There's a document detailing the setup for a local b2g at
http://bioinfo.cipf.es/blast2go --> Downloads --> Local B2G database
installation guide (howto_v1.3.tar.gz).

I followed all of the steps in the document (v1.3 - 29.08.2007) with
the following changes:

1.  Step 5c of Importing the data used for the mapping:
        Got the following error using the sun-java6-jdk on Ubuntu 7.10:
                $ javac -classpath . ImportPIR.java
                Note: ImportPIR.java uses unchecked or unsafe operations.
                Note: Recompile with -Xlint:unchecked for details.

After some searching online, this is because of how newer versions of
JDK handle Generics.  By running javac -Xlint:unchecked -classpath .
ImportPIR.java, I was able to compile the java class (with a warning).

2.  A new file from www.geneontology.org/external2go/ec2go was
downloaded (Feb 23, 2008).
When attempting to import the file (Step 3), the following error
occurs:
        mysqlimport: Error: Duplicate entry 'EC:3.6.3.14        GO:00469-'
for key 1, when using table: ec2go

Checking the following:
$ cat ec2go | grep 3.6.3.14
EC:3.6.3.14     GO:0046961
EC:3.6.3.14     GO:0046933

These GO terms are both for "hydrogen ion transporting ATP(ase)
(synthase) activity, rotational mechanism  -- the differences are in
parentheses.

Upon closer inspection of the ec2go file, there are other duplicates.
They are:
EC:2.5.1.46     GO:0034038
EC:2.5.1.46     GO:0050983

EC:2.7.1.119    GO:0008904
EC:2.7.1.119    GO:0034071

EC:3.5.99.7     GO:0008660
EC:3.5.99.7     GO:0034100

EC:3.6.3.15     GO:0046962
EC:3.6.3.15     GO:0046932

EC:3.6.5.1      GO:0003924
EC:3.6.5.1      GO:0005834

EC:3.6.5.3      GO:0003924
EC:3.6.5.3      GO:0006412

EC:3.6.5.4      GO:0003924
EC:3.6.5.4      GO:0005786

After manually comparing the 2 GO terms for each EC, I selectively
removed/deleted one of them.  (WARNING:  doing so may break previous
mappings.)  Once this was accomplished, the ec2go file could be
imported into database (Step 3).

3.  When importing the annex file to the database, a similar error of
duplicates was thrown.  I decided to leave this as is and stopped
there.  For accomplishing the Annex, I will just reset the database
connection to default.

General:
Fixes for the guide (Importing data for the Enzyme Code retrieval):
        In Step 2a, instead of replacing all ">" with ";", replace " > " as
well as " ; " with ";" (remove white space).
        Additonally, in Step 2c, remove the 2nd COLUMN (not row), as well as
the header information.