IRC log of HCLS on 2012-04-23
Timestamps are in UTC.
- 15:04:36 [RRSAgent]
- RRSAgent has joined #HCLS
- 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
- 17:30:18 [Zakim]
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- 18:02:34 [egonw]
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- 18:44:47 [egonw]
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- 19:35:18 [egonw]
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