16:03:25 <RRSAgent> RRSAgent has joined #hcls2
16:03:25 <RRSAgent> logging to http://www.w3.org/2011/10/06-hcls2-irc
16:03:33 <mscottm> Zakim, who is here?
16:03:41 <mscottm> Zakim, this is tmo
16:03:41 <bobP> bobP has joined #hcls2
16:04:03 <adrien> adrien has joined #HCLS2
16:04:04 <Zakim> sorry, mscottm, I don't know what conference this is
16:04:14 <Zakim> ok, mscottm; that matches SW_HCLS(TMO)11:00AM
16:04:20 <Zakim> On IRC I see bobP, RRSAgent, mscottm, matthias_samwald, ericP, Lena, Zakim, michel2
16:04:51 <Zakim> +??P55
16:05:03 <Zakim> +Bob_Powers
16:06:24 <Zakim> + +33.3.83.59.aabb
16:07:20 <bobP> scribenick bobP
16:07:28 <Zakim> +Tony
16:07:33 <BobF> BobF has joined #hcls2
16:08:09 <bobP> Michel: Look at use case template, think of task to perform
16:08:48 <bobP> ... this group can champion what we want to do with the KB
16:10:10 <bobP> Michel: Agenda: Matthias, develop use cases, and research
16:10:34 <bobP> Matthias: Thanks everybody for great collaboration
16:10:41 <adrien> thank you Matthias for submitting it!
16:10:53 <bobP> ... one of difficulties was that we did two things at once
16:11:25 <bobP> ... report on how semantics implemented, also design choices etc on the other hand
16:11:46 <Zakim> +??P7
16:12:01 <bobP> ... another paper will be research article in biomed semantics
16:12:19 <Zakim> +??P26
16:12:34 <iker> iker has joined #hcls2
16:12:53 <bobP> ... Special Report short paper, turned out to be longer, so wrote a proper review article
16:13:21 <bobP> ... produced a very interesting and useful piece of scientific literature
16:13:28 <bobP> ... can use as a basis to communicate
16:13:50 <bobP> Michel: Hit the level that we wanted; broad scope of utility
16:14:14 <bobP> ... readers will get the gist. Tech platform for what we are doing
16:15:03 <bobP> BobF: Thank you very much for driving this manuscript
16:15:51 <bobP> Matthias: Now that this is done, other paper should be easier
16:16:35 <bobP> ... can really focus on tech. Pgx in OWL will be very interesting
16:17:06 <bobP> ... pgx data and related data, at the end will be very interesting
16:17:41 <bobP> Michel: Would really like to see a list of design patterns for expressing data
16:18:19 <bobP> ... in line w. new interest group. More on the vocab side
16:18:37 <bobP> ... not much yet from w3c about representational patterns
16:19:08 <bobP> ... how to represent snp data, relation to pgx. Patterns, should be possible to marshal
16:19:34 <bobP> ... going to try to push this, beyond just strict RDF, but a bit more (disciplined)
16:20:04 <bobP> BobF: Absolutely.
16:20:17 <mscottm> 1+
16:20:20 <bobP> +1
16:21:12 <bobP> Michel: bio2rdf, need patterns for representation, not yet well developed
16:21:37 <bobP> ... we have always used obo ontologies in my research
16:22:07 <bobP> ... have a whole list of design patterns, then becomes like a recipe
16:22:19 <bobP> ... go the W3C and get the pattern.
16:23:43 <bobP> Michel: Next step. Use case template, would like to...
16:23:59 <michel2> https://docs.google.com/document/d/1I9xyVKhO9wG7My2fWu9S-wMwWZxG6PkRc98kOxUqH-o/edit?hl=en_US
16:24:46 <bobP> BobF: dbSNP last correspondence, mentioned that working here too
16:25:14 <bobP> ... development has been fairly good. We have a local copy, have stripped out immediate utility data
16:25:33 <bobP> ... can share by email. Plan is to load local DB here.
16:25:45 <bobP> ... how to expose for the rest of the group?
16:26:28 <bobP> Matthias: Problem may be larger? Ensure the scalability of the data
16:26:43 <bobP> Michel: Agree, going to make a note of this.
16:27:25 <bobP> BobF: Institutional guidlines are strict on external servers.
16:27:36 <bobP> ... approval to stand up an instance here
16:28:38 <bobP> Michel: You can load it at Carleton
16:29:06 <bobP> ... SWObjects, expose sparql endpoint?
16:29:24 <bobP> Scott: Iker has down exploratory work w d2r
16:29:56 <bobP> ... idea was to take specific data w dbSNP and access via sql mapped in swobjects
16:30:08 <bobP> ... not trying to expose everything
16:30:24 <bobP> ... Iker found that infra was the problem
16:30:45 <bobP> (I think he found that it was too big etc)
16:31:05 <Zakim> -??P7
16:31:38 <bobP> Iker: Did mapping w d2r, swobjects. Used a subset, here is the link
16:31:52 <iker> https://cgsmd.isi.edu/dbsnpq/
16:32:46 <bobP> ... first we should generate a subset of dbSNP that we will use. Huge
16:33:13 <bobP> Michel: BobF has done this part.
16:33:44 <bobP> BobF: Pulled out only those fields that are relevant. Excluded historical groupings of the RFs themselves
16:34:10 <bobP> ... contig mappings omitted. Just took SNPs, genes, classification etc
16:34:19 <iker> q+
16:34:21 <bobP> ... four different tables, but can extend from there.
16:34:49 <iker> SNP table at https://cgsmd.isi.edu/dbsnpq/downloads.php
16:34:57 <bobP> Michel: No contigs?
16:35:06 <iker> this table collects more or less the information Bob is talking about
16:35:13 <bobP> BobF: Yes, no contigs. Each build has its own mappings
16:35:31 <bobP> ... pulling in contig maps would imply pulling in the build data too
16:35:50 <bobP> ... but we can associate RS numbers w chromosomes
16:36:12 <bobP> ... also there will be some ambiguity in some
16:36:35 <bobP> ... not QC, just pulled data
16:36:56 <bobP> ... snp, chrome, validation info, locus id, proximity info, etc
16:37:04 <bobP> ... gene symbol with local ID
16:38:13 <bobP> Michel: (asking...)
16:38:35 <bobP> ... rewrite DB relations to swobjects forms
16:38:48 <bobP> Matthias: SWObjects in addition?
16:39:01 <iker> q+
16:39:45 <bobP> Michel: (implement to graph pattern - didn't quite get)
16:41:17 <bobP> Iker and Michel talking DB exchange
16:43:53 <bobP> Iker: ...Is ethnicity a requirement?
16:44:41 <bobP> Michel: Depends...longer term thing is to predict, related to pop genetics
16:45:16 <bobP> ScottScott: Scenario, have SNP for a particular patient
16:45:38 <bobP> ... might hapmap to see freq on pop. Pre-warfarin biomarker research
16:46:04 <bobP> ... warfarin, you already know whether patient has SNP or not.
16:46:57 <iker> could you provide a link to the wiki page of this work?
16:47:08 <bobP> Michel: Get trimmed down version of dbSNP up and running.
16:47:45 <bobP> Michel: Matthias' scalability issue. Would like to collaborate on a framework
16:48:50 <mscottm> @iker: we discussed that for initial versions of the paper so there is a wiki page and a few relevant google docs such as an article draft.
16:48:57 <bobP> Scott: Sustainability for HCLS, should have agree to have common method of methods, scripts, versions
16:49:22 <bobP> (that was Michel!)
16:49:36 <iker> @Scott, I am talking about the wiki page where we added the SPARQL queries of dbSNP I cannot find it
16:49:40 <bobP> Michel: Resources need to be kept up to date
16:50:25 <mscottm> for iker (in case you haven't seen this): http://www.w3.org/wiki/HCLSIG/TranslationalMedicine/pharmacogenomics
16:50:39 <bobP> Matthias: Miriam, identifiers.org, etc
16:50:52 <bobP> (that was Michel again!)
16:51:16 <iker> @Scott, maybe I am wrong but I think there was another wiki page with the SPARQL queries, I will check, thanks anyway
16:52:17 <bobP> Michel: Will try to take the medicine, on representation of pgx data.
16:52:55 <mscottm> @iker: maybe one of the google docs? Not this one (the modeling): https://docs.google.com/drawings/d/1OaqlmiTbIAkgHM6kCV-4xbRddHJiN1YZkCWdNHvwiGI/edit?authkey=CIT4rcwM&hl=en_US&authkey=CIT4rcwM
16:53:37 <matthias_samwald> maybe you meant http://www.w3.org/wiki/HCLSIG/pharmacogenomics_2011 ?
16:53:41 <Zakim> -??P26
16:54:22 <adrien> I wish you all a very good day. 
16:54:34 <Zakim> - +33.3.83.59.aabb
16:54:51 <bobP> Scott: One of Bob's Mayo people has project, sounds uncannily similar
16:55:07 <mscottm> http://informatics.mayo.edu/LCD/
16:56:12 <bobP> Scott: Project talks about LD, linking clinical records etc
16:56:40 <bobP> ... sent questions to LOD group, so contacted him
16:57:22 <bobP> ... can Mayo take advantage, and we can take advantage to get use cases and data
16:58:40 <bobP> BobF: Some of the work is what is offerring here
17:02:05 <Zakim> -Tony
17:02:09 <Zakim> -Bob_Powers
17:02:10 <Zakim> - +62427aaaa
17:02:14 <Zakim> -??P55
17:02:16 <Zakim> -??P22
17:02:18 <Zakim> SW_HCLS(TMO)11:00AM has ended
17:02:20 <Zakim> Attendees were +62427aaaa, Bob_Powers, +33.3.83.59.aabb, Tony
17:02:42 <bobP> rrsagent, draft minutes
17:02:42 <RRSAgent> I have made the request to generate http://www.w3.org/2011/10/06-hcls2-minutes.html bobP
17:02:58 <bobP> rrsagent, make logs public
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