HCLSIG/PharmaOntology/Meetings/2009-10-29 Conference Call

Conference Details

• Date of Call: Thursday October 29 2009
• Time of Call: 12:00 - 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: 1h
• Convener: Susie

Agenda

• Paper - All
• Ontology Update - Colin
• Data Conversion - Anja, Trish, Michel, Joanne, Susie
• Data Loading - Michel
• Mapping Data to Ontology - Susie
• User Interface Proposal - Bosse
• Use Case Questions - All
• AOB

Minutes

Attendees: Chris, Andreas, Michel, Bosse, Trish, EricP, Lyn, Julia, Elgar, Peter, Lee, Anja, Colin, Joanne, Christi, Matthias, Susie

<ericP> meeting: TMO

<ericP> chair: Susie

<ericP> scribenic: ericP

<ericP> topic: the paper

<ericP> Susie: paper deadline extended

<ericP> ... (perhaps for everybody?)

<cdenney> I can't get on the phone line - it says it is full.

<matthias_samwald> i also get a "this conference is full".

<cdenney> Glad to hear it wasn't personal. (blocking me)  :-)

<ericP> Susie: despite our extension to 30Nov, Barry would like an abstract tomorrow

<ericP> ... propose to start one this evening and get feedback from folks over tomorrow

<ericP> colin: trying to write one now in the google doc

<ericP> Susie: cool, will use that this evening

<ericP> colin: like the idea of putting philosophy into another paper

<ericP> ... currently lack a description of how the patient data was generated

<ericP> Susie: should have more this weekend

<ericP> colin: also need a short desc of the toy interface (pubby)

<ericP> colin: [something about indivo ont]

<ericP> Susie: need to work out paper authors and order

<ericP> ... like to be inclusive, i.e. two calls or more in last two months, plus offline contributions

<ericP> ... for abstract tomorrow, alphabetical order

<ericP> ... chose paper order nearer [real] deadline

<ericP> topic: ontology updates

<ericP> Susie: recent updates?

<ericP> colin: haven't touched it myself. elgar has added MeSH

<ericP> ... expect criticisms when folks pour it into the triple store

<ericP> elgar: edded all of the xref that i could find

<ericP> ... used best judgement selecting reasonable sources

<AnjaJentzsch> can someone invite me to the google doc? anjeve@gmail.com - thanks

<ericP> ... folks might want SNOMED

<ericP> ... have added comments to the overall structure into google project /doc directory

<ericP> [ericP and peter interested in reviewing and helping the ontology]

<ericP> i suspect matthias_samwald would be interested as well

<ericP> topic: imports into triple store

<ericP> AnjaJentzsch: converted to RDF

<ericP> ... unsure about Medicare Plan D over-the-counter drugs

<ericP> ... asking for help from d2r folks

<ericP> ... end point is up, folks can query the server

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

<ericP> Susie: you can pick up OTC's comments from last week's minutes

<ericP> ... my interpretation: folks are sometimes covered by both BCBS and Medicare

<ericP> AnjaJentzsch: ? and Jun submitted a demo to linked data

<AnjaJentzsch> http://tinyurl.com/yzdc9a5

<ericP> ... can query for alternative medicines

<ericP> ... might be busy for the next hours/days

<ericP> Susie: would be nice if Michel could get access to Medicare data ASAP

<ericP> AnjaJentzsch: can't fix d2r [myself], but will try

<ericP> Susie: alternative plans?

<ericP> AnjaJentzsch: any tool which queries the...

<ericP> Susie: we want to extract data from panel 2 from a DuBois paper

<ericP> ... has DSM codes

<ericP> ... Trish was going to look at correspondance

<ericP> ... also asked Joanne and Michel

<ericP> Trish: gone through part

<ericP> ... for diagnostics, finding MRI, ...

<ericP> ... was feading panel 2 text to NCBI's tagging tool

<ericP> ... matches found for e.g. memory recall issues

<ericP> Susie: good coverage from one ontology?

<ericP> Trish: hitting SNOMED NCIT, BirnLex

<ericP> ... not sure all that has gone into the neuroinformatics framework

<ericP> Susie: unsure of intersection of those

<ericP> ... Maryann Martone might have the answer

<ericP> Trish: spoked with Birn folks yesterday

<ericP> Susie: carry on with lead; let me know if you hit a dead end

<ericP> Joanne: think Trish has gotten more out of Panel 2

<ericP> ... met with Michel, who i expect is working on querying it

<ericP> Michel: you can stick in some text, and get some markup

<ericP> ... but you don't get ontology matches through the web interface

<ericP> ... have to fall back to the web service

<ericP> Trish: also having trouble with the web interface

<ericP> Joanne: you get back a cloud of terms, e.g. memory, referenced many times

<ericP> ... don't see the ontologies

<ericP> ... terminizer draws on fewer ontologies, but has more useful interface

<ericP> ... had exactly what i needed for the influenza ontology

<ericP> Trish: have time to continue on this

<ericP> Susie: one we see the best fit ontologies, need to choose

<ericP> ... seems like SNOMED and NCI were the best

<ericP> Lynn: am a PI on the Disease ontology

<ericP> ... can't distribute SNOMED on the web

<ericP> Susie: are there other criteria (besides liscencing) we should look for?

<ericP> Lynn: BFO ontology is very new

<ericP> Colin: propose OBO foundry

<ericP> Peter: some of the electronic medical records ontologies are based on their implementation system

<ericP> ... seen a bunch of source datasets

<ericP> ... is it exceptable to code towards ICD9 or LOINC?

<ericP> Susie: final focus is to develop TMO and develop an app to use it

<ericP> ... we've id'd a bunch of sources

<ericP> ... prolly best to map the data sources we're using to terminologies already applied there

<ericP> ... for EMR, we've been using Indivo where possible

<ericP> ... asked Ben Adida and Ken Mandel to make the rest available

<ericP> ... doesn't look like it will happen in time, so we're rolling our own

<ericP> ... makes sense to make it as like an EMR as possible

<ericP> ... we wouldn't seen LOINC or ICD9 in pharmas

<ericP> Lynn: we've mapped ICD9 to Disease Ontology

<cdenney> wondering about the last comment... wouldn't see icd-9 in pharma?

<cdenney> we are using icd-9

<ericP> peter: would like to look at the EMR data to see how it fits [oops, forgot]

<ericP> Colin: terms of use of LOINC are alarming, rules like "don't dillute"

<cdenney> is anyone using MedDRA terms?

<ericP> Elgar: test for no liscencing by seeing if the ontology has level 0 restriction in UMLS

<ericP> Lynn: also if it's in OBO foundry

<ericP> Susie: Trish, you're taking the lead on panel 2 of DuBois

<ericP> ... can you get us some mappings by next week?

<ericP> Trish: mostly seeing [matches on] terms related to cognitian rather than diagnsotic tests

<ericP> Susie: i've been generating fake patient data in Indivo where possible

<ericP> ... Peter has be reviewing and enhancing

<ericP> ... three sections:

<ericP> ... .. demographics, contact

<ericP> ... .. largely static medical information

<ericP> ... .. encounters

<ericP> ... Peter has improved demo and contact info, as well as static info

<ericP> ... put together some hemo data, cholesterol, ... in encounters

<ericP> ... hoping peter can help with realistic data for other encounters, e.g. patient presents symptoms

<ericP> ... would like to complete one patient and develop 5 more in a google doc

<ericP> ... have discussed the intended distribution of patient data

<ericP> ... Indivo is capturing XML data

<ericP> ... expect ericP to GRDDL it

<ericP> Peter: will try, have other high-priority projects

<ericP> ... can look at the first patient set this week, the other patient sets in the next two weeks

<ericP> ... hemotology was 2 hours

<ericP> ... another 2 hours for the other aspects

<ericP> ... quite a lot of evening time, maybe 6 hours?

<ericP> Joanne: what can you turf to others?

<ericP> Peter: two aspects:

<ericP> ... .. examine Indivo and look at expression therein

<ericP> ... .. translating coding terminology

<ericP> ... finding the codes which match the use case example data

<ericP> ... would help if the use case data were already input

<ericP> Susie: would like Peter to finish patient1 so others can contribute more patients

<ericP> Peter: will work on this patient this week, hope to have a template next week

<ericP> [XML template]

<ericP> Susie: already have list of patients (.doc), exchanged with Peter

<ericP> ... will make available

<ericP> Chris: interested in the display of the pharmacogenetics section

<ericP> Chris: sent you an exmaple of the bedside data needed to tailor substance adminstration

<ericP> Susie: that's the next step, would be nice to have an offline call to start

<ericP> topic: data loading

<ericP> topic: user interface

<ericP> Bosse: looked into Openvista which Chris proposed

<ericP> ... is already a good user interface

<ericP> ... enhancing for tailored medicine or treatment

<ericP> ... propose Emanual P of Novartis's approach

<ericP> ... menu of options

<ericP> ... e.g. point to a word

<ericP> ... link to a faceted browser

<ericP> ... have good answer from Chris, will extend

<ericP> ... i have not gotten OpenVista running

<ericP> ... saw video presentation

<ericP> ... is a structure/organized interface

<ericP> ... am not an expert developer any more

<ericP> ... need a developer

<ericP> Andreas: OpenVista is based on TCRS (the VA system)

<ericP> ... sent Chris a sample of TCRS

<ericP> ... i recommend adding a tab to OpenVista

<ericP> ... code is in C#

<ericP> ... adding a tab is easy

<ericP> ... TCRS can be accessed at http://www1.va.gov/cprsdemo/

<ericP> Andreas: would expect physicians faced with new problems would go to this tab

<ericP> Susie: we don't need a strong interface for the paper

<ericP> ... need to decide if the tool allows the physician enter symptoms and the tool does some inferencing

<ericP> ... or a tool for researchers

<ericP> ... need to decide what interface we want to demo and where to start

<ericP> Andreas: pretty sure that CTRS is available

<ericP> ... not sure if it's open source

<ericP> ... it's avail from Delphi

<ericP> topic: f2f logistics

<ericP> Susie: task break-out time allocated

<ericP> Susie: will re-send f2f agenda, highlight break-out session, and including dial-in logistics for TMO call