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

By B. Boyle, Nicole Hopkins, Zhenyuan Lu, J. R. Garay, D. Mozzherin, Anthony J. J. (Tony) Rees, Naim Matasci, M. Narro, W. H. Piel, S. McKay and 4 more. BMC Bioinformatics, 2013

515 citations recorded by the source corpus.

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/ and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/.

Subfields: Ecological Modeling, Nature and Landscape Conservation, Plant Science

View Paper: https://www.semanticscholar.org/paper/0223d1dc682b42daac2c6eb40aa1f4986d3d9ba6

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In Ecological Modeling

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Citations in the corpus

An Inventory of Crop Wild Relatives of the United States (2013, methodology): “Taxonomic verification was performed via the “Taxonomic Name Resolution Service” (Boyle et al., 2013) and GRIN taxonomy (USDA-ARS National Genetic Resources Program, 2012), the latter of which served as the final authority.”
GIFT – A Global Inventory of Floras and Traits for macroecology and biogeography (2019, methodology): “…all non-hybrid species names to a semi-automated taxonomic standardization and validation procedure based on taxonomic information provided by The Plant List 1.1 (TPL; The Plant List, 2013) and additional resources available via iPlant’s Taxonomic Name Resolution Service (TNRS; Boyle et al., 2013).”
sPlot – A new tool for global vegetation analyses (2019, methodology): “Taxon names were parsed and resolved using the Taxonomic Name Resolution Service web application (TNRS version 4.0; Boyle et al., 2013; iPlant Collaborative, 2015), using the five TNRS standard sources ranked by default.”
Running off the road: roadside non-native plants invading mountain vegetation (2018, background): “0 (Boyle et al. 2013; http://tnrs.iplantcollaborative.org/ TNRSapp.html, accessed April 2015) and local published floras.”
Big data for forecasting the impacts of global change on plant communities (2017, background): “Taxonomic misidentification and changes in nomenclature as well as changes in the concepts represented by species names (Franz & Peet, 2009; Wiser, 2016) also lead to data uncertainty for ecologists using aggregated species occurrence data (Graham et al. , 2004; Boyle et al. , 2013).”
taxize: taxonomic search and retrieval in R (2013, background): “For a data analysis a crucial data-cleaning step is to match species identities across di erent datasets Boyle et al. (2013). Taxonomic data is becoming increasingly available on the web, but scientists need an easy and reproducible way to access it. We present taxize Chamberlain and Szöcs (2013) - ”
Improved allometric models to estimate the aboveground biomass of tropical trees (2014, background): “Taxonomic information was carefully checked for consistency (Boyle et al., 2013).”
Mapping ignorance: 300 years of collecting flowering plants in Africa (2016, methodology): “Fourth, we assessed the validity of 52,537 taxa names by submitting all names to the Taxonomic Name Resolution Service (TNRS) version 3.2 (Boyle et al., 2013) in May 2013.”