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Encyclopedia of Systems Biology pp 1560Cite as

Ontologies

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Synonyms

Structured Terminologies

Definition

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).

Cross-References

Collaborative and Distributed Biomedical Applications

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References

  • Bodenreider O, Stevens R (2006) Bio-ontologies: current trends and future directions. Brief Bioinform 7(3):256–274. doi:10.1093/bib/bbl027

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  • 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 Systems

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  • Parsia B, Dumontier M (2011) Bio-ontologies. Wiley, Oxford

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Author information

Authors and Affiliations

  1. Department of Neurology, Massachusetts General Hospital and Harvard Medical School, 65 Landsdowne St., Suite 200, Boston, MA, 02139, USA

    Tim Clark

Authors
  1. Tim Clark
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Corresponding author

Correspondence to Tim Clark .

Editor information

Editors and Affiliations

  1. Biomedical Sciences Research Institute, University of Ulster, Coleraine, UK

    Werner Dubitzky

  2. Department of Computer Science, University of Rostock, Rostock, Germany

    Olaf Wolkenhauer

  3. Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea

    Kwang-Hyun Cho

  4. Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA

    Hiroki Yokota

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© 2013 Springer Science+Business Media, LLC

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Clark, T. (2013). Ontologies. In: Dubitzky, W., Wolkenhauer, O., Cho, KH., Yokota, H. (eds) Encyclopedia of Systems Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-9863-7_1471

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