15:00:43 <RRSAgent> RRSAgent has joined #hcls
15:00:43 <RRSAgent> logging to http://www.w3.org/2012/08/02-hcls-irc
15:00:50 <michel> zakim, this is hcls
15:00:51 <Zakim> "hcls" matches SW_HCLS()11:00AM, and SW_HCLS(TMO)11:00AM, michel
15:01:06 <michel> zakim, this is SW_HCLS
15:01:06 <Zakim> "SW_HCLS" matches SW_HCLS()11:00AM, and SW_HCLS(TMO)11:00AM, michel
15:01:20 <michel> zakim, this is SW_HCLS()
15:01:20 <Zakim> michel, I see SW_HCLS()11:00AM in the schedule but not yet started.  Perhaps you mean "this will be SW_HCLS()".
15:02:03 <michel> Chair: Michel Dumontier
15:02:05 <michel> Meeting: W3C HCLS – Pharmacogenomics
15:02:11 <harryhoch> harryhoch has joined #hcls
15:03:14 <matthias_samwald> matthias_samwald has joined #hcls
15:04:31 <michel> zakim, this is hcls
15:04:31 <Zakim> ok, michel; that matches SW_HCLS()11:00AM
15:04:37 <michel> zakim, who is here?
15:04:37 <Zakim> On the phone I see +1.412.624.aaaa, ??P20, +1.613.293.aabb
15:04:39 <Zakim> On IRC I see matthias_samwald, harryhoch, RRSAgent, Zakim, achille_zappa, michel, MacTed, egonw_, ericP
15:04:50 <michel> zakim, who is making noise?
15:05:01 <Zakim> michel, listening for 10 seconds I heard sound from the following: ??P20 (67%), +1.613.293.aabb (12%)
15:05:02 <harryhoch> hello +1 412 648 9300 is harryhoch  -Harry Hochheiser at Pittsburgh
15:05:24 <michel> zakim, +.aaaa is harryhoch
15:05:25 <Zakim> sorry, michel, I do not recognize a party named '+.aaaa'
15:05:28 <matthias_samwald> zakim, ??P20 is matthias_samwald
15:05:30 <michel> zakim, +aaaa is harryhoch
15:05:32 <Zakim> +matthias_samwald; got it
15:05:35 <Zakim> sorry, michel, I do not recognize a party named '+aaaa'
15:05:39 <michel> zakim, .aaaa is harryhoch
15:05:43 <Zakim> sorry, michel, I do not recognize a party named '.aaaa'
15:06:06 <michel> zakim, 1.412.624.aaaa is harryhoch
15:06:07 <Zakim> sorry, michel, I do not recognize a party named '1.412.624.aaaa'
15:06:12 <michel> zakim, +1.412.624.aaaa is harryhoch
15:06:15 <Zakim> +harryhoch; got it
15:07:59 <Joanne> Joanne has joined #hcls
15:09:00 <Zakim> +Joanne_Luciano
15:10:07 <michel> topic: pgx ontology
15:10:32 <michel> matthias: satisfying results with spreadsheet constructed ontology
15:10:52 <michel> ... in the past tried to build over tmo, other ontologies
15:11:12 <michel> ... this time tried to focus on the task of inferring haplotypes from pgx data
15:11:31 <michel> ... snps to haplotypes and alleles; alleles to definitions in cpic or dutch pgx group
15:11:34 <Lena> Lena has joined #hcls
15:11:48 <michel> ... from very basic patient data to clinical interpretations
15:12:03 <michel> ... results posted to the pgx mailing list
15:12:12 <michel> ... got some good feedback
15:12:34 <michel> ... powerful - seems to have what we need
15:12:41 <michel> ... challenge is to get it to work in practice
15:13:06 <michel> ... small subset of kb; most reasoners are not working well; not responding
15:13:30 <michel> ... next thing on the todo reduce the complexity ; possibly throw out some features
15:13:35 <michel> ... must work with large datases
15:13:45 <michel> ... scalable; fast results
15:14:06 <michel> ... michel offered suggestions to improve performance
15:14:13 <michel> ... TrOWL reasoner in particular
15:14:44 <Joanne> TrOWL classifies  in about a second
15:15:17 <Joanne> ...Michel: TrOWL classifies in about a second
15:15:43 <Joanne>  ...Matthias using 4.2 build 278 
15:15:51 <Joanne> ... of Protege
15:16:57 <Joanne> ...Michel using 4.1, not using too much of 4.2 and will double check (he's found an inconsistency)
15:18:11 <Joanne> ...TrOWL fast, but doesn't seem to support all features (may not so DLQuery, for example) but that is important because the SNPs are submitted as a DLQuery
15:18:59 <Joanne> ...TrOWL may not be up-to-date version .9 in May   // Michel will download latest version
15:19:24 <Joanne> ... issue with cardinality restrictions also
15:19:25 <BobF> BobF has joined #hcls
15:19:56 <Zakim> +Tony
15:19:57 <Joanne> Michel - switching to representation discussion:  
15:20:11 <Zakim> + +1.617.324.aacc
15:20:16 <ericP> Zakim, aacc is me
15:20:16 <Zakim> +ericP; got it
15:22:06 <BobF> zakim, Tony is BobF
15:22:06 <Zakim> +BobF; got it
15:24:07 <michel> https://dl.dropbox.com/u/6355381/ontology/pgx.owl
15:28:40 <michel> matthias: polymorphic variants are held by all individuals, for which each variant can have 2 values
15:30:03 <Joanne> For example, ApoE contains two SNPs that result in three possible alleles for this gene: E2, E3, and E4. Each allele differs by one DNA base  (is this what we're talking about?)
15:37:07 <Joanne> Discussion about the excel spreadsheet that the clinicians can update and OWL generated automatically (through Visual Basic programming within the spreadsheet) (Matthias correct if I didn't get this right)
15:37:18 <Joanne> output is Manchester Syntax
15:38:00 <michel> http://trowl.eu/?page_id=10
15:41:53 <michel> michel: after removing the snp from the disjoint set, i still get 6 unsatisfiable classes - H1,H2,H5,H7,H8,H9 for homozygous
15:56:57 <BobF> VKORC1 rs2884737 and rs7196161
15:57:10 <BobF> rs2884737 can be A or C
15:57:18 <BobF> rs7196161 can be G or A
15:57:30 <BobF> if patient is heterozygous at both loci
15:58:21 <BobF> the patient could be H1 (A at 737 and G at 161) and H5 (C and A, respectively)
15:58:30 <BobF> or H2 (C and G) and H?? (A and A)
15:59:27 <Joanne> How do you know you have found a new allele that hasn't been identified?  [Did I get your question correct?  Correct if not]
16:04:17 <michel> bobf: affy has a genotype to star nomenclature converter
16:10:48 <Zakim> -BobF
16:11:01 <harryhoch> thanks all.
16:11:02 <Zakim> -matthias_samwald
16:11:03 <Zakim> -harryhoch
16:11:06 <Zakim> - +1.613.293.aabb
16:11:20 <michel> rrsagent, draft minutes
16:11:20 <RRSAgent> I have made the request to generate http://www.w3.org/2012/08/02-hcls-minutes.html michel
16:11:26 <michel> rrsagent, make log world-visible
16:18:52 <matthias_samwald> matthias_samwald has joined #hcls
16:40:12 <Zakim> -Joanne_Luciano
16:40:16 <Zakim> -ericP
16:40:17 <Zakim> SW_HCLS()11:00AM has ended
16:40:17 <Zakim> Attendees were +1.613.293.aabb, matthias_samwald, harryhoch, Joanne_Luciano, +1.617.324.aacc, ericP, BobF
17:30:48 <Zakim> Zakim has left #hcls
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