<Sivaram> Sivaram here - 216 area code

<Sivaram> Thx. Joining this after a long long time

<JoanneandBob> Sivram, good to have you!

<JoanneandBob> Bob and I have to leave in about 10 minutes for an other meeting. Apologies

<Sivaram> Thx. good to see you here too

http://www.w3.org/wiki/HCLSIG/PharmaOntology/Meetings/2011-06-23_Conference_Call

<JoanneandBob> '' Agenda''' * Paper: deadlines (Scott) * Paper: introduction predictive methods * Paper: text-mining (Adrien) * Paper: ontology (Adrien, Michel, Scott, Matthias, BobF) * Paper: conversion + mapping of warfarin pharmacogenomic data (Joanne, Tim, ...) * Paper: kb development (Iker, EricP) * AOB

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

core scenerio on warfarin dosage

<JoanneandBob> +q

scott: patient data needs to be in a form where we query about snps and gwas outcomes

ack

joanne: what's the purpose?

scott: main message - importance of linked data to provide molecular knowledge to personalized patient care

<mscottm> joanne: still sounds like the focus is too much on information modelling

<JoanneandBob> we have to go. really sorry about the conflict

<mscottm> bye Joanne and Bob.

<ericP> i think that having a couple of motivating queries would demonstrate the value of the self-organizing/self-integrating data

bosse: personalized care will consider more than genetics

elgar: predictive algorithms use large feature vectors
... more information the better
... datasets all over the place
... accuracy of predictions - up to 52%
... improving would be good; having a tool that uses the different methods, and shows the overlap,

ericP: positive and negative indicators

elgar: FDA labels ~40%; pharmacogenomic predictor has 44% accuracy
... snps are expensive; the predictive value is comparable

scott: information is highly fragmented in hospitals; so getting additional info linked in has high value
... how do we make use of existing linked data resources?

<ericP> michel: want to see relationships, with a bit more genetic variation and outcomes

<ericP> ... we haven't been exposing new data sources

<ericP> mscottm: i thought that would come from dbSNP or SNPpedia or pharmaKB

dbsnp: ftp://ftp.ncbi.nih.gov/snp/database/

ER model: ftp://ftp.ncbi.nih.gov/snp/database/erd_dbSNP.pdf

<iker> this is the sql schema ftp://ftp.ncbi.nih.gov/snp/database/organism_schema/human_9606

<iker> semm to be updated

<ericP> Homo sapiens9606humanhs1999-11-05 17:30:00.02009-08-07 15:04:00.0pri human_9606humansp96060137.1

<iker> instructions to create a local copy at ftp://ftp.ncbi.nih.gov/snp/database/README.create_local_dbSNP.txt

<ericP> ethnicity, SNP score, reference sequence

<iker> eric, changed my appointment, I will be here within 40 min

<iker> talk through IRC?

<ericP> sure

<iker> great, then i will wait for you

<ericP> works well for me. i need to eat (if you don't want to read what i accidentally type as i collapse on the keyboard) but 40 mins should be plenty

<iker> jeje, ok

<mscottm> http://www.sciencemag.org/content/early/2011/05/18/science.1207018.abstract

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Got date from IRC log name: 23 Jun 2011
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