IRC log of hcls on 2012-10-04

Timestamps are in UTC.

15:01:39 [RRSAgent]
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logging to http://www.w3.org/2012/10/04-hcls-irc
15:01:44 [ericP]
Zakim, this is hcls
15:01:44 [Zakim]
ok, ericP; that matches SW_HCLS()11:00AM
15:01:50 [michel]
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+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
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rrsagent, make log world-visible
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