scribenick Bob

<michel> https://docs.google.com/document/d/1lKdDSb2uBBIeTEQAv2CyTHN_aVW63k9si1hmmilOMi0/edit?hl=en&authkey=CJGUtcwF#

<AmitSheth> there is nothing at http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/

<michel> https://docs.google.com/document/d/1lKdDSb2uBBIeTEQAv2CyTHN_aVW63k9si1hmmilOMi0/edit?hl=en&authkey=CJGUtcwF#

Michel: Use case plus the data and the ontological discussions
... paper is about SNPs pxgx, how SNP's might be recorded in patient records

<joanne> pls post link to paper again. i see only a link to rhetorical structure

https://docs.google.com/document/d/1lKdDSb2uBBIeTEQAv2CyTHN_aVW63k9si1hmmilOMi0/edit?hl=en&authkey=CJGUtcwF#

scribe: breast cancer case: info still tied around gene expression as a biomarker
... a little bit further away from what we wanted to embark

<joanne> 12:09 Bob https://docs.google.com/document/d/1lKdDSb2uBBIeTEQAv2CyTHN_aVW63k9si1hmmilOMi0/edit?hl=en&authkey=CJGUtcwF#

<joanne> for bo

Michel: Breast cancer case suited for collab w BioRDF

<AmitSheth> +q

Michel: maybe a separate paper. One paper for SNPs, one paper for pharmacogenomics

Joanne: TMO to bridge;

Michel: Introduction by Eiker(?), startup w breast cancer interest
... there is a front end that uses TMO; based on what we published
... Learned as much as there is about warfarin
... dosing, SNP ids; also prediciton algorithms, interesting to see lots of work

<AmitSheth> was this shared on this group? http://news.sciencemag.org/sciencenow/2011/04/computer-algorithm-may-speed-dru.html?ref=hp

Michel: pharmGKB is interested. Wonder if we can look at semantic web services

<AmitSheth> +q

Michel: would be well placed to do prediction for a speicific patient

Elgar: What are predictions based on?

Michel: Testing is done by int'l normalized ratio INR: how active is the pathway for coagulation
... amt of warfarin needs to be balanced
... there are home monitoring kits to manage dosing
... factors other than the two genes are diet, etc that can change
... this is already a nice patient-specific case

Joanne: bc w BioRDF; warf w...
... Lib of Personalized Med has published on warfarin

Michel: Also genetic tests for low $
... genetic component explains 40% of dosage variance
... FDA has published the table reproduced in the doc
... but the table is less effective than other research

Elgar: We have two things that determine dosing
... so there is an input vector for the algorithms
... dosage recommendation is not great for accuracy

<joanne> what are the inputs?

Elgar: we would like to look at 1) can we find other features to consider? and 2) look at diff prediction algorithms

Michel: There are papers that crit pgx approach; doesn't work for people >65
... reduced metabolism, loss of liver function, etc

<AmitSheth> Looks like being on the queue does not help: so here are questions/comments: (a) have you thought about the quality of data you are integrating? (b) quality of intergration?

Michel: consider a range of factors beyond genetics, should be able to account for more variance

(well, warfariin dosing is tough!)

Elgar: No idea at moment how data analysis and prediction would sound

Michel: Have touched the surface; maybe take closer look at prediction aspect

Joanne: Interested in prediction, along w Elgar

Michel: We need a better understanding of what they use to train
... one of papers in section on prediction; performance of the different approaches
... are there some elements that are being missed, even in state-of-the-art
... could we add more features to explain more variance?

<joanne> here's one tonellato warfarin avatar paper: http://www.google.com/url?sa=t&source=web&cd=4&sqi=2&ved=0CDAQFjAD&url=http%3A%2F%2Fpeople.dbmi.columbia.edu%2F~rip7002%2FSite%2FHome_files%2FSimulated%2520Comparison%2520of%2520Warfarin%2520Treatment%2520Protocols%2520Chi%25202010.pdf&ei=itDCTeG-K9PqgQeMlJHaBg&usg=AFQjCNGRNZdX7CCrLw3Mh5YJK3pIHkV7Yg&sig2=GmqL31HAsPP

What is quality of data that you are going to use?

Michel: Reduce dimensionality of data; can analytically find strong correlates in the input
... we would complement what they already use w new contributions

<joanne> Look at page 17 and 18 of this (at least!) http://docs.google.com/viewer?a=v&q=cache:gaOqmO8SKj4J:online.law.asu.edu/events/Personalized_Medicine/ppts/Monday/Afternoon/Session_III/Tonellato.pdf+tonellato+warfarin+filetype:PDF&hl=en&gl=us&pid=bl&srcid=ADGEESi-OP2QSvCcWEh-8WEj1Ukq0ApfCCv3_xqKfTNFBWbTdKlZ3_TzyCVp475MFh1xs1qbV8YTcHVXGWnfxpXHSE8HXiak2sH59WHNMhSzd

Amit(?): question about correlates and alignment

Michel: Can't comment on even their quality of data
... won't build a new algorithm for paper
... how do we represent facts; mostly focus on rep of knowledge
... we might build a better predictor later :-)
... Looked at pathways from pharmGKB; basically a diagram
... don't know how well maps out to Reactome or Kegg
... There was a GWAS on pharmGKB; want to convert patient data wrt outcomes

<michel> http://www.pharmgkb.org/do/serve?objId=PA135603152#tabview=tab2

that's not the right link!

here's another one:

<michel> http://www.pharmgkb.org/do/serve?objId=PA165291561&objCls=PhenotypeDataset#tabview=tab1

Michel: Based on clinical and other demo factors
... this is the most important dataset for us; need to convert to semantic set for individual
... convert to RDF; ensure that our representation has all the fields, and in ontologies
... ontological nature of the representations

Joanne: will do tab-to-RDF

Michel: Are there other datasets that we might consider?

Joanne: emailing warfarin paper to everyone
... can set parameters flexibility in the avatars

Michel: Which field; does our ont have the slots?
... vis-a-vis predictive stuff that Russ did? Which fields might be missing, overlap of these.

Joanne: Probably have captured all the important ones

Michel: Warfarin case: enough for good investigation

Bosse: Would like to see link to pharam co

Michel: Label has been updated twice; gene but no dosing
... 2009 updated w table, w variance accounted for
... What kind of data are required to make decision? expensive to do trials

Bosse: Clinical trial could be the angle here.

Michel: Also what data the FDA requires so that becomes part of the label?

Amit: Interested to see how this is realized. Issues of data access, quality etc
... have developed tools to produce RDF
... capturing data is what I would like

Matthias: Interested in clinical decision support; how pgx data can be used for alerts etc
... seamless integration into clincial workloads

Michel: Adrian Coulet and I will work on representations

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: Amit AmitSheth Bosse Elgar Joanne Matthias Michel bbalsa epichler hcls2 https iker joined
You can indicate people for the Present list like this:
        <dbooth> Present: dbooth jonathan mary
        <dbooth> Present+ amy


WARNING: No meeting title found!
You should specify the meeting title like this:
<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: 05 May 2011
Guessing minutes URL: http://www.w3.org/2011/05/05-hcls2-minutes.html
People with action items: 

WARNING: No "Topic: ..." lines found!  
Resulting HTML may have an empty (invalid) <ol>...</ol>.

Explanation: "Topic: ..." lines are used to indicate the start of 
new discussion topics or agenda items, such as:
<dbooth> Topic: Review of Amy's report