15:59:15 <RRSAgent> RRSAgent has joined #HCLS
15:59:15 <RRSAgent> logging to http://www.w3.org/2013/01/16-HCLS-irc
15:59:22 <michel> zakim, this will be hcls
15:59:22 <Zakim> ok, michel, I see SW_HCLS(LODD)11:00AM already started
15:59:35 <BobF> BobF has joined #HCLS
15:59:56 <BobF> zakim, who is here
15:59:56 <Zakim> BobF, you need to end that query with '?'
15:59:58 <Zakim> +michel
16:00:01 <michel> zakim, who is here?
16:00:02 <Zakim> On the phone I see Tony, egombocz, michel
16:00:02 <Zakim> On IRC I see BobF, RRSAgent, Zakim, egombocz, michel, egonw, TallTed, ericP
16:00:04 <egombocz> 510.705.8470 is me
16:00:17 <BobF> zakim Tony is BobF
16:00:32 <michel> zakim, Tony is BobF
16:00:33 <Zakim> +BobF; got it
16:01:02 <matthias_samwald> matthias_samwald has joined #hcls
16:01:07 <Zakim> +[IPcaller]
16:01:14 <Zakim> -[IPcaller]
16:01:18 <matthias_samwald> zakim, this is hcls
16:01:18 <Zakim> matthias_samwald, this was already SW_HCLS(LODD)11:00AM
16:01:20 <Zakim> ok, matthias_samwald; that matches SW_HCLS(LODD)11:00AM
16:01:36 <Zakim> +[IPcaller]
16:01:42 <Zakim> + +1.412.482.aaaa
16:02:07 <michel> zakim, aaaa is Harry
16:02:07 <Zakim> +Harry; got it
16:02:09 <matthias_samwald> zakim, [IPcaller] is matthias_samwald
16:02:09 <Zakim> +matthias_samwald; got it
16:02:15 <boycer> boycer has joined #hcls
16:02:27 <harry> harry has joined #HCLS
16:03:18 <Zakim> +[IPcaller]
16:03:51 <matthias_samwald> (note: the other IPcaller is rich boyce)
16:04:03 <michel> zakim, IPcaller is boycer
16:04:04 <Zakim> +boycer; got it
16:04:19 <boycer> Rich - I might need to call in with my cell phone - connection is low speed.
16:04:26 <michel> zakim, 8470 is egombocz
16:04:26 <Zakim> sorry, michel, I do not recognize a party named '8470'
16:04:28 <Zakim> +[GVoice]
16:04:35 <boycer> be right back
16:04:40 <Zakim> -boycer
16:05:01 <Zakim> +simon
16:05:06 <ericP> hey gang, i'm on the RDF WG call.
16:05:24 <ericP> hey gang, i'm on the RDF WG call.
16:05:57 <matthias_samwald> scribenick: matthias_samwald
16:06:03 <Atif_Khan> Atif_Khan has joined #HCLS
16:06:22 <matthias_samwald> michel: i have a lab at 11:30, so we should shift the timeslot a bit
16:06:36 <matthias_samwald> michel: would 10:00 also work for everyone?
16:06:38 <Zakim> + +1.206.371.aabb
16:06:53 <matthias_samwald> bobF: I would be able to join 10:30
16:07:17 <Atif_Khan> I am OK with 10:00 AM or 10:30 AM
16:07:48 <matthias_samwald> eric: a bit of a problem with a conflicting meeting every second week
16:07:57 <achille_zappa> achille_zappa has joined #hcls
16:08:04 <matthias_samwald> simon: okay for me, just make sure to change google calendar
16:08:07 <boycer> boycer is +1.206.371.aabb
16:08:34 <boycer> 10 or 10:30 ok with Rich Boyce
16:09:02 <matthias_samwald> matthias: 10:00 and 10:30 would work
16:10:01 <harry> 10:15-1:15 is fine.
16:10:03 <matthias_samwald> michel: 10:15 seems ideal
16:10:16 <matthias_samwald> 10:15 it is!
16:10:59 <michel> matthias : face to face meeting
16:11:25 <matthias_samwald> michel: i think this is a good idea. i am there from wednesday afternoon until friday evening?
16:11:36 <matthias_samwald> erich: i will also be at CSHALS
16:11:44 <michel> http://www.iscb.org/cshals2013
16:12:14 <matthias_samwald> michel: CSHALS will happen between february 27 and march 1
16:14:59 <matthias_samwald> matthias: next topic: Rich's work on annotation of pharmacogenomics statements in FDA labels with Annotation Ontology
16:15:34 <Zakim> -michel
16:16:01 <boycer> http://www.fda.gov/drugs/scienceresearch/researchareas/pharmacogenetics/ucm083378.htm
16:16:01 <matthias_samwald> 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.
16:18:08 <matthias_samwald> matthias: how did you select with what you started out with?
16:18:39 <matthias_samwald> rich: pharmacists selected that based on importance. also, at our university we are developing clinical guidelines for some of these drugs.
16:18:52 <boycer> https://code.google.com/p/swat-4-med-safety/source/browse/trunk/analyses/pharmgx-statement-annotation/figures/PGx-RDB-medinfo-submission-01042012.jpg
16:19:20 <matthias_samwald> rich: here is a graph that might be useful. it is a graphical representation of the semantic model.
16:20:19 <matthias_samwald> rich: tried to model pharmacogenomic statements in RDF, and also to see which ontologies could be useful.
16:21:25 <matthias_samwald> test
16:21:31 <boycer> http://www.openannotation.org/spec/beta/
16:21:32 <boycer> http://www.openannotation.org/spec/beta/
16:22:04 <matthias_samwald> rich: look at figure 1, the baseline model
16:23:43 <matthias_samwald> rich: 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.
16:24:12 <matthias_samwald> rich: the "target" is the product label document (available in many formats)
16:24:25 <matthias_samwald> rich: the "body" would be the pharmacogenomic statement
16:25:49 <matthias_samwald> rich: 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".
16:28:50 <matthias_samwald> test
16:30:19 <Zakim> +[GVoice.a]
16:30:26 <boycer> boycer has joined #HCLS
16:30:31 <boycer> http://dbmi-icode-01.dbmi.pitt.edu:8080/sparql
16:30:36 <boycer> https://code.google.com/p/swat-4-med-safety/source/browse/trunk/analyses/pharmgx-statement-annotation/scripts/example-queries.txt
16:30:41 <ericP> Zakim, GVoice.a is me
16:30:41 <Zakim> -simon
16:30:42 <Zakim> +ericP; got it
16:31:15 <matthias_samwald> rich: the first link points to a SPARQL endpoint, the second one contains sample SPARQL queries.
16:32:37 <matthias_samwald> (rich explains some of the queries)
16:33:51 <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
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16:37:26 <matthias_samwald> erich: this is very nice, i put the SPARQL into our knowledge explorer -- feel free to explore it.
16:37:56 <matthias_samwald> erich: i pasted in some of the sparql queries, it looks really nice!
16:38:47 <ericP> matthias_samwald: michel and i had opposing comments
16:38:57 <ericP> ... michel wanted deeper modeling
16:39:39 <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
16:39:48 <ericP> ... i wanted soemthing simpler, using the annotation ontology
16:40:10 <ericP> rich: i agree, that's what i was hearing from clinicians
16:40:19 <ericP> ... and pharmacists
16:41:22 <matthias_samwald> rich: the "value" property is a bit underdefined in the graphs
16:41:56 <boycer> http://www.fda.gov/drugs/scienceresearch/researchareas/pharmacogenetics/ucm083378.htm
16:42:31 <Zakim> -[GVoice]
16:42:35 <Zakim> + +31.62.427.aacc
16:42:55 <mscottm> Zakim, aacc is mscottm
16:42:55 <Zakim> +mscottm; got it
16:43:36 <ericP> matthias_samwald: how will you maintain this?
16:43:53 <ericP> ... will there be a nice user interface in addition to SPARQL
16:44:28 <matthias_samwald> matthias_samwald: any progress with using DOMEO
16:46:13 <matthias_samwald> rich: it would be exciting to making the annotations publicly accessible through a nice UI
16:46:29 <matthias_samwald> rich: i expect the next round of annotations between now and march
16:47:46 <ericP> -> http://bioportal.bioontology.org/ontologies ncbo ontology list
16:48:18 <ericP> -> http://bioportal.bioontology.org/ontologies/1567 pharmacovigilance ontology
16:48:49 <ericP> -> http://bioportal.bioontology.org/ontologies/1655 PharmGKB represented in OWL
16:49:17 <matthias_samwald> rich: pharmacovigilance ontology might not be a good fit, erich.
16:49:38 <matthias_samwald> erich: you could also take TMO... you don't need to use as-is, but use pieces.
16:52:55 <boycer> boycer has joined #HCLS
16:56:22 <BobF> BobF will be at AMIA, but exact dates are not known yet
16:58:02 <BobF> I am not planning to attend CSHALS this year
16:58:32 <matthias_samwald> rich: i will go to the AMIA summit and could print and present the poster.
16:59:20 <matthias_samwald> eric: another poster from us was accepted as well... could you present it as well?
16:59:24 <matthias_samwald> rich: okay :D
17:01:13 <Zakim> -BobF
17:01:13 <Zakim> -ericP
17:01:14 <Zakim> - +1.206.371.aabb
17:01:15 <Zakim> -egombocz
17:01:15 <Zakim> -mscottm
17:01:16 <Zakim> -matthias_samwald
17:01:33 <matthias_samwald> RRSagent, please draft minutes
17:01:33 <RRSAgent> I have made the request to generate http://www.w3.org/2013/01/16-HCLS-minutes.html matthias_samwald
17:01:45 <matthias_samwald> RRSagent, please make logs world-visible
17:06:16 <Zakim> disconnecting the lone participant, Harry, in SW_HCLS(LODD)11:00AM
17:06:17 <Zakim> SW_HCLS(LODD)11:00AM has ended
17:06:17 <Zakim> Attendees were egombocz, michel, BobF, +1.412.482.aaaa, Harry, matthias_samwald, boycer, [GVoice], simon, +1.206.371.aabb, ericP, +31.62.427.aacc, mscottm
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