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Comparative and Functional Genomics
Volume 5 (2004), Issue 6-7, Pages 537-544
http://dx.doi.org/10.1002/cfg.436
Conference paper

Ontology for Genome Comparison and Genomic Rearrangements

1School of Computing Science, University of Newcastle upon Tyne, Claremont Tower, Claremont Road, NE1 7RU, UK
2Department of Computing Science, University of Manchester, UK

Received 25 October 2004; Revised 27 October 2004; Accepted 1 November 2004

Copyright © 2004 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation.