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15:01:44 <ericP> Zakim, this is hcls
15:01:44 <Zakim> ok, ericP; that matches SW_HCLS()11:00AM
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15:01:56 <Zakim> +EricP
15:02:51 <matthias_samwald> zakim, [IPcaller] is matthias_samwald
15:02:54 <michel> zakim, this is hcls
15:03:01 <Zakim> +michel
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15:03:23 <Zakim> +matthias_samwald; got it
15:03:27 <Zakim> michel, this was already SW_HCLS()11:00AM
15:03:28 <ericP> Zakim, aaaa is harryh 
15:03:29 <Zakim> ok, michel; that matches SW_HCLS()11:00AM
15:03:45 <Zakim> +harryh; got it
15:03:45 <michel> Meeting: W3C HCLS – Pharmacogenomics
15:03:49 <michel> Chair: Michel Dumontier
15:03:51 <matthias_samwald> (reading the draft of the AMIA paper in the meanwhile...)
15:05:10 <bobP> scribenick: bobP
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15:05:37 <harryh> harryh@pitt.edu
15:05:44 <bobP> :)
15:06:43 <Zakim> + +31.62.427.aabb
15:07:04 <michel> zakim, aabb is mscottm
15:07:04 <Zakim> +mscottm; got it
15:07:58 <bobP> Michel: Discuss submission to AMIA in March 2013
15:08:32 <bobP> ... need to prepare one page podium presentation
15:09:25 <michel> https://docs.google.com/document/d/1v2L95VYL2OTBAUoRcSbFXpF5Qj_9HLb2EsDCmMfH7H4/edit
15:11:10 <bobP> ... either 1) an overview of W3C thrust to integrating data, or...
15:11:45 <bobP> 2) Bob Freimuth suggested about how allele defs can change thru time
15:12:09 <bobP> ... fits well with Matthias' solution, with class subsumption
15:12:25 <bobP> ... So, broader or more focussed??
15:12:29 <mscottm> Quick link to Google Drive (used to be called Google Documents): https://drive.google.com/?tab=mo&authuser=0
15:12:52 <bobP> Matthias: +1 for more focussed.
15:13:14 <bobP> ... addresses a clear need and allows us to advertise for other groups
15:13:28 <bobP> Scott: +100% w Matthias
15:13:43 <bobP> Harry: Agree, plenty to say w/o being vague
15:14:25 <bobP> ... there are oodles of important challenges here; and we solved this one first on the list
15:18:56 <bobP> Michel: (discussing *1 allele defintions), wild-type is a non-monotonic def
15:19:09 <bobP> Matthias: +1 this is true
15:19:56 <bobP> Michel: So we need a new classification of *1 w each new allele def
15:21:15 <bobP> Matthias: (discussion about logic about alleles)
15:21:59 <bobP> ... look at haplotypes; combinations of SNPs; logic about differentiating between alleles
15:22:32 <bobP> ... writing this down in description logic has advantage over procedural code
15:22:52 <bobP> Scott: Example?
15:23:44 <bobP> Matthias: (going deep w an example...)
15:24:16 <bobP> ... each instance of the rare allele target is also instance of the more common allele
15:25:06 <bobP> ... all alleles should be disjoint; can detect inconsistency if one is a subclass of another
15:25:54 <bobP> Scott: Nesting of alleles: location of mutation, tends to be grouped
15:26:29 <bobP> ... "nesting" b/c in the nomenclature it looks like nesting, so it's in the name itself
15:26:43 <bobP> ... new changes get added on to the old names
15:27:02 <bobP> ... subtypes arise in this
15:27:27 <bobP> Matthias: Evolutionary history, rate of change of alleles
15:27:54 <bobP> Michel: Focus the paper around genotype/haplotype effort.
15:28:48 <bobP> Matthias: I already have a lot of material to put in.
15:29:35 <bobP> Michel: Will also write about data around this
15:30:02 <bobP> ... will also take bobF's section and frame as background
15:31:15 <bobP> ... Matthias section + bobF section
15:32:06 <bobP> Scott: Do you have a sense of the audience level of interest?
15:32:50 <bobP> Michel: Varies. Most popular session was panel about drug interactions, side effects, drug re-purposing.
15:33:11 <bobP> ... interest in PGx is much less tangible, but it could change
15:34:10 <bobP> ... bigger story: now we can provide a treatment plan for an individual
15:34:26 <bobP> Matthias: Go from classifications to clinical guidlines
15:34:52 <bobP> (Michel: bobF was talking clinical guidelines, above)
15:35:13 <bobP> Matthias: Already have a spreadsheet of mature guidelines
15:35:29 <bobP> ... basically doing what I have done for haplotype definitions
15:35:48 <bobP> Michel: Would vastly increase the interest in the work
15:36:25 <bobP> Scott: Big picture, relate shift in medicine from cancer where is tumor, to molecular makeup of tumor
15:37:17 <bobP> ... nomenclature classification for patients might be meaningless (in 5 years?)
15:37:34 <bobP> ... our solution might change the particular recommended guidelines
15:38:00 <bobP> ... this gives a broader view to the issue of nomenclature
15:38:27 <bobP> Matthias: Traditional medicine needs precise ways to formalize the guidelines
15:38:35 <bobP> ... we have a toolset to do just that.
15:41:52 <bobP> Michel: want to include all the data, but we may have enough here w genotype/haplotype
15:45:06 <Zakim> -harryh
15:45:07 <Zakim> -matthias_samwald
15:45:08 <Zakim> -EricP
15:45:09 <Zakim> -mscottm
15:45:10 <Zakim> -Bob_Powers
15:45:12 <Zakim> SW_HCLS()11:00AM has ended
15:45:12 <Zakim> Attendees were Bob_Powers, +1.412.624.aaaa, EricP, michel, matthias_samwald, harryh, +31.62.427.aabb, mscottm
15:45:16 <michel> rrsagent, draft minutes
15:45:16 <RRSAgent> I have made the request to generate http://www.w3.org/2012/10/04-hcls-minutes.html michel
15:45:22 <michel> rrsagent, make log world-visible
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