See also: IRC log
Bob from Mayo Clinic is here.
Scott: How to manage pgx
knowledge to harness for personalized medicine apps
... context is warfarin b/c well documented and important
Bob: -1 to semweb in title
Bosse: This title is more consistent w purpose
Scott: Nice title, and
improvement
... introduction has been smoothed by Matthias
... talking re pgx being incorporated in HC practice, via
product labels
... intro leads up to new product label for diff alleles of
warfarin gene variants
... should explain our allele notation
... the star* notation
Matthias: In table?
Scott: Or bring it up when
talking re HSGV naming scheme, LRG etc
... need to explain that we focus on SNPs rather than all
genetic variants
... unambiguous IDs, round out discussion
... already in TMO we have example data that make use of SNP
notation
... for particular patients. Could influence a canonical
representation
... demo data vs. IDs in our own KB
... VKORC1 and CYC2C9
Matthias: Map between IDs?
... return to the problem of partial solution(?)
Scott: Don't need to figure out
whole solution
... for SNPs, could have procedural call to mutalyzer
... extra effort here.
Matthias: There are diff ways of
spelling out the variation
... look at dbSNP
Scott: Main dbSNP IDs were classic names; also point to HSGV names when there
<matthias_samwald> http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=104894542
try rs9923231
<mscottm> http://www.lrg-sequence.org/page.php?page=about
Discussion of whether we should talk re HVGS ids
Scott: Should try to explain how these relate to HVGS
<mscottm> http://www.hgvs.org/mutnomen/
Scott: Also good idea to explain
GWAS, perhaps in the context of drug development
... important to bring up that a SNP is an assertion based on
statistical evidence
... slightly different kind of knowledge than what people
normally represent
... have discussed representing ethnicity
... but now how to represent hapmap, if indeed SNP is relative
to geopolitical boundary
... refer to pop, plus refer to boundary
... refer to ethnicity when talking SNPs always?
Matthias: Must pick the reference
population
... hapmap mostly defined by geography
... guess we should try to focus on hapmap pops at the
moment
... Michel already has some class to define SNPs
... hapmap pop might not be relative to some race
Scott: Distiinguished from ethnicity?
Matthias: Ethnicity irrelevant from genetic point of view; strictly culturally defined
ericP: But good correlation for certain genotypes?
Scott: Ethnicity is described in
context of warfarin SNPs
... warfarin lit refers to Asians, blacks, Caucasians,
etc
... we should probably change the race class to something more
palatable?
... Let's keep this in mind for update!
BobF: Question of how to define race/ethnicity?
Scott: Choosing a label; more
just a problem of what we're going to call it
... genes related to categories of ancestry
BobF: Race/ethnicity have strict
defn relative to OMG in US, for collecting clinical trial
info
... there is a clear distinction about what is race, what is
ethnicity
... Had email exchange w Michel in May
(I remember, but couldn't find you either :-)
Scott: Try to fill out paper;
done by EO next week
... competency questions
<BobF> US National Cancer Institute standards for race and ethnicity: https://cabig.nci.nih.gov/workspaces/VCDE/Data_Standards/CDC_Race_Eth.zip
Matthias: pharmGKB has been
converted by Tim and by Michel
... should collect all the datasets on wiki for
transparency
<BobF> Ethnicity data element: https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192217&version=2.0
<BobF> Race data element: https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192199&version=1.0
Scott: One view is that we have
several diff dbs, including text-mined data
... showcase data sources, as well as bring in others?
Matthias: But do not have
concensus on how to represent variations in TMO
... representation of large amount of data w all sorts of
restrictions
Scott: Summarize here, to put out on pgx list
<BobF> OMB directive for race/ethnicity (see appendix 1): http://www.whitehouse.gov/omb/fedreg_directive_15 (this may be too restrictive for the purposes of this paper, but could serve as a starting point)
Elgar: Strongly +1 support
putting on wiki all the sources
... one sentence summary of each.
... who is converting what?
Current version:
https://docs.google.com/document/d/1I9xyVKhO9wG7My2fWu9S-wMwWZxG6PkRc98kOxUqH-o/edit?hl=en_US
Matthias: Redundancy for dbSNP and pharmGKB
Elgar: Relevant DBs, are all sources listed in table?
Matthias: Not able to convert all of them certainly at the moment
Elgar: +1
Scott: pharmGKB conversions: Be
practical here
... Michel wrote script; review w Tim and Joanne
... which one may not be important for paper; need not use one
or the other
... ericP has done a lot of mapping in the KB
... to map RDF consistent w TMKB
... maybe also use SWObjects to get access
... we don't even need to talk about federation; automatically
routed to different stores
ericP: Different mappings to RDF;
might have use case discussion to resolve
... also suggestion to send off to google discussion list;
Would prefer to push to HCLS list
Scott: Trying to wrap up rather than unwrap it
Bob: -1 here
Scott: Part of issue is how to
use a reasoner and how we would do that
... Matthias points out that reasoner would require separate
section
... Michel has talked re ethnicity via restrictions in
owl
... something convincing for reasoning would be good, not
necessary
(BobF - would you please spell your name here?)
BobF: Would like to get a better understanding w/o distracting.
Scott: Jump in!
<ericP> matthias_samwald, i don't mean to complicate modeling decisions et. al. if you'd rather discuss in smaller setting, i understand
ericP: Goal is the modeling. Need
to go into ID issues
... inferencing is something we do only when motivated by use
cases
BobF: How does work overlap w SO, etc?
ericP: Would need to do homework.
(Michel would be the expert in this area.)
Scott: Broader sense, lots of
efforts to describe genotypes, phenotypes w ontologies
... Michel has pointed out foundational difficulties w SO
... pgx ontologies, there aren't really any around (yet)
BobF: pharmGKB started at one time work on an ontology
(breaking up)
BobF: very interested in learning
hello??
(muting confusion here :-)
BobF: Want to learn more about overlap w other work
(echo now)
BobF: PGRN pharmacogenomics research network
<mscottm> http://pgrn.org
<BobF> http://pgrn.org/display/pgrnwebsite/PHONT+Profile
<epichler> need to run - on vacation for the next 2 weeks - see you all again in August - e2.
Scott: PGRN related directly to pharmGKB
BobF: PGRN is parent project,
funded to be research site
... since then pharmGKB is funded separately but still closely
associated
<mscottm> mscottmarshall@gmail.com
<ericP> cheers all
rssagent, draft minutes
This is scribe.perl Revision: 1.136 of Date: 2011/05/12 12:01:43 Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ Guessing input format: RRSAgent_Text_Format (score 1.00) No ScribeNick specified. Guessing ScribeNick: BobP Inferring Scribes: BobP WARNING: No "Topic:" lines found. WARNING: No "Present: ... " found! Possibly Present: Bob BobF BobP Bob_ Bosse Elgar Matthias Scott bbalsa epichler ericP hcls2 https joined matthias_samwald mscottm You can indicate people for the Present list like this: <dbooth> Present: dbooth jonathan mary <dbooth> Present+ amy WARNING: No meeting title found! You should specify the meeting title like this: <dbooth> Meeting: Weekly Baking Club Meeting WARNING: No meeting chair found! You should specify the meeting chair like this: <dbooth> Chair: dbooth Got date from IRC log name: 14 Jul 2011 Guessing minutes URL: http://www.w3.org/2011/07/14-hcls2-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]