1FlyBase (http://www. flybase. bio. indiana. edu). 2Berkeley Drosophila Genome Project (http://fruitfly. bdgp. berkeley. edu). 3Saccharomyces Genome Database (http://genome-www. stanford. edu). 4Mouse Genome Database and Gene Expression Database (http://www. informatics. jax. org). Correspondence should be addressed to JMC (e-mail: cherry@ stanford. edu) and DB (e-mail: botstein@ genome. stanford. edu), Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.

The accelerating availability of molecular sequences, particularly the sequences of entire genomes, has transformed both the theory and practice of experimental biology. Where once biochemists characterized proteins by their diverse activities and abundances, and geneticists characterized genes by the phenotypes of their mutations, all biologists now acknowledge that there is likely to be a single limited universe of genes and proteins, many of which are conserved in most or all living cells. This recognition has fuelled a grand unification of biology; the information about the shared genes and proteins contributes to our understanding of all the diverse organisms that share them. Knowledge of the biological role of such a shared protein in one organism can certainly illuminate, and often provide strong inference of, its role in other organisms. Progress in the way that biologists describe and conceptualize the shared biological elements has not kept pace with sequencing. For the most part, the current systems of nomenclature for genes and their products remain divergent even when the experts appreciate the underlying similarities. Interoperability of genomic databases is limited by this lack of progress, and it is this major obstacle that the Gene Ontology (GO) Consortium was formed to address.