16 Jan 2013

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.

<boycer> https://code.google.com/p/swat-4-med-safety/source/browse/trunk/analyses/pharmgx-statement-annotation/figures/PGx-RDB-medinfo-submission-01042012.jpg

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.


<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".


<boycer> http://dbmi-icode-01.dbmi.pitt.edu:8080/sparql

<boycer> https://code.google.com/p/swat-4-med-safety/source/browse/trunk/analyses/pharmgx-statement-annotation/scripts/example-queries.txt

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

Summary of Action Items

[End of minutes]

Minutes formatted by David Booth's scribe.perl version 1.137 (CVS log)
$Date: 2013-01-16 17:01:39 $

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Got date from IRC log name: 16 Jan 2013
Guessing minutes URL: http://www.w3.org/2013/01/16-HCLS-minutes.html
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