HCLSIG/PharmaOntology/Meetings/2009-10-22 Conference Call
Conference Details
- Date of Call: Thursday October 22 2009
- Time of Call: 11:00am - 1pm 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
- Data Conversion - Anja, Trish, Susie
- Data Loading - Michel
- Mapping Data to Ontology - Susie
- User Interface Update - All
- Use Case Questions - All
- Paper - Colin
- AOB
Minutes
Attendees: Michel, Jun, Julia, Matthias, Elgar, Joanne, Bosse, EricP, Chris, Susie
Apologies: Christi, Colin
<ericP> scribenic: michel
<michel> susie: update on ontology
<michel> susie: data conversion
<susie> Susie: loading data
<michel> susie: mapping of data to ontology
<susie> susie: interface
<michel> susie: paper
<michel> susie: update on ontology - colin provided notes
<Susie> Colin's notes: Ontology update: namespace, thanks Susie; useful suggestions from Elgar that I haven't actioned yet; you are all free to make the necessary changes to the ontology based on the mapping exercise and I will adjust ontology OR say what you need and I will tweak.
<michel> susie: w3c namespace : http://www.w3.org/2001/sw/hcls/ns/transmed/tmo
<michel> susie: data conversion
<michel> susie: anya -> mapping of medicare D listed drugs into RDF, from HTML, linked with drugbank & dailymed, will have data for loading soon
<michel> susie: on medicare website seems that a key used, brand in uppercase, generic in lowercase, over the counter light grey colour
<michel> susie: can be eligible for medicare, but through some plan?
<michel> susie: medicare has over the counter, so should be in medicare plan; but people on medicare might also be on insured plan, but don't thave access to over the counter drugs - so why is medicare offering these?
<michel> susie: in use case, none of our patients should be taking the over the counter.... messy and confusing
<michel> joanne: might be a problem in delivery of health care?
<michel> susie: could be discussed
<michel> susie: trish working on diagnostic info available - what terms used in diagnostic information, mapping to existing ontologies
<michel> susie: data sources - some commercial - chris identified a paper with some diagnostic criteria, public data sources are available
<michel> susie: can use bioportal to do the markup
<michel> joanne: todo
<michel> susie: created one patient using indivo PHCR
<michel> susie: contact, medication currently on, lifestyle, pre-existing conditions, immunization, genetic information (family)
<michel> susie: generated physician encounter - getting a medical - biochemistry, hematology, blood pressure, weight, height, etc
<michel> susie: encounter - forgetfulness; sees various experts (cognition test, MRI)
<michel> susie: hopes that Peter Kos to get back with more encounters
<michel> susie: once made, need to convert to RDF and load into triple store
<michel> susie: how much genetic information / drug interactions should be included in the PCHR?
<michel> joanne: google health?
<michel> susie: setup account, but haven't investigated it further.
<michel> joanne: patient-centric, providers can be given access
<michel> susie: still in development with health care partners; lifestyle companies getting involved
<michel> susie: the PHCR schema is useful because it has diverse, requisite and useful fields
<susie> Susie: loading data
<michel> susie: progress with triple store?
<michel> michel: still waiting for more data
<michel> send me the PCHR data when it comes in
<michel> eric: conversion of xml to rdf
<michel> susie: based on indiva schema
<michel> eric: grddl could be used
<michel> i'll just write a quick and dirty script
<michel> susie: mapping of data to ontology
<michel> will query for the types found in the data, can generate the mappings from the list obtained, should be straightforward
<michel> susie: TMO interface design call
<michel> susie: need to think about the questions that people want answers to; begin with basic mockup; get feedback on useability
<michel> susie: multiple interfaces could be designed : physician, researcher, patient
<michel> susie: having a polished interface not realistic for deadline; pubby for now, paper should include some text about the future of the interface
<Susie> http://esw.w3.org/topic/HCLSIG/PharmaOntology/Interface
<michel> susie: tabs to give views, each catered to the topic
<michel> susie: started mockup in ppt file on wiki page
<michel> eric: ODM? has lots of forms
<michel> joanne: categorical forms restrict data entry, which is good, but also bad because it prevent information from being captured
<michel> susie: would be good to have event drivers that can pull information about some entity (right click behaviour)
<michel> ericP: HTML + JS?
<michel> susie: depends on what's available - promising
<michel> susie: what's the user going to do; have been ignoring data entry; browsing the data; querying the data; visualization of result
<michel> chris: should have profiles for each of the roles that we've identified
<michel> susie: we'll focus on interface after the paper
<michel> susie: need to think about what an interface should look like for a physician
<michel> chris: avoid reinventing the wheel - US veterans hospital association - all electronic & clinical, simple, graphical, tracked history, easy to use
<michel> ericp: might be able to get a demo/view at VA system
<michel> bosse: worth pursuing
<michel> chris: extra features brought in by this group will enrich the interface
<michel> chris: pathways, metabolism, biomarkers, treatments and drug responses - could answer questions about the relationship between disease and genetics and drug response
<michel> susie: home page, data entry fields, if there is anything about genetics, responses
<ericP> action ericP to ask Liz V to grab: home page enter patient info patient summary adverse events genetics blood tests
<ericP> action: ericP to ask Liz V to grab: home page enter patient info patient summary adverse events genetics blood tests
<michel> chris: how do their systems displays diagnostic results
<ericP> e.g. graph of blood changes
<michel> lots of interest to discuss this further at the F2F
<michel> Susie: the goal of the ontology is to integrate genomics, side effects, clinical info -> how much should be contained in the PCHR?
<michel> ericP: if the data is not stable, then makinga copy would make sense
<michel> chris: patient records should contain their specific information
<michel> chris: but in this new system, the knowledge is integrated
<michel> chris: user can include relevant info
<michel> Susie: paper - needs contributions from medical people
<michel> Susie: everybody should look at the paper and contribute/edit
<michel> Susie: make sure the messages are put forward
<michel> Susie: extension - no confirmation yet from Trish; will write Barry
<michel> Susie: asks chris medicare d question
<michel> chris: pharmacist enters all the info, submit electronically to insurer, which says covered/not-covered & deductibles; different plans, including medicaid, can allow double billing - two insurers will cover the whole amount. medicare d will double with various carriers, over the counter is plan exclusion, but one or the other might cover it
<ElgarPichler> http://code.google.com/p/translationalmedicineontology/
<michel> action: everybody to look at paper; add comments into the text; if adding text use a colour - legend at the top