15:59:32 <RRSAgent> RRSAgent has joined #hcls2
15:59:32 <RRSAgent> logging to http://www.w3.org/2011/06/30-hcls2-irc
15:59:36 <michel>  rrsagent, make logs public 
15:59:50 <michel> michel has changed the topic to: #hcls2 pharmacogenomics paper (michel)
16:00:04 <michel> zakim, this is tmo
16:00:04 <Zakim> michel, I see SW_HCLS(TMO)11:00AM in the schedule but not yet started.  Perhaps you mean "this will be tmo".
16:00:10 <bbalsa> bbalsa has joined #HCLS2
16:00:11 <michel> zakim, this will be tmo
16:00:11 <Zakim> ok, michel; I see SW_HCLS(TMO)11:00AM scheduled to start 60 minutes ago
16:00:31 <michel> agenda?
16:00:47 <mscottm> mscottm has joined #hcls2
16:01:28 <matthias_samwald> matthias_samwald has joined #hcls2
16:01:51 <Zakim> SW_HCLS(TMO)11:00AM has now started
16:01:56 <fred> fred has joined #hcls2
16:01:57 <Zakim> +??P26
16:02:00 <Zakim> +??P61
16:02:06 <michel> zakim, ??P26 is michel
16:02:06 <Zakim> +michel; got it
16:02:17 <matthias_samwald> zakim, ??P61 is matthias_samwald
16:02:17 <Zakim> +matthias_samwald; got it
16:02:34 <Zakim> +mscottm
16:02:44 <mscottm> I am muted
16:02:46 <Zakim> + +1.518.276.aaaa
16:02:49 <Zakim> +??P62
16:02:56 <mscottm> Zakim, who is here?
16:03:07 <Zakim> On the phone I see matthias_samwald, michel, mscottm, +1.518.276.aaaa, ??P62
16:03:18 <Zakim> + +1.714.616.aabb
16:03:24 <michel> zakim, who is making noise
16:03:26 <mscottm> Zakim, who is making noise?
16:03:32 <Zakim> On IRC I see fred, matthias_samwald, mscottm, bbalsa, RRSAgent, Zakim, michel, Joanne, ericP
16:04:07 <Zakim> I don't understand 'who is making noise', michel
16:04:18 <Zakim> mscottm, listening for 10 seconds I heard sound from the following: 6 (52%), michel (96%)
16:04:28 <mscottm> Zakim was behind..
16:04:33 <mscottm> latency
16:04:36 <Zakim> + +1.781.431.aacc
16:04:36 <epichler> epichler has joined #HCLS2
16:08:19 <michel> scott: idea is to get dbsnp into linked data form for proof of concept and to validate models
16:08:36 <michel> scott: iker has run into problems because of the large size of data (250GB disk) 
16:09:02 <michel>  ... took a subset - 30M SNPs - what are the criteria?
16:09:28 <michel>  ... genes related to warfarin; dbSNP queries in SQL to retrieve snp information related to those genes
16:10:42 <michel>  ... waiting on ericP/other to setup SWObjects
16:10:51 <michel>  ... need to choose RDF rendering to translate SQL
16:11:16 <michel>  ... let's look at the scenarios 
16:11:40 <michel>  ... spoke with Bob and Joanne, to brainstorm about article and how to spin it
16:12:17 <michel>  ... title change to "On the application of pharmacogenomic knowledge in the personalized medicine setting"
16:12:37 <matthias_samwald> zakim, unmute matthias_samwald
16:12:37 <Zakim> matthias_samwald was not muted, matthias_samwald
16:13:32 <michel>  ... personalized medicne, snps, linked data
16:14:14 <michel>  ... pseudo patients with snp data using the scenarios we create
16:15:24 <michel>  ... use tmo + linked data, but not much detail - refer to prior publications
16:15:43 <michel>  ... information needs of a clinical patient pipeline
16:16:16 <michel>  ... applying biomarkers in a clinical setting
16:19:48 <michel> Joanne: try to target this paper to Future Medicne's pharmacogenomics journal http://www.futuremedicine.com/loi/pgs
16:20:09 <michel> aims and scope: Pharmacogenomics (ISSN 1462-2416) is a peer-reviewed journal presenting reviews and reports by the researchers and decision-makers closely involved in this rapidly developing area. Key objectives are to provide the community with an essential resource for keeping abreast of the latest developments in all areas of this exciting field. Pharmacog
16:20:16 <michel> Pharmacogenomics focuses on those aspects that have the most direct relevance to the pharmaceutical industry and wider clinical community, including:
16:20:31 <michel> The emergence of new pharmacogenomic initiatives and their impact on R&D and regulatory strategies
16:20:35 <michel> Emerging technologies for accessing and exploiting genomic information
16:20:40 <michel> Reviews of genotyping and clinical data in particular therapeutic areas
16:20:45 <michel> Development of novel diagnostic products and strategies
16:21:42 <michel> matthias: don't think we need to convince this audience of the benefit of pharmacogenomics
16:22:33 <michel> scott: integrated pipeline; exists?
16:22:48 <michel> fred: physicians receive incentive to make use of EHR
16:25:11 <epichler> michel: paper needs to address how SW technologies facilitates access to pharmacogenomics data, how to make this part of future approach
16:26:05 <michel> scott: difference between stated aims of hospitals and those in practice
16:26:51 <michel>  ... good for us to show that it's not as hard as it seems
16:26:57 <michel>  ... bottom up is good
16:27:50 <michel> matthias_samwald: focus on potential, capabilities - but should also talk about technical aspects, but not too much detail
16:29:02 <michel> michel: think our sell is with semantic web
16:30:27 <michel> scott: the use cases are important
16:30:46 <michel> matthias_samwald: use cases are quite detailed - we need to focus on some aspects
16:31:22 <Joanne> to michel, say more re: sell w/ sem web.  I think i agree (Scott, Bob and I discussed this at length).
16:31:38 <Joanne> Note: I'm stepping away for a moment to get some food (just out my door). brb
16:32:11 <michel> matthias_samwald: what can we do with our knowledge model to sensibly represent data
16:32:35 <michel>  ... leave use cases for the moment and focus on the development
16:34:02 <michel> michel: so let's discuss the ontology  - material entity vs informational entity
16:36:13 <michel> matthias_samwald: IAO - gives 'about' property to link 'information content entities' with physical objects; 
16:37:14 <michel>  ... genotypes; alleles;   part hood is fine, but use owl individuals  instead of classes
16:43:33 <michel> michel: for material entities - the idea is that when we make a measurement on some sample, we are making a measurement of a collection of material objects (dna and their parts)
16:48:17 <michel> fred: bridge the gap with the audience and also explain what you are doing
16:48:38 <michel> joanne: make sure what you do is most relevant
16:50:01 <michel> fred: use of genomics in the clinic is developing and there is a lot of confusion; if you want to write a paper for physicians; not everything has been verified or is clinically valid; what data has reached clinical significance and is clinically useable
16:52:26 <michel> scott: if you look at genes related to warfarin in the LOD cloud; dbsnp is too far from this use case
16:54:34 <michel> fred: a large percentage of the conclusions in the literature is wrong or insufficient supported
16:55:41 <michel>  ... clinicians will operate on the clinical guidelines
17:00:04 <Zakim> - +1.518.276.aaaa
17:00:14 <michel> matthias_samwald: need competency questions
17:00:35 <mscottm> want to suggest having two extra telcons in the next week 1/2 hour long
17:00:57 <michel>  ... when creating the knowledge model, i pondered how to query alleles from snp data. etc
17:02:55 <ericP> weak, i forgot this meeting
17:03:02 <ericP> anything i should try to join for?
17:03:14 <mscottm> I'll fill you in - in a minute.
17:03:17 <Zakim> - +1.781.431.aacc
17:03:19 <ericP> ok
17:03:20 <Zakim> -??P62
17:03:21 <Zakim> - +1.714.616.aabb
17:03:25 <Zakim> -matthias_samwald
17:03:36 <mscottm> shall we talk?
17:03:37 <michel>  rrsagent, draft minutes 
17:03:37 <RRSAgent> I have made the request to generate http://www.w3.org/2011/06/30-hcls2-minutes.html michel
17:03:38 <Zakim> -michel
17:04:03 <mscottm> Zakim, dial ericP (how does it go?)
17:04:03 <Zakim> I don't understand 'dial ericP (how does it go?)', mscottm
17:05:01 <ericP> mscottm, should i call you?
17:06:12 <Zakim> -mscottm
17:06:14 <Zakim> SW_HCLS(TMO)11:00AM has ended
17:06:16 <Zakim> Attendees were michel, matthias_samwald, mscottm, +1.518.276.aaaa, +1.714.616.aabb, +1.781.431.aacc
17:06:29 <epichler> epichler has left #HCLS2
17:33:37 <ericP> patient trans:feature
17:33:37 <ericP> 1       tag:eric@w3.org:2009/tmo/translator#variant_VKOR
17:33:37 <ericP> 1       tag:eric@w3.org:2009/tmo/translator#variant_CPC9
17:33:37 <ericP> 1       tag:eric@w3.org:2009/tmo/translator#variant_APOE4
17:33:37 <ericP> 2       tag:eric@w3.org:2009/tmo/translator#variant_APOE4
17:33:40 <ericP> 2       tag:eric@w3.org:2009/tmo/translator#variant_CYP2C19
17:33:42 <ericP> 2       tag:eric@w3.org:2009/tmo/translator#variant_RP4-669P10_2
17:33:45 <ericP> 4       tag:eric@w3.org:2009/tmo/translator#variant_APOE4
17:33:47 <ericP> 6       tag:eric@w3.org:2009/tmo/translator#variant_APOE4
17:33:50 <ericP> 7       tag:eric@w3.org:2009/tmo/translator#variant_APOE4
18:19:29 <matthias_samwald> matthias_samwald has joined #hcls2
19:08:44 <Zakim> Zakim has left #hcls2
19:45:13 <matthias_samwald> matthias_samwald has joined #hcls2
20:58:55 <matthias_samwald> matthias_samwald has joined #hcls2
20:59:07 <matthias_samwald> matthias_samwald has left #hcls2