The use of ontologies has become a mainstream activity within bioinfor-matics. 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 com-putational 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 characteris-tics, 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 ontol-ogy and ontology-like artifacts. We present a series of case studies and conclude by describing the current state and future directions for bio-ontologies.
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