I actually did an exercise that described how to get GO IDs and GO terms from UCSC Table Browser at the request of the ENCODE project folks who are doing similar stuff.

In the UCSC Table Browser tutorial materials ( http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28 ) click the Exercises button. See Exercise 3 to walk through it.

Mary

Mary Mangan, PhD

President

OpenHelix LLC

65 Main St.

Somerville MA 02145

phone: 888-861-5051 x9

email: mmangan@openhelix.com

http://blog.openhelix.com

From: galaxy-user-bounces@lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of Oscar V Camacho
Sent: Tuesday, December 08, 2009 5:44 PM
To: galaxy-user@bx.psu.edu
Subject: [galaxy-user] ChIP-Seq and Gene Ontology with Galaxy-UCSC

Hi,
I am currently doing some ChIP-Seq experiments, to analyze the data I get from the PeakFinder of my choice I'm using the Galaxy tool from the UCSC browser to manipulate my intervals. What I have is a file in .BED format with the chromosome number, Start, End of the position and then I fetch the closest features and up to this moment everything is perfect but now that I have the positions of the nearest features to my putative binding sites I would like to get the gene symbol, description y GO for each one of them in a sort of table so as I can analyze it later on and make relationships.
Is there a direct  tool between Galaxy and a Gene ontology database?
Any help about this topic will be appreciated.
Thank you in advance.