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