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

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

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

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

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

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

author email corresponding author email

Genome Biology 2005, 6:R44doi:10.1186/gb-2005-6-5-r44


Published:	29 April 2005

Subject areas: Bioinformatics, Methods, Genome studies, Molecular biology

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.