See also: IRC log
hi all
mscottm: today start discussing remaining issues for expression rdf document
there has been a publication already
link follows:
<mscottm> https://plus.google.com/u/0/114642613065018821852/posts/XYJuMDFfkK6
(michael joined)
<mscottm> https://plus.google.com/u/0/114642613065018821852/posts/XYJuMDFfkK6
paper uses swobjects
http://sourceforge.net/projects/swobjects/
that GDoc discusses using RDF for gene expression
biggest missing pieces
a general tool that converts MageTab into RDF
take interesting gene list and convert into RDF, including exp details, etc
mscottm: I did not full get that last major point
<JimMcCusker> http://code.google.com/p/magetab2rdf/source/browse/trunk/magetab2magerdf/mapping.ttl
jim: general framework for converting MageTAB into RDF...
<JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/virtuoso/sparql
<JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/
<JimMcCusker> http://purl.org/twc/arrayexpress/
<JimMcCusker> http://purl.org/twc/arrayexpress/E-GEOD-17089
<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?
<pekkoh> This is a ToxBank/SEURAT-1 consortium project (Egon knows). Can convert automatically mage2ISA and then ISA2RDF.
<mscottm> Pekka - Jim mentioned "ISA" a few minutes ago as a way to reference assays, IIR
<michael> hi pekkoh, yes we are, but we've started with MAGE-TAB, ISA-TAB would be similar
<pekkoh> OK.
<JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/P-GSE17089-4.html
JimMcCusker talks the telcon through some of the patterns
mscottm noted that the .ttl link did not work, may have been misrepresented, said JimMcCusker
<mscottm> bnode used to represent implicit input to the activity in the provenance for the protocol
OBI is used to refer to general processes...
<JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17089.html
protocols realize some process (more than one?), e.g. http://aquarius.tw.rpi.edu/projects/lobi/P-GSE17089-4.html
and investigation (:investigation, prov:Activity) has protocol realizations as parts (has_part)
study designs are represented using EFO: http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17089/studyDesign.html
egonw: is there an ordering of has_part linked protocols...
JimMcCusker: that order is implied by input and output of protocols
ok, thanx :)
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
this happens to be a cell line, A375P
here modeled as a "material entity" (BFO_0000040)
<JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/P-GSE17089-1.html
primary use case: discoverability, reuseability of results
JimMcCusker has visualizations, e.g. showing how methods changed over time
? suggests the example of a refuted cancer study...
which could be looked up in microarray dbs
practical problems in the data analysis which may have been tracked with a systematic approach
mscottm asks what is missing in JimMcCusker's work
JimMcCusker: one problem is samples from human, which are not instantiations of humans
so, tricky to pick the right OBI/... predicate
<michael> reanalisis of duke gene expression experiment: http://www.economist.com/node/21528593
<mscottm> Scott confirms understanding of use case application: Find studies that make use of same assay, protocol, enzyme, analysis, etc.
that is: how to encode "is a sample originating from human"
closest now is "has characteristic"
btw, I need to leave in 4 minutes...
<mscottm> tx for the warning
if we are not done by then, can someone scribe the remaining few minutes?
<mscottm> sure
<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
<JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17275/sourcename/GSM429727_2.html
ok, I have to leave
I note that our group does this pipeline:
and will see if people here can be interested in magetab2rdf
cheers!
<mscottm> tx egon!
<JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17275/sourcename/GSM429727_2.html
<mscottm> There's a characteristic for homo sapiens for the sample (in the URL Jim just posted above)
<egombocz> I've to leave, but very good discussions!
<mscottm> tried Zooma but it doesn't get you all the way to the URI for the ontology class.
<JimMcCusker> http://purl.org/twc/arrayexpress/E-GEOD-17089
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