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15:04:36 <RRSAgent> logging to http://www.w3.org/2012/04/23-HCLS-irc
15:07:26 <egonw> hi all
15:08:13 <egonw> mscottm: today start discussing remaining issues for expression rdf document
15:08:20 <egonw> there has been a publication already
15:08:29 <egonw> link follows:
15:08:49 <mscottm> https://plus.google.com/u/0/114642613065018821852/posts/XYJuMDFfkK6
15:09:17 <egonw> (michael joined)
15:09:30 <michael> michael has joined #hcls
15:10:11 <mscottm> https://plus.google.com/u/0/114642613065018821852/posts/XYJuMDFfkK6
15:10:28 <egonw> paper uses swobjects
15:10:44 <egonw> http://sourceforge.net/projects/swobjects/
15:12:23 <mscottm> https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?authkey=CK-y8Y8C
15:12:43 <egonw> that GDoc discusses using RDF for gene expression
15:13:03 <egonw> biggest missing pieces
15:13:15 <egonw> a general tool that converts MageTab into RDF
15:13:40 <egonw> take interesting gene list and convert into RDF, including exp details, etc
15:13:46 <ericP> hi all, i'm pushing to get some stuff presentable for an hl7 meeting.
15:14:18 <ericP> s/hi all, i'm pushing to get some stuff presentable for an hl7 meeting.//
15:15:30 <egonw> mscottm: I did not full get that last major point
15:17:25 <JimMcCusker> http://code.google.com/p/magetab2rdf/source/browse/trunk/magetab2magerdf/mapping.ttl
15:17:44 <egonw> jim: general framework for converting MageTAB into RDF...
15:20:45 <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/virtuoso/sparql
15:21:10 <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/
15:21:23 <JimMcCusker> http://purl.org/twc/arrayexpress/
15:22:03 <JimMcCusker> http://purl.org/twc/arrayexpress/E-GEOD-17089
15:25:09 <egonw> .ttl did not work for me either
15:26:07 <pekkoh> Hello. I know i am a bit new at this (Pekka Kohonen  from Karolinska Institutet) but are you aware of the ISA-TAB and the ISA2RDF tools?
15:27:12 <pekkoh> This is a ToxBank/SEURAT-1 consortium project (Egon knows). Can convert automatically mage2ISA and then ISA2RDF.
15:27:32 <mscottm> Pekka - Jim mentioned "ISA" a few minutes ago as a way to reference assays, IIR
15:27:43 <michael> hi pekkoh, yes we are, but we've started with MAGE-TAB, ISA-TAB would be similar
15:29:03 <pekkoh> OK.
15:29:24 <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/P-GSE17089-4.html
15:29:35 <egonw> JimMcCusker talks the telcon through some of the patterns
15:29:53 <egonw> mscottm noted that the .ttl link did not work, may have been misrepresented, said JimMcCusker
15:33:27 <mscottm> bnode used to represent implicit input to the activity in the provenance for the protocol
15:34:53 <egonw> OBI is used to refer to general processes...
15:35:11 <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17089.html
15:35:16 <egonw> protocols realize some process (more than one?), e.g. http://aquarius.tw.rpi.edu/projects/lobi/P-GSE17089-4.html
15:36:12 <egonw> and investigation (:investigation, prov:Activity) has protocol realizations as parts (has_part)
15:36:57 <egonw> study designs are represented using EFO: http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17089/studyDesign.html
15:38:28 <egonw> egonw: is there an ordering of has_part linked protocols...
15:38:42 <egonw> JimMcCusker: that order is implied by input and output of protocols
15:38:53 <egonw> ok, thanx :)
15:40:56 <egonw> JimMcCusker: prov:used is used to refer to the samples, materials, etc... e.g. http://purl.org/twc/arrayexpress/E-GEOD-17089/sourcename/GSM427343_1
15:41:09 <egonw> this happens to be a cell line, A375P
15:41:39 <egonw> here modeled as a "material entity" (BFO_0000040)
15:43:06 <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/P-GSE17089-1.html
15:45:35 <egonw> primary use case: discoverability, reuseability of results
15:45:55 <egonw> JimMcCusker has visualizations, e.g. showing how methods changed over time
15:47:31 <egonw> ? suggests the example of a refuted cancer study...
15:47:43 <egonw> which could be looked up in microarray dbs
15:52:16 <egonw> practical problems in the data analysis which may have been tracked with a systematic approach
15:52:37 <egonw> mscottm asks what is missing in JimMcCusker's work
15:53:21 <egonw> JimMcCusker: one problem is samples from human, which are not instantiations of humans
15:53:33 <egonw> so, tricky to pick the right OBI/... predicate
15:53:51 <michael> reanalisis of duke gene expression experiment: http://www.economist.com/node/21528593
15:53:58 <mscottm> Scott confirms understanding of use case application: Find studies that make use of same assay, protocol, enzyme, analysis, etc.
15:54:57 <egonw> that is: how to encode "is a sample originating from human"
15:55:33 <egonw> closest now is "has characteristic"
15:55:59 <egonw> btw, I need to leave in 4 minutes...
15:56:10 <mscottm> tx for the warning
15:56:11 <egonw> if we are not done by then, can someone scribe the remaining few minutes?
15:56:15 <mscottm> sure
15:57:26 <Helena> <michael> reanalisis of duke gene expression experiment: http://www.economist.com/node/21528593 -> michael: I know Keith Baggerly and Kevin Coombes (the statistians who uncovered the fraud) - they spent at least 3 years attempting to reanalize the data
15:58:57 <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17275/sourcename/GSM429727_2.html
15:59:36 <egonw> ok, I have to leave
15:59:43 <egonw> I note that our group does this pipeline:
15:59:49 <egonw> http://arrayanalysis.org/
16:00:06 <egonw> and will see if people here can be interested in magetab2rdf
16:00:09 <egonw> cheers!
16:01:49 <mscottm> tx egon!
16:05:16 <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17275/sourcename/GSM429727_2.html
16:05:56 <mscottm> There's a characteristic for homo sapiens for the sample (in the URL Jim just posted above)
16:12:19 <michael> michael has left #hcls
16:12:55 <egombocz> I've to leave, but very good discussions!
16:13:17 <mscottm> tried Zooma but it doesn't get you all the way to the URI for the ontology class.
16:14:54 <JimMcCusker> http://purl.org/twc/arrayexpress/E-GEOD-17089
16:18:42 <mscottm> RRSAgent, please draft minutes.
16:18:42 <RRSAgent> I'm logging. I don't understand 'please draft minutes.', mscottm.  Try /msg RRSAgent help
16:20:24 <mscottm> RRSAgent, please draft minutes
16:20:24 <RRSAgent> I have made the request to generate http://www.w3.org/2012/04/23-HCLS-minutes.html mscottm
16:20:42 <mscottm> RRSAgent, please make minutes public
16:20:42 <RRSAgent> I'm logging. I don't understand 'please make minutes public', mscottm.  Try /msg RRSAgent help
16:21:09 <Helena> scott, I think it's 'world visible' instead of public
16:21:20 <Helena> RRSAgent, please make minutes world-visible
16:21:20 <RRSAgent> I'm logging. I don't understand 'please make minutes world-visible', Helena.  Try /msg RRSAgent help
16:21:41 <Helena> RRSAgent, please make minutes world visible
16:21:41 <RRSAgent> I'm logging. I don't understand 'please make minutes world visible', Helena.  Try /msg RRSAgent help
16:21:49 <Helena> aaarhhrhhhgggggggg
16:22:33 <Helena> RRSAgent, please set logs world-visible
16:23:03 <Helena> tks for logging
16:23:13 <mscottm> thanks Lena! 
16:23:36 <mscottm> LOL - aaaarhhhhrrrrggggg
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