Ontologies in biology: design, applications and future challenges

  title={Ontologies in biology: design, applications and future challenges},
  author={Jonathan B. L. Bard and Seung Yon Rhee},
  journal={Nature Reviews Genetics},
  • J. BardS. Rhee
  • Published 1 March 2004
  • Computer Science, Philosophy
  • Nature Reviews Genetics
Biological knowledge is inherently complex and so cannot readily be integrated into existing databases of molecular (for example, sequence) data. An ontology is a formal way of representing knowledge in which concepts are described both by their meaning and their relationship to each other. Unique identifiers that are associated with each concept in biological ontologies (bio-ontologies) can be used for linking to and querying molecular databases. This article reviews the principal bio… 

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  • 2008
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A Survey of Semantic Integration Approaches in Bioinformatics

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  • J. Bard
  • Computer Science
    BioEssays : news and reviews in molecular, cellular and developmental biology
  • 2003
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Linking Molecular Imaging Terminology to the Gene Ontology (GO)

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Many of the most common single gene disorders are present in WordNet, as well as many high-level concepts in Gene Ontology, and WordNet is likely to be a useful source of lay knowledge in the framework of a consumer health information system on genetic diseases.

MGD: the Mouse Genome Database

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Protégé-2000: An Open-Source Ontology-Development and Knowledge-Acquisition Environment: AMIA 2003 Open Source Expo

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