GOTaxExplorer

Download

GOTaxExplorer is available as download. This version includes binaries of all programs that are necessary to build GOTaxDB from the flat files. Additionally, FSST is made available with an included embedded database. The FSST database contains all pairwise simRel scores between Gene Ontology terms contained in the current GOTaxDB release. If you are interested only in one of the ontologies (biological process, molecular function, cellular component) it may be possible to provide a smaller version of the database.
In such cases, please contact us at: gotax [at] mpi-inf [dot] mpg [dot] de.
Download one of the packages here.

Web Start Version

Start GOTaxExplorer via Java Web Start:

Online GOTaxDB 6.0:

UniProt 2012_01
Gene Ontology, monthly release from January 2012
GOA, release from January 2012
NCBI Taxononmy, release from 13 February 2012
Pfam 26.0
SMART from InterPro 35

The list of species contained in the current version of the online database can be found here.
How many proteins of a specific species are annotated with

GO biological process terms? See here
GO molecular function terms? See here
GO cellculat component terms? See here
Pfam families? See here
SMART families? See here

SOAP Server

You can access the SOAP server under the URL: http://gotax.bioinf.mpi-inf.mpg.de/GOTaxSOAP.php.
The WSDL file describing the server is available here.