Publications by authors named "Yde de Jong"

17 Publications

  • Page 1 of 1

Fauna Europaea: Hymenoptera - Symphyta & Ichneumonoidea.

Biodivers Data J 2017 27(5):e14650. Epub 2017 Jul 27.

University of Amsterdam - Faculty of Science, Amsterdam, Netherlands.

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 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. 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 Hymenoptera, taxonomic data from one grade (Symphyta) and one Superfamily (Ichneumonoidea), including 15 families and 10,717 species, are included. Ichneumonoidea is the largest superfamily of Hymenoptera and consisting of two extant families, Ichneumonidae and Braconidae. The costal cell of the fore wing is absent, the fore wing has at least two closed cells, the constriction between the mesosoma (thorax + first abdominal segment or propodeum) and the metasoma (remainder of abdomen) is distinct and the parasitoid larvae usually spin a silken cocoon. Also, the metasoma is ventrally partly desclerotized in the vast majority of ichneumonoids.
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http://dx.doi.org/10.3897/BDJ.5.e14650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5572943PMC
July 2017

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.

BMC Ecol 2016 10 20;16(1):49. Epub 2016 Oct 20.

Fraunhofer Institute for Intelligent Analysis and Information Systems (IAIS), Schloss Birlinghoven, 53757, Sankt Augustin, Germany.

Background: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited.

Results: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity.

Conclusions: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.
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http://dx.doi.org/10.1186/s12898-016-0103-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5073428PMC
October 2016

Fauna Europaea - Orthopteroid orders.

Biodivers Data J 2016 29(4):e8905. Epub 2016 Jun 29.

University of Amsterdam - Faculty of Science, Amsterdam, Netherlands; Museum für Naturkunde, Berlin, Germany.

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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http://dx.doi.org/10.3897/BDJ.4.e8905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018117PMC
September 2016

PESI - a taxonomic backbone for Europe.

Biodivers Data J 2015 28(3):e5848. Epub 2015 Sep 28.

Muséum national d'Histoire naturelle, Département Systématique & Evolution, UMR 7205 MNHN-CNRS-UPMC-EPHE, (ISyEB), Paris, France.

Background: Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.

New Information: This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.
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http://dx.doi.org/10.3897/BDJ.3.e5848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609752PMC
October 2015

Fauna Europaea: Gastrotricha.

Biodivers Data J 2015 14(3):e5800. Epub 2015 Aug 14.

University of Amsterdam - Faculty of Science, Amsterdam, Netherlands ; Museum für Naturkunde, Berlin, Germany.

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 Macrodasyida incertae 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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http://dx.doi.org/10.3897/BDJ.3.e5800DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4563153PMC
September 2015

Fauna Europaea: Annelida - Terrestrial Oligochaeta (Enchytraeidae and Megadrili), Aphanoneura and Polychaeta.

Biodivers Data J 2015 11(3):e5737. Epub 2015 Sep 11.

University of Amsterdam - Faculty of Science, Amsterdam, Netherlands ; Museum für Naturkunde, Berlin, Germany.

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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http://dx.doi.org/10.3897/BDJ.3.e5737DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568407PMC
September 2015

Fauna Europaea: Mollusca - Bivalvia.

Biodivers Data J 2015 17(3):e5211. Epub 2015 Jul 17.

University of Amsterdam - Faculty of Science, Amsterdam, Netherlands ; Museum für Naturkunde, Berlin, Germany.

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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http://dx.doi.org/10.3897/BDJ.3.e5211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4549642PMC
August 2015

Fauna europaea: neuropterida (raphidioptera, megaloptera, neuroptera).

Biodivers Data J 2015 17(3):e4830. Epub 2015 Apr 17.

University of Amsterdam - Faculty of Science, Amsterdam, Netherlands ; University of Eastern Finland, Joensuu, Finland.

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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http://dx.doi.org/10.3897/BDJ.3.e4830DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4411496PMC
May 2015

Fauna Europaea: Coleoptera 2 (excl. series Elateriformia, Scarabaeiformia, Staphyliniformia and superfamily Curculionoidea).

Biodivers Data J 2015 9(3):e4750. Epub 2015 Apr 9.

Museum and Institute of Zoology, Warsaw, Poland.

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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http://dx.doi.org/10.3897/BDJ.3.e4750DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4399155PMC
April 2015

Fauna Europaea: Hymenoptera - Apocrita (excl. Ichneumonoidea).

Biodivers Data J 2015 20(3):e4186. Epub 2015 Mar 20.

University of Amsterdam - Faculty of Science, Amsterdam, Netherlands ; University of Eastern Finland, Joensuu, Finland.

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. 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. Hymenoptera is one of the four largest orders of insects, with about 130,000 described species. In the Fauna Europaea database, 'Hymenoptera - Apocrita (excluding Ichneumonoidea)' comprises 13 superfamilies, 52 families, 91 subfamilies, 38 tribes and 13,211 species. The paper includes a complete list of taxa dealt with, the number of species in each and the name of the specialist responsible for data acquisition. As a general conclusion about the European fauna of Hymenoptera, the best known countries in terms of recorded species are those from northwestern Europe, with the least known fauna probably in the more eastern and southeastern parts of Europe.
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http://dx.doi.org/10.3897/BDJ.3.e4186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385900PMC
April 2015

Fauna europaea: Diptera - brachycera.

Biodivers Data J 2015 20(3):e4187. Epub 2015 Feb 20.

University of Stavanger, Stavanger, Norway.

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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http://dx.doi.org/10.3897/BDJ.3.e4187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4339814PMC
March 2015

A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control.

Biodivers Data J 2014 11(2):e4221. Epub 2014 Dec 11.

School of Computer Science, University of Manchester, Manchester, United Kingdom.

The compilation and cleaning of data needed for analyses and prediction of species distributions is a time consuming process requiring a solid understanding of data formats and service APIs provided by biodiversity informatics infrastructures. We designed and implemented a Taverna-based Data Refinement Workflow which integrates taxonomic data retrieval, data cleaning, and data selection into a consistent, standards-based, and effective system hiding the complexity of underlying service infrastructures. The workflow can be freely used both locally and through a web-portal which does not require additional software installations by users.
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http://dx.doi.org/10.3897/BDJ.2.e4221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267104PMC
December 2014

Fauna Europaea: Annelida - Hirudinea, incl. Acanthobdellea and Branchiobdellea.

Biodivers Data J 2014 14(2):e4015. Epub 2014 Nov 14.

University of Eastern Finland, Joensuu, Finland ; University of Amsterdam - Faculty of Science, Amsterdam, Netherlands.

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. Hirudinea is a fairly small group of Annelida, with about 680 described species, most of which live in freshwater habitats, but several species are (sub)terrestrial or marine. In the Fauna Europaea database the taxon is represented by 87 species in 6 families. Two closely related groups, currently treated as distinct lineages within the Annelida, are the Acanthobdellea (2 species worldwide, of which 1 in Europe) and the Branchiobdellea (about 140 species worldwide, of which 10 in Europe). This paper includes a complete list of European taxa belonging to the Hirudinea, Acanthobdellea and Branchiobdellea. Recent research on a limited number of taxa suggests that our current appreciation of species diversity of Hirudinea in Europe is still provisional: on the one hand, cryptic, unrecognised taxa are expected to emerge; on the other, the status of some taxa currently treated as distinct species deserves revisiting.
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http://dx.doi.org/10.3897/BDJ.2.e4015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4238066PMC
November 2014

Fauna Europaea - all European animal species on the web.

Biodivers Data J 2014 17(2):e4034. Epub 2014 Sep 17.

Institute of Biodiversity & Ecosystem Research, Bulgarian Academy of Sciences and Pensoft Publishers, Sofia, Bulgaria ; Pensoft Publishers, Sofia, Bulgaria.

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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http://dx.doi.org/10.3897/BDJ.2.e4034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4206781PMC
October 2014

Fauna europaea: helminths (animal parasitic).

Biodivers Data J 2014 17(2):e1060. Epub 2014 Sep 17.

University of Eastern Finland, Joensuu, Finland ; University of Amsterdam - Faculty of Science, Amsterdam, Netherlands.

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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http://dx.doi.org/10.3897/BDJ.2.e1060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4206782PMC
October 2014

A decadal view of biodiversity informatics: challenges and priorities.

BMC Ecol 2013 Apr 15;13:16. Epub 2013 Apr 15.

School of Computer Science and Informatics, Cardiff University, Queens Buildings, 5 The Parade, Cardiff, CF24 3AA, UK.

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.
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http://dx.doi.org/10.1186/1472-6785-13-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3843378PMC
April 2013

New species in the Old World: Europe as a frontier in biodiversity exploration, a test bed for 21st century taxonomy.

PLoS One 2012 23;7(5):e36881. Epub 2012 May 23.

UMR 7204, Muséum National d'Histoire Naturelle, Paris, France.

The number of described species on the planet is about 1.9 million, with ca. 17,000 new species described annually, mostly from the tropics. However, taxonomy is usually described as a science in crisis, lacking manpower and funding, a politically acknowledged problem known as the Taxonomic Impediment. Using data from the Fauna Europaea database and the Zoological Record, we show that contrary to general belief, developed and heavily-studied parts of the world are important reservoirs of unknown species. In Europe, new species of multicellular terrestrial and freshwater animals are being discovered and named at an unprecedented rate: since the 1950s, more than 770 new species are on average described each year from Europe, which add to the 125,000 terrestrial and freshwater multicellular species already known in this region. There is no sign of having reached a plateau that would allow for the assessment of the magnitude of European biodiversity. More remarkably, over 60% of these new species are described by non-professional taxonomists. Amateurs are recognized as an essential part of the workforce in ecology and astronomy, but the magnitude of non-professional taxonomist contributions to alpha-taxonomy has not been fully realized until now. Our results stress the importance of developing a system that better supports and guides this formidable workforce, as we seek to overcome the Taxonomic Impediment and speed up the process of describing the planetary biodiversity before it is too late.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0036881PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359328PMC
October 2012
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