[Bioperl-l] Gene Expression Omnibus Data interface?

Sean Davis 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
database.   See:

http://gbnci.abcc.ncifcrf.gov/geo/
http://bioconductor.org/packages/release/bioc/html/GEOmetadb.html

Sean


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