HCLSIG/PharmaOntology/Meetings/2009-11-19 Conference Call
Conference Details
- Date of Call: Thursday November 19 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
- Diagnostic Data - Michel
- PCHR Data - Susie
- Data Loading and Mapping - Michel
- Paper (intro, intro box, UI, etc.) - All
- AOB
Minutes
Attendees: Colin, Michel, Elgar, Bosse, Eric, Priti, Anja, Chris, Matthias, Christi, Trish
Apologies: Joanne, Jim
<michel> susie: no call next week
<michel> ontology
<michel> elgar: notation issues, classes that are not classified, sanctioning what we have so far
<michel> elgar: notation - how to label classes and label relations
<michel> elgar: latest version cannot be loaded in protege
<michel> elgar: orphan classes, we need to meet to deal with those
<michel> elgar: need approval for changes for all classes in the ontology
<michel> elgar: being put forward as a recommendation by the ontology group
<michel> susie: might want to include multiple biomarker classes
<michel> bosse: or could a biomarker have different qualifiers
<michel> colin: looking at having multiple roles
<michel> susie: biomarker in discovery wouldn't have to be validated, unlike in the clinic
<michel> bosse: would prefer qualifier
<michel> bosse: which class would it go in?
<michel> colin: toxicity - need to distinguish different types
<michel> susie: toxicity and safety seem interrelated
<michel> chris: toxicity can be quantified
<michel> colin: safety hard ontologically - perhaps better handled by the front end (software)
<michel> ericP: datasets?
<michel> susie: Sider - adverse events like nausea
<michel> susie: things that are relative safe all the way to lethal
<michel> susie: also related to risk-benefit analysis
<michel> colin: safety criterion?
<michel> colin: does a drug satisfy certain safety criteria?
<michel> bosse: drugs have known risk factors
<michel> chris: side affects have to be stratified
<michel> colin: use the "issues" at the google code project to register any issues
<michel> diagnostic data: http://lodd.semanticscience.org/describe/?url=http://bio2rdf.org/tmo:panel2
<michel> susie: PCHR data - finished patient 1, 2; gaps in genotyping/SNPs, hard to find this information,
<michel> susie: for those preparing the PCHR, send snps you need info for, will have staff look into it
<michel> susie: need license # (state), DEA # (federal/institution)
<michel> susie: would a patient have access to this info
<michel> chris: yes, it can be looked up - pharmacist, online
<michel> susie: one patient suffering from depression; would the diagnostic be a depression score
<michel> chris: 12-16 criteria available, need 6+ over some period, can use scales
<michel> chris: ask questions from a list - questionnaires - consultation gets the story from the patient
<michel> susie: when would the follow up be?
<michel> chris: depends on the extent of depression
<michel> chris: one or two weeks would be reasonable
<michel> anja: should we putting in the their names or the identifiers?
<michel> susie: more likely to use the names
<michel> susie: a hospital based system might use the identifiers
<michel> chris: contact information - name, address, + speciality
<michel> bosse: still have a lot to do
<michel> chris: lab values - conflict with units - need to pick one system
<michel> susie: suggests US system, since addresses etc are in the US
<michel> bosse: for the drugs we have metric, but for the rest it appears as US
- ericP aren't they *all* metric systems?
- michel SI vs imperial vs US
<michel> anja: still need to understand how to capture lab data in xml
<michel> susie: patient 6;
<michel> matthias_samwald: a bit complex,
<michel> chris: multiple presenting symptoms, complications
<michel> susie: PCHR have tie in to hospital / clinic
<michel> susie: high levels of detail may not reflect typical report, but is important for pharma
<michel> susie: depending on the role of the person accessing the system, would present different info
<michel> susie: be good to get all of these completed and converted into RDF - ericP
<michel> ericP: look at TMO, generate XSLT to convert PHCR XML to RDF,
<ericP> http://www.w3.org/2009/11/19-TMO-xslt/AD_PCHR_1_Reviewed.rdf
<ericP> http://www.w3.org/2009/11/19-TMO-xslt/AD_PCHR_1_Reviewed.rdf
<michel> susie: how often are we able to connect data to TMO
<michel> colin: use of classes instead of relations
<michel> susie: need to get the profiles finished early next week
<michel> susie: conversion end of the week, then loaded
<michel> ericP: had to patch patient 1 to make it valid xml
<michel> ericP: funny MS quotes into normal quotes
- michel suggest Oxygen XML editor
- michel or http://xml-copy-editor.sourceforge.net/
<michel> http://bio2rdf.org/pharmgkb:PA334
<michel> lodd + tmo + pharmgkb + panel2 = http://tm.semanticscience.org/sparql/
<michel> Paper
<michel> susie: working through the paper
<michel> susie: at one point will want to generate a word document
<michel> susie: will have to pass between participants - with some kind of exclusion mechanism
<michel> susie: perhaps by posting on wiki, and indicating that you have checked it out
<michel> susie: work on queries when the data is in
<michel> 1) Ontology: Bridging the Gap From Bedside to Bench with a Patient Centric Approach 2) A Translational Medicine Ontology: A Patient-Centric Approach to Personalize Therapy and Bridge the Gap From Bedside to Bench 3) A Translational Medicine Ontology : A Patient-Centric Approach to Bridge the Gap from Bedside to Bench… 4) A Translational Medicine Ontology : A
<michel> 4) A Translational Medicine Ontology : A Tailored Therapeutic Approach to Bridge the Gap from Bedside to Bench… 5) A Translational Medicine Ontology : Applications to Personalize Therapy and Bridge the Gap from Bedside to Bench 6) A Translational Medicine Ontology : An Application to Personalize Therapy and Bridge the Gap from Bedside to Bench
<michel> change from "A" to "The"
<michel> title debated: "The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to bench "
<michel> keywords settled: "keywords: Biomedical Informatics; Drug Discovery and Development; Healthcare; Ontology; Patient; Personalized Medicine; Health Record; Semantic Web; Tailored Therapeutics; Translational Medicine"
<michel> Anja, Jun, Michel, Matthias should look into queries