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      Match Algorithms for Scientific Names in FlorItaly, the Portal to the Flora of Italy

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      Author(s): , , *
      Editor(s):
      Publication date (Electronic):
      Journal: Plants
      Publisher: MDPI
      Keywords: checklist, database, nomenclature, synonym, taxon

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          Abstract

          Scientific names are not part of everyday language in any modern country, and their input as strings in a query system can be easily associated with typographical errors. While globally unique identifiers univocally address a taxon name, they can hardly be used for querying a database manually. Thus, matching algorithms are often used to overcome misspelled names in query systems in several data repositories worldwide. In order to improve users’ experience in the use of FlorItaly, the Portal to the Flora of Italy, a near match algorithm to resolve misspelled scientific names has been integrated in the query systems. In addition, a novel tool in FlorItaly, capable of rapidly aligning any list of names to the nomenclatural backbone provided by the national checklists, has been developed. This manuscript aims at describing the potential of these new tools.

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

          Brad Boyle, Nicole Hopkins, Zhenyuan Lu … (2013)
          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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            An updated checklist of the vascular flora native to Italy

            L Poldini, A. Selvaggi, F Selvi … (2018)
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              Names are key to the big new biology.

              Arthur J L Cooper, David Remsen, Scott D. Patterson … (2010)
              Those who seek answers to big, broad questions about biology, especially questions emphasizing the organism (taxonomy, evolution and ecology), will soon benefit from an emerging names-based infrastructure. It will draw on the almost universal association of organism names with biological information to index and interconnect information distributed across the Internet. The result will be a virtual data commons, expanding as further data are shared, allowing biology to become more of a 'big science'. Informatics devices will exploit this 'big new biology', revitalizing comparative biology with a broad perspective to reveal previously inaccessible trends and discontinuities, so helping us to reveal unfamiliar biological truths. Here, we review the first components of this freely available, participatory and semantic Global Names Architecture. Copyright © 2010 Elsevier Ltd. All rights reserved.
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                Author and article information

                Contributors
                Filippo Maggi: Role: Academic Editor
                Journal
                Journal ID (nlm-ta): Plants (Basel)
                Journal ID (iso-abbrev): Plants (Basel)
                Journal ID (publisher-id): plants
                Title: Plants
                Publisher: MDPI
                ISSN (Electronic): 2223-7747
                Publication date (Electronic): 13 May 2021
                Publication date Collection: May 2021
                Volume: 10
                Issue: 5
                Electronic Location Identifier: 974
                Affiliations
                Department of Life Sciences, University of Trieste, via L. Giorgieri 10, I-34127 Trieste, Italy; matt.ciao@ 123456gmail.com (M.C.); nimis@ 123456units.it (P.L.N.)
                Author notes
                [* ]Correspondence: martelst@ 123456units.it
                Author information
                https://orcid.org/0000-0001-5201-8948
                Article
                Publisher ID: plants-10-00974
                DOI: 10.3390/plants10050974
                PMC ID: 8153551
                PubMed ID: 34068389
                SO-VID: 675ccd08-2d94-4724-a8e0-364f578943a4
                Copyright © © 2021 by the authors.
                License:

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( https://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 30 March 2021
                Date accepted : 08 May 2021
                Categories
                Subject: Article

                Keywords: checklist,database,nomenclature,synonym,taxon
                Data availability:
                Keywords: checklist, database, nomenclature, synonym, taxon

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