While most ontologies have been used only by the groups who created them and for their initially defined purposes, the Gene Ontology (GO), an evolving structured controlled vocabulary of nearly 16,000 terms in the domain of biological functionality, has been widely used for annotation of biological-database entries and in biomedical research. As a set of learned lessons offered to other ontology developers, we list and briefly discuss the characteristics of GO that we believe are most responsible for its success: community involvement; clear goals; limited scope; simple, intuitive structure; continuous evolution; active curation; and early use. © 2004 Elsevier B.V. All rights reserved.