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

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Creator
  • Boyle, Brad
    • Other Affiliation: Department of Ecology and Evolutionary Biology, University of Arizona
  • Hopkins, Nicole
    • Other Affiliation: The iPlant Collaborative, Thomas W. Keating Bioresearch Building
  • Lu, Zhenyuan
    • Other Affiliation: The iPlant Collaborative, Thomas W. Keating Bioresearch Building
  • Raygoza Garay, Juan Antonio
    • Other Affiliation: The iPlant Collaborative, Thomas W. Keating Bioresearch Building
  • Mozzherin, Dmitry
    • Other Affiliation: 7 MBL street, Center for Library and Informatics, Marine Biological Laboratory
  • Rees, Tony
    • Other Affiliation: Divisional Data Centre, CSIRO Marine and Atmospheric Research
  • Matasci, Naim
    • Other Affiliation: Department of Ecology and Evolutionary Biology, University of Arizona Tucson
  • Narro, Martha L
    • Other Affiliation: The iPlant Collaborative, Thomas W. Keating Bioresearch Building
  • Piel, William H
    • Other Affiliation: Yale-NUS College
  • Mckay, Sheldon J
    • Other Affiliation: The iPlant Collaborative, Thomas W. Keating Bioresearch Building
  • Lowry, Sonya
    • Other Affiliation: The iPlant Collaborative, Thomas W. Keating Bioresearch Building
  • Freeland, Chris
    • Other Affiliation: Missouri Botanical Garden
  • Peet, Robert K.
    • Affiliation: College of Arts and Sciences, Department of Biology
  • Enquist, Brian J
    • Other Affiliation: Department of Ecology and Evolutionary Biology, University of Arizona Tucson
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/ and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/.
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DOI
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Resource type
  • Article
Rights statement
  • In Copyright
Rights holder
  • Brad Boyle et al.; licensee BioMed Central Ltd.
License
Journal title
  • BMC Bioinformatics
Journal volume
  • 14
Journal issue
  • 1
Page start
  • 16
Language
  • English
Is the article or chapter peer-reviewed?
  • Yes
ISSN
  • 1471-2105
Bibliographic citation
  • BMC Bioinformatics. 2013 Jan 16;14(1):16
Publisher
  • BioMed Central Ltd
Access right
  • Open Access
Date uploaded
  • January 24, 2013

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Thumbnail Title Date Uploaded Visibility Actions
file details 1471-2105-14-16.pdf 2019-05-06 Public Download
file details Taxonomic names used to compare performance of TNRS, Plantminer and GNResolver. 2019-05-06 Public Download
file details List of submitted names, expected targets, and descriptions of errors for names which failed matching by one or more name resolution applications. 2019-05-06 Public Download
file details 1471-2105-14-16.xml 2019-05-06 Public Download
file details Example R script which uses the TNRS API to correct names on a phylogeny. 2019-05-06 Public Download