See also: IRC log
<egombocz> 510.705.8470 is me
<BobF> zakim Tony is BobF
(note: the other IPcaller is rich boyce)
<boycer> Rich - I might need to call in with my cell phone - connection is low speed.
<boycer> be right back
<ericP> hey gang, i'm on the RDF WG call.
<ericP> hey gang, i'm on the RDF WG call.
<scribe> scribenick: matthias_samwald
michel: i have a lab at 11:30, so
we should shift the timeslot a bit
... would 10:00 also work for everyone?
bobF: I would be able to join 10:30
<Atif_Khan> I am OK with 10:00 AM or 10:30 AM
eric: a bit of a problem with a conflicting meeting every second week
simon: okay for me, just make sure to change google calendar
<boycer> boycer is +1.206.371.aabb
<boycer> 10 or 10:30 ok with Rich Boyce
matthias: 10:00 and 10:30 would work
<harry> 10:15-1:15 is fine.
michel: 10:15 seems ideal
10: 15 it is!
<michel> matthias : face to face meeting
michel: i think this is a good idea. i am there from wednesday afternoon until friday evening?
erich: i will also be at CSHALS
<michel> http://www.iscb.org/cshals2013
michel: CSHALS will happen between february 27 and march 1
matthias: next topic: Rich's work on annotation of pharmacogenomics statements in FDA labels with Annotation Ontology
<boycer> http://www.fda.gov/drugs/scienceresearch/researchareas/pharmacogenetics/ucm083378.htm
RIch: We created a graph detailing pharmacogenomic statements. Done with a group of 5 pharmacists as annotators. We started with a list of 29 biomarker-drug relationships from the FDA table of pharmacogenomic biomarkers.
matthias: how did you select with what you started out with?
rich: pharmacists selected that based on importance. also, at our university we are developing clinical guidelines for some of these drugs.
rich: here is a graph that might
be useful. it is a graphical representation of the semantic
model.
... tried to model pharmacogenomic statements in RDF, and also
to see which ontologies could be useful.
test
<boycer> http://www.openannotation.org/spec/beta/
<boycer> http://www.openannotation.org/spec/beta/
rich: look at figure 1, the
baseline model
... we found AO useful for this use-case. There is a single
product label for each drug. The AO model provides a way of
distinguishing the context of where something is stated from
information what is stated.
... the "target" is the product label document (available in
many formats)
... the "body" would be the pharmacogenomic statement
... in the upper left corner of the JPEG i sent you, there is a
cluster with "annotation". if you look at that, there is an
arrow that points to a "pharmacogenomicsstatement".
test
<boycer> http://dbmi-icode-01.dbmi.pitt.edu:8080/sparql
rich: the first link points to a SPARQL endpoint, the second one contains sample SPARQL queries.
(rich explains some of the queries)
<ericP> note that i think that query 1 is outside of the SPARQL spec (selecting variables which weren't GROUPED) and therefor not terribly portable
erich: this is very nice, i put
the SPARQL into our knowledge explorer -- feel free to explore
it.
... i pasted in some of the sparql queries, it looks really
nice!
<ericP> matthias_samwald: michel and i had opposing comments
<ericP> ... michel wanted deeper modeling
<egombocz> IO informatics current free version of Knowledge Explorer can be downloaded here (we will have a new version available at CSHALS): http://www.io-informatics.com/download_KE_PersEd_B.html
<ericP> ... i wanted soemthing simpler, using the annotation ontology
<ericP> rich: i agree, that's what i was hearing from clinicians
<ericP> ... and pharmacists
rich: the "value" property is a bit underdefined in the graphs
<boycer> http://www.fda.gov/drugs/scienceresearch/researchareas/pharmacogenetics/ucm083378.htm
<ericP> matthias_samwald: how will you maintain this?
<ericP> ... will there be a nice user interface in addition to SPARQL
matthias_samwald: any progress with using DOMEO
rich: it would be exciting to
making the annotations publicly accessible through a nice
UI
... i expect the next round of annotations between now and
march
<ericP> ncbo ontology list
<ericP> pharmacovigilance ontology
<ericP> PharmGKB represented in OWL
rich: pharmacovigilance ontology might not be a good fit, erich.
erich: you could also take TMO... you don't need to use as-is, but use pieces.
<BobF> BobF will be at AMIA, but exact dates are not known yet
<BobF> I am not planning to attend CSHALS this year
rich: i will go to the AMIA summit and could print and present the poster.
eric: another poster from us was accepted as well... could you present it as well?
rich: okay :D
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: matthias_samwald Inferring Scribes: matthias_samwald WARNING: No "Topic:" lines found. WARNING: No "Present: ... " found! Possibly Present: Atif_Khan GVoice IPcaller TallTed Tony aaaa aabb aacc achille_zappa bobF boycer egombocz egonw eric ericP erich harry https matthias matthias_samwald michel mscottm rich scribenick simon 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: 16 Jan 2013 Guessing minutes URL: http://www.w3.org/2013/01/16-HCLS-minutes.html People with action items: WARNING: Input appears to use implicit continuation lines. You may need the "-implicitContinuations" option. 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]
