Application of Ontologies in Bioinformatics

  • Robert Stevens
  • Phillip Lord
Part of the International Handbooks on Information Systems book series (INFOSYS)


The use of ontologies has become a mainstream activity within bioinformatics. In a largely descriptive science such as biology, the need to have a common understanding of things described is obvious. The need to be able to apply computational methods to the large quantities of data being produced also suggests a computational requirement to standardise descriptions in biology.

As a mechanism for describing the categories of entities and their characteristics, ontologies offer many of the features that can support a descriptive science. The main use of ontologies in bioinformatics has been the delivery of controlled vocabularies. In this chapter we explore this use of ontology, but also other uses, especially those that have a deeper computational aspect. We take a broad view of ontology to include many ontology-like resources and classify the uses of ontology and ontology-like artifacts. We present a series of case studies and conclude by describing the current state and future directions for bio-ontologies.


Gene Ontology Directed Acyclic Graph Semantic Similarity Control Vocabulary Phosphoglucose Isomerase 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  1. 1.School of Computer ScienceUniversity of ManchesterManchesterUK
  2. 2.School of Computing ScienceNewcastle UniversityNewcastleUK

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