[BioC] ArrayExpress and GEO datasets

Helen Parkinson parkinson at ebi.ac.uk
Tue Jul 14 12:52:38 CEST 2009


I wanted to clarify the GEO - ArrayExpress content discussion. To date 
ArrayExpress and GEO have no formal data exchange agreement to date for 
array based data. ArrayExpress imports GEO single channel data on 
commercial platforms by converting SOFT files into MAGE-TAB and also 
some two colour data.

MAGE-ML is a deprecated format for ArrayExpress - we still accept 
submissions but we do not encourage new pipelines for example.

Where GEO  = GEO data sets (GDS) these are re-curated by ArrayExpress, 
for GSE these are simply imported. We do reject some datasets based on 
data file fails etc. If people would like data to be in AE that's not 
been curated which originates with GEO this can be requested.

We are working towards a data exchange agreement for high throughput 
sequence data as the short read archives at NCBI and EBI already have 
such an agreement, and we hope to have something in place soon and data 
exchange working,



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