16:04:51 <RRSAgent> RRSAgent has joined #HCLS
16:04:51 <RRSAgent> logging to http://www.w3.org/2012/12/05-HCLS-irc
16:05:05 <michel> michel has changed the topic to: #hcls  W3C HCLS – Clinical Pharmacogenomics
16:05:12 <michel> Meeting: W3C HCLS – Clinical Pharmacogenomics
16:05:21 <michel> Chair: michel
16:05:36 <bobP> scribenick bobP
16:05:47 <mscottm> mscottm has joined #hcls
16:07:07 <matthias_samwald> zakim, who is here?
16:07:07 <Zakim> sorry, matthias_samwald, I don't know what conference this is
16:07:09 <Zakim> On IRC I see mscottm, RRSAgent, Zakim, BobF, michel, boycer, matthias_samwald, bobP, MacTed, ericP
16:07:19 <matthias_samwald> zakim, this is hcls
16:07:19 <Zakim> ok, matthias_samwald; that matches SW_HCLS(LODD)11:00AM
16:07:27 <matthias_samwald> zakim, who is here?
16:07:28 <Zakim> On the phone I see Bob_Powers, [IPcaller], [IPcaller.a], Tony, +1.613.293.aaaa
16:07:30 <Zakim> On IRC I see mscottm, RRSAgent, Zakim, BobF, michel, boycer, matthias_samwald, bobP, MacTed, ericP
16:07:49 <Zakim> +Joanne_Luciano
16:07:53 <matthias_samwald> zakim, IPcaller is matthias_samwald
16:07:53 <Zakim> +matthias_samwald; got it
16:07:55 <mscottm> Zakim keeps hanging up on me
16:07:55 <michel> zakim, +aaaa is michel
16:07:55 <Zakim> sorry, michel, I do not recognize a party named '+aaaa'
16:07:56 <matthias_samwald> (probably)
16:08:01 <michel> zakim, aaaa is michel
16:08:01 <Zakim> +michel; got it
16:08:23 <Zakim> +[IPcaller]
16:08:52 <bobP> Michel: CSHALS submission, plus...
16:09:11 <bobP> Matthias: AMIA(?)
16:09:12 <matthias_samwald> IMIA Medinfo
16:09:44 <bobP> Matthias: Deadlines are coming up. CHALS today, IMIA Dec 10
16:10:06 <bobP> ... we should be at both conferences
16:10:28 <bobP> ... think about integration of resources that we have
16:11:05 <bobP> ... cshals, we can use what we have now; re-use resources from summit next year
16:11:41 <bobP> ... slightly different audiences: AMIA translational, CSHALS more people from pharma
16:11:41 <mscottm> Zakim is telling me that 4257 is not a valid passcode.. ?
16:11:50 <Zakim> +??P37
16:12:14 <bobP> Joanne: CSHALS focussed on pharma, but well aware of semweb tech
16:12:43 <Zakim> +??P38
16:13:16 <bobP> Matthias: CSHALS relatively short submission
16:13:19 <mscottm> Wow, thanks Zakim for letting me in! with passcode 4257 even.
16:15:24 <achille_zappa> achille_zappa has joined #hcls
16:16:01 <Zakim> -??P37
16:17:49 <mscottm> echo echo
16:17:51 <bobP> Michel: Happy to do CSHALS presentation
16:18:39 <bobP> ... SWAT4LS was last week in Paris
16:21:30 <mscottm> https://docs.google.com/document/d/1LIO2X7PL3MTHWX5XhIy0Dd8h2yFr0Pk4d8lBG8A6CgY/edit
16:23:41 <bobP> Michel: Should list resources and dates accessed
16:24:21 <boycer> codehop.dev
16:27:01 <bobP> Michel: add more than the OWL KB?
16:27:53 <bobP> Matthias: KB, only referring to the OWL ontology; but includes other data: Michel's data++
16:28:06 <bobP> Michel: OWL profile?
16:28:13 <bobP> Matthias: DL
16:28:38 <bobP> Michel: Can reason, dump inferences to OWLim for query
16:29:14 <bobP> ... or set up website too, or just a file for query
16:29:27 <bobP> Matthias: Just a file for now
16:29:51 <bobP> ... parts of Bio2RDF + Richard's data, but no real interface
16:30:07 <bobP> Michel: PharmGKB, dbSNP, OMIM
16:30:24 <bobP> Scott: What is the biological use case?
16:30:48 <bobP> ... we have snps, structured product labels
16:31:21 <bobP> Matthais; Show how to integrate different datasets, then demo how OWL reasoning can connect to clinical guidlines
16:33:25 <bobP> Michel: Brainstorm, w product label for codeine(?)
16:33:36 <michel> that's rich ;)
16:33:43 <bobP> ... statement applied to pregnant women
16:34:27 <bobP> Rich: Interesting part was that sem model could capture PGx (view)
16:35:09 <bobP> Matthias: Could use owl for automated reasoning and for matching pts to clinical guidelines
16:35:34 <bobP> ... RDF model for capturing slightly more (subtle rules)
16:35:54 <bobP> ... would be hard to capture everything in clincial rule sets
16:36:05 <bobP> ... OWL inferencing would add here
16:36:13 <bobP> Rich: +1
16:36:34 <bobP> Michel: Matthias' point is very good
16:36:55 <bobP> ... RDF can express opaque relationships
16:37:22 <bobP> ... we can cherry pick RDF parts, then construct much more powerful ontological inference
16:38:39 <bobP> Matthias: 3-4 coherent, not too complex in presentation
16:39:10 <mscottm> http://informatics.mayo.edu/adepedia/index.php/Main_Page
16:39:15 <bobP> Scott: Another idea: We are bringing in structured product labels; should we address adverse events
16:39:38 <bobP> ... sparql resource for AE reporting systems
16:40:01 <bobP> ... we could use this resource in our scenario
16:40:31 <bobP> Matthias: but time constrant
16:41:13 <bobP> Scott: Can use AE pdf w sparql endpoint
16:41:31 <BobF> As full disclosure, the developer of ADEpedia is located directly across the hall from my office :-)
16:41:44 <mscottm> lol
16:42:11 <bobP> BobF(?): There has not yet been rigorous validation of the quality
16:42:35 <bobP> ... (someone else) addressed validation
16:42:54 <bobP> ... to bring it in, there has to be a connection between PGx and AE
16:43:03 <BobF> (Rich Boyce is speaking)
16:43:47 <bobP> Rich: Something to think about in the big picture, very nice to address AE outcomes
16:44:06 <bobP> ... 3rd resource is SIDER, slightly different process
16:44:24 <bobP> Michel: SWAT4LS I wrote a parser for SIDER
16:44:41 <bobP> Rich: SIDER has 900 drugs, not yet complete
16:45:38 <bobP> ... dbPedia value is the cloud platform
16:46:00 <bobP> ... Jian Yu(?)
16:46:00 <BobF> Qian Zhu - another colleague of mine
16:46:16 <BobF> ADEpedia:  Guoqian Jiang
16:47:04 <bobP> (discussion that BobF is geographically close to ADEpedia :)
16:47:35 <bobP> Matthias: ADEpedia, RDF does not contain much other than drug -> side effect
16:47:56 <bobP> ... not not much info on (context, provenance)
16:48:06 <bobP> ... still under development(?)
16:48:41 <bobP> Rich(?): Part of the proposal is to include this provenance
16:49:11 <bobP> ... item for further discussion, to develop metadata standard for structured labelling
16:49:56 <Zakim> +[GVoice]
16:50:06 <bobP> ... manually annotated AE + structured label: these are claims about the drug
16:50:23 <bobP> ... should be tied to evidence
16:50:47 <bobP> ... to be more concrete, should be SBML
16:51:25 <bobP> Michel: We had a group on SciDisc, out of which come other ongoing groups
16:51:52 <bobP> ... not too difficult to assemble from these semweb assets
16:52:13 <bobP> ericP: Anybody else w curated stuff?
16:52:53 <bobP> Rich: FDA has indexing initiative; there is some validation
16:53:13 <bobP> ... ericP: have done homework on this.
16:53:54 <bobP> Michel: Trying to link PGx aspects; when talk about drugs we get AE, drug-drug. All connected
16:54:13 <bobP> ... AE, mining structure product label are key endpoints
16:54:30 <bobP> ... for PGx: Do we have what we *can* have?
16:55:00 <bobP> ... PGx has a lot of assertions, needs curation(?)
16:55:35 <bobP> ... excited about pulling out facts w provenance from lots of different sources
16:56:02 <bobP> ... connect to other resources; what is the process to curate the lit?
16:56:40 <bobP> Matthias: People can go overboard w complex ontologies; 10=headache :)
16:57:13 <bobP> BobF: One of things to be careful: Separate knowledge from interpretation!
16:58:07 <bobP> ... PGx line greys easily; genotype-phenotype, PGx has habit of tying to intermediate metabolites
16:58:26 <bobP> ... but these are arbitrary, historical in nature but w/o good semantic meaning
16:58:42 <bobP> ... for assertions, consider how much of PGx to include in this project
16:58:56 <bobP> Joanne: +1 on observations
16:59:10 <bobP> ... worth re-stating this.
16:59:39 <bobP> ... for medical conference
17:00:19 <bobP> Matthias: Address intermediate metabolite info problems
17:01:00 <Zakim> -ericP
17:02:26 <bobP> BobF: Talking re data, resources, queries outside of PGx; but (ex) intermediate metabolite connections between genes may lead us to bad inferences
17:03:08 <bobP> ... primary data sources like pubs, we can have provenance; but then there are lab-to-lab differences
17:03:32 <bobP> ... see this periodically; careful of this trap.
17:04:10 <bobP> Thanks to Matthias for taking the lead!
17:04:17 <Zakim> -[IPcaller]
17:04:17 <Zakim> -[IPcaller.a]
17:04:19 <Zakim> -Tony
17:04:20 <Zakim> -michel
17:04:20 <Zakim> -Bob_Powers
17:04:21 <Zakim> -Joanne_Luciano
17:04:21 <Zakim> -??P38
17:04:28 <michel> rrsagent, draft minutes
17:04:28 <RRSAgent> I have made the request to generate http://www.w3.org/2012/12/05-HCLS-minutes.html michel
17:04:34 <Zakim> -matthias_samwald
17:04:34 <michel> rrsagent, make log world-visible
17:04:35 <Zakim> SW_HCLS(LODD)11:00AM has ended
17:04:35 <Zakim> Attendees were Bob_Powers, Tony, +1.613.293.aaaa, Joanne_Luciano, matthias_samwald, michel, [IPcaller], ericP
17:08:38 <matthias_samwald> I added a link to the minutes to the wiki page of the call.
17:08:40 <matthias_samwald> bye!
17:08:49 <matthias_samwald> matthias_samwald has left #hcls
19:16:25 <Zakim> Zakim has left #hcls