See also: IRC log
<matthias_samwald> argh
<scribe> scribenick: ericP
matthias_samwald: presented a few
months ago at AMIA
... BobF and simon_lin were there
... how do we give pharmacogenomic data to clinicians without
too many privacy or centralization issues?
<matthias_samwald> http://safety-code.org/
matthias_samwald: also
sidestepping the sluggish uptake of EHRs
... QR-code with the ~400 SNPs of most pharmacogenomic
interest
... populated by microarrays or nextgen
... QR-code points a URL
... avoiding centralization
... genetic data is associated with many privacy issues:
... .. (personal) genetic data
... .. serves as a genetic fingerprint
matthias_samwald: law in Austria avoids genetic data
simon_lin: this URL includes the data
matthias_samwald: exactly, ~250 chars. can be carried with you
BobF: so your URL will decode the data and present the info
matthias_samwald: yes
... you can interpret such a medicine safety code can be
interpreted by most phones
BobF: but your server is
responsible for keeping the guidelines up to date?
... that's not a trivial task
matthias_samwald: indeed. so far just a research datatype
<BobF> ericP - the questions were from BobF (not BobF) :-)
s/boyver/BobF/g
simon_lin: given your
compression, how much info can you put in?
... i assume the size of the QRcode is a design constraint
matthias_samwald: putting lots of data in a code makes it very complex and hard to scan
BobF: how many can you fit now?
matthias_samwald: i'm fitting ~400 SNPs. can't exceed ~800 with current compression
ericP: this is good for 5 years?
matthias_samwald: around 10 probably
boycer: you've got a good set of
phase I/phase II
... pharmacodynamics is what your body does
... there are a hand-full of enzymes for phase I
(oxidizing/reducing)
... pharmacokinetics won't change much over the next years
<matthias_samwald> http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=12&Itemid=27
boycer: but pharmacodynamics will
explode over the next few years
... it's easier to predict pharmacokinetics
... but e.g. statin doesn't have a clear safe range
matthias_samwald: the 400 i use
were compiled from the PharmGKB "VIP" genes (those with
existing clinical evidence)
... combined with a list from pharma adne (SP?)
... added also those listed in FDA drug labels
<boycer> Matthias - what was the pharma database (I heard Pharma ad & e?)
<matthias_samwald> http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=12&Itemid=27
<boycer> Found it: www.pharmaadme.org/
matthias_samwald:
pharmacodynamics would seem more interesting than
pharmacokinetics, but the latter are further along
... CPIC SNPs are primarily kinetic
BobF: we're working on a schema
for conveying guidelines which can be hooked into a clinical
support engine
... could you use that to update safety-code.org?
<matthias_samwald> https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AiGT-vnkGcoLdFFVMEdqcFdYaDFqS0xHTnlUT0N3cEE&output=html
matthias_samwald: that'd be
helpful
... in the last few days, i've updated this spreadsheet with
CPIC and Dutch Pharmacogenomics WG guidelines from
PharmaGKB
... i'd like to further curate the data to create CDS rules in
SPARQL
... but it would be great the have machine-readable CPIC
guidelines
BobF: that's my goal
data: application/medsafetycode+qrcode/qm70W00I2KZ0u-A01N103HmXRp0W80080zIe0oWW0vL4kC8441HTCCCfOA03U0uW020013mICe00I8wyFnk6Qo4m20e7Nq0m0500G03RG90e56407xu6O0000000000000000000000000000
ericP: use RDF/XML with controlled schema? GRDDL? conneg?
matthias_samwald: i think RDF/XML
is the worst of both worlds
... the rows in the spreadsheet represent multiple SNP
combos
... we can break up some of the CPIC guidelines in this table
into smaller rows
BobF: i didn't intend to create a
comprehensive pharmacogenomics domain model
... just serialize CPIC guidelines
... there are national efforts in the US to create generic CDS
rules
... i'd like to link the schema to those rules so there's a
path from the CPIC guidelines to what the hospitals can
implement
ericP: how complex are these rules?
<matthias_samwald> example of guideline and boolean logic: http://pharmgkb.org/gene/PA128
BobF: most are single
drug/geneotype combo
... warfarin is the most complex with a 2X2 matrix
<matthias_samwald> bite tge second row in the second table.
<matthias_samwald> note the second row in the second table
BobF: as we apply more systems
bio, this will get more complex
... need to distinguish between broad clinical practics and
specific guidelines
... each institution will have to decide the latter
ericP: would you want your expressivity to cover quatitative dosing even though you're not using all of that expressivity?
BobF: i'd like it to be extensible but i can't populate it now
matthias_samwald: the more complex the expressivity, the harder it is for clinicians to understand and the harder it is to validate
boycer: is the safety-code.org infrastructure going to be public?
matthias_samwald: it's a jenna back-end and i'll make the SPARQL rules open-source
UNKNOWN_SPEAKER: we're doing a
trial looking at 80 genes via nextgen
... we're analyzing the impact of markers to see how we can
change our practice
... marshfield clinic also has an insurance subsidiary
... we'd like to put medicine safety codes and drug
interactions into an insurance card
... Mayo clinic and about 8 participants in Emerge
... expect recruitment next year
<boycer> https://www.mc.vanderbilt.edu/victr/dcc/projects/acc/index.php/About
This is scribe.perl Revision: 1.136 of Date: 2011/05/12 12:01:43 Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ Guessing input format: RRSAgent_Text_Format (score 1.00) FAILED: s/boyver/BobF/g Succeeded: s/boycer/BobF/g Succeeded: s/pharmacogenetics/pharmacokinetics/ Succeeded: s/put SNPs and drug interactions/put medicine safety codes and drug interactions/ Found ScribeNick: ericP Inferring Scribes: ericP WARNING: No "Present: ... " found! Possibly Present: BobF MacTed P15 Tony aaaa aabb boycer data egonw ericP https matthias_samwald scribenick simon_lin 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: 14 Jun 2012 Guessing minutes URL: http://www.w3.org/2012/06/14-hcls-minutes.html People with action items:[End of scribe.perl diagnostic output]