Where can I view or download the complete sets of GO annotations?
As with the vocabularies, the gene product sets (gene association files) from contributing groups are freely available; you can download them from the annotation downloads section of the GO website. The files are in tab-delimited text; the file format is described in the GO annotation guide. Gene association files contain all evidence pertinent to the annotation, including database IDs and gene product names, as well as citation and evidence data.
As with the vocabularies, the gene product/GO association sets from contributing groups are available at the GO web site. Tab-delimited files of the associations between gene products and GO terms that are made by the member organizations are available from their individual FTP sites, from the GO FTP site (ftp://ftp.geneontology.org/pub/go/gene-association), or from a link on the Current Annotations table. The gene association file format is described in the GO annotation guide. These files store IDs for objects (genes/gene products) in the database that contributed the file (e.g. FlyBase IDs, Swiss-Prot accession IDs for proteins) as well as citation and evidence data. There are also files containing Swiss-Prot/TrEMBL protein sequence identifiers for gene products that have been annotated using GO terms; they are available via FTP. You can also download the annotations in mySQL format from GO Database Downloads. Note however that the mysql database dumps shouldn’t be treated as flat f
