Open Access Highly Accessed Software

The taxonomic name resolution service: an online tool for automated standardization of plant names

Brad Boyle12*, Nicole Hopkins23, Zhenyuan Lu24, Juan Antonio Raygoza Garay23, Dmitry Mozzherin5, Tony Rees6, Naim Matasci123, Martha L Narro23, William H Piel7, Sheldon J Mckay234, Sonya Lowry23, Chris Freeland8, Robert K Peet9 and Brian J Enquist110

Author Affiliations

1 Department of Ecology and Evolutionary Biology, University of Arizona Tucson, P.O. Box 210088, Tucson, AZ, 85721, USA

2 The iPlant Collaborative, Thomas W. Keating Bioresearch Building, 1657 East Helen Street, Tucson, AZ, 85721, USA

3 BIO5 Institute, 1657 East Helen Street, PO Box 210240, Tucson, AZ, 85721-0240, USA

4 Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724-2202, USA

5 7 MBL street, Center for Library and Informatics, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA

6 Divisional Data Centre, CSIRO Marine and Atmospheric Research, GPO Box 1538, Hobart, Tasmania, 7001, Australia

7 Yale-NUS College, 6 College Avenue East, Singapore, 138614, Singapore

8 Missouri Botanical Garden, 4344 Shaw Blvd. |, St. Louis, MO, 63110, USA

9 Department of Biology, CB 3280, University of North Carolina, Chapel Hill, NC, 27599-3280, USA

10 The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA

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BMC Bioinformatics 2013, 14:16  doi:10.1186/1471-2105-14-16

Published: 16 January 2013

Abstract

Background

The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science.

Results

The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets.

Conclusions

We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ webcite and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/ webcite.

Keywords:
Biodiversity informatics; Database integration; Taxonomy; Plants