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