<matthias_samwald> (reading the draft of the AMIA paper in the meanwhile...)

<scribe> scribenick: bobP

<harryh> harryh@pitt.edu

:)

Michel: Discuss submission to AMIA in March 2013
... need to prepare one page podium presentation

<michel> https://docs.google.com/document/d/1v2L95VYL2OTBAUoRcSbFXpF5Qj_9HLb2EsDCmMfH7H4/edit

Michel: either 1) an overview of W3C thrust to integrating data, or...

2) Bob Freimuth suggested about how allele defs can change thru time

scribe: fits well with Matthias' solution, with class subsumption
... So, broader or more focussed??

<mscottm> Quick link to Google Drive (used to be called Google Documents): https://drive.google.com/?tab=mo&authuser=0

Matthias: +1 for more focussed.
... addresses a clear need and allows us to advertise for other groups

Scott: +100% w Matthias

Harry: Agree, plenty to say w/o being vague
... there are oodles of important challenges here; and we solved this one first on the list

Michel: (discussing *1 allele defintions), wild-type is a non-monotonic def

Matthias: +1 this is true

Michel: So we need a new classification of *1 w each new allele def

Matthias: (discussion about logic about alleles)
... look at haplotypes; combinations of SNPs; logic about differentiating between alleles
... writing this down in description logic has advantage over procedural code

Scott: Example?

Matthias: (going deep w an example...)
... each instance of the rare allele target is also instance of the more common allele
... all alleles should be disjoint; can detect inconsistency if one is a subclass of another

Scott: Nesting of alleles: location of mutation, tends to be grouped
... "nesting" b/c in the nomenclature it looks like nesting, so it's in the name itself

<scribe> ... new changes get added on to the old names

UNKNOWN_SPEAKER: subtypes arise in this

Matthias: Evolutionary history, rate of change of alleles

Michel: Focus the paper around genotype/haplotype effort.

Matthias: I already have a lot of material to put in.

Michel: Will also write about data around this
... will also take bobF's section and frame as background
... Matthias section + bobF section

Scott: Do you have a sense of the audience level of interest?

Michel: Varies. Most popular session was panel about drug interactions, side effects, drug re-purposing.
... interest in PGx is much less tangible, but it could change
... bigger story: now we can provide a treatment plan for an individual

Matthias: Go from classifications to clinical guidlines

(Michel: bobF was talking clinical guidelines, above)

Matthias: Already have a spreadsheet of mature guidelines
... basically doing what I have done for haplotype definitions

Michel: Would vastly increase the interest in the work

Scott: Big picture, relate shift in medicine from cancer where is tumor, to molecular makeup of tumor
... nomenclature classification for patients might be meaningless (in 5 years?)
... our solution might change the particular recommended guidelines
... this gives a broader view to the issue of nomenclature

Matthias: Traditional medicine needs precise ways to formalize the guidelines
... we have a toolset to do just that.

Michel: want to include all the data, but we may have enough here w genotype/haplotype

This is scribe.perl Revision: 1.137  of Date: 2012/09/20 20:19:01  
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Default Present: Bob_Powers, +1.412.624.aaaa, EricP, michel, matthias_samwald, harryh, +31.62.427.aabb, mscottm
Present: Bob_Powers +1.412.624.aaaa EricP michel matthias_samwald harryh +31.62.427.aabb mscottm
Got date from IRC log name: 04 Oct 2012
Guessing minutes URL: http://www.w3.org/2012/10/04-hcls-minutes.html
People with action items: 

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<dbooth> Topic: Review of Amy's report