Automated assembly of a reference taxonomy for phylogenetic data synthesis

By

Rees, Jonathan
Cranston, Karen

Type

Article

Date of Publication

2017-05-22

Original Publication

Biodiversity data journal

Volume

5

Pages

1--32

Subjects

taxonomy phylogeny automation pipeline synthesis

Contributed by

Pensoft Publishers

Language

English

Published by

Sofia Pensoft Publishers [2013]-

Identifiers

DOI: https://doi.org/10.3897/BDJ.5.e12581
eLocator: e12581

 

Abstract

Taxonomy and nomenclature data are critical for any project that synthesizes biodiversity data, as most biodiversity data sets use taxonomic names to identify taxa. Open Tree of Life is one such project, synthesizing sets of published phylogenetic trees into comprehensive summary trees. No single published taxonomy met the taxonomic and nomenclatural needs of the project. Here we describe a system for reproducibly combining several source taxonomies into a synthetic taxonomy, and we discuss the challenges of taxonomic and nomenclatural synthesis for downstream biodiversity projects.