Taxonome: a software package for linking biological species data


Correspondence: Thomas A. Kluyver, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom. Tel: +44 114 222 0146; Fax: +44 114 222 0002; E-mail:


Online databases of biological information offer tremendous potential for evolutionary and ecological discoveries, especially if data are combined in novel ways. However, the different names and varied spellings used for many species present major barriers to linking data. Taxonome is a software tool designed to solve this problem by quickly and reproducibly matching biological names to a given reference set. It is available both as a graphical user interface (GUI) for simple interactive use, and as a library for more advanced functionality with programs written in Python. Taxonome also includes functions to standardize distribution information to a well-defined set of regions, such as the TDWG World Geographical Scheme for Recording Plant Distributions. In combination, these tools will help biologists to rapidly synthesize disparate datasets, and to investigate large-scale patterns in species traits.