16:01:08 <RRSAgent> RRSAgent has joined #hcls2
16:01:08 <RRSAgent> logging to http://www.w3.org/2011/06/02-hcls2-irc
16:01:15 <mscottm> Zakim, who is here?
16:01:15 <Zakim> sorry, mscottm, I don't know what conference this is
16:01:17 <Zakim> On IRC I see RRSAgent, Zakim, bbalsa, iker, mscottm, Fred, ericP
16:01:26 <mscottm> Zakim, this is TM
16:01:27 <Zakim> TM matches both WAI_PFWG(HTML TF)11:00AM and SW_HCLS(TMO)11:00AM, mscottm
16:01:34 <mscottm> Zakim, this is TMO
16:01:34 <Zakim> ok, mscottm; that matches SW_HCLS(TMO)11:00AM
16:03:57 <matthias_samwald> matthias_samwald has joined #hcls2
16:04:04 <Zakim> +Adrien
16:04:47 <BobP> BobP has joined #hcls2
16:05:21 <ericP> Zakim, please dial ericP-office
16:05:21 <Zakim> ok, ericP; the call is being made
16:05:23 <Zakim> +EricP
16:05:28 <michel> michel has joined #hcls2
16:06:18 <Zakim> +??P15
16:06:46 <matthias_samwald> zakim, ??P15 is matthias_samwald
16:06:46 <Zakim> +matthias_samwald; got it
16:07:06 <mscottm> Zakim, who is here?
16:07:06 <Zakim> On the phone I see +1.714.616.aaaa, +31.62.427.aabb, ??P34, Adrien, EricP, matthias_samwald
16:07:09 <Fred> I'm hearing MIchel
16:07:11 <Zakim> On IRC I see michel, BobP, matthias_samwald, RRSAgent, Zakim, bbalsa, iker, mscottm, Fred, ericP
16:08:06 <Zakim> +Bob_Powers
16:08:08 <michel> 6132938657
16:08:28 <BobP> scribenick BobP
16:09:20 <michel> rrsagent, make logs public
16:12:02 <BobP> Hi Fred!
16:13:23 <Fred> Hi Bob
16:14:03 <BobP> Michel: Changes to agenda?
16:14:22 <Zakim> +elgar
16:14:28 <BobP> Scott: Looking across data, are we going to try to move SNPs into model?
16:15:18 <BobP> Michel: Iker has some data too
16:19:25 <michel> http://phenomebrowser.net/
16:20:30 <michel> robert hoehndorf
16:20:41 <mscottm> Robert Hoehndorf - Phenomebrowser rat, mouse, human, yeast, few others, links genotypes to phenotypes
16:20:43 <BobP> Fred(?): Try thrombolism
16:20:44 <Fred> thromboembolism
16:20:48 <michel> http://phenomebrowser.net/explore.php?val=OMIM_188050
16:21:18 <BobP> Fred: I am consultant in clinical applications of genomics
16:21:32 <BobP> ... have Genomics Education Initiative
16:21:53 <BobP> Fred: Joanne asked me join in
16:22:43 <BobP> https://docs.google.com/document/d/1lKdDSb2uBBIeTEQAv2CyTHN_aVW63k9si1hmmilOMi0/edit?hl=en&authkey=CJGUtcwF#
16:32:05 <Joanne> Joanne has joined #hcls2
16:32:55 <Zakim> +joanne
16:33:37 <iker> my regrets but i must leave
16:33:46 <Zakim> -??P34
16:37:04 <BobP> Michel: Focus of paper is how to represent
16:37:37 <BobP> Bosse: Generalizing from warfarin is a good example
16:38:17 <Zakim> -matthias_samwald
16:38:38 <Zakim> +??P10
16:39:26 <BobP> Scott: Add in reference to warfarin's being problematical
16:40:38 <matthias_samwald> matthias_samwald has joined #hcls2
16:40:45 <BobP> Elgar: Predictive pgx, still working on
16:41:31 <BobP> ... have gone through Michel's papers
16:41:45 <BobP> ... papers on methods and algorithms
16:42:07 <BobP> ... can summarize at the bottom of google doc
16:43:02 <BobP> Joanne: Conversion, talked to Tim
16:43:28 <BobP> ... Linked open biodata, have done one provenance enhancement parameter
16:44:09 <BobP> ... we did the warfarin data, have detailed notes about the conversion
16:45:17 <BobP> ... running through converted takes no time; but adding parameters and value add - using our brains
16:45:58 <BobP> Scott: Part of problem is which vocabularies, which terms
16:46:15 <BobP> Joanne: Manual process to create the right mapping
16:46:52 <BobP> Michel: Using BioPortal?
16:47:27 <BobP> Scott: Yes, this is the hard part about converting to RDF
16:47:55 <BobP> ... once chosen vocab, then which terms to use. Lots of variability
16:51:05 <BobP> Michel: For TMO we had a spreadsheet of all terms to start
16:51:31 <BobP> ... then looked up terms in BioPortal to find the meanings that we wanted
16:51:43 <mscottm> Phenex Onto Pheno Diversity http://precedings.nature.com/documents/4068/version/1/files/npre20094068-1.pdf
16:51:50 <BobP> ... we might have to do this for our work now
16:52:17 <BobP> ... Should we use TMO? on mailing list
16:52:42 <BobP> ... maybe entries in table move to spreadsheet
16:52:59 <BobP> Elgar: -1 to spreadsheet
16:53:51 <mscottm> Another belated link related to the phenome browser: https://www.phenoscape.org/wiki/Main_Page
16:54:01 <BobP> Michel: Pull terms into ontology, then create mapping
16:54:26 <BobP> Michel: Seq Ont, but do not want to import the whole thing
16:54:52 <BobP> ... we can create 'like' versions of terms
16:55:29 <BobP> Scott: Trish told us about a way to refer to a term, w. some functionality in ?
16:55:58 <BobP> Michel: Protege server, can query BioPortal
16:56:27 <BobP> Scott: Option is BioPortal Reference plugin for protege
16:56:51 <BobP> ... slightly different from LODD and Term, use of proxy ontology or reference ontology
16:57:08 <BobP> ... like a spreadsheet, but put terms directly into ontology
16:57:19 <BobP> ... seeAlso for terms in other ontologies
16:58:07 <BobP> Michel: We can play around w. web protege to help us make decision
16:58:29 <BobP> Matthias: If we are using TMO, how should we go about it?
16:58:39 <BobP> ... add TMO directly in?
16:58:44 <BobP> Michel: Yes
16:58:50 <BobP> Scott: +1
16:59:28 <BobP> Michel: Iker's Virtuoso is loaded
16:59:45 <BobP> ... are there other RDF datasets for KB?
17:00:29 <BobP> Scott: Take all warfarin SNPs; start w. dbSNP, authoritative, stable approach
17:01:03 <BobP> ... name checker seems to be able to handle SNP nomenclature
17:01:32 <BobP> ... id warfarin SNPs, make URI or map
17:02:18 <BobP> ... future work: look for SNPs that would effect warfarin pathways
17:03:10 <BobP> ... there aren't that many warfarin SNPs
17:03:16 <BobP> Bob: +1 here
17:03:24 <Joanne> regrests - have to go -- the CSHALS org call is now and I need to go.
17:03:29 <Zakim> -joanne
17:04:12 <matthias_samwald> (i need to leave now as well, bye!)
17:04:20 <Zakim> -??P10
17:04:34 <mscottm> http://www.snpedia.com/index.php/Warfarin
17:07:00 <Zakim> -Bob_Powers
17:07:03 <Zakim> - +1.714.616.aaaa
17:07:04 <Zakim> -elgar
17:07:06 <Zakim> -Adrien
17:07:08 <Zakim> - +31.62.427.aabb
17:07:28 <michel> rrsagent, draft minutes
17:07:28 <RRSAgent> I have made the request to generate http://www.w3.org/2011/06/02-hcls2-minutes.html michel
17:12:08 <Zakim> disconnecting the lone participant, EricP, in SW_HCLS(TMO)11:00AM
17:12:11 <Zakim> SW_HCLS(TMO)11:00AM has ended
17:12:12 <Zakim> Attendees were +1.714.616.aaaa, +31.62.427.aabb, Adrien, EricP, matthias_samwald, Bob_Powers, elgar, joanne
18:20:26 <Zakim> Zakim has left #hcls2
18:30:31 <BobP> BobP has joined #hcls2