19 May 2011

See also: IRC log


Bob_Powers, mscottm, [IPcaller], Tony, +, +1.781.431.aabb, ericP


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

Michel: Agenda 1) demo, like Iker, then 2) paper

Iker, can you dial in?

<iker> one moment please

Good, thx!

<iker> i am having problems with my VoiP service

Michel: Discussion of paper

paper from Chest http://chestjournal.chestpubs.org/content/133/6_suppl/160S.full.pdf

Bosse: Use case in a care situation might be difficult
... could develop how info could help in pharma
... interested in making case for pharma; even if just around clinical trials

<michel> action item - Bosse to develop pharma-oriented use case for pharmacogenomics - will be nice to tie to a patient use case

Elgar: Can look at algorithms that have already been developed
... everything ties into the use case

Michel: Portion of use case: doctor gathers info, warfarin-dosing.org(?)

Elgar: Interested in analysis part
... want to understand where others did not have sufficient info
... have data, mash them up, then drill down; if we use the data, can we deal w. one of the algorithms than they did?

Michel: Ambitious?

Matthias: Editors sent requirement, top of google doc
... review or research article?

Scott: Will review original email.

<BobF> Michel: http://www.warfarindosing.org is the correct URL

Scott: suggested that we do pgx paper

<mscottm> The answer to this paste was yes: >>>>> Thank you for the invitation to write on the �Development of Multi-SNP

<mscottm> >>>>> Predictive Models in Pharmacogenomics�. We have been working on

<mscottm> >>>>> incorporating SNP's into our Translational Medicine Knowledge Base in

<mscottm> >>>>> one of the task forces of the W3C Health Care and Life Sciences

<mscottm> >>>>> Interest Group (HCLS IG). We would like to write a paper about an

<mscottm> >>>>> approach for integrating SNP's into multidisclipinary studies for

<mscottm> >>>>> translational medicine. Would that fit your needs?

ericP and Michel in discussion about false negatives, false positives

ericP: Sounds like low yield use case?
... machine gets to make decision and it always errs in one direction
... radiologist did not match microcalcification
... so machine can help where you otherwise might have missed

Elgar: This is clinical decision support, part of what we are trying to represent
... based on this genotype, we expect that patient is higher- or lower-metabolizer
... original idea is to focus on clinical decision support alone
... research, etc, other scenarios can use one pgx representation
... patient can be influenced by warfarin-genotype

Scott: Started on breast cancer: reason to go to warfarin is that bc is only expression profiles
... expression profiles are more challenging to model than SNPs
... warfarin use case is more clear cut
... agree w. Matthias; use of pgx for translational medicine purposes
... also come up w representations for other biomarkers?

ericP: If is has both false negs and false positives, clincian always has to monitor patient anyway

Scott: Tumor stratification has a nicer (skit?)

ericP: Vigilance is use case here?

Michel: Dosage ranges do change; standard warfarin dosing is wrong > 50%

Matthias: Modeling all this in OWL is nontrivial

Michel: We can highlight this in paper: chance of hurting patient w/o info
... warfarin on pharmGKB site, need to convert to RDF

<michel> http://www.pharmgkb.org/do/serve?objId=PA162355460&objCls=PhenotypeDataset#tabview=tab2

BobF: On a call w pharmGKG, talking about representing in RDF; want to monitor this

<mscottm> http://www.snpedia.com/index.php/Warfarin

ericP: converting vs chartering :-)

Michel: Ontology.

<iker> sorry, but i am definitely unable to join the conversation

Michel: can you do sparql query?
... share a raw RDF file.

Web Protege is a good idea.

Michel: Would need to understand axioms w. web Protege

Scott: Need your own server.

Michel: Protege 3 has client-server, configure acct etc

<iker> we have got an instance of webprotege with breast cancer ontology at

Scott: Would like to get feedback on web Protege

<iker> you can check

Iker: Could you set up a project for us?

<michel> iker would you be able to setup an instance of webprotege for our project?

<iker> yes, no problem at all


<matthias_samwald> hooray!

Matthias: Easier to use a good client than just a doc
... Web Protege has notes etc

Scott: PatientsLikeMe has written back. "What are your specific areas of interest?"

<iker> Would we start the project from scratch or do we have any ontology already implemented?

<Adrien> on google doc there is a diagram that will help start the ontology

Summary of Action Items

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