<michel> zakim ?PP9 is michel

<michel> +1.781.431.aadd is epichler

<epichler> thanks matthias!

<matthias_samwald> you can do the same for RRSagent, which is actually more helpful for the minutes

<matthias_samwald> (i think)

<michel> wiki page: http://esw.w3.org/HCLSIG/PharmaOntology/Paper

<whetzel> a discussion on the HCLS & TMO structure and activities. Michel Confirmed

Michel: 1) will add paragraph on weekly calls etc
... Paper should indicate that the KB is an important component, plus patient records

<whetzel> agree

Trish: Ontology is just a framework for something more interesting

Michel: Bridge patient records over the LODD
... would like to see the paper more about the entire effort

Joanne: We talk about research to clinic and back again, but the research component isn't really addressed
... 15) talk about it from a research perspective

Michel: 2) Ref. ontologies try to cover comprehensively; but we are much more applied
... text should describe our evaluation
... need to contrast our effort vs. efforts of the reference ontologies

Joanne: 3) 5) and 10) are covered by PeterT and PeterK

Michel: 4) Eric has come up w. framework for unit testing

<mscottm> ericP has come up - ericP's bot is now alerted ;)

Michel: convert to Indivo XML, converted then to RDF in a quad format
... final piece for unit testing, will translate to RDF, describe your sparql
... system needs to be described

Scott: It's a really cool system

Yes.

Joanne: Scott for number 4)

<Joanne> Authors- add scott

Michel: 5) detailing consistency; came from reviewer comments

<Jim> Scott, what is your affiliation?

<Joanne> Michel suggests, all agree keep 1st and last and rest will be alphabetical

<mscottm> I had trouble hearing Michel just now too

Michel: 6) BigOWLIM

Matthias: Checked consistency of TMO + LODD
... can try to execute sparql queries, but need to check datasets

<Joanne> Scott's afiliation (scott, please correct) Leiden University Medical Center and the University of Amsterdam.

Michel: 7) overview figure, next couple of days
... 8) figure for Fig.1, Chime's got it done

<mscottm> I have double affil.. LUMC and University of Amsterdam

<Joanne> thanks Scott!

<michel> http://esw.w3.org/HCLSIG/PharmaOntology/Diagrams

<mscottm> If it gets too crowded, just use the LUMC. :)

Michel: Fig. 1 will be overview, then a query diagram
... 9) mapping to CPR: EricP and Chime have to do this

Eric: Documenting what the queries, here's how the mapping works, etc
... talked about Indivo XML, Michel also suggested testing framework
... Bragging points: If you have a sense of test coverage from user community
... then you can get messages saying which queries failed and can get quick feedback
... don't have to gang up all the testing at the end

Scott: Xtreme programming for ontological development

XPOD!!

Eric: Every sparql implementation has this functionality

Michel: Update KB w. patient data?
... see if it fits at the last minute
... Query that spans more or all datasets
... 14) related work is now broader than before: snomed, nci thesaurus

Jim McCusker: Send your suggestions re related work

Michel: 15) Research use case

Joanne: 13) and 15) are two different aspects of just about the same thing
... a) Enabling eScience on a much larger scale
... b) focussed on pharma might miss the message of having a translational medicine ontology
... users of different roles; Message should be clear that different users can view w diff lenses
... a) If we could say something important re eScience

Scott: NL trying to get Science Center established
... eSci sometimes start talking re big data
... TMO talks about something in the gene list that might be useful
... I will give it a go. This is important.

<ericP> my model for a high-throuput analysis lab is Fred Hutchinson Cancer Research

<ericP> they were the folks who convinced me that they weren't good users of SemWeb stuff

Chat on the document itself! Go to the 'Share' button and add your email.

https://docs0.google.com/document/d/1sh0lttGpqXZuQL-WxTSqj5ZjMRFeYUciHhkHfqRSrTk/edit?hl=en&authkey=CK7D5YYO&pli=1#

<Joanne> https://docs.google.com/document/d/1sh0lttGpqXZuQL-WxTSqj5ZjMRFeYUciHhkHfqRSrTk/edit?authkey=CK7D5YYO&hl=en#

<michel> scribenick bobP

This is scribe.perl Revision: 1.135  of Date: 2009/03/02 03:52:20  
Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/

Guessing input format: RRSAgent_Text_Format (score 1.00)

No ScribeNick specified.  Guessing ScribeNick: Bob
Inferring Scribes: Bob

WARNING: No "Topic:" lines found.


WARNING: No "Present: ... " found!
Possibly Present: Bo_Anderson Bob Bob_Powers Eric Jim Joanne Matthias Michel P24 P9 Scott Trish aaaa aacc aadd epichler ericP https matthias_samwald mscottm whetzel
You can indicate people for the Present list like this:
        <dbooth> Present: dbooth jonathan mary
        <dbooth> Present+ amy


WARNING: No meeting title found!
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<dbooth> Meeting: Weekly Baking Club Meeting


WARNING: No meeting chair found!
You should specify the meeting chair like this:
<dbooth> Chair: dbooth

Got date from IRC log name: 11 Nov 2010
Guessing minutes URL: http://www.w3.org/2010/11/11-hcls2-minutes.html
People with action items: 

WARNING: No "Topic: ..." lines found!  
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Explanation: "Topic: ..." lines are used to indicate the start of 
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<dbooth> Topic: Review of Amy's report