See also: IRC log
<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 Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ Guessing input format: RRSAgent_Text_Format (score 1.00) Found ScribeNick: bobP Inferring Scribes: bobP WARNING: No "Topic:" lines found. 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: WARNING: No "Topic: ..." lines found! Resulting HTML may have an empty (invalid) <ol>...</ol>. Explanation: "Topic: ..." lines are used to indicate the start of new discussion topics or agenda items, such as: <dbooth> Topic: Review of Amy's report[End of scribe.perl diagnostic output]