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