[Bioperl-l] Gene Expression Omnibus Data interface?
sdavis2 at mail.nih.gov
Wed Apr 21 10:40:26 EDT 2010
On Mon, Apr 19, 2010 at 5:31 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 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,
>> 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:
I forgot to mention an RSS feed that we set up using the above tools. The
feed tracks released data from NCBI GEO. The GEO folks are working on such
a thing themselves, but to my knowledge have not made it available yet. The
blog post describing the technology is here:
The GEO RSS feed is here:
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