16:03:08 <RRSAgent> RRSAgent has joined #hcls
16:03:08 <RRSAgent> logging to http://www.w3.org/2010/02/08-hcls-irc
16:03:15 <kei> Zakim, this will be BioRDF
16:03:15 <Zakim> ok, kei, I see SW_HCLS(BioRDF)11:00AM already started
16:04:44 <Zakim> +jun
16:05:23 <Zakim> +[IPcaller]
16:07:02 <rfrost> rfrost has joined #HCLS
16:10:50 <mscottm> http://hackathon3.dbcls.jp/
16:11:39 <kei> scott: concept alliance -- programmers hack rdf
16:11:55 <kei> scott: uniprot 
16:13:24 <Donald_Doherty> Michael Miller joins BioRDF for 1st time
16:13:33 <Donald_Doherty> was with Prosetta Software
16:13:45 <Donald_Doherty> now at Terranode
16:14:08 <ericP> Zakim, please dial ericP-office
16:14:08 <Zakim> ok, ericP; the call is being made
16:14:09 <Zakim> +EricP
16:14:22 <mscottm> s/Rosetta/Prosetta/
16:15:19 <Donald_Doherty> New data sources for the HCLS KB
16:16:56 <ericP> 5x5
16:18:37 <Donald_Doherty> Suggest post example queries for the HCLS KB
16:19:13 <ericP> the query federation queries are in an SWObjects test suite
16:19:20 <ericP> i suggest the same for HCLS KB
16:19:44 <mscottm> http://linkedlifedata.com/
16:20:13 <Donald_Doherty> kei: talk about RDF structures
16:20:30 <Donald_Doherty> kei: RDF structures for experimental context
16:22:33 <Donald_Doherty> kei: gene list - usually not machine friendly
16:23:58 <Donald_Doherty> kei: authors often make electronic version of gene list available in tabular or Excel format
16:25:13 <Donald_Doherty> kei: can we come up with a general RDF structure to represent gene lists?
16:25:44 <Donald_Doherty> kei: other efforts are interested in this such as SharedNames effort
16:26:32 <Zakim> -EricP
16:26:44 <ericP> Zakim, please dial ericP-office
16:26:44 <Zakim> ok, ericP; the call is being made
16:26:46 <Zakim> +EricP
16:26:52 <kei> http://www.tgen.org/research/index.cfm?pageid=502
16:30:03 <Donald_Doherty> +
16:31:26 <Donald_Doherty> We're looking at Excel document from above link "U133 plus 2.0 AD tangle vs AD control (99% CI)"
16:33:14 <Donald_Doherty> kei: this is a typical structure.
16:34:49 <Donald_Doherty> eric: this is not normalized. typical?
16:35:47 <Donald_Doherty> michael miller: can be normalized
16:36:51 <mscottm> q+
16:36:54 <Zakim> -EricP
16:38:08 <mscottm> scott: normalization from a database perspective (table structure) vs. normalization of microarray probe values
16:38:08 <ericP> the RDB2RDF WG will need a reallistic database, not a simplified form of it
16:38:16 <ericP> otherwise, they won't be able to meet our needs
16:38:31 <ericP> and they won't be motivated to adopt the use cases we give them
16:47:35 <Donald_Doherty> kei: lena has created a draft RDF structure and will post on a wiki page
16:50:45 <Donald_Doherty> kei: discuss app
16:52:40 <Donald_Doherty> Purpose: identify aging and neurodegenerative disease biomarkers at the gene and protein levels
16:57:25 <kei> don: input -- location, species, 
16:57:53 <kei> don: output -- phenotypes, genes, pathways, proteins ..
17:05:35 <mscottm> tx
17:06:43 <mscottm> gotta run to Terminology
17:07:20 <Zakim> - +1.206.605.aaaa
17:07:21 <Zakim> -mscottm
17:07:22 <Zakim> -Kei_Cheung
17:07:29 <jun> exit
17:07:31 <jun> exit
17:07:33 <Donald_Doherty> ericP are you saving this?
17:07:38 <Zakim> -Don_Doherty
17:07:44 <Zakim> -[IPcaller]
17:07:47 <Donald_Doherty> i've forgotten how
17:09:38 <kei> RRSAgent, please draft minutes
17:09:38 <RRSAgent> I have made the request to generate http://www.w3.org/2010/02/08-hcls-minutes.html kei
17:09:45 <kei> RRSAgent, please make log world-visible
17:12:44 <Zakim> disconnecting the lone participant, jun, in SW_HCLS(BioRDF)11:00AM
17:12:48 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
17:12:49 <Zakim> Attendees were +1.206.605.aaaa, Don_Doherty, mscottm, Kei_Cheung, jun, [IPcaller], EricP
18:35:38 <egonw> egonw has joined #hcls