IRC log of hcls2 on 2011-10-06

Timestamps are in UTC.

16:03:25 [RRSAgent]
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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]
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16:04:03 [adrien]
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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]
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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]
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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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