Conference Details
- Date of Call: Monday, April 23, 2012
- Time of Call: 17:00 CEST
- Dial-In #: +1.617.761.6200 (Cambridge, MA)
- Participant Access Code: 4257 ("HCLS")
- VOIP: To be added
- IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for IRC access.
- Duration: ~1 hour
- Convener: Scott Marshall
- Scribe: User:Ewilligh
IRC Transcript
[Monday, April 23, 2012] [03:38:40 PM] Join MacTed has joined this channel (Thud@63.119.36.36).
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[Monday, April 23, 2012] [05:01:33 PM] * Helena can't join audio due to overlapping meeting but happy to read the minutes :)
[Monday, April 23, 2012] [05:01:50 PM] * egonw notices he is late once again
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[Monday, April 23, 2012] [05:04:48 PM] <RRSAgent> logging to http://www.w3.org/2012/04/23-HCLS-irc
[Monday, April 23, 2012] [05:07:38 PM] <egonw> hi all
[Monday, April 23, 2012] [05:07:55 PM] * egonw will scribe
[Monday, April 23, 2012] [05:08:24 PM] <egonw> mscottm: today start discussing remaining issues for expression rdf document
[Monday, April 23, 2012] [05:08:32 PM] <egonw> there has been a publication already
[Monday, April 23, 2012] [05:08:41 PM] <egonw> link follows:
[Monday, April 23, 2012] [05:09:01 PM] <mscottm> https://plus.google.com/u/0/114642613065018821852/posts/XYJuMDFfkK6
[Monday, April 23, 2012] [05:09:29 PM] <egonw> (michael joined)
[Monday, April 23, 2012] [05:09:42 PM] Join michael has joined this channel (d17cbd27@78.129.202.38).
[Monday, April 23, 2012] [05:10:23 PM] <mscottm> https://plus.google.com/u/0/114642613065018821852/posts/XYJuMDFfkK6
[Monday, April 23, 2012] [05:10:40 PM] <egonw> paper uses swobjects
[Monday, April 23, 2012] [05:10:56 PM] <egonw> http://sourceforge.net/projects/swobjects/
[Monday, April 23, 2012] [05:12:34 PM] <mscottm> https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?authkey=CK-y8Y8C
[Monday, April 23, 2012] [05:12:54 PM] <egonw> that GDoc discusses using RDF for gene expression
[Monday, April 23, 2012] [05:13:14 PM] <egonw> biggest missing pieces
[Monday, April 23, 2012] [05:13:27 PM] <egonw> a general tool that converts MageTab into RDF
[Monday, April 23, 2012] [05:13:52 PM] <egonw> take interesting gene list and convert into RDF, including exp details, etc
[Monday, April 23, 2012] [05:13:58 PM] <ericP> hi all, i'm pushing to get some stuff presentable for an hl7 meeting.
[Monday, April 23, 2012] [05:14:08 PM] * ericP can you ping me here if you need me for a short moment?
[Monday, April 23, 2012] [05:14:30 PM] <ericP> s/hi all, i'm pushing to get some stuff presentable for an hl7 meeting.//
[Monday, April 23, 2012] [05:14:40 PM] * ericP doesn't want to leave crap in the log
[Monday, April 23, 2012] [05:15:42 PM] <egonw> mscottm: I did not full get that last major point
[Monday, April 23, 2012] [05:17:37 PM] <JimMcCusker> http://code.google.com/p/magetab2rdf/source/browse/trunk/magetab2magerdf/mapping.ttl
[Monday, April 23, 2012] [05:17:56 PM] <egonw> jim: general framework for converting MageTAB into RDF...
[Monday, April 23, 2012] [05:20:57 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/virtuoso/sparql
[Monday, April 23, 2012] [05:21:22 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/
[Monday, April 23, 2012] [05:21:35 PM] <JimMcCusker> http://purl.org/twc/arrayexpress/
[Monday, April 23, 2012] [05:22:15 PM] <JimMcCusker> http://purl.org/twc/arrayexpress/E-GEOD-17089
[Monday, April 23, 2012] [05:25:21 PM] <egonw> .ttl did not work for me either
[Monday, April 23, 2012] [05:26:18 PM] <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?
[Monday, April 23, 2012] [05:27:24 PM] <pekkoh> This is a ToxBank/SEURAT-1 consortium project (Egon knows). Can convert automatically mage2ISA and then ISA2RDF.
[Monday, April 23, 2012] [05:27:44 PM] <mscottm> Pekka - Jim mentioned "ISA" a few minutes ago as a way to reference assays, IIR
[Monday, April 23, 2012] [05:27:54 PM] <michael> hi pekkoh, yes we are, but we've started with MAGE-TAB, ISA-TAB would be similar
[Monday, April 23, 2012] [05:29:15 PM] <pekkoh> OK.
[Monday, April 23, 2012] [05:29:36 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/P-GSE17089-4.html
[Monday, April 23, 2012] [05:29:47 PM] <egonw> JimMcCusker talks the telcon through some of the patterns
[Monday, April 23, 2012] [05:30:04 PM] <egonw> mscottm noted that the .ttl link did not work, may have been misrepresented, said JimMcCusker
[Monday, April 23, 2012] [05:33:39 PM] <mscottm> bnode used to represent implicit input to the activity in the provenance for the protocol
[Monday, April 23, 2012] [05:35:05 PM] <egonw> OBI is used to refer to general processes...
[Monday, April 23, 2012] [05:35:22 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17089.html
[Monday, April 23, 2012] [05:35:28 PM] <egonw> protocols realize some process (more than one?), e.g. http://aquarius.tw.rpi.edu/projects/lobi/P-GSE17089-4.html
[Monday, April 23, 2012] [05:36:24 PM] <egonw> and investigation (:investigation, prov:Activity) has protocol realizations as parts (has_part)
[Monday, April 23, 2012] [05:37:08 PM] <egonw> study designs are represented using EFO: http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17089/studyDesign.html
[Monday, April 23, 2012] [05:38:39 PM] <egonw> egonw: is there an ordering of has_part linked protocols...
[Monday, April 23, 2012] [05:38:53 PM] <egonw> JimMcCusker: that order is implied by input and output of protocols
[Monday, April 23, 2012] [05:39:05 PM] <egonw> ok, thanx :)
[Monday, April 23, 2012] [05:41:08 PM] <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
[Monday, April 23, 2012] [05:41:21 PM] <egonw> this happens to be a cell line, A375P
[Monday, April 23, 2012] [05:41:51 PM] <egonw> here modeled as a "material entity" (BFO_0000040)
[Monday, April 23, 2012] [05:43:18 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/P-GSE17089-1.html
[Monday, April 23, 2012] [05:45:47 PM] <egonw> primary use case: discoverability, reuseability of results
[Monday, April 23, 2012] [05:46:07 PM] <egonw> JimMcCusker has visualizations, e.g. showing how methods changed over time
[Monday, April 23, 2012] [05:47:43 PM] <egonw> ? suggests the example of a refuted cancer study...
[Monday, April 23, 2012] [05:47:55 PM] <egonw> which could be looked up in microarray dbs
[Monday, April 23, 2012] [05:52:28 PM] <egonw> practical problems in the data analysis which may have been tracked with a systematic approach
[Monday, April 23, 2012] [05:52:49 PM] <egonw> mscottm asks what is missing in JimMcCusker's work
[Monday, April 23, 2012] [05:53:33 PM] <egonw> JimMcCusker: one problem is samples from human, which are not instantiations of humans
[Monday, April 23, 2012] [05:53:45 PM] <egonw> so, tricky to pick the right OBI/... predicate
[Monday, April 23, 2012] [05:54:03 PM] <michael> reanalisis of duke gene expression experiment: http://www.economist.com/node/21528593
[Monday, April 23, 2012] [05:54:10 PM] <mscottm> Scott confirms understanding of use case application: Find studies that make use of same assay, protocol, enzyme, analysis, etc.
[Monday, April 23, 2012] [05:55:08 PM] <egonw> that is: how to encode "is a sample originating from human"
[Monday, April 23, 2012] [05:55:45 PM] <egonw> closest now is "has characteristic"
[Monday, April 23, 2012] [05:56:11 PM] <egonw> btw, I need to leave in 4 minutes...
[Monday, April 23, 2012] [05:56:22 PM] <mscottm> tx for the warning
[Monday, April 23, 2012] [05:56:23 PM] <egonw> if we are not done by then, can someone scribe the remaining few minutes?
[Monday, April 23, 2012] [05:56:26 PM] <mscottm> sure
[Monday, April 23, 2012] [05:57:00 PM] * egonw wonderes how the proteomics does this with "human protein"
[Monday, April 23, 2012] [05:57:38 PM] <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
[Monday, April 23, 2012] [05:59:09 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17275/sourcename/GSM429727_2.html
[Monday, April 23, 2012] [05:59:47 PM] <egonw> ok, I have to leave
[Monday, April 23, 2012] [05:59:54 PM] <egonw> I note that our group does this pipeline:
[Monday, April 23, 2012] [06:00:00 PM] <egonw> http://arrayanalysis.org/
[Monday, April 23, 2012] [06:00:18 PM] <egonw> and will see if people here can be interested in magetab2rdf
[Monday, April 23, 2012] [06:00:21 PM] <egonw> cheers!
