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15:00:09 <RRSAgent> logging to http://www.w3.org/2012/06/14-hcls-irc
15:00:16 <matthias_samwald> zakim, who is here
15:00:16 <Zakim> matthias_samwald, you need to end that query with '?'
15:00:27 <matthias_samwald> zakim, who  is here?
15:00:27 <Zakim> On the phone I see +1.412.624.aaaa, ??P15
15:00:28 <Zakim> On IRC I see RRSAgent, boycer, matthias_samwald, Zakim, MacTed, egonw, ericP
15:00:44 <matthias_samwald> zakim, ??P15 is matthias_samwald
15:00:45 <Zakim> +matthias_samwald; got it
15:01:04 <BobF> BobF has joined #hcls
15:01:16 <Zakim> +Tony
15:01:20 <matthias_samwald> zakim, +1.412.624.aaaa is boycer
15:01:22 <Zakim> +boycer; got it
15:01:47 <matthias_samwald> zakim, who is here
15:01:47 <Zakim> matthias_samwald, you need to end that query with '?'
15:01:51 <matthias_samwald> argh
15:01:53 <matthias_samwald> zakim, who is here?
15:01:53 <Zakim> On the phone I see boycer, matthias_samwald, Tony
15:01:56 <Zakim> On IRC I see BobF, RRSAgent, boycer, matthias_samwald, Zakim, MacTed, egonw, ericP
15:02:02 <Zakim> + +1.715.389.aabb
15:02:30 <matthias_samwald> zakim, Tony is BobF
15:02:48 <Zakim> +BobF; got it
15:04:20 <matthias_samwald> zakim, +1.715.389.aabb is simon_lin
15:04:20 <Zakim> +simon_lin; got it
15:07:20 <Zakim> +EricP
15:08:22 <ericP> scribenick: ericP 
15:09:11 <ericP> topic: Medicine Safety Code project
15:09:32 <ericP> matthias_samwald: presented a few months ago at AMIA
15:09:54 <ericP> ... BobF and simon_lin were there
15:10:48 <ericP> ... how do we give pharmacogenomic data to clinicians without too many privacy or centralization issues?
15:10:59 <matthias_samwald> http://safety-code.org/
15:11:10 <ericP> ... also sidestepping the sluggish uptake of EHRs
15:12:01 <ericP> ... QR-code with the ~400 SNPs of most pharmacogenomic interest
15:12:10 <ericP> ... populated by microarrays or nextgen
15:13:43 <ericP> ... QR-code points a URL
15:14:18 <ericP> ... avoiding centralization
15:14:30 <ericP> ... genetic data is associated with many privacy issues:
15:14:43 <ericP> ... .. (personal) genetic data
15:14:54 <ericP> ... .. serves as a genetic fingerprint
15:15:44 <matthias_samwald> http://safety-code.org/v0.1/qm70W00I2KZ0u-A01N103HmXRp0W80080zIe0oWW0vL4kC8441HTCCCfOA03U0uW020013mICe00I8wyFnk6Qo4m20e7Nq0m0500G03RG90e56407xu6O0000000000000000000000000000
15:15:49 <ericP> ... law in Austria avoids genetic data
15:16:57 <ericP> simon_lin: this URL includes the data
15:17:13 <ericP> matthias_samwald: exactly, ~250 chars. can be carried with you
15:17:54 <ericP> boycer: so your URL will decode the data and present the info
15:18:48 <ericP> matthias_samwald: yes
15:18:57 <ericP> ... you can interpret such a medicine safety code can be interpreted by most phones
15:19:17 <ericP> boycer: but your server is responsible for keeping the guidelines up to date?
15:19:22 <ericP> ... that's not a trivial task
15:19:35 <ericP> matthias_samwald: indeed. so far just a research datatype
15:19:57 <BobF> ericP - the questions were from BobF (not boycer) :-)
15:20:19 <ericP> s/boyver/BobF/g
15:20:28 <ericP> s/boycer/BobF/g
15:21:00 <ericP> simon_lin: given your compression, how much info can you put in?
15:21:15 <ericP> ... i assume the size of the QRcode is a design constraint
15:21:53 <ericP> matthias_samwald: putting lots of data in a code makes it very complex and hard to scan
15:23:16 <ericP> BobF: how many can you fit now?
15:23:47 <ericP> matthias_samwald: i'm fitting ~400 SNPs. can't exceed ~800 with current compression
15:25:34 <ericP> ericP: this is good for 5 years?
15:25:41 <ericP> matthias_samwald: around 10 probably
15:26:19 <ericP> boycer: you've got a good set of phase I/phase II
15:27:26 <ericP> ... pharmacodynamics is what your body does
15:27:54 <ericP> ... there are a hand-full of enzymes for phase I (oxidizing/reducing)
15:28:23 <ericP> ... pharmacogenetics won't change much over the next years
15:28:28 <BobF> BobF has joined #hcls
15:29:03 <matthias_samwald> http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=12&Itemid=27
15:29:45 <ericP> s/pharmacogenetics/pharmacokinetics/
15:30:28 <ericP> ... but pharmacodynamics will explode over the next few years
15:30:55 <ericP> ... it's easier to predict pharmacokinetics
15:32:01 <ericP> ... but e.g. statin doesn't have a clear safe range
15:33:08 <ericP> matthias_samwald: the 400 i use were compiled from the PharmGKB "VIP" genes (those with existing clinical evidence)
15:33:23 <ericP> ... combined with a list from pharma adne (SP?)
15:33:35 <ericP> ... added also those listed in FDA drug labels
15:33:49 <boycer> Matthias - what was the pharma database (I heard Pharma ad & e?)
15:34:42 <matthias_samwald> http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=12&Itemid=27
15:34:54 <boycer> Found it: www.pharmaadme.org/
15:35:01 <ericP> ... pharmacodynamics would seem more interesting than pharmacokinetics, but the latter are further along
15:35:56 <ericP> ... CPIC SNPs are primarily kinetic
15:36:31 <ericP> BobF: we're working on a schema for conveying guidelines which can be hooked into a clinical support engine
15:36:46 <ericP> ... could you use that to update safety-code.org?
15:36:49 <matthias_samwald> https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AiGT-vnkGcoLdFFVMEdqcFdYaDFqS0xHTnlUT0N3cEE&output=html
15:36:52 <ericP> matthias_samwald: that'd be helpful
15:37:38 <ericP> ... in the last few days, i've updated this spreadsheet with CPIC and Dutch Pharmacogenomics WG guidelines from PharmaGKB
15:37:58 <ericP> ... i'd like to further curate the data to create CDS rules in SPARQL
15:38:40 <ericP> ... but it would be great the have machine-readable CPIC guidelines
15:38:55 <ericP> BobF: that's my goal
15:41:54 <ericP> data:application/medsafetycode+qrcode/qm70W00I2KZ0u-A01N103HmXRp0W80080zIe0oWW0vL4kC8441HTCCCfOA03U0uW020013mICe00I8wyFnk6Qo4m20e7Nq0m0500G03RG90e56407xu6O0000000000000000000000000000
15:44:43 <ericP> ericP: use RDF/XML with controlled schema? GRDDL? conneg?
15:45:00 <ericP> matthias_samwald: i think RDF/XML is the worst of both worlds
15:46:00 <ericP> ... the rows in the spreadsheet represent multiple SNP combos
15:46:04 <ericP> ... we can break up some of the CPIC guidelines in this table into smaller rows
15:46:39 <ericP> BobF: i didn't intend to create a comprehensive pharmacogenomics domain model
15:46:53 <ericP> ... just serialize CPIC guidelines
15:47:25 <ericP> ... there are national efforts in the US to create generic CDS rules
15:47:55 <ericP> ... 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
15:48:49 <ericP> ericP: how complex are these rules?
15:48:58 <matthias_samwald> example of guideline and boolean logic: http://pharmgkb.org/gene/PA128
15:49:04 <ericP> BobF: most are single drug/geneotype combo
15:49:29 <ericP> ... warfarin is the most complex with a 2X2 matrix
15:49:31 <matthias_samwald> bite tge second row in the second table.
15:49:38 <matthias_samwald> note the second row in the second table
15:49:50 <ericP> ... as we apply more systems bio, this will get more complex
15:51:14 <ericP> ... need to distinguish between broad clinical practics and specific guidelines
15:51:42 <ericP> ... each institution will have to decide the latter
15:53:06 <ericP> ericP: would you want your expressivity to cover quatitative dosing even though you're not using all of that expressivity?
15:53:28 <ericP> BobF: i'd like it to be extensible but i can't populate it now
15:53:58 <ericP> matthias_samwald: the more complex the expressivity, the harder it is for clinicians to understand and the harder it is to validate
15:56:51 <ericP> boycer: is the safety-code.org infrastructure going to be public?
15:57:30 <ericP> matthias_samwald: it's a jenna back-end and i'll make the SPARQL rules open-source
15:58:57 <ericP> topic: simon_lin intro
15:59:17 <ericP> ... we're doing a trial looking at 80 genes via nextgen
15:59:44 <ericP> ... we're analyzing the impact of markers to see how we can change our practice
16:00:03 <ericP> ... marshfield clinic also has an insurance subsidiary
16:00:32 <ericP> ... we'd like to put SNPs and drug interactions into an insurance card
16:01:29 <ericP> ... Mayo clinic and about 8 participants in Emerge
16:01:38 <ericP> ... expect recruitment next year
16:02:15 <ericP> s/put SNPs and drug interactions/put medicine safety codes and drug interactions/
16:02:15 <boycer> https://www.mc.vanderbilt.edu/victr/dcc/projects/acc/index.php/About
16:03:33 <Zakim> -simon_lin
16:03:34 <Zakim> -BobF
16:03:38 <ericP> http://www.w3.org/People/Eric/ericP-foaf
16:08:00 <Zakim> -boycer
16:08:53 <ericP> RRSAgent, please draft minutes
16:08:53 <RRSAgent> I have made the request to generate http://www.w3.org/2012/06/14-hcls-minutes.html ericP
16:09:02 <ericP> RRSAgent, please make log world-readable
16:34:10 <Zakim> -EricP
16:34:11 <Zakim> SW_HCLS()11:00AM has ended
16:34:11 <Zakim> Attendees were matthias_samwald, boycer, BobF, simon_lin, EricP
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