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Open Access Database

TBMap: a taxonomic perspective on the phylogenetic database TreeBASE

Roderic DM Page

Author Affiliations

Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, UK

BMC Bioinformatics 2007, 8:158  doi:10.1186/1471-2105-8-158

Published: 18 May 2007

Abstract

Background

TreeBASE is currently the only available large-scale database of published organismal phylogenies. Its utility is hampered by a lack of taxonomic consistency, both within the database, and with names of organisms in external genomic, specimen, and taxonomic databases. The extent to which the phylogenetic knowledge in TreeBASE becomes integrated with these other sources is limited by this lack of consistency.

Description

Taxonomic names in TreeBASE were mapped onto names in the external taxonomic databases IPNI, ITIS, NCBI, and uBio, and graph G of these mappings was constructed. Additional edges representing taxonomic synonymies were added to G, then all components of G were extracted. These components correspond to "name clusters", and group together names in TreeBASE that are inferred to refer to the same taxon. The mapping to NCBI enables hierarchical queries to be performed, which can improve TreeBASE information retrieval by an order of magnitude.

Conclusion

TBMap database provides a mapping of the bulk of the names in TreeBASE to names in external taxonomic databases, and a clustering of those mappings into sets of names that can be regarded as equivalent. This mapping enables queries and visualisations that cannot otherwise be constructed. A simple query interface to the mapping and names clusters is available at http://linnaeus.zoology.gla.ac.uk/~rpage/tbmap webcite.