The completion of the human genome has shifted the attention from deciphering the sequence to the identification and characterization of the encoded components. The identification and functional annotation of the proteome is here of special interest and starts with the identification of genes and transcripts as a prerequisite of proteome annotation. Gene predictions are very powerful in predicting most of the exons in a genome, but reliable gene structure predictions of both known and novel genes are dependent on existing transcript and protein information. An enormous amount of data already exists on the function of many human proteins, but this is scattered over many resources. Public domain databases are required to manage and collate this information and present it to the user community in both a human and machine readable manner.