Examples of Gene Ontology. Three examples illustrate the structure and style used by GO to represent the gene ontologies and to associate genes with nodes within an ontology. The ontologies are built from a structured, controlled vocabulary. The illustrations are the products of work in progress and are subject to change when new evidence becomes available. For simplicity, not all known gene annotations have been included in the figures. a, Biological process ontology. This section illustrates a portion of the biological process ontology describing DNA metabolism. Note that a node may have more than one parent; for example, ‘DNA ligation’ has three parents, ‘DNA-dependent DNA replication’, ‘DNA repair’ and ‘DNA recombination’. b, Molecular function ontology. The ontology is not intended to represent a reaction pathway, but instead reflects conceptual categories of gene-product function. A gene product can be associated with more than one node within an ontology, as illustrated by the MCM proteins. These proteins have been shown to bind chromatin and to possess ATP-dependent DNA helicase activity, and are annotated to both nodes. c, Cellular component ontology. The ontologies are designed for a generic eukaryotic cell, and are flexible enough to represent the known differences between diverse organisms.