HCLSIG/Meetings/2008-10-16 Conference Call

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Conference Details

  • Date of Call: Thursday October 16, 2008
  • 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 #: + (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: Chime, Scott, Susie



<Zakim> On the phone I see EricP, chimezie, Susie, mscottm, Kei_Cheung, matthias_samwald, Don_Doherty, June, MaryK, John_Madden

<Zakim> On IRC I see mkennedy, Donald_Doherty_, Jun, Huajun, kei, mscottm, chimezie, Susie, matthias_samwald, RRSAgent, Zakim, johnM, ericP

<chimezie> Zakim, pick a scribe

<Zakim> Not knowing who is chairing or who scribed recently, I propose John_Madden

<ericP> scribenick: johnM

<johnM> where is biordf?

<ericP> scribenick: ericP

  • ericP thinks that means we're both scribes now

<ericP> Topic: Task Force Updates

<ericP> [BioRDF]

<ericP> kei: won't be at the f2f

<ericP> ... will have a representative from matthias_samwald at the f2f

<johnM> kei: last few biordf calls have had presentations

<ericP> ... invited a number of presenters over the last couple calls

<johnM> ...about related interest group activities

<johnM> ... and Olivier Bodenreider did one recently

<johnM> ...and wants to do an RDF implementation of MeSH

<johnM> ...(Olivier is from NLM)

<johnM> ...kei asked if can incorporate >1 language in addition to English (i.e. Chinese)

<johnM> ...in Olivier's RDF MeSH conversion

<johnM> ...and this is under consideration

<johnM> kei: another sub-update is scheduling of next BioRDF call

<johnM> ...there is a conflict with F2F, and will probably skip next call

<johnM> susie: could you please cancel the next call?

<johnM> ...because there is a conflict with a large group discussion scheduled at f2f

<johnM> kei: yes, we will cancel next call

<johnM> [Clinical Decision Support]

<johnM> chime: not much to report here, need use cases, please give us some!!!

<johnM> [COI]

<johnM> ericP: have a demo of the ontology mapping tool at the ISWC tutorial

<ericP> -> http://www.w3.org/mid/20081011161136.GB13414@w3.org queries

<ericP> cat stdt.rq | SWtransformer -q - hl7-sdtm.rq | SWtransformer db-sl7.rq -s http://sql.example/DB/

<johnM> ...above is a set of queries and mappings among a number of terminologies

<johnM> ericP: so this demonstrates a long pipeline of query transforms that eventuate in sql queries

<johnM> ericP: there is a second target that may or may not materialize that involves query optimization

<johnM> mscottm: eric, would you show this at technical plenary?

<johnM> ericP: we could do that

<johnM> susie: we have a slot at tpac, and could incorpoarte this if ready

<johnM> ericP: this is inter-ontology transforms and inter-database transforms

<johnM> ...and this is reusable for any use case, i.e. not COI-specific

<johnM> ...and want to use it subsequently to do query federation

<johnM> ...Recently talked to Jim Ostell at NCI and he is interested in using it to federate SPARQL queries on NCI

<johnM> [LODD]

<johnM> susie: Olivier Bodenreider has developed a framework for integrating a large number of heterogeneous

<johnM> ...drug datasets

<johnM> susie: have also identified about 20 datasets that could actually be used in the demo

<johnM> ...and looked at licensing issues on these

<johnM> susie: and third, we have defined some use cases.

<johnM> ...we want a use case that has three "perspectives"

<johnM> ... 1. patient perspective

<johnM> ... 2. physician perspective

<johnM> ... 3. pharma company

<johnM> ...and each perspective has its own characteristic questions

<johnM> ... and it would make sense to put ClinicalTrials.gov as the centerpiece

<johnM> susie: there will be special issue on linked data on Int'l J of SemWeb & Info Systems

<johnM> ... and hope to submit to that issue, deadline coming up fast

<johnM> [Scientific Discourse]

<johnM> susie: Tim Clark is organizer and they are "making progress"

<johnM> ... a new version of SWAN is coming out, and they will hopefully have the SWAN and SIOC ontologies interlinked

<johnM> ... and they next want to add some bibliography ontologies

<johnM> [Terminology]

<ericP> johnM: next task was to redo the SNOMED mapping using more expressive skos relations

<ericP> ... holgerS says he wrote a groovy script to do this

<ericP> ... when i get it from him, i'll put it on our Sesame server

<ericP> ... hope to have clarification on SNOMED licensing issues next week

<ericP> ... expect that it will be ok to use SNOMED so long as you don't download the entire vocab

<ericP> mscottm: what will you put on the Sesame server? SKOS mapping? SNOMED ontology? both?

<ericP> johnM: both. we'll put up the SNOMED ct identifiers as URLs, with synonyms and @@ expressed as SKOS

<ericP> ... our brainstorming site shows how we're mapping SNOMED isa relations and other relations to SKOS

<ericP> mscottm: we have web services that can talk SKOS or directly to your Sesame server

<ericP> johnM: Sesame server down due to hardware migration. expect up soon

<ericP> topic: F2F Agenda

<johnM> susie: f2f next week

<johnM> susie: 36 are registered

<johnM> susie: and a number are dialing in remotely

<johnM> ericP: for the 8 hours of the meeting

<johnM> ... we should have access for 20 people

<johnM> johnm: what is the number?

<Susie> -> http://esw.w3.org/topic/HCLSIG/F2F/2008-10_F2F HCLS F2F

<johnM> susie: we currently have 11 dial-in committers

<johnM> susie: several talks will be given

<johnM> ... and the agenda with all the speakers is up on the website link above

<johnM> susie: we will also have updates for "sibling" groups in W3C

<johnM> susie: and finally we will have a big presentation on the standards landscape

<johnM> ... including HL7, and chime will do this

<johnM> topic: coordinating high level ontologies for health + pharma

<johnM> susie: at Lilly, we are interested in doing better:

<johnM> ... 1. query across silos

<johnM> ... 2. query across collaborators' data

<johnM> ... in respect to silos in our own enterprise, we need a bridging ontology

<johnM> ... that we're thinking ought to be patient-centric

<johnM> susie: an emerging strategy in pharma is to identify patient groups

<johnM> ... and then link these to biological mechanisms

<johnM> ... and then link from there further to pharmacology, etc.

<johnM> ... so it seem like the central concept ought to be patient

<johnM> susie: we want a completely open ontology here

<johnM> ... because if we want to use it to link to extra-enterprise collaborators, we would want a lot of generic uptake

<johnM> chime: high-level cross-domain ontologies might require more bandwidth than a taskforce

<johnM> susie: let's try it as a taskforce, and see later if we might want to spin off to a different wrapper

<johnM> susie: here's a question for everyone:

<johnM> ... we think to best design this ontology, we need to consider the questions

<johnM> ... that we will want to ask with it

<johnM> ... and susie has developed a list of questions

<johnM> ... but maybe others would like to contribute some

<johnM> susie: we want to avoid compound-centric, traditional drug ontologies

<johnM> ... and stick with patient-centric

<johnM> ... and this coould interoperate with linking drug data work

<johnM> chime: we've been doing some intra-enterprise clinical registry integration work at Cleveland Clinic

<johnM> ... and we might like to work on this too

<mscottm> http://www.alert-project.org/

<johnM> mscottm: drug safety project with 50,000,000 electronic patient records

<johnM> ... scott said should look at LODD taskforce

<johnM> ... but also seems like some links to susie's proposal

<johnM> ... and one of these dudes is part of ELIXIR project which is european infrastructure for bioinformatics

<johnM> susie: will look at link

<johnM> Topic: outreach activities

<johnM> susie: many such activities are emerging

<johnM> ... 1. Scott will lead a lightning demo at tpac

<johnM> ... lightning means 4 minutes

<johnM> ... 2. tutorial at ISWC

<johnM> ... and there is still some space available -- sign up now!!!

<johnM> ... because this tutorial will be a good recruitment opportunity

<johnM> ... 3. eric & susie will present at Boston Area Group for Informatics & Modeling

<johnM> ... 4. Tool for Life Sciences in Edinburgh

<johnM> ... 5. HCLS Turorial at Asian Semantic Web Conference

<johnM> ... 6. CSHALS conference early next year

<johnM> ... 7. susie to present at DIA meeting in Berlin in March

<johnM> ... 8. club for pharmaceutical gurus in Switzerland in May

<johnM> susie: let's all keep an eye open for conferences where we can have some face time for HCLS

<johnM> chime: any other issues?

<johnM> chime: thanks all