IRC log of hcls on 2012-08-02

Timestamps are in UTC.

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

18:14:27 [matthias_samwald]

matthias_samwald has joined #hcls