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The Sequence Ontology: a tool for the unification of genome annotations

Karen Eilbeck1, Suzanna E Lewis1, Christopher J Mungall2, Mark Yandell2, Lincoln Stein3, Richard Durbin4 and Michael Ashburner5*

Author Affiliations

1 Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729-3200, USA

2 Howard Hughes Memorial Institute, Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729-3200, USA

3 Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA

4 Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK

5 Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK

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Genome Biology 2005, 6:R44  doi:10.1186/gb-2005-6-5-r44

Published: 29 April 2005

Abstract

The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data. Because SO treats part-whole relationships rigorously, data described with it can become substrates for automated reasoning, and instances of sequence features described by the SO can be subjected to a group of logical operations termed extensional mereology operators.