16:02:34 <RRSAgent> RRSAgent has joined #hcls2
16:02:34 <RRSAgent> logging to http://www.w3.org/2011/09/29-hcls2-irc
16:04:08 <epichler> epichler has joined #HCLS2
16:05:47 <micheldumontier> micheldumontier has joined #hcls2
16:06:03 <micheldumontier> on my way
16:07:07 <adrien> HI everyone - unfortunately I have to leave at 18h20
16:07:18 <micheldumontier> we'll make it short
16:07:26 <micheldumontier> zakim, who is here?
16:07:26 <Zakim> sorry, micheldumontier, I don't know what conference this is
16:07:27 <Zakim> On IRC I see micheldumontier, epichler, RRSAgent, Zakim, mscottm, BobF, adrien, bobP, ericP
16:07:34 <micheldumontier> zakim, this is hcls
16:07:34 <Zakim> ok, micheldumontier; that matches SW_HCLS(TMO)11:00AM
16:07:45 <micheldumontier> zakim, who is here?
16:07:45 <Zakim> On the phone I see Bob_Powers, Scott_Bauer, +31.62.427.aaaa, +33.3.83.59.aabb, Scott_Bauer.a, +1.781.431.aadd, ??P27
16:07:47 <Zakim> On IRC I see micheldumontier, epichler, RRSAgent, Zakim, mscottm, BobF, adrien, bobP, ericP
16:07:51 <ericP> micheldumontier, will be there in 5 mins
16:08:51 <Zakim> + +1.301.443.aaee
16:09:44 <mscottm> I sent a note to Fred Whipple to ask him to join us since he was involved in the formative months.
16:09:47 <DaveHau> DaveHau has joined #HCLS2
16:10:08 <bobP> scribenick bobP
16:11:10 <bobP> Michel: discussing large sets of interconnected dbs...
16:11:42 <bobP> ... next step, need to demonstrate the integration
16:12:04 <bobP> ... should show URIs for docs etc
16:12:27 <bobP> ... motivation for the owl section
16:12:56 <bobP> ... how to communicate the essence of the tech, so readers have a grip
16:14:32 <bobP> Adrien: Lots of data expressed in natural language
16:17:51 <bobP> ... (missed some here..)
16:19:04 <bobP> Scott: Chris Baker has reference here..
16:19:05 <mscottm> http://www.biomedcentral.com/1471-2164/11/S4/S24
16:19:28 <bobP> Scott: Mutation impacts, from text mining
16:19:48 <bobP> ... closely aligned with what we are describing
16:20:22 <ericP> Zakim, please dial ericP-office
16:20:22 <Zakim> ok, ericP; the call is being made
16:20:24 <Zakim> +EricP
16:22:21 <adrien> I have to run - have a good meeting
16:22:32 <ericP> i'll cover for you
16:22:33 <bobP> Michel: Figure for cds clincical decision support
16:22:39 <adrien> tks
16:23:30 <Zakim> - +33.3.83.59.aabb
16:24:49 <bobP> ... table has several levels - (I see it)
16:25:22 <bobP> BobF: Level 1, before variant can be used in pheno-geno, needs to be validated etc
16:25:44 <bobP> ... there is work around clean-up and nail-down before clinical application
16:26:14 <bobP> Michel: Level 1 is basic research; don't know yet re importance
16:26:36 <bobP> ... don't yet know relationship to pheno
16:27:08 <bobP> BobF: Reading tightly; if includes assay and validation then it's OK
16:27:23 <bobP> ... validation that it's real, not an artifact
16:27:36 <bobP> Michel: Level 1 is appropriate for validation too
16:28:05 <bobP> BobF: Today most of SNPs go thru one level of validation
16:29:05 <bobP> Michel: RHS has orders of magnitude, can we give reference?
16:29:48 <bobP> BobF: Thought about, not sure so easy
16:30:10 <bobP> ... good for graph representation of funnel shape rather than exact numbers
16:31:05 <bobP> Scott: Funnel shape gets the idea across
16:31:30 <bobP> BobF: Numbers might tie this to time
16:32:10 <ericP> funnel shape will be familar to folks who've seen popular representations of the attrition of drug leads in a development pipeline
16:32:39 <bobP> Michel: Need a bang-for-the-buck ending
16:32:53 <bobP> Scott: Need one more bullet at least
16:33:27 <bobP> BobF: Title is focussed on infra and tech, and how they facilitate
16:33:41 <bobP> ... concluding portion should help reinforce that
16:34:03 <bobP> ... many different components: datasets, onts, etc
16:34:31 <bobP> ... bring all of threads together; real advance in brining all these resources to bear
16:35:03 <bobP> ... (this is too good to miss - write it out!)
16:36:11 <bobP> Michel: Should end in a different place?
16:36:42 <bobP> Scott: Need a punch line. Everybody is after mapping geno-pheno
16:37:22 <bobP> ... look at that as a bottleneck; When we have these mappings then easy to share
16:37:50 <bobP> ... one of the promises of semweb, describe sets of phenos in commonly accepted form
16:38:18 <bobP> ... and access snps in global namespace, then harness to make statements understood here to China
16:39:33 <bobP> BobF: Many of datasources have evolved over time, become internally standarized
16:39:48 <bobP> ... dbSNP great effort to make unique IDs
16:40:16 <bobP> ... single term for concepts. But this evolution is still in silos!
16:40:38 <bobP> ... semweb can start us to more seamlessly normalize across silos
16:41:49 <bobP> Elgar: Main concern, why do all of this, what is the real advantage of owl, need example?
16:42:36 <bobP> ... meaning of interlinking data. Matthias has shown how to make queries across dbs
16:43:09 <bobP> ... section on owl inference, using genetic info to stratify patients
16:43:38 <bobP> ... would be nice to show that w owl can be easy
16:44:13 <bobP> ... under figure on integration, using the functionalities of owl...
16:44:47 <bobP> ... nice to show how things are much easier
16:45:17 <bobP> ericP: Here's how traditional query, vs here's how to do w owl
16:45:39 <mscottm> immediate advantages to SPARQL endpoint: subsumption reasoning, federation 
16:45:45 <bobP> ... can mock up SQL w a couple of hospital dbs
16:46:17 <bobP> Michel: Patient has some disease, affects some morphological part
16:47:03 <bobP> Elgar: Agree, but want one simple example of superiority.
16:48:05 <bobP> Elgar: Under figure by Matthias, we can conceptualize...as a pipeline...
16:48:23 <bobP> ... don't quite see the analogy here.
16:50:37 <micheldumontier> https://docs.google.com/document/d/1bsJ3YWuH1k3gdXtSN2PXfmUIavtR-hDXhHMn0bKB5pk/edit?hl=en_US
16:50:56 <bobP> DaveHau: will look at report
16:51:58 <bobP> Scott: Deadline tomorrow :)
16:52:57 <Zakim> -Scott_Bauer.a
16:55:09 <bobP> Scott: Need to be clear about benefits of clinical practice vs clinical research
16:55:21 <bobP> ... Fred Whipple was pointing this out.
16:55:33 <micheldumontier> dave: i need you to request access to the document
16:55:51 <bobP> ... info retrieval, hypothesis testing need to be kept separate
16:56:05 <bobP> ... we are saying that both will benefit.
16:56:44 <bobP> ... clinical software should alert to dose-response w allele
16:57:06 <bobP> ... too difficult for doctor to do like a researcher
16:57:25 <bobP> ... this is a benefit of semweb infra (to automate this?)
16:58:19 <bobP> Dave Hau: There is a feedback between clinical practice and research(?)
17:00:29 <mscottm> The notion of feedback (Dave mentioned) is probably worth mentioning in the 'future prospective' section.
17:08:05 <Zakim> -Scott_Bauer
17:08:07 <Zakim> -EricP
17:08:08 <Zakim> -Bob_Powers
17:08:08 <Zakim> -??P27
17:08:08 <Zakim> - +1.301.443.aaee
17:08:10 <Zakim> - +31.62.427.aaaa
17:08:10 <Zakim> - +1.781.431.aadd
17:08:11 <Zakim> SW_HCLS(TMO)11:00AM has ended
17:08:12 <Zakim> Attendees were Bob_Powers, Scott_Bauer, +31.62.427.aaaa, +33.3.83.59.aabb, +1.781.431.aacc, +1.781.431.aadd, +1.301.443.aaee, EricP
17:08:30 <bobP> rrsagent, draft minutes
17:08:30 <RRSAgent> I have made the request to generate http://www.w3.org/2011/09/29-hcls2-minutes.html bobP
17:08:45 <bobP> rrsagent, make logs public
17:08:47 <mscottm> Forgot to mention: today was a Jewish holiday, esp. in the Boston area. 
18:32:20 <Zakim> Zakim has left #hcls2