HCLSIG/PharmaOntology/Meetings/2009-11-05 Conference Call

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Conference Details

  • Date of Call: Thursday November 5 2009
  • Time of Call: 11:00am - 1:00pm ET
  • 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)
  • Mibbit instructions: go to http://www.mibbit.com/chat and click the server link. Enter irc.w3.org:6665 into that box, enter a nickname, and enter #HCLS2 for the channel
  • Duration: 2h
  • Convener: Susie

Agenda

  • Ontology Update - Colin
  • Medicare Data - Anja
  • Diagnostic Data - Trish
  • PCHR Data - Susie
  • Data Loading and Mapping - Michel
  • RelFinder - Anja
  • User Interface - Bosse
  • Paper - All
  • AOB

Minutes

Attendees: Matthias, Bosse, Michel, Jim, Anja, Christi, Chris, Eric, Philipp, Elgar, Susie

<Susie> Ontology

<Susie> Colin doesn't have an update on the ontology

<Susie> Was asking for information on the fake patient data in order to possibly tweak the ontology

<ericP> i have the impression that roles are attached to people instead of an event, so doctor Bob acting as a patient in a consultation is indistinguishable from him asking as a doctor

<Susie> Medicare Data

<AnjaJentzsch> http://www4.wiwiss.fu-berlin.de/medicare/

<Susie> Is up and running with D2R

<Susie> Linked to other LODD data sets

<Susie> There is also a dump available

<Susie> Can also link to DBpedia

<Susie> Diagnostic Data

<Susie> Information in the panel in the DuBois paper can link to many ontologies

<michel> NCI thesaurus, CTV, MESH, GALEN, CHEBI

<Susie> Let's map to 5 ontologies for now

<AnjaJentzsch> Michel to inform Trish we agreed on the above 5 datasets, and see if she's happy with Michel taking the lead on the work

<Susie> Michel agrees to have data in RDF in time for the next call

<AnjaJentzsch> PCHR Data

<Susie> Created new wiki page for data related information

<Susie> http://esw.w3.org/topic/HCLSIG/PharmaOntology/Data

<AnjaJentzsch> Susie shared data on one fake patient

<Susie> http://esw.w3.org/topic/HCLSIG/PharmaOntology/Data/FakePatients

<Susie> To be used as the template for other fake patients

<AnjaJentzsch> PCHR contains a medical code for each patient, demographic information, drug prescriptions, conditions

<philippHeim> that is great data, thank you

<AnjaJentzsch> additional information: allergies, lifestyle, family history information, siblings

<AnjaJentzsch> encounters with physicians (tests undertaken, blood results etc)

<AnjaJentzsch> we still need to create 5 patient data sheets

<philippHeim> just a question: terms like "hypertension" are not uniquely defined in the database, aren't they?

<philippHeim> "hypertension" appears in the section about conditions in AD_PCHR_1_Template

<AnjaJentzsch> Susie: Would including gender differences in brain structure be interesting?

<AnjaJentzsch> Chris: concentrate on patient background

<AnjaJentzsch> Susie: track effects/outcome of prescribed drugs

<AnjaJentzsch> Susie & Chris to enhance patient data with more on symptoms, diagnoses, drugs, doses, genotype by Monday

<AnjaJentzsch> Christi to add a 7th patient

<AnjaJentzsch> Chris: Down Syndrome in young patients might lead to AD (around the 30ies)

<AnjaJentzsch> Bosse to complete one patient

<AnjaJentzsch> http://esw.w3.org/topic/ESWEditorsGroup

<AnjaJentzsch> Christi, Anja to add demographic and medical data for 1 patient each

<AnjaJentzsch> Jim to add data for one patient

<AnjaJentzsch> Data Loading and Mapping

<michel> http://bio2rdf.semanticscience.org:8017/sparql

<AnjaJentzsch> Michel has loaded several datasets in the triple store

<michel> http://bio2rdf.semanticscience.org:8017/fct

<michel> diseasome dailymed drugbank linkedct medicare pharmgkb sider tcm tmo

<AnjaJentzsch> Anja and Michel to work on the datasets (linking?)

<Susie> UI

<philippHeim> http://relfinder.semanticweb.org/RelFinder.swf?id=lodd

<philippHeim> http://www.vis.uni-stuttgart.de/~heimpp/videos/relFinder/relFinder_screencast.html

<AnjaJentzsch> Philipp: Can you imagine any use case for RelFinder?

<AnjaJentzsch> Susie: interface should be like known interfaces for physicians

<AnjaJentzsch> Susie: enhance existing interfaces rather than take new tools

<AnjaJentzsch> Philipp: can look into integrating RelFinder into OpenVista or any other tool

<AnjaJentzsch> Bosse: enhancing OpenVista probably out of scope (concerning timeline and technical background)?

<AnjaJentzsch> Chris: better to build on known systems

<AnjaJentzsch> Philipp: RelFinder is a Flash applications, uses SPARQL endpoints to search for instance data

<ericP> i found the send link, the video, very instructive

<AnjaJentzsch> try "Lepirudin"

<AnjaJentzsch> and "Dysprothrombinemia"

<AnjaJentzsch> Susie: work on duplicate detection / data cleansing

<AnjaJentzsch> Bosse: propose OpenVista as a known interface

<AnjaJentzsch> Bosse: describe paradigms and tools

<AnjaJentzsch> Chris: describe the model where we like to go and probably somebody catches up on this

<AnjaJentzsch> Susie: make a web interface mockup

<AnjaJentzsch> Susie: based on OpenVista

<AnjaJentzsch> Paper

<AnjaJentzsch> Susie: feedback from Barry Smith for the abstract was very positive

<Susie> Call on tuesday covered title, author order, keywords, abstract, introduction, and UI

<Susie> will work on paper over the weekend

<Susie> Move to word with tracking by next Thursday