16:07:38 RRSAgent has joined #hcls2 16:07:38 logging to http://www.w3.org/2011/05/19-hcls2-irc 16:07:50 Adrien has joined #HCLS2 16:07:59 Zakim, who is here? 16:07:59 sorry, mscottm, I don't know what conference this is 16:08:00 On IRC I see Adrien, RRSAgent, Zakim, michel, epichler, mscottm, Bob, iker, BobF, bbalsa, matthias_samwald, ericP 16:09:36 https://docs.google.com/document/d/1lKdDSb2uBBIeTEQAv2CyTHN_aVW63k9si1hmmilOMi0/edit?hl=en&authkey=CJGUtcwF# 16:12:04 Michel: Agenda 1) demo, like Iker, then 2) paper 16:12:16 Iker, can you dial in? 16:12:22 one moment please 16:12:39 Good, thx! 16:12:41 i am having problems with my VoiP service 16:13:10 Michel: Discussion of paper 16:15:05 paper from Chest http://chestjournal.chestpubs.org/content/133/6_suppl/160S.full.pdf 16:17:26 Bosse: Use case in a care situation might be difficult 16:17:36 iker_ has joined #hcls2 16:18:02 ... could develop how info could help in pharma 16:18:48 ... interested in making case for pharma; even if just around clinical trials 16:19:29 action item - Bosse to develop pharma-oriented use case for pharmacogenomics - will be nice to tie to a patient use case 16:20:27 Elgar: Can look at algorithms that have already been developed 16:20:39 ... everything ties into the use case 16:21:39 Michel: Portion of use case: doctor gathers info, warfarin-dosing.org(?) 16:22:06 Elgar: Interested in analysis part 16:23:17 ... want to understand where others did not have sufficient info 16:25:15 ... have data, mash them up, then drill down; if we use the data, can we deal w. one of the algorithms than they did? 16:25:34 Michel: Ambitious? 16:26:26 Zakim, this is hcls 16:26:26 ok, ericP; that matches SW_HCLS(TMO)11:00AM 16:26:29 -??P2 16:26:29 Zakim, who is here? 16:26:31 On the phone I see Bob_Powers, mscottm, [IPcaller], Tony, +46.4.63.3.aaaa, +1.781.431.aabb, ??P6, Tom 16:26:34 On IRC I see iker_, Adrien, RRSAgent, Zakim, michel, epichler, mscottm, Bob, BobF, bbalsa, matthias_samwald, ericP 16:26:39 Zakim, Tom is really ericP 16:26:39 +ericP; got it 16:28:23 Matthias: Editors sent requirement, top of google doc 16:28:37 ... review or research article? 16:29:35 Scott: Will review original email. 16:29:54 Michel: http://www.warfarindosing.org is the correct URL 16:29:56 ... suggested that we do pgx paper 16:30:20 +??P21 16:33:29 The answer to this paste was yes: >>>>> Thank you for the invitation to write on the ‘Development of Multi-SNP 16:33:29 >>>>> Predictive Models in Pharmacogenomics’. We have been working on 16:33:29 >>>>> incorporating SNP's into our Translational Medicine Knowledge Base in 16:33:29 >>>>> one of the task forces of the W3C Health Care and Life Sciences 16:33:29 >>>>> Interest Group (HCLS IG). We would like to write a paper about an 16:33:30 >>>>> approach for integrating SNP's into multidisclipinary studies for 16:33:32 >>>>> translational medicine. Would that fit your needs? 16:34:34 ericP and Michel in discussion about false negatives, false positives 16:35:17 ericP: Sounds like low yield use case? 16:35:42 ... machine gets to make decision and it always errs in one direction 16:36:10 ... radiologist did not match microcalcification 16:36:27 ... so machine can help where you otherwise might have missed 16:37:17 Elgar: This is clinical decision support, part of what we are trying to represent 16:37:51 ... based on this genotype, we expect that patient is higher- or lower-metabolizer 16:38:08 ... original idea is to focus on clinical decision support alone 16:38:35 ... research, etc, other scenarios can use one pgx representation 16:39:00 ... patient can be influenced by warfarin-genotype 16:39:34 Scott: Started on breast cancer: reason to go to warfarin is that bc is only expression profiles 16:39:52 ... expression profiles are more challenging to model than SNPs 16:40:02 ... warfarin use case is more clear cut 16:40:34 ... agree w. Matthias; use of pgx for translational medicine purposes 16:40:57 ... also come up w representations for other biomarkers? 16:41:43 ericP: If is has both false negs and false positives, clincian always has to monitor patient anyway 16:42:12 Scott: Tumor stratification has a nicer (skit?) 16:42:35 ericP: Vigilance is use case here? 16:43:28 Michel: Dosage ranges do change; standard warfarin dosing is wrong > 50% 16:44:10 Matthias: Modeling all this in OWL is nontrivial 16:44:46 Michel: We can highlight this in paper: chance of hurting patient w/o info 16:44:53 iker has joined #hcls2 16:46:51 Michel: warfarin on pharmGKB site, need to convert to RDF 16:46:56 http://www.pharmgkb.org/do/serve?objId=PA162355460&objCls=PhenotypeDataset#tabview=tab2 16:47:36 BobF: On a call w pharmGKG, talking about representing in RDF; want to monitor this 16:48:31 http://www.snpedia.com/index.php/Warfarin 16:49:56 ericP: converting vs chartering :-) 16:50:27 Michel: Ontology. 16:51:30 sorry, but i am definitely unable to join the conversation 16:53:28 ... can you do sparql query? 16:54:55 ... share a raw RDF file. 16:55:41 Web Protege is a good idea. 16:56:14 Michel: Would need to understand axioms w. web Protege 16:56:18 -ericP 16:57:43 Scott: Need your own server. 16:58:02 Michel: Protege 3 has client-server, configure acct etc 16:58:47 we have got an instance of webprotege with breast cancer ontology at http://85.48.202.13:8080/webprotege/WebProtege.html 16:58:49 Scott: Would like to get feedback on web Protege 16:58:58 you can check 16:59:35 Iker: Could you set up a project for us? 16:59:36 iker would you be able to setup an instance of webprotege for our project? 16:59:47 yes, no problem at all 16:59:56 good!! 16:59:58 hooray! 17:01:11 Matthias: Easier to use a good client than just a doc 17:01:46 Matthias: Web Protege has notes etc 17:02:19 Scott: PatientsLikeMe has written back. "What are your specific areas of interest?" 17:02:53 Would we start the project from scratch or do we have any ontology already implemented? 17:03:47 -Tony 17:03:49 on google doc there is a diagram that will help start the ontology 17:04:08 -[IPcaller] 17:04:08 -Bob_Powers 17:04:10 - +46.4.63.3.aaaa 17:04:10 -??P6 17:04:12 - +1.781.431.aabb 17:04:16 -mscottm 17:04:16 -??P21 17:04:18 SW_HCLS(TMO)11:00AM has ended 17:04:20 Attendees were Bob_Powers, mscottm, [IPcaller], Tony, +46.4.63.3.aaaa, +1.781.431.aabb, ericP 17:04:23 rrsagent, draft minutes 17:04:23 I have made the request to generate http://www.w3.org/2011/05/19-hcls2-minutes.html michel 17:04:33 rrsagent, make log world-visible 17:21:19 epichler has left #HCLS2 17:53:46 jodi has joined #hcls2 18:36:58 Zakim has left #hcls2 20:41:14 jodi has left #hcls2 21:43:01 matthias_samwald has joined #hcls2 22:11:21 matthias_samwald has joined #hcls2