Hi Michael et al,
Thanks for pointing to this generic approach of RDF representation of
datasets. A list of differentially expressed genes may be associated
with values such as P-values, fold-change, gene symbols, etc. Also, it's
important to capture metadata/provenance associated with the gene list.
This may include the type of statistical test (e.g., ANOVA) and the
array platform employed (e.g., Affymetrix U133A). This may be an
interesting discussion topic at the F2F meeting.
Cheers,
-Kei
mdmiller wrote:
hi all,
on a different HCLS thread i saw this proposal from jeni tennison for
specifying a generic dataset, it might be a useful way to encode a
list of differentially expressed genes. it looks like one could do
this encoding on the fly, so that the data itself at the source could
be in whatever format is natural.
http://sw.joanneum.at/scovo/schema.html
cheers,
michael
Michael Miller
mdmille...@comcast.net
----- Original Message ----- From: "Kei Cheung" <kei.che...@yale.edu>
To: "Helen Parkinson" <parkin...@ebi.ac.uk>
Cc: "HCLS" <public-semweb-lifesci@w3.org>; "Tony Burdett"
<tburd...@ebi.ac.uk>
Sent: Wednesday, October 14, 2009 7:03 PM
Subject: Re: Action Items from call today
Thanks, Helen.
To make it more concrete. I've been thinking about some example
queries that I hope can be answered by the RDF data once converted. I
wonder if the following example quereis can be answered:
Retrieve a list of differentially expressed genes between different
brain regions (e.g., hippocampus and entorhinal cortex) for normally
aged human subjects.
Retrieve a list of differentially expressed genes for the same brain
region of normal human subjects and AD patients.
Using these lists of genes one can issue (federated) queries to
retrieve addtional information about the genes for various types of
analyses (e.g., GO term enrichment).
Just a thought.
Cheers,
-Kei
Helen Parkinson wrote:
Hi
here are my action items from the call today
1. MAGE-TAB->RDF, Lena requested details.
Code here: https://sourceforge.net/projects/limpopo/
Java Parser for MAGE-TAB developed by EBI, used by several groups.
Contact Tony Burdett tburd...@ebi.ac.uk for details. Tony estimates
for a simple RDF dump a few days work. Lena if you are interested in
working on this java code please contact Tony as he's already
designed with rdf export in mind
2. MAGE-TAB->MAGE-ML - code from Junmin Liu at UPenn
https://sourceforge.net/projects/tab2mage/files/ - see mage2tab
Pretty much all public MAGE-ML comes from AE and is available from
Arrayexpress ftp dirs as mage-tab already. Exceptions are Rosetta's
mage-ml importer, and non public data
3. EBI experimental factor ontology (EFO) slides, attached
see also www.ebi.ac.uk/efo
4. Noted that an RDF dump of atlas data and triple store access will
be useful, we'll announce when these are available
thanks
Helen