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
