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Mora MA, Araya JE. Semi-automatic Extraction of Plants Morphological Characters from Taxonomic Descriptions Written in Spanish. Biodivers Data J 2018; 6:e21282. [PMID: 29991903 PMCID: PMC6030177 DOI: 10.3897/bdj.6.e21282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 06/11/2018] [Indexed: 12/02/2022] Open
Abstract
Taxonomic literature keeps records of the planet's biodiversity and gives access to the knowledge needed for its sustainable management. Unfortunately, most of the taxonomic information is available in scientific publications in text format. The amount of publications generated is very large; therefore, to process it in order to obtain high structured texts would be complex and very expensive. Approaches like citizen science may help the process by selecting whole fragments of texts dealing with morphological descriptions; but a deeper analysis, compatible with accepted ontologies, will require specialised tools. The Biodiversity Heritage Library (BHL) estimates that there are more than 120 million pages published in over 5.4 million books since 1469, plus about 800,000 monographs and 40,000 journal titles (12,500 of these are current titles). It is necessary to develop standards and software tools to extract, integrate and publish this information into existing free and open access repositories of biodiversity knowledge to support science, education and biodiversity conservation. This document presents an algorithm based on computational linguistics techniques to extract structured information from morphological descriptions of plants written in Spanish. The developed algorithm is based on the work of Dr. Hong Cui from the University of Arizona; it uses semantic analysis, ontologies and a repository of knowledge acquired from the same descriptions. The algorithm was applied to the books Trees of Costa Rica Volume III (TCRv3), Trees of Costa Rica Volume IV (TCRv4) and to a subset of descriptions of the Manual of Plants of Costa Rica (MPCR) with very competitive results (more than 92.5% of average performance). The system receives the morphological descriptions in tabular format and generates XML documents. The XML schema allows documenting structures, characters and relations between characters and structures. Each extracted object is associated with attributes like name, value, modifiers, restrictions, ontology term id, amongst other attributes. The implemented tool is free software. It was developed using Java and integrates existing technology as FreeLing, the Plant Ontology (PO), the Plant Glossary, the Ontology Term Organizer (OTO) and the Flora Mesoamericana English-Spanish Glossary.
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Abstract
Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all extant European terrestrial and freshwater animals, their geographical distribution at the level of countries and major islands (west of the Urals and excluding the Caucasus region), and some additional information. The Fauna Europaea project comprises about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. Fauna Europaea represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. The “Orthopteroid orders“ is one of the 58 Fauna Europaea major taxonomic groups. It contains series of mostly well-known insect orders: Embiodea (webspinners), Dermaptera (earwigs), Phasmatodea (walking sticks), Orthoptera s.s. (grasshoppers, crickets, bush-crickets) and Dictyoptera with the suborders Mantodea (mantids), Blattaria (cockroaches) and Isoptera (termites). For the Orthopteroid orders, data from 35 families containing 1,371 species are included in this paper.
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Affiliation(s)
| | - Horst Bohn
- Zoologische Staatssammlung Munchen, Munich, Germany
| | - Fabian Haas
- Staatliches Museum fur Naturkunde, Stuttgart, Germany
| | | | - Yde de Jong
- University of Amsterdam - Faculty of Science, Amsterdam, Netherlands; Museum für Naturkunde, Berlin, Germany
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Rota E, de Jong Y. Fauna Europaea: Annelida - Terrestrial Oligochaeta (Enchytraeidae and Megadrili), Aphanoneura and Polychaeta. Biodivers Data J 2015; 3:e5737. [PMID: 26379463 PMCID: PMC4568407 DOI: 10.3897/bdj.3.e5737] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 09/07/2015] [Indexed: 11/12/2022] Open
Abstract
Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. This paper provides updated information on the taxonomic composition and distribution of the Annelida - terrestrial Oligochaeta (Megadrili and Enchytraeidae), Aphanoneura and Polychaeta, recorded in Europe. Data on 18 families, 11 autochthonous and 7 allochthonous, represented in our continent by a total of 800 species, are reviewed, beginning from their distinctness, phylogenetic status, diversity and global distribution, and following with major recent developments in taxonomic and faunistic research in Europe. A rich list of relevant references is appended. The Fauna Europaea Annelida - terrestrial Oligochaeta data-set, as completed in 2004, will be updated accordingly.
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Affiliation(s)
| | - Yde de Jong
- University of Amsterdam - Faculty of Science, Amsterdam, Netherlands
- Museum für Naturkunde, Berlin, Germany
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4
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Balsamo M, D Hondt JL, Kisielewski J, Todaro MA, Tongiorgi P, Guidi L, Grilli P, de Jong Y. Fauna Europaea: Gastrotricha. Biodivers Data J 2015:e5800. [PMID: 26379467 PMCID: PMC4563153 DOI: 10.3897/bdj.3.e5800] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 08/12/2015] [Indexed: 11/12/2022] Open
Abstract
Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Gastrotricha are a meiobenthic phylum composed of 813 species known so far (2 orders, 17 families) of free-living microinvertebrates commonly present and actively moving on and into sediments of aquatic ecosystems, 339 of which live in fresh and brackish waters. The Fauna Europaea database includes 214 species of Chaetonotida (4 families) plus a single species of Macrodasyidaincertae sedis. This paper deals with the 224 European freshwater species known so far, 9 of which, all of Chaetonotida, have been described subsequently and will be included in the next database version. Basic information on their biology and ecology are summarized, and a list of selected, main references is given. As a general conclusion the gastrotrich fauna from Europe is the best known compared with that of other continents, but shows some important gaps of knowledge in Eastern and Southern regions.
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Affiliation(s)
| | | | | | | | | | | | | | - Yde de Jong
- University of Amsterdam - Faculty of Science, Amsterdam, Netherlands ; Museum für Naturkunde, Berlin, Germany
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5
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Abstract
Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. For the Mollusca-Bivalvia, data from 5 families (Margaritiferidae, Unionidae, Sphaeriidae, Cyrenidae, Dreissenidae) containing 55 species are included in this paper. European freshwater bivalves belong to the Orders Unionoida and Cardiida. All the European unionoids are included in the superfamily Unionoidea, the freshwater mussels or naiads. The European cardiids belong to the following three superfamilies: Cardioidea, Cyrenoidea and Dreissenoidea. Among the Unionoidea there are the most imperilled animal groups on the planet while the Cardioidea includes the cosmopolitan genus Pisidium, the Cyrenoidea the Asiatic clam (Corbiculafluminea) and the Dreissenoidea the famous invasive zebra mussel (Dreissenapolymorpha). Basic information is summarized on their taxonomy and biology. Tabulations include a complete list of the current estimated families, genera and species.
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Affiliation(s)
| | - Yde de Jong
- University of Amsterdam - Faculty of Science, Amsterdam, Netherlands ; Museum für Naturkunde, Berlin, Germany
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Aspöck U, Aspöck H, Letardi A, de Jong Y. Fauna europaea: neuropterida (raphidioptera, megaloptera, neuroptera). Biodivers Data J 2015:e4830. [PMID: 25941450 PMCID: PMC4411496 DOI: 10.3897/bdj.3.e4830] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 03/24/2015] [Indexed: 11/14/2022] Open
Abstract
Fauna Europaea provides a public web-service with an index of scientific names of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. For Neuropterida, data from three Insect orders (Raphidioptera, Megaloptera, Neuroptera), comprising 15 families and 397 species, are included.
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Affiliation(s)
- Ulrike Aspöck
- Natural History Museum Vienna, 2nd Zoological Department, Burgring 7, 1010, Vienna, Austria
| | - Horst Aspöck
- Institute of Specific Prophylaxis and Tropical Medicine, Medical Parasitology, Medical University (MUW), Kinderspitalgasse 15, 1090, Vienna, Austria
| | - Agostino Letardi
- ENEA, Technical Unit for Sustainable Development and Agro-industrial innovation, Sustainable Management of Agricultural Ecosystems Laboratory, Rome, Italy
| | - Yde de Jong
- University of Amsterdam - Faculty of Science, Amsterdam, Netherlands ; University of Eastern Finland, Joensuu, Finland
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Audisio P, Alonso Zarazaga MA, Slipinski A, Nilsson A, Jelínek J, Taglianti AV, Turco F, Otero C, Canepari C, Kral D, Liberti G, Sama G, Nardi G, Löbl I, Horak J, Kolibac J, Háva J, Sapiejewski M, Jäch M, Bologna MA, Biondi M, Nikitsky NB, Mazzoldi P, Zahradnik P, Wegrzynowicz P, Constantin R, Gerstmeier R, Zhantiev R, Fattorini S, Tomaszewska W, Rücker WH, Vazquez-Albalate X, Cassola F, Angelini F, Johnson C, Schawaller W, Regalin R, Baviera C, Rocchi S, Cianferoni F, Beenen R, Schmitt M, Sassi D, Kippenberg H, Zampetti MF, Trizzino M, Chiari S, Carpaneto GM, Sabatelli S, de Jong Y. Fauna Europaea: Coleoptera 2 (excl. series Elateriformia, Scarabaeiformia, Staphyliniformia and superfamily Curculionoidea). Biodivers Data J 2015; 3:e4750. [PMID: 25892924 PMCID: PMC4399155 DOI: 10.3897/bdj.3.e4750] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 03/31/2015] [Indexed: 11/16/2022] Open
Abstract
Fauna Europaea provides a public web-service with an index of scientific names (including synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Coleoptera represent a huge assemblage of holometabolous insects, including as a whole more than 200 recognized families and some 400,000 described species worldwide. Basic information is summarized on their biology, ecology, economic relevance, and estimated number of undescribed species worldwide. Little less than 30,000 species are listed from Europe. The Coleoptera 2 section of the Fauna Europaea database (Archostemata, Myxophaga, Adephaga and Polyphaga excl. the series Elateriformia, Scarabaeiformia, Staphyliniformia and the superfamily Curculionoidea) encompasses 80 families (according to the previously accepted family-level systematic framework) and approximately 13,000 species. Tabulations included a complete list of the families dealt with, the number of species in each, the names of all involved specialists, and, when possible, an estimate of the gaps in terms of total number of species at an European level. A list of some recent useful references is appended. Most families included in the Coleoptera 2 Section have been updated in the most recent release of the Fauna Europaea index, or are ready to be updated as soon as the FaEu data management environment completes its migration from Zoological Museum Amsterdam to Berlin Museum für Naturkunde.
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Affiliation(s)
- Paolo Audisio
- Sapienza Rome University, Department of Biology and Biotechnologies 'C. Darwin', Rome, Italy
| | | | | | | | | | - Augusto Vigna Taglianti
- Sapienza Rome University, Department of Biology and Biotechnologies 'C. Darwin', Rome, Italy
| | | | - Carlos Otero
- Departamento de Biología Animal, Santiago de Compostela, Spain
| | | | - David Kral
- Charles University, Prague, Czech Republic
| | | | | | - Gianluca Nardi
- MiPAAF, Corpo Forestale dello Stato, Centro Nazionale per lo Studio e la Conservazione della Biodiversità Forestale “Bosco Fontana” di Verona, Sede di Bosco Fontana, Strada Mantova 29, I-46045, Marmirolo (MN), Italy
| | - Ivan Löbl
- Museum d'Histoire naturelle Geneve, Geneve, Switzerland
| | - Jan Horak
- K Hádku 1567, Dubeček, CZ-107 00 Praha 10, Prague, Czech Republic
| | | | - Jirí Háva
- Dermestidae World, Prague, Czech Republic
| | | | | | | | - Maurizio Biondi
- University of L`Aquila, Department of Health, Life and Environmental Sciences, L`Aquila - Coppito, Italy
| | | | | | - Petr Zahradnik
- Forestry and Game Management Research Institute, Praha, Czech Republic
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Cosimo Baviera
- University of Messina, Department of Biological and Environmental Sciences, Messina, Italy
| | - Saverio Rocchi
- University of Florence, Natural History Museum, Zoological Section 'La Specola', Florence, Italy
| | - Fabio Cianferoni
- University of Florence, Natural History Museum, Zoological Section 'La Specola', Florence, Italy
- Institute of Agroenvironmental and Forest Biology, CNR - National Research Council of Italy, Monterotondo Scalo (Rome), Italy
| | - Ron Beenen
- Naturalis Biodiversity Center, Leiden, Netherlands
| | | | - David Sassi
- c/o Museo Civico di Storia Naturale, Milano, Italy
| | | | | | - Marco Trizzino
- Department of Genetics, University of Pennsylvania, Philadelphia, United States of America
| | - Stefano Chiari
- Sapienza Rome University, Department of Biology and Biotechnologies 'C. Darwin', Rome, Italy
| | | | - Simone Sabatelli
- Sapienza Rome University, Department of Biology and Biotechnologies 'C. Darwin', Rome, Italy
| | - Yde de Jong
- University of Eastern Finland, Joensuu, Finland
- University of Amsterdam - Faculty of Science, Amsterdam, Netherlands
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Pape T, Beuk P, Pont AC, Shatalkin AI, Ozerov AL, Woźnica AJ, Merz B, Bystrowski C, Raper C, Bergström C, Kehlmaier C, Clements DK, Greathead D, Kameneva EP, Nartshuk E, Petersen FT, Weber G, Bächli G, Geller-Grimm F, Van de Weyer G, Tschorsnig HP, de Jong H, van Zuijlen JW, Vaňhara J, Roháček J, Ziegler J, Majer J, Hůrka K, Holston K, Rognes K, Greve-Jensen L, Munari L, de Meyer M, Pollet M, Speight MCD, Ebejer MJ, Martinez M, Carles-Tolrá M, Földvári M, Chvála M, Barták M, Evenhuis NL, Chandler PJ, Cerretti P, Meier R, Rozkosny R, Prescher S, Gaimari SD, Zatwarnicki T, Zeegers T, Dikow T, Korneyev VA, Richter VA, Michelsen V, Tanasijtshuk VN, Mathis WN, Hubenov Z, de Jong Y. Fauna europaea: Diptera - brachycera. Biodivers Data J 2015:e4187. [PMID: 25733962 PMCID: PMC4339814 DOI: 10.3897/bdj.3.e4187] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/12/2015] [Indexed: 11/12/2022] Open
Abstract
Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all extant multicellular European terrestrial and freshwater animals and their geographical distribution at the level of countries and major islands (east of the Urals and excluding the Caucasus region). The Fauna Europaea project comprises about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. Fauna Europaea represents a huge effort by more than 400 contributing taxonomic specialists throughout Europe and is a unique (standard) reference suitable for many user communities in science, government, industry, nature conservation and education. The Diptera-Brachycera is one of the 58 Fauna Europaea major taxonomic groups, and data have been compiled by a network of 55 specialists. Within the two-winged insects (Diptera), the Brachycera constitute a monophyletic group, which is generally given rank of suborder. The Brachycera may be classified into the probably paraphyletic 'lower brachyceran grade' and the monophyletic Eremoneura. The latter contains the Empidoidea, the Apystomyioidea with a single Nearctic species, and the Cyclorrhapha, which in turn is divided into the paraphyletic 'aschizan grade' and the monophyletic Schizophora. The latter is traditionally divided into the paraphyletic 'acalyptrate grade' and the monophyletic Calyptratae. Our knowledge of the European fauna of Diptera-Brachycera varies tremendously among families, from the reasonably well known hoverflies (Syrphidae) to the extremely poorly known scuttle flies (Phoridae). There has been a steady growth in our knowledge of European Diptera for the last two centuries, with no apparent slow down, but there is a shift towards a larger fraction of the new species being found among the families of the nematoceran grade (lower Diptera), which due to a larger number of small-sized species may be considered as taxonomically more challenging. Most of Europe is highly industrialised and has a high human population density, and the more fertile habitats are extensively cultivated. This has undoubtedly increased the extinction risk for numerous species of brachyceran flies, yet with the recent re-discovery of Thyreophoracynophila (Panzer), there are no known cases of extinction at a European level. However, few national Red Lists have extensive information on Diptera. For the Diptera-Brachycera, data from 96 families containing 11,751 species are included in this paper.
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Affiliation(s)
- Thomas Pape
- Natural History Museum of Denmark, Copenhagen, Denmark
| | - Paul Beuk
- Natural History Museum Maastricht / Diptera.info, Maastricht, Netherlands
| | | | | | | | - Andrzej J Woźnica
- Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Bernhard Merz
- Muséum d'histoire naturelle Genève, Paris, Switzerland
| | - Cezary Bystrowski
- Forest Research Institute, Department of Forest Protection, Warszawa, Poland
| | - Chris Raper
- Tachinidae Recording Scheme, London, United Kingdom
| | | | - Christian Kehlmaier
- Senckenberg Natural History Collections Dresden, Museum of Zoology, Dresden, Germany
| | | | | | | | - Emilia Nartshuk
- Zoological Institute Russian Academy of Sciences, St Petersburg, Russia
| | - Frederik T Petersen
- Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marc Pollet
- Research Institute for Nature and Forest, Brussels, Belgium
| | | | | | - Michel Martinez
- INRA, UMR Centre de Biologie pour la Gestion des Populations, Montferrier-sur-Lez, France
| | | | - Mihály Földvári
- MTA-DE 'Lendület' Behavioural Ecology Research Group, Department of Evolutionary Zoology, University of Debrecen, Debrecen, Hungary
| | | | | | | | | | | | - Rudolf Meier
- National University of Singapore, Singapore, Singapore
| | | | | | - Stephen D Gaimari
- California Department of Food and Agriculture, Sacramento, California, United States of America
| | | | | | - Torsten Dikow
- National Museum of Natural History, Smithsonian Institution, Washington DC, United States of America
| | | | | | | | | | - Wayne N Mathis
- National Museum of Natural History, Smithsonian Institution, Washington DC, United States of America
| | | | - Yde de Jong
- University of Eastern Finland, Joensuu, Finland ; University of Amsterdam - Faculty of Science, Amsterdam, Netherlands
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de Jong Y, Verbeek M, Michelsen V, Bjørn PDP, Los W, Steeman F, Bailly N, Basire C, Chylarecki P, Stloukal E, Hagedorn G, Wetzel FT, Glöckler F, Kroupa A, Korb G, Hoffmann A, Häuser C, Kohlbecker A, Müller A, Güntsch A, Stoev P, Penev L. Fauna Europaea - all European animal species on the web. Biodivers Data J 2014:e4034. [PMID: 25349527 PMCID: PMC4206781 DOI: 10.3897/bdj.2.e4034] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 09/17/2014] [Indexed: 12/02/2022] Open
Abstract
Fauna Europaea is Europe's main zoological taxonomic index, making the scientific names and distributions of all living, currently known, multicellular, European land and freshwater animals species integrally available in one authoritative database. Fauna Europaea covers about 260,000 taxon names, including 145,000 accepted (sub)species, assembled by a large network of (>400) leading specialists, using advanced electronic tools for data collations with data quality assured through sophisticated validation routines. Fauna Europaea started in 2000 as an EC funded FP5 project and provides a unique taxonomic reference for many user-groups such as scientists, governments, industries, nature conservation communities and educational programs. Fauna Europaea was formally accepted as an INSPIRE standard for Europe, as part of the European Taxonomic Backbone established in PESI. Fauna Europaea provides a public web portal at faunaeur.org with links to other key biodiversity services, is installed as a taxonomic backbone in wide range of biodiversity services and actively contributes to biodiversity informatics innovations in various initiatives and EC programs.
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Affiliation(s)
- Yde de Jong
- University of Eastern Finland, Joensuu, Finland ; University of Amsterdam - Faculty of Science, Amsterdam, Netherlands
| | | | | | | | - Wouter Los
- University of Amsterdam, Amsterdam, Netherlands
| | | | | | | | | | - Eduard Stloukal
- Department of Zoology, Comenius University, Bratislava, Slovakia
| | - Gregor Hagedorn
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Florian Tobias Wetzel
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Falko Glöckler
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Alexander Kroupa
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Günther Korb
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Anke Hoffmann
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Christoph Häuser
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | | | | | | | - Pavel Stoev
- National Museum of Natural History and Pensoft Publishers, Sofia, Bulgaria
| | - Lyubomir Penev
- Institute of Biodiversity & Ecosystem Research, Bulgarian Academy of Sciences and Pensoft Publishers, Sofia, Bulgaria ; Pensoft Publishers, Sofia, Bulgaria
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Gibson DI, Bray RA, Hunt D, Georgiev BB, Scholz T, Harris PD, Bakke TA, Pojmanska T, Niewiadomska K, Kostadinova A, Tkach V, Bain O, Durette-Desset MC, Gibbons L, Moravec F, Petter A, Dimitrova ZM, Buchmann K, Valtonen ET, de Jong Y. Fauna europaea: helminths (animal parasitic). Biodivers Data J 2014; 2:e1060. [PMID: 25349520 PMCID: PMC4206782 DOI: 10.3897/bdj.2.e1060] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 05/10/2014] [Indexed: 11/12/2022] Open
Abstract
Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Helminths parasitic in animals represent a large assemblage of worms, representing three phyla, with more than 200 families and almost 4,000 species of parasites from all major vertebrate and many invertebrate groups. A general introduction is given for each of the major groups of parasitic worms, i.e. the Acanthocephala, Monogenea, Trematoda (Aspidogastrea and Digenea), Cestoda and Nematoda. Basic information for each group includes its size, host-range, distribution, morphological features, life-cycle, classification, identification and recent key-works. Tabulations include a complete list of families dealt with, the number of species in each and the name of the specialist responsible for data acquisition, a list of additional specialists who helped with particular groups, and a list of higher taxa dealt with down to the family level. A compilation of useful references is appended.
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Affiliation(s)
| | | | | | | | - Tomaš Scholz
- Biology Centre (CAS), České Budějovice, Czech Republic
| | | | | | | | | | | | - Vasyl Tkach
- University of North Dakota, Grand Forks, United States of America
| | - Odile Bain
- Museum National d'Histoire Naturelle, Paris, France
| | | | | | | | - Annie Petter
- Museum National d'Histoire Naturelle, Paris, France
| | | | | | | | - Yde de Jong
- University of Eastern Finland, Joensuu, Finland
- University of Amsterdam - Faculty of Science, Amsterdam, Netherlands
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11
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Abstract
Multimedia data held by Natural History Museums and Universities are presently not readily accessible, even within the natural history community itself. The EU project OpenUp! is an effort to mobilise scientific biological multimedia resources and open them to a wider audience using the EUROPEANA data standards and portal. The connection between natural history and EUROPEANA is accomplished using well established BioCASe and GBIF technologies. This is complemented with a system for data quality control, data transformation and semantic enrichment. With this approach, OpenUp! will provide at least 1,1 Million multimedia objects to EUROPEANA by 2014. Its lean infrastructure is sustainable within the natural history community and will remain functional and effective in the post-project phase.
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Affiliation(s)
- Walter G Berendsohn
- Department of Biodiversity Informatics and Laboratories, Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Straße 6-8, D-14195 Berlin, Germany
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Baker E, Johnson KG, Young JR. The future of the past in the present: biodiversity informatics and geological time. Zookeys 2011:397-405. [PMID: 22207819 PMCID: PMC3234446 DOI: 10.3897/zookeys.150.2350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 11/23/2011] [Indexed: 11/12/2022] Open
Abstract
The biological and palaeontological communities have approached the problem of informatics separately, creating a divide between communities that is both technological and sociological in nature. In this paper we describe one new advance towards solving this problem - expanding the Scratchpads platform to deal with geological time. In creating this system we have attempted to make our work open to existing communities by providing a webservice of geological time data via the GBIF Vocabularies site. We have also ensured that our system can adapt to changes in the definition of geological time intervals and is capable of querying datasets independently of the format of geological age data used.
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Affiliation(s)
- Edward Baker
- Department of Entomology, Natural History Museum, London, United Kingdom
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