[Bioperl-l] Gene Expression Omnibus Data interface?

Sean Davis 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,
>> 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
>
>
Robert,

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:

http://bio-blue.blogspot.com/2010/03/rss-feed-for-ncbi-geo-submissions-using.html

The GEO RSS feed is here:

http://feeds.feedburner.com/ncbiGeo

Sean


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