23 Apr 2012

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


<mscottm> https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?authkey=CK-y8Y8C

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

.ttl did not work for me either

<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


<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

Summary of Action Items

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