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Briefings in Bioinformatics Advance Access originally published online on August 9, 2006
Briefings in Bioinformatics 2006 7(3):256-274; doi:10.1093/bib/bbl027
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© The Author 2006. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Bio-ontologies: current trends and future directions

Olivier Bodenreider and Robert Stevens

Corresponding author. Olivier Bodenreider, National Library of Medicine, 8600 Rockville Pike - MS 3841, Bethesda, MD 20894, USA. Tel: (1) 301 435-3246; Fax: (1) 301 480-3035; E-mail: olivier{at}nlm.nih.gov

In recent years, as a knowledge-based discipline, bioinformatics has been made more computationally amenable. After its beginnings as a technology advocated by computer scientists to overcome problems of heterogeneity, ontology has been taken up by biologists themselves as a means to consistently annotate features from genotype to phenotype. In medical informatics, artifacts called ontologies have been used for a longer period of time to produce controlled lexicons for coding schemes. In this article, we review the current position in ontologies and how they have become institutionalized within biomedicine. As the field has matured, the much older philosophical aspects of ontology have come into play. With this and the institutionalization of ontology has come greater formality. We review this trend and what benefits it might bring to ontologies and their use within biomedicine.

Keywords: bio-ontology, medical ontology, annotation, knowledge, knowledge representation, history


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