Ontologies, in computer science and informatics, are formally structured terminology systems. Ontologies specify a set of concepts within a domain, with their mutual relationships, definitions, and properties. If specified in a sufficiently formal way, such as with the Web Ontology Language, OWL (http://www.w3.org/2004/OWL/), computational reasoning may be performed on the concepts and relationships in an ontology (Chandrasekaran et al. 1999).
Ontologies are used extensively, and increasingly formally, in bioinformatics and computational systems biology. They provide essential infrastructure for Web 3.0 or “semantic web” technologies (see World Wide Web), which are increasingly being applied to biomedical collaboratories as knowledge organizing, interchange and integration tools (Bodenreider and Stevens 2006; Parsia and Dumontier 2011).