HCLSIG/PharmaOntology/Meetings/2010-06-24 Conference Call

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Conference Details 

* Date of Call: Thursday June 24 2010 
* Time of Call: 12:00pm - 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 quick start: Click on mibbit for instant IRC access
* Duration: 1h 
* Convener: Susie


Agenda


Minutes

Attendees: Bob, Christi, Trish, Joanne, Matthias, Elgar, Chris, Scott, EricP, Susie

<Joanne> Brainstorming as to next steps. Outreach closely tied to OR and Strategy

<Joanne> SS: 1. Outreach

<Joanne> SS: 2. Ongoing

<Joanne> SS: 3. New ideas

<Joanne> SS: Outreach

<Susie> http://jointsummits2011.amia.org/

<Joanne> SS: Outreach: Susie got email from Nigam Shah, re a new Translational Bioinformatics Summit, we had a poster and heard it was a good meeting

<Joanne> SS: wondering if was a good meeting for us to have our next paper

<Joanne> Paper proposals due 16 AUG, 18 OCT Panel, and 15 Dec Abstract prop. Suggests Paper Proposal fo r16 Aug.

<Joanne> 4 tracks: methodological innovations, concepts tools and techs to integrate ... , integrat analy, representaing and relating, ... clinical practice

<Joanne> SS: thinks concepts and tools may be best fit. Now asks for input:

<Joanne> Asks what we could get done in that time frame?

<Joanne> Seems tight.

<Joanne> Talking about extending BioOntology practice of taking one of the papers and expanding them for journal publicaions

<Joanne> Trish: could EMERGE work included? VA System and Conor

<Joanne> Susie - it could be interesting to reach out to Conor to see if we can collaborate to get something out for submission - he may be busy

<Joanne> Chris: Could be, haven't wanted to push him, but is a good idea, plans are in place and they do want to work with us. May be possible for Michel and Luke to get involved and take it forward

<Joanne> SS: Suggests sending Conor an email about working together on a submission and see what response is

<Joanne> SS: we could always go for the abstract submission deadline, which gives us time.

<Joanne> Trish - yes, if we can't put in for a paper, then go for abstract

<Joanne> Chris will send email to Conner checking his interest.

<Joanne> SS - suspects we'll be invited by biointologies to submit a longer paper for submission to journal of web semantics

<bobP> Susie: Deadline should be Oct timeframe

<bobP> ...Any other Oct deadline meetings?

<Joanne> Joanne is stepping a way for a minute and is on Mute because I need to move my car

<bobP> Trish: looking through meetings;

<Trish> Here are some conference listings: http://www.bioontology.org/news

<bobP> Scott: TRX-10 translational research excellence, Australia

<bobP> Susie: Looking for deadline in Oct, rather than meeting in Oct

<mscottm> http://www.swat4ls.org/

<bobP> ...Maybe we should continue to look for meetings...

<bobP> Scott: SWAT-LS(?) not sure about submission date

<bobP> Trish: Looks like Oct 18 deadline

<mscottm> http://www.swat4ls.org/2010/info.php#dates

<bobP> Susie: ISMB ? meeting is in a couple of weeks; look into ISMB 2011?

<bobP> Susie: ISMB 2011 Vienna, website doesn't exist yet; 6-month lead-time might have Dec deadline

<bobP> ...Bio-IT World doesn't require papers

<bobP> Joanne/Chris: didn't hear back from ITMAP

<Trish> http://www.itmat.upenn.edu/symposium.shtml

<bobP> Joanne: ITMAP Oct 26,27 Gerret(?) Fitzgerald

<Joanne> Molly J. Reagan Executive Assistant to Garret A. FitzGerald, MD Department of Pharmacology Institute for Translational Medicine and Therapeutics

<Trish> 2nd International Conference on Biomedical Ontologies, 2011 Barry Smith announced at the OBO Foundry workshop this week that the 2nd International Conference on Biomedical Ontologies will be held in Buffalo, New York, US on the July 29th-31st 2011.

<bobP> Susie: Chris will follow up w. Conor re AMIA TBI paper

<bobP> ...Submit abstract in Dec for AMIA TBI talk

<bobP> ...Accept invitation to Bioinformatics if offerred

<bobP> ...Keep eye on ISMB 2011

<bobP> ...SWAT4LS may be academic; looking for pharma/industry too

<bobP> Scott: Swat4LS would probably welcome our contribution

<bobP> ...If we continue along EHR proof-of-concept then we could probably get in

<bobP> ...Europe has influenced Swat, bioinformatics emphasis

<bobP> Susie: IEEE bioinformatics meeting Hong Kong Dec

<Susie> http://www.math.hkbu.edu.hk/BIBM2010/

<bobP> TMO would fit into this Hong Kong workshop

<bobP> This week in Shanghai in Nov 1st Int Wkshp August deadline

<epichler> http://www.ontologydynamics.org/od/index.php/seres2010/

<bobP> Susie: Maybe we should try for non-semweb meetings

<bobP> Susie: I will produce a list of upcoming options for meetings

<bobP> Susie: Ongoing work

<bobP> ...Patient records: make sure they're interconnected w. other data

<bobP> ...Did ask Indivo to join our call; We're really busy, look at the website

<bobP> Eric: Chasing down Indivo

<bobP> Matthias has set up webinar, plus semantic wiki

<bobP> Matthias: discussion about semantic wiki, HL7

<bobP> Susie: Tom Jones at Oracle supported HL7, but didn't know him

<bobP> Look at interface? is there RDF?

<bobP> Matthias: Demo looks quite intuitive

<bobP> Susie: To date we've been translating to triple-store

<bobP> ...Do we want to continue w. triple store aaproach, as likely better suited to Indivo

<bobP> Matthias: CTO knows more about it; may be able to tell us more

<bobP> Susie: AOB about patient records?

<bobP> ...EHR interface is interesting; but it not something we nec. put our weight behind

<bobP> ...Maybe find if Terminology group could work on the EHR side; we have limited bandwidth here

<bobP> ...Maybe we could combine efforts w. Term., possibly separate calls

<bobP> Scott: Terminology summary: We have sample path + radiology reports

<bobP> ...Would like to model these reports in RDF, extract info of interest from free text

<bobP> ...Find discrepancies in report, where biopsy doesn't hit the mark.

<bobP> (Bob: totally cool)

<bobP> ...John Madden, Daniel Rubin, have discussed possiblities where biopsy is wrong

<bobP> ...See what kind of RDF we need, then find if RDF can contain Lab-x, snomed, TMO

<bobP> ...Would be an opp for TMO to be involved in actual clinical reports

<bobP> ...Maybe scale up if we can do this the right way.

<bobP> Chris: This is where I'd like to spend some time, put together a step-by-step plan, for clinicians to comply w. standards

<bobP> ...You have 30/40% of records electronic; Can we dump your data into these stores and demo?

<bobP> Scott: We might be able to make mid-Aug deadline

<bobP> ...Issue has been to get our hands on the data

<bobP> ...Mammogram scenario, biopsies, markers, look for clinical trials; this all might be interesting

<bobP> ...Can link out from mammogram use case

<bobP> Susie: Introduce idea: improving links around patient records; like EHR being done w. Terminology

<bobP> ...Should also think about TMO work: can we use ont to integrate info about drug targets

<bobP> ...Compare/contrast human/animal models and data

<susie> Christi: Can look at existing documented use cases for ideas

<bobP> ...Would like to discuss these things on next call.

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