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Open Access Methodology article

An anatomy ontology to represent biological knowledge in Dictyostelium discoideum

Pascale Gaudet1*, Jeffery G Williams2, Petra Fey1 and Rex L Chisholm1

Author Affiliations

1 dictyBase, Northwestern University, Center for Genetic Medicine, 676 N. St. Clair, Chicago, IL, 60611, USA

2 School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK

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BMC Genomics 2008, 9:130  doi:10.1186/1471-2164-9-130

Published: 18 March 2008

Abstract

Background

Dictyostelium discoideum is a model system for studying many important physiological processes including chemotaxis, phagocytosis, and signal transduction. The recent sequencing of the genome has revealed the presence of over 12,500 protein-coding genes. The model organism database dictyBase hosts the genome sequence as well as a large amount of manually curated information.

Results

We present here an anatomy ontology for Dictyostelium based upon the life cycle of the organism.

Conclusion

Anatomy ontologies are necessary to annotate species-specific events such as phenotypes, and the Dictyostelium anatomy ontology provides an essential tool for curation of the Dictyostelium genome.