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dc.contributor.authorBoyle, Brad  Concept link
dc.contributor.authorHopkins, Nicole  Concept link
dc.contributor.authorLu, Zhenyuan  Concept link
dc.contributor.authorGaray, Juan Antonio Raygoza  Concept link
dc.contributor.authorMozzherin, Dmitry  Concept link
dc.contributor.authorRees, Tony  Concept link
dc.contributor.authorMatasci, Naim  Concept link
dc.contributor.authorNarro, Martha L.  Concept link
dc.contributor.authorPiel, William H.  Concept link
dc.contributor.authorMckay, Sheldon J.  Concept link
dc.contributor.authorLowry, Sonya  Concept link
dc.contributor.authorFreeland, Chris  Concept link
dc.contributor.authorPeet, Robert K.  Concept link
dc.contributor.authorEnquist, Brian J.  Concept link
dc.date.accessioned2013-02-28T16:42:13Z
dc.date.available2013-02-28T16:42:13Z
dc.date.issued2013-01-16
dc.identifier.citationBMC Bioinformatics 14 (2013): 16en_US
dc.identifier.urihttps://hdl.handle.net/1912/5791
dc.description© 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.en_US
dc.description.abstractThe 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.en_US
dc.description.sponsorshipBJE was supported by NSF grant DBI 0850373 and TR by CSIRO Marine and Atmospheric Research, Australia,. BB and BJE acknowledge early financial support from Conservation International and TEAM who funded the development of early prototypes of taxonomic name resolution. The iPlant Collaborative (http://www.iplantcollaborative.org) is funded by a grant from the National Science Foundation (#DBI-0735191).en_US
dc.format.mimetypeapplication/pdf
dc.format.mimetypeapplication/vnd.ms-excel
dc.format.mimetypetext/csv
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dc.language.isoenen_US
dc.publisherBioMed Centralen_US
dc.relation.urihttps://doi.org/10.1186/1471-2105-14-16
dc.rightsAttribution 2.0 Generic*
dc.rights.urihttp://creativecommons.org/licenses/by/2.0*
dc.subjectBiodiversity informaticsen_US
dc.subjectDatabase integrationen_US
dc.subjectTaxonomyen_US
dc.subjectPlantsen_US
dc.titleThe taxonomic name resolution service : an online tool for automated standardization of plant namesen_US
dc.typeArticleen_US
dc.identifier.doi10.1186/1471-2105-14-16


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