16:01:16 <RRSAgent> RRSAgent has joined #hcls2
16:01:16 <RRSAgent> logging to http://www.w3.org/2011/06/23-hcls2-irc
16:01:21 <Sivaram> Sivaram has joined #hcls2
16:01:22 <michel> rrsagent, make logs public
16:01:30 <michel> zakim, this is tmo
16:01:32 <Zakim> ok, michel; that matches SW_HCLS(TMO)11:00AM
16:02:05 <Zakim> +??P0
16:02:16 <Zakim> +??P2
16:02:28 <Zakim> + +33.3.83.59.aaaa
16:02:43 <Zakim> + +1.216.373.aabb
16:02:48 <mscottm> Zakim, who is here?
16:02:48 <Zakim> On the phone I see Joanne_Luciano, mscottm, ??P0, ??P2, +33.3.83.59.aaaa, +1.216.373.aabb
16:02:51 <Zakim> On IRC I see Sivaram, RRSAgent, mscottm, Zakim, michel, iker, bbalsa, ericP
16:02:57 <adrien> adrien has joined #HCLS2
16:03:05 <Sivaram> Sivaram here  - 216 area code
16:03:39 <JoanneandBob> JoanneandBob has joined #hcls2
16:04:20 <Zakim> +??P13
16:04:32 <Sivaram> Thx. Joining this after a long long time
16:04:38 <michel> zakim, ??P13 is bbalsa
16:04:38 <Zakim> +bbalsa; got it
16:04:49 <michel> zakim, ??P0 is michel
16:04:49 <Zakim> +michel; got it
16:04:54 <JoanneandBob> Sivram, good to have you!
16:05:19 <JoanneandBob> Bob and I have to leave in about 10 minutes for an other meeting. Apologies
16:05:26 <epichler> epichler has joined #HCLS2
16:05:39 <Sivaram> Thx. good to see you here too
16:05:50 <michel> http://www.w3.org/wiki/HCLSIG/PharmaOntology/Meetings/2011-06-23_Conference_Call
16:05:50 <Zakim> + +1.617.324.aacc
16:06:18 <ericP> Zakim, aacc is me
16:06:18 <Zakim> +ericP; got it
16:07:22 <Zakim> + +1.781.431.aadd
16:07:30 <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
16:07:33 <mscottm> https://docs.google.com/document/d/1lKdDSb2uBBIeTEQAv2CyTHN_aVW63k9si1hmmilOMi0/edit?hl=en_US&authkey=CJGUtcwF
16:10:31 <michel> core scenerio on warfarin dosage
16:11:01 <JoanneandBob> +q
16:11:02 <michel> scott: patient data needs to be in a form where we query about snps and gwas outcomes
16:11:22 <michel> ack
16:11:47 <Zakim> -ericP
16:12:01 <Zakim> +ericP
16:12:45 <michel> joanne: what's the purpose?
16:13:44 <michel> scott: main message - importance of linked data to provide molecular knowledge to personalized patient care
16:14:57 <mscottm> joanne: still sounds like the focus is too much on information modelling
16:16:57 <JoanneandBob> we have to go.  really sorry about the conflict
16:18:27 <mscottm> bye Joanne and Bob.
16:18:40 <Zakim> -Joanne_Luciano
16:18:45 <ericP> i think that having a couple of motivating queries would demonstrate the value of the self-organizing/self-integrating data
16:19:12 <michel> bosse: personalized care will consider more than genetics
16:21:57 <michel> elgar: predictive algorithms use large feature vectors
16:22:01 <michel> elgar: more information the better
16:22:16 <michel> elgar: datasets all over the place 
16:23:16 <Zakim> -bbalsa
16:23:56 <michel> elgar: accuracy of predictions - up to 52%
16:24:01 <Zakim> +??P9
16:24:24 <michel> elgar: improving would be good; having a tool  that uses the different methods, and shows the overlap, 
16:26:17 <michel> ericP: positive and negative indicators
16:27:39 <michel> elgar: FDA labels ~40%; pharmacogenomic predictor has 44% accuracy
16:28:22 <michel> elgar: snps are expensive; the predictive value is comparable
16:30:27 <michel> scott: information is highly fragmented in hospitals; so getting additional info linked in has high value
16:33:05 <Zakim> -ericP
16:33:17 <Zakim> +ericP
16:38:44 <michel> scott: how do we make use of existing linked data resources?
16:40:49 <ericP> michel: want to see relationships, with a bit more genetic variation and outcomes
16:40:58 <ericP> ... we haven't been exposing new data sources
16:41:48 <ericP> mscottm: i thought that would come from dbSNP or SNPpedia or pharmaKB
16:42:39 <michel> dbsnp: ftp://ftp.ncbi.nih.gov/snp/database/
16:44:09 <iker> q+
16:44:54 <michel> ER model: ftp://ftp.ncbi.nih.gov/snp/database/erd_dbSNP.pdf
16:50:23 <iker> this is the sql schema ftp://ftp.ncbi.nih.gov/snp/database/organism_schema/human_9606
16:50:32 <iker> semm to be updated
16:50:43 <ericP> Homo sapiens9606humanhs1999-11-05 17:30:00.02009-08-07 15:04:00.0pri   human_9606humansp96060137.1
16:51:20 <iker> instructions to create a local copy at ftp://ftp.ncbi.nih.gov/snp/database/README.create_local_dbSNP.txt
16:51:50 <ericP> ethnicity, SNP score, reference sequence
16:56:33 <iker> eric, changed my appointment, I will be here within 40 min
16:56:39 <iker> talk through IRC?
16:57:00 <ericP> sure
16:57:13 <iker> great, then i will wait for you
16:58:29 <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
16:58:55 <iker> jeje, ok
17:01:01 <mscottm> http://www.sciencemag.org/content/early/2011/05/18/science.1207018.abstract
17:01:06 <Zakim> -ericP
17:01:07 <Zakim> - +1.216.373.aabb
17:01:08 <Zakim> - +33.3.83.59.aaaa
17:01:09 <Zakim> -michel
17:01:11 <Zakim> - +1.781.431.aadd
17:01:13 <Zakim> -??P9
17:01:21 <michel> rrsagent, draft minutes
17:01:21 <RRSAgent> I have made the request to generate http://www.w3.org/2011/06/23-hcls2-minutes.html michel
17:01:51 <mscottm> the link that I just added points to a paper that shows large differences between DNA and RNA in individuals
17:48:33 <mscottm> Zakim, who is here?
17:48:33 <Zakim> On the phone I see mscottm, ??P2
17:48:34 <Zakim> On IRC I see RRSAgent, mscottm, Zakim, michel, iker, ericP
17:48:47 <Zakim> -mscottm
17:53:47 <Zakim> disconnecting the lone participant, ??P2, in SW_HCLS(TMO)11:00AM
17:53:51 <Zakim> SW_HCLS(TMO)11:00AM has ended
17:53:52 <Zakim> Attendees were Joanne_Luciano, mscottm, +33.3.83.59.aaaa, +1.216.373.aabb, bbalsa, michel, +1.617.324.aacc, ericP, +1.781.431.aadd
17:54:21 <iker> hello
17:54:40 <iker> anybody there?
17:58:49 <mscottm> I am kind of here (with my 6 year old boy who is finishing his dinner, wife and daughter went to the store)
17:59:30 <mscottm> Somebody probably intercepted ericP on the way to his sandwich.
17:59:59 <mscottm> I haven't heard him sound that tired in a long time.
18:00:39 <iker> ok, thanks scott
18:02:26 <mscottm> If ericP shows up, I can call you on a landline and Skype you in to Zakim, if that helps. I will have to step away to bring my son to bed.
18:03:17 <iker> ok, thanks my skype id is iker.huerga
18:03:28 <iker> nice dreams to your son
18:04:33 <mscottm> Zakim, room for 3? 
18:04:34 <Zakim> ok, mscottm; conference Team_(hcls2)18:04Z scheduled with code 42572 (HCLS2) for 60 minutes until 1904Z
18:10:23 <Zakim> Team_(hcls2)18:04Z has now started
18:10:24 <Zakim> +mscottm
18:13:54 <mscottm> http://www.stanford.edu/~rubin/projects.html
18:23:38 <Zakim> +ericP
18:23:39 <Zakim> -ericP
18:23:39 <Zakim> +ericP
18:25:47 <mscottm> I'm muted now. mic and speakers.
18:38:02 <iker> ftp://ftp.ncbi.nih.gov/snp/database/README.create_local_dbSNP.txt
18:58:32 <iker> http://85.48.202.13:8890/sparql?default-graph-uri=&query=PREFIX+sider%3A+%3Chttp%3A%2F%2Fwww4.wiwiss.fu-berlin.de%2Fsider%2Fresource%2Fsider%2F%3E%0D%0APREFIX+diseasome%3A+%3Chttp%3A%2F%2Fwww4.wiwiss.fu-berlin.de%2Fdiseasome%2Fresource%2Fdiseasome%2F%3E%0D%0Aselect+distinct+%3FsideEffect+%3FgenesRelated%0D%0Awhere{%0D%0A%3Chttp%3A%2F%2Fwww4.wiwiss.fu-berlin.d
19:06:31 <iker> http://code.google.com/p/lindenb/source/browse/trunk/src/xsl/dbsnp2rdf.xsl
19:07:54 <ericP> FIELDS TERMINATED BY '\t' ENCLOSED BY '' ESCAPED BY '\\'
19:07:55 <ericP> LINES TERMINATED BY '\n' STARTING BY ''
19:10:18 <iker> http://ben90.com/2011/06/import-bcp-output-file-into-mysql-database/
19:11:46 <ericP> mkfifo
19:15:00 <ericP> sudo su - mysql /bin/bash
19:16:08 <ericP> http://dev.mysql.com/doc/refman/5.1/en/load-data.html
19:20:06 <ericP> mysql> LOAD DATA INFILE 'Allele.bcp' INTO TABLE Allele;
19:20:06 <ericP> ERROR 29 (HY000): File '/var/lib/mysql/dbsnp/Allele.bcp' not found (Errcode: 2)
19:20:37 <Zakim> -ericP
19:25:37 <Zakim> disconnecting the lone participant, mscottm, in Team_(hcls2)18:04Z
19:25:41 <Zakim> Team_(hcls2)18:04Z has ended
19:25:41 <Zakim> Attendees were mscottm, ericP
20:10:23 <Zakim> Zakim has left #hcls2