The taxonomic name resolution service : an online tool for automated standardization of plant names
Additional file 1: Example R script which uses the TNRS API to correct names on a phylogeny. (1.826Kb)
Additional file 2: Taxonomic names used to compare performance of TNRS, Plantminer and GNResolver. (20.46Kb)
Garay, Juan Antonio Raygoza
Narro, Martha L.
Piel, William H.
Mckay, Sheldon J.
Peet, Robert K.
Enquist, Brian J.
MetadataShow full item record
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. 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. 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.
© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 14 (2013): 16, doi:10.1186/1471-2105-14-16.
Suggested CitationArticle: Boyle, Brad, Hopkins, Nicole, Lu, Zhenyuan, Garay, Juan Antonio Raygoza, Mozzherin, Dmitry, Rees, Tony, Matasci, Naim, Narro, Martha L., Piel, William H., Mckay, Sheldon J., Lowry, Sonya, Freeland, Chris, Peet, Robert K., Enquist, Brian J., "The taxonomic name resolution service : an online tool for automated standardization of plant names", BMC Bioinformatics 14 (2013): 16, DOI:10.1186/1471-2105-14-16, https://hdl.handle.net/1912/5791
The following license files are associated with this item:
Showing items related by title, author, creator and subject.
Salguero-Gomez, Roberto; Jones, Owen R.; Archer, C. Ruth; Buckley, Yvonne M.; Che-Castaldo, Judy; Caswell, Hal; Hodgson, David; Scheuerlein, Alexander; Conde, Dalia A.; Brinks, Erik; de Buhr, Hendrik; Farack, Claudia; Gottschalk, France; Hartmann, Alexander; Henning, Anne; Hoppe, Gabriel; Romer, Gesa; Runge, Jens; Ruoff, Tara; Wille, Julia; Zeh, Stefan; Davison, Raziel; Vieregg, Dirk; Baudisch, Annette; Altwegg, Res; Colchero, Fernando; Dong, Ming; de Kroon, Hans; Lebreton, Jean-Dominique; Metcalf, Charlotte J. E.; Neel, Maile M.; Parker, Ingrid M.; Takada, Takenori; Valverde, Teresa; Velez-Espino, Luis A.; Wardle, Glenda M.; Franco, Miguel; Vaupel, James W. (John Wiley & Sons, 2014-11-09)Schedules of survival, growth and reproduction are key life-history traits. Data on how these traits vary among species and populations are fundamental to our understanding of the ecological conditions that have shaped ...
Response of plant nutrient stoichiometry to fertilization varied with plant tissues in a tropical forest Mo, Qifeng; Zou, Bi; Li, Yingwen; Chen, Yao; Zhang, Weixin; Mao, Rong; Ding, Yongzhen; Wang, Jun; Lu, Xiankai; Li, Xiaobo; Tang, Jianwu; Li, Zhian; Wang, Faming (Nature Publishing Group, 2015-09-29)Plant N:P ratios are widely used as indices of nutrient limitation in terrestrial ecosystems, but the response of these metrics in different plant tissues to altered N and P availability and their interactions remains ...
Macromolecular rate theory (MMRT) provides a thermodynamics rationale to underpin the convergent temperature response in plant leaf respiration Liang, Liyin L.; Arcus, Vickery; Heskel, Mary; O'Sullivan, Odhran S.; Weerasinghe, Lasantha K.; Creek, Danielle; Egerton, John J. G.; Tjoelker, Mark; Atkin, Owen K.; Schipper, Louis A. (2017-10)Temperature is a crucial factor in determining the rates of ecosystem processes, e.g. leaf respiration (R) − the flux of plant respired CO2 from leaves to the atmosphere. Generally, R increases exponentially with temperature ...