Encyclopedia of Systems Biology

2013 Edition
| Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota


Reference work entry
DOI: https://doi.org/10.1007/978-1-4419-9863-7_1471



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).



  1. Bodenreider O, Stevens R (2006) Bio-ontologies: current trends and future directions. Brief Bioinform 7(3):256–274. doi:10.1093/bib/bbl027PubMedGoogle Scholar
  2. Chandrasekaran B, Josephson JR, Benjamins VR (1999) What are ontologies, and why do we need them? Intell syst Appl IEEE 14(1):20–26, IEEE Intelligent SystemsGoogle Scholar
  3. Parsia B, Dumontier M (2011) Bio-ontologies. Wiley, OxfordGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Department of NeurologyMassachusetts General Hospital and Harvard Medical SchoolBostonUSA