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

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/.

Figure 1

Transformed scientific name match score (SNMS_tr) versus original, untransformed score (SNMS) of a submitted binomial, showing the differing degrees of certainty defined by the transformation function. In the two regions of certainty, small score differences have a smaller impact on the outcome: either there is a mismatch (SNMS=-2) or a perfect match (SNMS=2). Similarly, in the region of uncertainty, small score differences do not help to distinguish between matches and mismatches. In the regions of discrimination, instead, there is already a preference towards matches or mismatches, and small differences can help tip the balance.

Figure 2

Screenshot of the main TNRS user interface. Up to 5000 names, one per line, may be entered manually or pasted into the “Enter list” text box. Larger lists are uploaded using the "Upload and Submit List" tab. Name processing settings are adjusted prior to submitting the names using the controls in the upper left box. Best match settings, on the upper left of the results display, are set after results are returned, and affect how multiple results for the same name are ranked and therefore how the single best match is selected. The "(+n more)" link allows the user to view and select any alternative matches found. The "Details" hyperlink displays the results and match scores for each name component (genus, species, author, etc.). The remaining hyperlinks link to entries in the original source databases. "Download settings" displays a report of all settings used to resolve the current batch of names. The "Download results" button displays options for downloading results as a plain text file.