TMO -- 29 Oct 2009

yes

scribenic: ericP

the paper

Susie: paper deadline extended
... (perhaps for everybody?)

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

<cdenney> yes

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

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

Susie: despite our extension to 30Nov, Barry would like an abstract tomorrow
... propose to start one this evening and get feedback from folks over tomorrow

colin: trying to write one now in the google doc

Susie: cool, will use that this evening

colin: like the idea of putting philosophy into another paper
... currently lack a description of how the paitent data was generated

Susie: should have more this weekend

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

cdenney, matthias_samwald, i've asked for the limit to be bumped up, but seen no live bodies to respond

colin: [something about indivo ont]

Susie: need to work out paper authors and order
... like to be inclusive, i.e. two calls or more in last two months, plus offline contributions
... for abstract tomorrow, alphabetical order
... chose paper order nearer [real] deadline

ontology updates

Susie: recent updates?

colon: haven't touched it myself. elgar has added MeSH
... expect criticisms when folks pour it into the triple store

elgar: edded all of the xref that i could find
... used best judgement selecting reasonable sources

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

elgar: folks might want SNOMED
... have added comments to the overall structure into google project /doc directory

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

i suspect matthias_samwald would be interested as well

[elgar unable to connect via Mibbit]

<matthias_samwald> (i am still unable to connect via audio, giving up now. will read the irc though)

matthias_samwald, you could try *0

imports into triple store

AnjaJentzsch: converted to RDF
... unsure about Medicare Plan D over-the-counter drugs
... asking for help from d2r folks

<Joanne> what's *0 ? ( I was muted myself -- i sent Elgar and Peter Kos an email with each other's email address)

AnjaJentzsch: end point is up, folks can query the server

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

Susie: you can pick up @@1's comments from last week's minutes
... my interpreation: folks are sometimes covered by both BCBS and Medicare

AnjaJentzsch: @@2 and Jun submitted a demo to linked data

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

AnjaJentzsch: can query for alternative medicines
... might be busy for the next hours/days

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

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

Susie: alternative plans?

AnjaJentzsch: any tool which queries the...

Susie: we want to extract data from panel 2 from a DuBois paper
... has DSM codes
... Trish was going to look at correspondance
... also asked Joanne and Michel

Trish: gone through part
... for diagnostics, finding MRI, ...
... was feading panel 2 text to NCBI's tagging tool
... matches found for e.g. memory recall issues

Susie: good coverage from one ontology?

Trish: hitting SNOMED NCIT, BirnLex
... not sure all that has gone into the neuroinformatics framework

Susie: unsure of intersection of those
... Mary Anne Martone might have the answer

Trish: spoked with Birn folks yesterday

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

Joanne: think Trish has gotten more out of Panel 2
... met with Michel, who i expect is working on querying it

Michel: you can stick in some text, and get some markup
... but you don't get ontology matches through the web interface
... have to fall back to the web service

Trish: also having trouble with the web interface

Joanne: you get back a cloud of terms, e.g. memory, referenced many times
... don't see the ontologies
... terminizer draws on fewer ontologies, but has more useful interface
... had exactly what i needed for the influenza ontology

Trish: have time to continue on this

Susie: one we see the best fit ontologies, need to choose
... seems like SNOMED and NCI were the best

Lynn: am a PI on the Disease Ontology ontology
... can't distribute SNOMED on the web

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

Lynn: BFO ontology is very new

Colin: propose OBO foundry

Peter: some of the electronic medical records ontologies are based on their implementation system
... seen a bunch of source datasets
... is it exceptable to code towards ICD9 or LOINC?

Susie: final focus is to develop TMO and develop an app to use it
... we've id'd a bunch of sources
... prolly best to map the data sources we're using to terminilogies already applied there
... for EMR, we've been using Indivo where possible
... asked Ben Adida and Ken Mandel to make the rest available
... doesn't look like it will happen in time, so we're rolling our own
... makes sense to make it as like an EMR as possible
... we wouldn't seen LOINC or ICD9 in pharmas

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

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

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

<cdenney> is anyone using MedDRA terms?

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

Lynn: also if it's in OBO foundry

Susie: Trish, you're taking the lead on panel 2 of DuBois
... can you get us some mappings by next week?

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

Susie: i've been generating fake patient data in Indivo where possible
... Peter has be reviewing and enhancing
... three sections:
... .. demographitcs, contact
... .. genetics profile
... .. encounters
... Peter has improvied demo and contact info, as well as static info
... put together some hemo data, cholestoral, ... in encounters
... hoping peter can help with realistic data for other encounters, e.g. patient presents symptoms
... would like to complete one patient and develop 5 more in a google doc
... have discussed the intended distribution of patient data
... Indivo is capturing XML data
... expect ericP to GRDDL it

Peter: will try, have other high-priority projects
... can look at the first patient set this week, the other patient sets in the next two weeks
... hemotology was 2 hours
... another 2 hours for the other aspects
... quite a lot of evening time, maybe 6 hours?

Joanne: what can you turf to others?

Peter: two aspects:
... .. examine Indivo and look at expression therein
... .. translating coding terminology
... finding the codes which match the use case example data
... would help if the use case data were already input

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

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

[XML template]

Susie: already have list of patients (.doc), exchanged with Peter
... will make available

Chris: intrested in the display of the pharmacogenetics section
... sent you an exmaple of the bedside data needed to tailor substance adminstration

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

data loading

Susie: user interface

user interface

Bosse: looked into Openvista which Chris proposed
... is already a good user interface
... enhancing for tailored medicine or treatment
... propose Emanual P of Novartis's approach
... menu of options
... e.g. point to a word
... link to a faceted browser
... have good answer from Chris, will extend
... i have not gotten OpenVista running
... saw video presentation
... is a structure/organized interface
... am not an expert developer any more
... need a developer

Andreas: OpenVista is based on TCRS (the VA system)
... sent Chris a sample of TCRS
... i recommend adding a tab to OpenVista
... code is in C#
... adding a tab is easy

<scribe> ACTION: Andreas to send said link to Susie to incorporate into minutes [recorded in http://www.w3.org/2009/10/29-hcls2-minutes.html#action01]

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

Susie: we don't need a strong interface for the paper
... need to decide if the tool allows the physician enter symptoms and the tool does some inferencing
... or a tool for researchers
... need to decide what interface we want to demo and where to start

Andreas: pretty sure that CTRS is available
... not sure if it's open source
... it's avail from Delphi

f2f logistics

Susie: task break-out time allocated
... will re-send f2f agenda, hilighting break-out session, and including dial-in logistics for TMO call

- DRAFT -

TMO

29 Oct 2009

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