HCLSIG/PharmaOntology/Meetings/2009-11-19 Conference Call

From W3C Wiki

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> 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