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Erschienen in:
What Is an Ontology? Kapitel lesen Erstes Kapitel lesen

2009 | OriginalPaper | Buchkapitel

Application of Ontologies in Bioinformatics

verfasst von : Robert Stevens, Phillip Lord

Erschienen in: Handbook on Ontologies

Verlag: Springer Berlin Heidelberg

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Summary

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.

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Vorheriges Kapitel Ontologies for Knowledge Management
Nächstes Kapitel Semantic Portals for Cultural Heritage
Fußnoten
1
Here we take a broad definition of bioinformatics to mean the storage, management and analysis of biological data by computational means to answer biological questions.
 
3
The less common term “poset” or partially ordered set is also used.
 
5
At least judged by the number of tools available; microarray tools form the largest subsection of related tools on the GO website (http://​www.​geneontology.​org/​GO.​tools.​shtml).
 
6
In this section, we will talk exclusively about GO, as it is the ontology which has been statistically analysed most widely. Most of the techniques could also apply to other ontologies.
 
7
The left-hand side of the reaction.
 
8
The right-hand side of the reaction.
 
9
The enzyme classification number.
 
11
The sequence of amino acid residues in a protein determine how the protein “folds” into a three-dimensional shape. This shape determines the functionality of the protein. Biologists have determined some patterns of amino acid residue that indicate certain features of these “shapes” that are diagnostic for functionality.
 
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Metadaten
Titel
Application of Ontologies in Bioinformatics
verfasst von
Robert Stevens
Phillip Lord
Copyright-Jahr
2009
Verlag
Springer Berlin Heidelberg
Buch
Handbook on Ontologies

Print ISBN: 978-3-540-70999-2

Electronic ISBN: 978-3-540-92673-3

Copyright-Jahr: 2009

DOI
https://doi.org/10.1007/978-3-540-92673-3_33