See also: IRC log
scribenick bobP
<mscottm> thanks bobP!
<joanne> hello!
<joanne> What's "Idler's" mean (on the right hand side of mibbit)
<michel> elgar presented TMO at bio-it world
Michel: Discussion of paper, more
detail about use case
... Adrian Coulet w. sopharm; We are lucky to have Adrian
participate
<adriencoulet> thank you !
Michel: 1) warfarin 2) breast cancer; 2) let's talk about this story
Scott: Talked w Daniel Rueben(?) and John Madden about bc
<adriencoulet> Daniel Rubin
<adriencoulet> ?
Scott: lots of people understand
the terminology involved
... consider oncoDX and Mammaprint(?)
... making use of molecular info about patient in order to
stratify, to make better choices
... also discover clinical trials and drugs in
development
... easily understandable to the audience; reduces costs and
needless suffering
<michel> OncoDX: http://www.oncotypedx.com/en-US/Breast/HealthcareProfessional/ClinicalSummary.aspx
Scott: increases patient care. All nice goals for theoretical use cases
<michel> Mammaprint: http://www.agendia.com/pages/mammaprint/21.php
Scott: note that each use case
applied to millions of women
... also clinician-single patient application. Still needs to
be implemented in hospital IT
<michel> paper: https://docs.google.com/document/d/1lKdDSb2uBBIeTEQAv2CyTHN_aVW63k9si1hmmilOMi0/edit?hl=en&authkey=CJGUtcwF#
Scott: I wrote a few things
in
... not sitting on bc data, but we do have some kidney
transplant data.
... might be able to get some data from Mammaprint people
Joanne: Data are critical; any
public bc datasets?
... can bring in IO too
Scott - breaking up!
Scott: ... data did not have info, embedded in a giant object model
<scribe> ... dropped effort b/c did not want to parse thru it all.
UNKNOWN_SPEAKER: working w
theoretical scenarios, hardest challenge is to come up w
realistic gx profile
... nobody reading article will need to look at differential
expression
... we are putting forth a proof-of-concept
... but, true, the more realistic the better
<adriencoulet> http://www.pharmgkb.org/do/serve?objId=PA443560&objCls=Disease#tabview=tab6
<adriencoulet> some PGx about breast neoplasms
Joanne: Knows group w/in Zach's
dept
... Ponolacco(?)
Michel: Adrian has posted this link w. data
<joanne> thanks Adrien!
We lost Adrian
<joanne> Peter Tonellato <Peter_Tonellato at hms.harvard.edu>
Michel: Shows down to
alleles
... mostly tamoxifen datasets
<mscottm> All: when you aren't speaking, please mute (it should help us to get rid of the echo)
<joanne> Web Site for Peter Tonellato's group: http://lpm.hms.harvard.edu/
Michel: #7 looks good! Joanne agrees
<michel> http://www.pharmgkb.org/do/serve?objId=PA646603&objCls=PhenotypeDataset#tabview=tab2
Males do get bc.
Michel: Cool w. alleles, but no
outcomes here. Need to read the paper to understand
remission
... convert to RDF, then query?
... these are the actual data; Not been formalized to RDF
yet.
... will require some significant curation. Columnn headers
require some work.
... base change definitions, we will have to parse this on a
case-by-case basis
Matthias: commenting here
Joanne will develop use cases
Michel: Need to download the data and parse
<matthias_samwald> e.g., http://www.snpedia.com/index.php/CYP3A5 lists the allele names (*1, *5 etc.), but unfortunately not in a way that would make it show up in the current RDF version of SNPedia.
Joanne: TMO or separate ontology?
Matthias: Started ont, tried to
align everything w TMO and other authorities
... raw at the moment. Want to use it for clinical decision
support
Scott: Do you have use cases? Interviewing clinician?
Matthias: Blue sky research at the moment.
<mscottm> Univ. of Nancy
Adrian: PhD pharmacogenomics text mining
<mscottm> Adrien: Prof at Univ of Nancy, did PhD with PharmGKB, from Mark Musen's lab (just returned from NCBO to France)
<mscottm> Adrien recently published work on SO-Pharm
Michel: Submit 1st week in May(?)
<adriencoulet> http://www.loria.fr/~coulet/
Michel: important to develop use case, as it relates to PharmGKB website
Scott: Maybe hook up w Terminology call
Michel: Look at diagram, a
general model in advance of use case
... ontology would be purple boxes
Matthias asking about gene variant as attribute of population and not of person
Scott: Better to have sample population associated w gene frequency
<joanne> i have to leave now. Would someone volunteer to contact me later and be willing to go over the diagram with me - preferably tomorrow? Michel, ideally, but if you can't someone else who understands it as well (not having generated)
Scott: (Scott was asking here...)
<joanne> bye.
Matthias: Arrow from freq to pop?
<adriencoulet> bye :)
Michel: Gene variant is still
part of an individual
... to assoc freq, has to be a sub-type
... variant in population is a sub-class of variant in
individual(?), has more property restriction
Matthias: In my view, it's not really a subclass
Scott: One class of snp, diff freqs of measurement in different population
Michel: But we do assign(?) these genes to specific individuals
Scott: We could have a number of
models; test would be how to find w owl or sparql
... demonstate the differences of how the different models
work
... brca1 has certain freq in pop, but fewer known alleles
which are known to be associated w cancer
... compared to snps which are known to be associated w
cancer
... gwas might have millions of snps to go thru for
genome
... brca measure is more like a read-out of a prognosis.
... Carry out further w. email exchange.
Michel: Add this discussion to the paper
<mscottm> Scott was actually saying that the BRCA1 allele is directly associated with a type of cancer.
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) Succeeded: s/Nanoprint/Mammaprint/ No ScribeNick specified. Guessing ScribeNick: bobP Inferring Scribes: bobP WARNING: No "Topic:" lines found. WARNING: No "Present: ... " found! Possibly Present: Adrian Adrien All Bob_Powers Joanne Mammaprint Matthias Michel OncoDX P13 P4 Scott aabb aacc aadd adriencoulet bbalsa bobP ericP https matthias_samwald mscottm paper You can indicate people for the Present list like this: <dbooth> Present: dbooth jonathan mary <dbooth> Present+ amy Regrets: Elgar Trish 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: 14 Apr 2011 Guessing minutes URL: http://www.w3.org/2011/04/14-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[End of scribe.perl diagnostic output]