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      RAINBIO: a mega-database of tropical African vascular plants distributions

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      1 , 2 , 3 , 4 , 5 , 16 , 12 , 1 , 6 , 9 , 7 , 19 , 4 , 6 , 9 , 10 ,   16 , 7 , 6 , 17 , 18 , 10 , 2 , , 11 , 21 , 7 , 11 , 20 , 13 , 19 , 6 , 15 , 11 , 9 , 7 , 6 , 7 , 10 , 7 , 5 , 14 , 19 , 11 , 12 , 1 , 9 , 11
      PhytoKeys
      Pensoft Publishers
      Herbarium specimens, tropical forests, georeferencing, taxonomic backbone, habit, digitization, native species, cultivated species, biodiversity assessment

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          Abstract

          Abstract

          The tropical vegetation of Africa is characterized by high levels of species diversity but is undergoing important shifts in response to ongoing climate change and increasing anthropogenic pressures. Although our knowledge of plant species distribution patterns in the African tropics has been improving over the years, it remains limited. Here we present RAINBIO, a unique comprehensive mega-database of georeferenced records for vascular plants in continental tropical Africa. The geographic focus of the database is the region south of the Sahel and north of Southern Africa, and the majority of data originate from tropical forest regions. RAINBIO is a compilation of 13 datasets either publicly available or personal ones. Numerous in depth data quality checks, automatic and manual via several African flora experts, were undertaken for georeferencing, standardization of taxonomic names and identification and merging of duplicated records. The resulting RAINBIO data allows exploration and extraction of distribution data for 25,356 native tropical African vascular plant species, which represents ca. 89% of all known plant species in the area of interest. Habit information is also provided for 91% of these species.

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          Most cited references16

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

          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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            A new land-cover map of Africa for the year 2000

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              Challenging Wallacean and Linnean shortfalls: knowledge gradients and conservation planning in a biodiversity hotspot

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                Author and article information

                Journal
                PhytoKeys
                PhytoKeys
                PhytoKeys
                PhytoKeys
                Pensoft Publishers
                1314-2011
                1314-2003
                2016
                7 November 2016
                : 74
                : 1-18
                Affiliations
                [1 ]Institut de Recherche pour le Développement (IRD), UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France
                [2 ]Laboratoire d’évolution Biologique et Ecologie, Faculté des Sciences, Université Libre de Bruxelles, CP160/12, avenue F.D. Roosevelt 50, 1050 Bruxelles, Belgium
                [3 ]CESAB / FRB, Domaine du Petit Arbois, Av. Louis Philibert, Aix-en-Provence, 13100, France
                [4 ]Institut de Recherche pour le Développement (IRD), UMR AMAP, Boulevard de la Lironde TA A-51 / PS 2 34398 Montpellier, France
                [5 ]Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
                [6 ]Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050 Bruxelles, Belgium
                [7 ]Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium
                [8 ]Royal Botanic Garden Edinburgh, 20A Inverleith Row Edinburgh, United Kingdom
                [9 ]Laboratoire de Botanique Systématique et d’Écologie, École Normale Supérieure, Université de Yaoundé I, PO Box 047, Yaoundé, Cameroon
                [10 ]Missouri Botanical Garden, Africa & Madagascar Department, St. Louis, United States of America
                [11 ]Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
                [12 ]Wageningen University, Biosystematics Group, Droevendaalsesteeg 1 6708 PB Wageningen, The Netherlands
                [13 ]Institut für Geobotanik und Botanischer Garten, University Halle-Wittenberg, Neuwerk 21, 06108 Halle, Germany
                [14 ]Laboratoire des Sciences du Climat et de l’Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
                [15 ]Laboratoire d'Ecologie végétale et Biogéochimie, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050 Bruxelles, Belgium
                [16 ]Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
                [17 ]CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto. Campus Agrário de Vairão, Vairão, Portugal
                [18 ]CEABN/InBio, Centro de Ecologia Aplicada “Professor Baeta Neves”, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
                [19 ]Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
                [20 ]Department of Ecology, Faculty of Science, Charles University, Vinicna 7, CZ-12843, Prague, Czech Republic
                [21 ]Picturae, De Droogmakerij 12, 1851LX Heiloo, The Netherlands
                Author notes

                Academic editor: Pavel Stoev

                [*]

                These authors contributed equally.

                Article
                10.3897/phytokeys.74.9723
                5234546
                6455ae89-16b1-41f0-b0e5-bc69156de355
                Gilles Dauby, Rainer Zaiss, Anne Blach-Overgaard, Luís Catarino, Theo Damen, Vincent Deblauwe, Steven Dessein, John Dransfield, Vincent Droissart, Maria Cristina Duarte, Henry Engledow, Geoffrey Fadeur, Rui Figueira, Roy E. Gereau, Olivier J. Hardy, David J. Harris, Janneke de Heij, Steven Janssens, Yannick Klomberg, Alexandra C. Ley, Barbara A. Mackinder, Pierre Meerts, Jeike L. van de Poel, Bonaventure Sonké, Marc S. M. Sosef, Tariq Stévart, Piet Stoffelen, Jens-Christian Svenning, Pierre Sepulchre, Xander van der Burgt, Jan J. Wieringa, Thomas L. P. Couvreur

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 30 June 2016
                : 4 September 2016
                Categories
                Data Paper

                Plant science & Botany
                herbarium specimens,tropical forests,georeferencing,taxonomic backbone,habit,digitization,native species,cultivated species,biodiversity assessment

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