What is the best way to obtain the GO annotations for a list of UniProt Accession Numbers in batch?

With UniProt accession numbers, you can obtain all GO annotations by parsing a GOA gene association file, which are provided in a simple tab-delimited format. These files are available from the GOA FTP site.

The GOA project offers users a number of different files; for example:

  • all UniProtKB proteins with GO annotation
  • human proteins
  • if you were only interested in proteins from a particular species, we also provide non-redundant, species-specific files for human, mouse, rat, zebrafish, chicken, cow and Arabidopsis proteins (these files are created using the International Protein Index (IPI) - which provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms)

Further information on the content and format of our gene association files can be found in the ReadMe.

Please contact GOA help for further assistance.