[Bioperl-l] Gene Expression Omnibus Data interface?
sdavis2 at mail.nih.gov
Mon Apr 19 17:31:26 EDT 2010
On Mon, Apr 19, 2010 at 4:03 PM, Robert Bradbury
<robert.bradbury at gmail.com>wrote:
> Next question is whether BioPerl has an interface to the NCBI GEO database
> that would allow BioPerl programs to (regularly) query the datasets to
> determine data relating to specific genes or organisms has been added?
> I'm trying to automate my requests to various databases (PubMed, GEO, etc.)
> to construct an expanding (topic specific) knowledge base.
You could look at the GEOmetadb package for R. The package provides an
interface to a standard SQLite database that we update weekly with ALL
metadata from GEO. Additionally, there is an online version of the
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