HCLSIG/PharmaOntology/Meetings/2009-02-19 Conference Call

From W3C Wiki

Conference Details

  • Date of Call: Thursday February 19, 2009
  • Time of Call: 12:00pm Eastern Daylight Time (EDT), 17:00 Greenwich Mean Time (GMT), 18:00 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: 42572 ("HCLS2").
  • IRC Channel: irc.w3.org port 6665 channel #HCLS2 (see W3C IRC page for details, or see Web IRC)
  • Duration: ~1h
  • Convener: Susie

Agenda

  • Refinement of use cases
  • Review ontologies
  • Outreach efforts (e.g. survey, C-SHALS)
  • Define next steps
  • F2F plans

Minutes

Attendees: David S., Lynn, Sandor, Christi, Claudia, Elgar, Susie, David, Matthias, Trish, EricP

Apologies: Bosse

<matthias_samwald> Susie: Christi, please give a recap of where we are in terms of creating roles and assigning questions to these roles

<matthias_samwald> Christi: The use cases are listed on the wiki page

<matthias_samwald> Christi: Use-case: a person looking at the bigger picture -- what diseases are out there

<matthias_samwald> ... and some more focussed views.

<matthias_samwald> (Christi goes through the roles listed in http://esw.w3.org/topic/HCLSIG/PharmaOntology/UseCases )

<matthias_samwald> Christi: I have not found ontologies for some of these, feel free to add to the wiki

<matthias_samwald> Susie: regarding health care plans

<matthias_samwald> ... Christi and I had a chat with someone from Kaiser Peramente

<matthias_samwald> ... We talked to some IT staff that might assist us

<matthias_samwald> ... We also worked with Chimezie

<matthias_samwald> ... John Madden would also be interested

<matthias_samwald> ... That could help us make progress on the health care side.

<matthias_samwald> ... We think that the "concepts of interest" can help in creating bridges.

<matthias_samwald> David Sedlock: the legal role might be missing

<matthias_samwald> Susie: This is partly covered by the "Strategy/Portfolio" role

<matthias_samwald> ... what could be added?

<matthias_samwald> David: patents, litigations etc. I could contact our legal staff about this

<matthias_samwald> Susie: maybe the informatician role should be a subset of the other roles? Should it be separate?

<matthias_samwald> ... We will spend the next two weeks in those roles whether they agree with the questions we have collected.

<matthias_samwald> ... We will first create a light-weight patient-centric ontology, then try to work with it in a few particular areas and see how it works out.

<matthias_samwald> Elgar: The list looks daunting, I am glad you say you will focus on some of the questions further down the line.

<matthias_samwald> Susie: Yes. But I would like to have a high-level framework (20 30 classes)

<matthias_samwald> Matthias: Did you look into what actual applications to use -- Oracle, Virtuoso, TopBraid..?

<matthias_samwald> Susie: I will post proposed time frame and actions on the wiki... We have calls every two weeks. I was thinking that we should spend some weeks on identifying the roles, and then get feedback ... this takes us to mid of March

<matthias_samwald> ... then we can spend another 4 weeks on specifying 2 or 3 use cases

<matthias_samwald> ... This should be finalized by April 16th

<matthias_samwald> ... Then we can spend 4 weeks on identifying the concepts in the bridging ontology

<matthias_samwald> ... This could be finalized mid of May.

<matthias_samwald> Then we could look into domain ontologies

<matthias_samwald> And after that we can look into what software products to use... by June 11

<matthias_samwald> Elgar: I have some concerns... All of these steps are very interesting projects

<matthias_samwald> ... but building the ontology alone... I have not made good experiences doing this in a community

<matthias_samwald> ... how are we using data?

<matthias_samwald> ... Do we provide data? Do we provide tools that have access control?

<matthias_samwald> Susie: My thinking was along the lines of developing a high-level framework with a minimal number of classes.

<matthias_samwald> ... The use-cases alone would be already a very valuable resource.

<matthias_samwald> ... The light-weight ontology and linking things together would also be a good achievement.

<matthias_samwald> ... I think that this group would be building a demo, not a production-ready system

<matthias_samwald> Lynn: Building a small ontology, with a use-case in mind, should be fairly simple

<matthias_samwald> Matthias: but even small ontologies can be a daunting task. Good community process and having right people in charge is important.

<matthias_samwald> TOPIC -- Existing ontologies.

<matthias_samwald> Lynn: My work is concerned with tracking pathogens for national security

<matthias_samwald> ... most of those ontologies are domain ontologies (e.g., disease ontology)

<matthias_samwald> ... or geographic ontology

<matthias_samwald> ... environmental ontology (ENVO)

<matthias_samwald> ... influenza ontology --- brings together components from several domain ontologies

<matthias_samwald> ... in the OBO Foundry I am editor of several ontologies

<matthias_samwald> Susie: Elisabeth Wu helped us to create a more focused use-case concerning Alzheimer's

<matthias_samwald> Lynn: One use case regarding symptom ontology... Patient describes symptoms, doctor writes down signs and has to write billing code

<matthias_samwald> Susie: Now that pharma companies are increasingly using EHR for analysis of drug efficacy, an innacurate representation of signs and symptoms is very problematic

<matthias_samwald> Lynn: atypical symptoms are not captured in a knowledge base

<matthias_samwald> ... but physicians are looking for that information

<matthias_samwald> ... patient history is also usually lost... this knowledge base is missing

<matthias_samwald> ... names of things tend to change -- another problem

<matthias_samwald> TASK for Lynn: Look at the physician use-case and identify ontologies

<matthias_samwald> Susie: I did not make much progess with reviewing Chimezie's ontology

<matthias_samwald> ... having problems with Protege, need to fix that

<matthias_samwald> ... feel free to add relevant ontologies to the wiki

<Susie1> http://esw.w3.org/topic/HCLSIG/PharmaOntology/Resources

<matthias_samwald> Susie: the criteria for inclusion are very loose... anything that might be helpful for the questions we have collected

<matthias_samwald> ... I thought someone from Pfizer might also be able to share an ontology.

<matthias_samwald> TOPIC -- Outreach

<matthias_samwald> Susie: I put a list of names on the wiki page

<matthias_samwald> ... there will be the C-SHALS conference in Cambridge next week

<matthias_samwald> ... Eric Neumann is the lead organizer

<matthias_samwald> ... We will be able to discuss the Pharma ontology work at that meeting

<matthias_samwald> ... David made the suggestion of doing a survey about the individual goals of participation

<matthias_samwald> ... But maybe this can be found out from the telecons

<matthias_samwald> ... The main beneficiaries of the pharma ontology are pharma companies

<matthias_samwald> Trish: Do you envision this to be used in publication and competitive intelligence work?

<matthias_samwald> Susie: If you want to reach out to this community, great! This could become a "strategic portfolio manager" view.

<matthias_samwald> ... The HCLS group will have a F2F meeting.

<matthias_samwald> ... it will be at a point when we are finalizing the use-cases

<matthias_samwald> ... there are 6 task forces, overlaps (participants, topics)

<matthias_samwald> ... John Madden has done some work on SNOMED etc

<matthias_samwald> ... He would like to have the terminology group meet with the Pharma ontology group

<matthias_samwald> ... Vipul Kashyap from COI also mentioned opportunity for collaboration

<matthias_samwald> ... LODD is working to converting some relevant datasets+

<matthias_samwald> ... LODD would like to have an ontology that could be used for some of the mappings

<RRSAgent> I have made the request to generate http://www.w3.org/2009/02/19-hcls2-minutes.html matthias_samwald

<matthias_samwald> rrsagent, make minutes world-readable

<matthias_samwald> rrsagent, set logs world-visible

<RRSAgent> I have made the request, matthias_samwald

<matthias_samwald> Bye!

Retrieved from "https://www.w3.org/wiki/index.php?title=HCLSIG/PharmaOntology/Meetings/2009-02-19_Conference_Call&oldid=43386"