16:02:35 RRSAgent has joined #hcls2 16:02:35 logging to http://www.w3.org/2011/07/14-hcls2-irc 16:05:14 mscottm has joined #hcls2 16:05:30 Zakim has joined #hcls2 16:06:14 Bob_ has joined #HCLS2 16:07:30 Bob from Mayo Clinic is here. 16:08:06 epichler has joined #HCLS2 16:09:48 https://docs.google.com/document/d/1lKdDSb2uBBIeTEQAv2CyTHN_aVW63k9si1hmmilOMi0/edit?authkey=CJGUtcwF&hl=en_US&pli=1 16:10:31 Scott: How to manage pgx knowledge to harness for personalized medicine apps 16:11:47 ... context is warfarin b/c well documented and important 16:12:41 Bob: -1 to semweb in title 16:13:33 Bosse: This title is more consistent w purpose 16:13:48 Scott: Nice title, and improvement 16:14:29 ... introduction has been smoothed by Matthias 16:15:09 ... talking re pgx being incorporated in HC practice, via product labels 16:15:39 ... intro leads up to new product label for diff alleles of warfarin gene variants 16:15:52 ... should explain our allele notation 16:16:08 ... the star* notation 16:16:21 Matthias: In table? 16:16:41 Scott: Or bring it up when talking re HSGV naming scheme, LRG etc 16:17:09 ... need to explain that we focus on SNPs rather than all genetic variants 16:17:46 ... unambiguous IDs, round out discussion 16:18:02 ... already in TMO we have example data that make use of SNP notation 16:18:35 ... for particular patients. Could influence a canonical representation 16:19:05 ... demo data vs. IDs in our own KB 16:19:19 ... VKORC1 and CYC2C9 16:19:35 Matthias: Map between IDs? 16:20:09 ... return to the problem of partial solution(?) 16:20:33 Scott: Don't need to figure out whole solution 16:20:56 ... for SNPs, could have procedural call to mutalyzer 16:21:04 ... extra effort here. 16:21:28 Matthias: There are diff ways of spelling out the variation 16:21:34 ... look at dbSNP 16:22:05 Scott: Main dbSNP IDs were classic names; also point to HSGV names when there 16:22:34 http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=104894542 16:23:09 try rs9923231 16:23:23 http://www.lrg-sequence.org/page.php?page=about 16:24:03 Discussion of whether we should talk re HVGS ids 16:24:32 Scott: Should try to explain how these relate to HVGS 16:24:41 http://www.hgvs.org/mutnomen/ 16:25:31 Scott: Also good idea to explain GWAS, perhaps in the context of drug development 16:26:40 ... important to bring up that a SNP is an assertion based on statistical evidence 16:26:59 ... slightly different kind of knowledge than what people normally represent 16:27:09 ... have discussed representing ethnicity 16:27:40 ... but now how to represent hapmap, if indeed SNP is relative to geopolitical boundary 16:28:01 ... refer to pop, plus refer to boundary 16:28:29 ... refer to ethnicity when talking SNPs always? 16:28:43 Matthias: Must pick the reference population 16:28:54 ... hapmap mostly defined by geography 16:29:15 ... guess we should try to focus on hapmap pops at the moment 16:29:37 ... Michel already has some class to define SNPs 16:30:06 ... hapmap pop might not be relative to some race 16:30:40 Scott: Distiinguished from ethnicity? 16:31:08 Matthias: Ethnicity irrelevant from genetic point of view; strictly culturally defined 16:31:25 ericP: But good correlation for certain genotypes? 16:31:52 Scott: Ethnicity is described in context of warfarin SNPs 16:32:14 ... warfarin lit refers to Asians, blacks, Caucasians, etc 16:32:38 ... we should probably change the race class to something more palatable? 16:33:08 Scott: Let's keep this in mind for update! 16:33:28 BobF: Question of how to define race/ethnicity? 16:33:51 Scott: Choosing a label; more just a problem of what we're going to call it 16:34:04 ... genes related to categories of ancestry 16:34:35 BobF: Race/ethnicity have strict defn relative to OMG in US, for collecting clinical trial info 16:34:54 ... there is a clear distinction about what is race, what is ethnicity 16:35:14 BobF: Had email exchange w Michel in May 16:35:40 (I remember, but couldn't find you either :-) 16:36:19 Scott: Try to fill out paper; done by EO next week 16:37:25 BobF has joined #hcls2 16:38:11 ... competency questions 16:38:22 US National Cancer Institute standards for race and ethnicity: https://cabig.nci.nih.gov/workspaces/VCDE/Data_Standards/CDC_Race_Eth.zip 16:38:48 Matthias: pharmGKB has been converted by Tim and by Michel 16:39:06 ... should collect all the datasets on wiki for transparency 16:39:11 Ethnicity data element: https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192217&version=2.0 16:39:37 Race data element: https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192199&version=1.0 16:39:49 Scott: One view is that we have several diff dbs, including text-mined data 16:40:04 ... showcase data sources, as well as bring in others? 16:40:31 Matthias: But do not have concensus on how to represent variations in TMO 16:41:12 ... representation of large amount of data w all sorts of restrictions 16:41:38 Scott: Summarize here, to put out on pgx list 16:41:38 OMB directive for race/ethnicity (see appendix 1): http://www.whitehouse.gov/omb/fedreg_directive_15 (this may be too restrictive for the purposes of this paper, but could serve as a starting point) 16:42:04 Elgar: Strongly +1 support putting on wiki all the sources 16:42:19 ... one sentence summary of each. 16:42:29 ... who is converting what? 16:43:00 Current version: 16:43:03 https://docs.google.com/document/d/1I9xyVKhO9wG7My2fWu9S-wMwWZxG6PkRc98kOxUqH-o/edit?hl=en_US 16:43:27 Zakim, who is on the phone? 16:43:27 sorry, mscottm, I don't know what conference this is 16:43:28 On IRC I see BobF, epichler, Bob_, Zakim, mscottm, RRSAgent, bbalsa, matthias_samwald, BobP, ericP 16:43:34 Zakim, this is TM 16:43:34 TM matches both SW_HCLS(TMO)11:00AM and INC_(HTMLSPEECH)11:30AM, mscottm 16:43:36 Zakim, who is on the phone? 16:43:36 sorry, mscottm, I don't know what conference this is 16:43:38 On IRC I see BobF, epichler, Bob_, Zakim, mscottm, RRSAgent, bbalsa, matthias_samwald, BobP, ericP 16:43:49 Matthias: Redundancy for dbSNP and pharmGKB 16:44:28 Elgar: Relevant DBs, are all sources listed in table? 16:44:52 Matthias: Not able to convert all of them certainly at the moment 16:45:14 Elgar: +1 16:45:34 Scott: pharmGKB conversions: Be practical here 16:45:59 ... Michel wrote script; review w Tim and Joanne 16:46:36 ... which one may not be important for paper; need not use one or the other 16:46:59 ... ericP has done a lot of mapping in the KB 16:47:14 Zakim, this is tmo 16:47:14 ok, ericP; that matches SW_HCLS(TMO)11:00AM 16:47:16 ... to map RDF consistent w TMKB 16:47:18 Zakim, who is here? 16:47:18 On the phone I see no one 16:47:19 On IRC I see BobF, epichler, Zakim, mscottm, RRSAgent, bbalsa, matthias_samwald, BobP, ericP 16:47:32 ... maybe also use SWObjects to get access 16:48:02 ... we don't even need to talk about federation; automatically routed to different stores 16:48:45 ericP: Different mappings to RDF; might have use case discussion to resolve 16:49:17 ... also suggestion to send off to google discussion list; Would prefer to push to HCLS list 16:50:30 Scott: Trying to wrap up rather than unwrap it 16:50:36 Bob: -1 here 16:51:08 Scott: Part of issue is how to use a reasoner and how we would do that 16:51:40 ... Matthias points out that reasoner would require separate section 16:52:03 ... Michel has talked re ethnicity via restrictions in owl 16:52:29 ... something convincing for reasoning would be good, not necessary 16:54:01 (BobF - would you please spell your name here?) 16:54:49 BobF: Would like to get a better understanding w/o distracting. 16:54:59 Scott: Jump in! 16:55:03 matthias_samwald, i don't mean to complicate modeling decisions et. al. if you'd rather discuss in smaller setting, i understand 16:55:53 ericP: Goal is the modeling. Need to go into ID issues 16:56:14 ... inferencing is something we do only when motivated by use cases 16:56:42 BobF: How does work overlap w SO, etc? 16:56:59 ericP: Would need to do homework. 16:57:28 (Michel would be the expert in this area.) 16:57:53 Scott: Broader sense, lots of efforts to describe genotypes, phenotypes w ontologies 16:58:32 ... Michel has pointed out foundational difficulties w SO 16:58:51 ... pgx ontologies, there aren't really any around (yet) 16:59:10 BobF: pharmGKB started at one time work on an ontology 16:59:23 (breaking up) 16:59:45 BobF: very interested in learning 16:59:54 hello?? 17:00:21 (muting confusion here :-) 17:00:42 BobF: Want to learn more about overlap w other work 17:00:47 (echo now) 17:01:14 BobF: PGRN pharmacogenomics research network 17:01:31 http://pgrn.org 17:01:43 http://pgrn.org/display/pgrnwebsite/PHONT+Profile 17:02:08 need to run - on vacation for the next 2 weeks - see you all again in August - e2. 17:02:20 Scott: PGRN related directly to pharmGKB 17:02:39 BobF: PGRN is parent project, funded to be research site 17:02:58 ... since then pharmGKB is funded separately but still closely associated 17:04:33 mscottmarshall@gmail.com 17:05:12 cheers all 17:05:42 rssagent, draft minutes 17:06:04 rrsagent, draft minutes 17:06:04 I have made the request to generate http://www.w3.org/2011/07/14-hcls2-minutes.html BobP 17:06:15 rrsagent, make logs public 17:09:43 Zakim, who is on the phone? 17:09:43 On the phone I see no one 17:10:02 Zakim, who is here? 17:10:02 On the phone I see no one 17:10:03 On IRC I see mscottm, RRSAgent, ericP 17:10:40 SW_HCLS(TMO)11:00AM has ended 17:10:42 Attendees were 19:32:53 Zakim has left #hcls2