The goal of the Pathway Ontology is to cover all types of biological pathways, including altered and disease pathways, and to capture the relationships between them within the hierarchical structure of a Directed Acyclic Graph (DAG). The five nodes of the ontology are: classic metabolic, regulatory, signaling, drug and disease pathways. An extensive survey of the review literature along with searches of existing pathway databases have been used to choose terms and their position within the tree. The ontology is continually expanding along with the development of Pathway and Disease Portals at RGD. Mapping of pathways in other databases to terms in PW as synonyms further increased the content of the ontology. It also provided the means to bring in annotations made by these databases and link to their sites via automatic pipelines built at RGD. The ontology allows for the standardized annotation of rat as well as human and mouse genes to pathway terms. It also serves as a vehicle to connect between genes and ontology reports, between reports and interactive pathway diagrams, between pathways that directly connect to one another within a diagram or between pathways that in some fashion are globally related in pathway suites and suite networks. Metabolic, regulatory or signaling pathway terms have associated terms for the altered version of the pathway and the level at which the alteration(s) may occur. Proteins with mutations known to affect a particular pathway can be annotated to the normal and altered version(s) of the pathway and to a disease pathway, if known. Both the provision of terms for the altered versions of pathways and the representation of disease pathway diagrams as a collection of altered pathways are unique to the PW ontology and RGD's pathway data. The Pathway ontology is distributed under the terms of the Creative Commons Attribution license version 3.0 Unported (CC BY 3.0), see http://creativecommons.org/licenses/by/3.0 for details.