[Gofriends] Best practice for integration of GO annotation ?

[K. Shameer]

Hello GOFriends,

I am looking for a best-practice method used by GO friends for integration
of GO annotation for genes in model organism. I need to store the GO data
for several model organisms in a local databases and retrieve the
annotation as a part of a web server based on requirement. I obtained GO
IDs using BioMart, using the GO IDs, I tried different perl modules to
obtain GO term from ID, but I find the processing is really slow - its
taking approximately 15 seconds to get term using a GO ID. Is there a
better approach to get the Gene ID, GO ID, GO Terms for model organisms as
a flat file ? I am also curious to know how GO friends obtain GO
annotations for genomes of interest - any best practices ?

Thanks in advance,
Khader Shameer
NCBS - TIFR
Bangalore