HCLSIG/PharmaOntology/Meetings/2010-01-07 Conference Call

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Conference Details

  • Date of Call: Thursday January 7 2009
  • Time of Call: 12:00am - 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: 1h
  • Convener: Susie

Agenda

  • AMIA TBI update - Susie
  • Ontology Update - Colin
  • Next Steps
    • Structuring inclusion/exclusion criteria - Michel, Susie
    • Mapping drug codes - Michel
    • Physician UI - All
    • Drug ontology - Susie
  • Outeach
    • BioOntologies SIG - Susie
    • UPenn Translational Medicine - Chris
    • CSHALS - Elgar
  • AOB

Minutes

Attendees: Chris, Colin, Bosse, Trish, Elgar, Christi, EricP, Scott, Susie

Apologies: Michel

<Susie2> AMIA TBI Submission

<Susie2> Trish: AMIA TBI submission accepted as a poster

<Susie2> Trish: Disappointing that it wasn't accepted as a talk

<Susie2> Trish: General decision was to go ahead

<Susie2> Trish: Dates are March 10-12

<Susie2> Trish and Chris will be at the meeting

<Susie2> Trish: Jan. 14 the resubmission is due

<Susie2> Trish: Don't think we need to make changes

<Susie2> Trish: Think abstract for a poster submission was the same as a poster for a short paper submission

<Susie2> Christi: Need to give 2 weeks notice on submissions

<Susie2> Trish: Will ask for a week's extension

<Susie2> Elgar: Good to do initial drafts on GoogleDoc, then move to word

<Susie2> Susie: Good to get to Word early so can be reviewed

<Susie2> Susie: Aim to get the poster complete by 3rd week of Feb.

<Susie2> Trish: I can print the poster

<Susie2> Susie: Feedback was that there wasn't enough content on anything

<Susie2> Susie: Yet they had set the page limit

<Susie2> Colin: The abstract was focused on aspiration

<Susie2> Christi: Maybe people are concerned that anyone in the world could contribute to a wiki

<Susie2> Susie: Could name the project rather than individuals on submissions

<Susie2> Susie: Would depend upon the place we make the submission

<Susie2> Bosse: Important to promote the collaborate aspect of the wiki

<Susie2> EricP: Big stength of Semantic Web is to promote collaboration

<mscottm> 1+

<Susie2> Ontology Update

<Susie2> Colin: Talking to Barry with the ontology his collaborators have been working on

<Susie2> Colin: Barry's group has been doing a lot of work on clinical aspects

<Susie2> Colin: Looking at how we can align

<Susie2> Colin: Should be able to off load some of the clinical aspects

<Susie2> Colin: They are happy to let us look after the conceptual space

<colin> http://code.google.com/p/ogms/

<Susie2> Colin: Will give a detailed ontology update during the next call

<Susie2> Next steps

<Susie2> Susie: Michel has rdfized the NDC dataset, but there aren’t any outward links

<Susie2> Here’s an example entry:

<Susie2> http://bio2rdf.semanticscience.org:8012/describe/?url=http://bio2rdf.org/ndc:listing_851

<Susie2> so he looked at one or two of the NDC codes used in the patient data e.g.

<Susie2> http://bio2rdf.semanticscience.org:8017/describe/?url=nodeID://b46849&sid=56

<Susie2> but the numbers didn't match up?

<Susie2> The NDC Labeler code is 5 digits and the product code is 3 or 4 digits.

<Susie2> Michel is looking to map inclusion/exclusion criteria to NCBO ontologies

<Susie2> Colin: He's looking to do this the right way

<Susie2> Chris: think this is going to blossom in future years

<Susie2> Chris: Isolating patient groups isn't going to be static going forwards

<Susie2> Chris: Need to filter data in various ways

<Susie2> Bosse: I agree it's a good area

<Susie2> Bosse: Inclusion and Exclusion are really the opposite of each other

<Susie2> Bosse: Really relates to the phenotypes

<Susie2> Bosse: Physicians in pharma do tend to use what was done before when selecting criteria

<Susie2> Chris: To narrow down to groups need to have full control

<Susie2> Chris: Will need new criteria going forwards

<ericP> there are probably lots of unspoken criteria embedded in the patient acquisition protocol and the interpretation of "obvious" requirements on the part of the folks contribing patients

<Susie2> Susie: Physician interface

<Susie2> Susie: Would be nice to demonstrate our work

<Susie2> Susie: But would need people to do the work

<Susie2> Susie: Have a call focused on the UI

<Susie2> Susie: Bosse lead the work?

<Susie2> Bosse: Yes, still interested

<Susie2> Bosse: Chris and I will discuss, and then we'll cover it in a call

<Susie2> Drug Ontology

<Susie2> Susie: became interest when noticed it was a gap when we developed tmo and in the LODD work

<Susie2> Susie: very useful as companies become more networked

<Susie2> Elgar: This would also be key for many public domain and commercial enterprises

<Susie2> Colin: Would be happy to put an initial report together

<Susie2> Colin: Lots done by ChEBI and ChEMBL

<Susie2> Bosse: Would IMI work be relevant?

<Susie2> Bosse: Very important that efforts are aligned

<Susie2> Bosse: IMI might be at a different level

<bbalsa> imi call: http://www.imi.europa.eu/calls-02_en.html

<Susie2> Susie: What happened to Samson's drug ontology

<Susie2> Trish: Will ask him

<Susie2> Colin: Saw a pre-released version

<Susie2> EricP: Used a piece of it for the COI demonstrator

<Susie2> Susie: Let's skip outreach today

<Susie2> Susie: How frequently show we have calls? Want to make good progress.

<Susie2> Colin: Having a goal is important for us to make progress too.

<Susie2> Chris: Let's mull over ideas over January, and set goals in early Feb.