anja, Chris are actively involved ...
  • <kei> susie: C-SHALS slides: overview and stuff extracted from the paper, there is a potenial for live demo ...
  • <kei> susie: f2f -- haven't had a chance to discuss with the lodd group yet and will do so soon ...
  • <kei> scott: what browswer was used?
  • <Susie> http://visinav.deri.org/hcls/
  • <Susie> http://visinav.deri.org/hcls/list?keyword=varenicline
  • <kei> matthias: specialized swse browser, but we still need a way to ask meaningful questions
  • <kei> susie: this is a important step forward
  • <kei> susie: pharma ontology group update
  • <kei> susie: currently focusing on identifying use cases
  • <kei> susie: life science, health care and drug research angles to ask questions
  • <kei> susie: maybe 3 use cases can be identified
  • <kei> susie: high level framework specifying how data objects can be connected to each other ...
  • <kei> susie: refine the ontology and build application to use the ontology
  • <kei> susie: limited but useful scope
  • <Susie> http://esw.w3.org/topic/HCLSIG/PharmaOntology
  • <kei> susie: 10 pharma co's, several organizations and a couple of academic institutions are currently involved ....
  • <kei> scott: impressive!
  • <kei> susie: doesn't have a slot at c-shals but there will be a lot of opportunities of discussion at c-shals
  • <kei> susie: f2f meeting -- aligning efforts with terminology and coi groups
  • <kei> susie: help guide us what to do next ...
  • <kei> scott: question -- lodd, terminology and pharma ontology linked unambiguously
  • <kei> scott: disambiguiation mechanisms
  • <kei> susie: rules are explored
  • <kei> susie: VoID, etc are explored