How we classify the genes, products and complexes that are present or absent in genomes, transcriptomes, proteomes and other datasets helps us place biological objects into subsystems with common functions, see how molecular functions are used to implement biological processes and compare the biology of different species and strains. Gene Ontology (GO) is one of the most successful systems for classifying biological function. Although GO is widely used for eukaryotic genomics, it has not yet been widely used for bacterial systems. The potential applications of GO are currently limited by the need to improve the annotation of bacterial genomes with GO and to improve how prokaryotic biology is represented in the ontology. Here, we discuss why GO should be adopted by microbiologists, and describe recent efforts to build and maintain high-quality GO annotation for Escherichia coli as a model system.