Latest Articles from Biodiversity Data Journal Latest 47 Articles from Biodiversity Data Journal https://bdj.pensoft.net/ Thu, 28 Mar 2024 13:38:01 +0200 Pensoft FeedCreator https://bdj.pensoft.net/i/logo.jpg Latest Articles from Biodiversity Data Journal https://bdj.pensoft.net/ The diversity of macromycetes in peatlands: nine years of plot-based monitoring and barcoding in the raised bog "Mukhrino", West Siberia https://bdj.pensoft.net/article/105111/ Biodiversity Data Journal 11: e105111

DOI: 10.3897/BDJ.11.e105111

Authors: Nina Filippova, Elena Zvyagina, Elena Rudykina, Alevtina Dobrynina, Sergey Bolshakov

Abstract: Peatland ecosystems are defined by soils with sufficient under-decomposed organic layer, called peat, formed under anoxic conditions. Peatlands are widespread around the world, with several highly paludified regions, one of which is the Western Siberian Plain. Peatlands store large amounts of carbon and are important in their intact state to counteract climate change, as well as for a variety of other ecosystem functions. From the practical aspect, these ecosystems are used as a source of peat for fuel, peat-based fertilisers and growing media, berries and Sphagnum plantations. Fungi are the key part of the decomposer community of peatlands, playing a critical role in the aerobic decomposition in the upper peat layer. The community of peatland fungi is adapted to decomposition of peat and dead parts of Sphagnum in wet acidic conditions; they form specific mycorrhizal associations with a variety of plants. Thus, the research of fungal diversity of peatlands is important for several reasons: 1) adding knowledge of peatland fungal diversity to local or global biodiversity databases; 2) studying carbon cycling in peatlands; 3) using peat and peatlands for different applications, such as cultivation of Sphagnum with regards to some parasitic species of fungi and 4) peatland restoration and conservation, to mention a few.The community of macromycetes of the raised bog “Mukhrino” in Western Siberia was studied using plot-based monitoring throughout a 9-year observation period. The revealed species diversity is represented by approximately 500 specimens in the Fungarium of Yugra State University collection. Selected specimens were used for barcoding of the ITS region to reveal a total of 95 species from 33 genera and three classes. The barcoding effort confirmed morphological identifications for most specimens and identified a number of cryptic species and several potentially new taxa. Based on regular all-season observations, we describe the phenology of the community sporophore production. The quantitative community structure, based on sporophores, revealed a difference in abundance between species by four orders of magnitude, with rare species representing nearly half of the species list. The inter-annual fruiting abundance varied several times by the total number of sporophores per year. To make the comparisons with global studies, we created an open access database of literature-based observations of fungi in peatlands, based on about 120 published papers (comprising about 1300 species) and compared our species list with this database.As a result, the study created an accurate representation of taxonomic and quantitative structure of the community of macromycetes in raised bogs in the region. The raw data of plot-based counts was published as a sampling-event dataset and the sequenced specimens with the sequence information as an DNA-derived extension dataset in GBIF.

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Taxonomy & Inventories Fri, 20 Oct 2023 10:32:25 +0300
Yugra State University Biological Collection (Khanty-Mansiysk, Russia): general and digitisation overview https://bdj.pensoft.net/article/77669/ Biodiversity Data Journal 10: e77669

DOI: 10.3897/BDJ.10.e77669

Authors: Nina Filippova, Galina Ganasevich, Ilya Filippov, Anastasia Meshcheryakova, Elena Lapshina, Dmitry Karpov

Abstract: The history of biological collections and digitisation initiatives in northern West Siberia is relatively new due to recent development of the region. The Center for Biodiversity Data Mobilization was established to promote the initiative, led by the Yugra State University. This organisation itself has a relatively young collection of biological specimens, which was, until recently, in a disintegrated state and only partly mobilised. The Yugra State University Biological Collection (YSU BC) currently includes three subdivisions differring by history and taxonomic groups, but also by details of management and storage conditions: the Fungarium, the Bryological collection and the Herbarium collection of YSU.The paper describes the general structure of the Yugra State University Biological Collection, its history, storage conditions, management practices, geographical, temporal and taxonomical coverage. The paper is underlined by three datasets of the collections databases published in GBIF, which are described in detail. The databases are managed in Specify 6 and 7 software and accessed through Specify Web Portal and through GBIF.The Yugra State University Biological Collection made an active reorganisation of physical storage conditions and data management recently, providing the model for other collections in the region. This paper describes the history, general structure, management practices and data management of all three parts of this collection for the first time.Although one part of the collection (Fungarium YSU) was mobilised earlier, last year, we mobilised data of the Bryological and Vascular plants (Herbarium) collections. The three datasets of the corresponding collections in GBIF were increased by about 6000 georeferenced records during the last year.

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Data Paper Thu, 20 Jan 2022 19:15:00 +0200
Diversity and distribution of Oxytropis DC. (Fabaceae) species in Asian Russia https://bdj.pensoft.net/article/78666/ Biodiversity Data Journal 10: e78666

DOI: 10.3897/BDJ.10.e78666

Authors: Denis Sandanov, Anastasiia Dugarova, Elena Brianskaia, Inessa Selyutina, Natalia Makunina, Sergey Dudov, Victor Chepinoga, Zhiheng Wang

Abstract: The dataset providing information on the geographic distribution of Oxytropis species on the territory of Asian Russia is discussed. The data were extracted from different sources including prominent floras and check-lists, Red Data books, published research on congeneric species and authors’ field observations and mainly cover less-studied, remote regions of Russia. The dataset should be of value to applied, basic and theoretical plant biologists and ecologists interested in the Oxytropis species.The dataset includes 5172 distribution records for 143 species and 15 subspecies of genus Oxytropis DC. (Fabaceae Lindl.) in Asian Russia. The dataset fills gaps in the distribution of locoweeds in the study area and contains precise coordinates for many of rare and endemic species.

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Data Paper Thu, 20 Jan 2022 12:10:00 +0200
The fungal literature-based occurrence database for southern West Siberia (Russia) https://bdj.pensoft.net/article/76789/ Biodiversity Data Journal 9: e76789

DOI: 10.3897/BDJ.9.e76789

Authors: Nina Filippova, Dmitry Ageev, Sergey Bolshakov, Evgeny Davydov, Aleksandra Filippova, Ilya Filippov, Sergei Gashkov, Irina Gorbunova, Ludmila Kalinina, Nadezhda Kudashova, Ekaterina Palomozhnykh, Natalia Shabanova, Maria Tomoshevich, Olga Vayshlya, Anastasia Vlasenko, Vyacheslav Vlasenko, Irina Vorob'eva, Lidia Yakovchenko, Elena Zvyagina

Abstract: The paper presents the initiative on literature-based occurrence data mobilisation of fungi and fungi-related organisms (literature-based occurrences, Darwin Core MaterialCitation) to develop the Fungal literature-based occurrence database for the southern West Siberia (FuSWS). The initiative on mobilisation of literature-based occurrence data started in the northern part of West Siberia in 2016. The present project extends the initiative to the southern regions and includes ten administrative territories (Tyumen Region, Sverdlovsk Region, Chelyabinsk Region, Omsk Region, Kurgan Region, Tomsk Region, Novosibirsk Region, Kemerovo Region, Altai Territory and Republic of Altai). The area occupies the central to southern part of the West Siberian Plain and extends for about 1.5 K km from the west to the east from the eastern slopes of the Ural Mountains to Yenisey River and from north to south—about 1.3 K km. The total area equals about 1.4 million km2.The initiative is actively growing in spatial, collaboration and data accumulation terms. The working group of about 30 mycologists from eight organisations dedicated to the data mobilisation was created as part of the Siberian Mycological Society (informal organisation since 2019). They have compiled the almost complete bibliographic list of mycology-related papers for the southern West Siberia, including over 900 publications for the last two centuries (the earliest dated 1800). All literature sources were digitised and an online library was created to integrate bibliography metadata and digitised papers using Zotero bibliography manager. The analysis of published sources showed that about two-thirds of works contain occurrences of fungi for the scope of mobilisation.At the time of the paper submission, the database had been populated with a total of about 8 K records from 93 sources. The dataset is uploaded to GBIF, where it is available for online search of species occurrences and/or download. The project's page with the introduction, templates, bibliography list, video-presentations and written instructions is available (in Russian) at the web site of the Siberian Mycological Society. The initiative will be continued in the following years to extract the records from all published sources.The paper presents the first project with the aim of literature-based occurrence data mobilisation of fungi and fungi-related organisms in the southern West Siberia. The full bibliography and a digital library of all regional mycological publications created for the first time includes about 900 published works. By the time of paper submission, nearly 8 K occurrence records were extracted from about 90 literature sources and integrated into the FuSWS database published in GBIF.

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Data Paper Mon, 13 Dec 2021 09:15:00 +0200
BEXIS2: A FAIR-aligned data management system for biodiversity, ecology and environmental data https://bdj.pensoft.net/article/72901/ Biodiversity Data Journal 9: e72901

DOI: 10.3897/BDJ.9.e72901

Authors: Javad Chamanara, Jitendra Gaikwad, Roman Gerlach, Alsayed Algergawy, Andreas Ostrowski, Birgitta König-Ries

Abstract: Obtaining fit-to-use data associated with diverse aspects of biodiversity, ecology and environment is challenging since often it is fragmented, sub-optimally managed and available in heterogeneous formats. Recently, with the universal acceptance of the FAIR data principles, the requirements and standards of data publications have changed substantially. Researchers are encouraged to manage the data as per the FAIR data principles and ensure that the raw data, metadata, processed data, software, codes and associated material are securely stored and the data be made available with the completion of the research.We have developed BEXIS2 as an open-source community-driven web-based research data management system to support research data management needs of mid to large-scale research projects with multiple sub-projects and up to several hundred researchers. BEXIS2 is a modular and extensible system providing a range of functions to realise the complete data lifecycle from data structure design to data collection, data discovery, dissemination, integration, quality assurance and research planning. It is an extensible and customisable system that allows for the development of new functions and customisation of its various components from database schemas to the user interface layout, elements and look and feel.During the development of BEXIS2, we aimed to incorporate key aspects of what is encoded in FAIR data principles. To investigate the extent to which BEXIS2 conforms to these principles, we conducted the self-assessment using the FAIR indicators, definitions and criteria provided in the FAIR Data Maturity Model. Even though the FAIR data maturity model is developed initially to judge the conformance of datasets, the self-assessment results indicated that BEXIS2 remarkably conforms and supports FAIR indicators. BEXIS2 strongly conforms to the indicators Findability and Accessibility. The indicator Interoperability is moderately supported as of now; however, for many of the lesssupported facets, we have concrete plans for improvement. Reusability (as defined by the FAIR data principles) is partially achieved.This paper also illustrates community deployment examples of the BEXIS2 instances as success stories to exemplify its capacity to meet the biodiversity and ecological data management needs of differently sized projects and serve as an organisational research data management system.

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Software Description Fri, 5 Nov 2021 10:45:00 +0200
Fleroff goes digital: georeferenced records from "Flora des Gouvernements Wladimir" (Fleroff, 1902) https://bdj.pensoft.net/article/75299/ Biodiversity Data Journal 9: e75299

DOI: 10.3897/BDJ.9.e75299

Authors: Alexey P. Seregin, Yurii Basov

Abstract: Global Biodiversity Information Facility (GBIF) has uneven data coverage across taxonomic, spatial and temporal dimensions. Temporal imbalances in the data coverage are particularly dramatic. Thus, 188.3M GBIF records were made in 2020, more than the whole lot of the currently available pre-1986 electronic data. This underscores the importance of reliable and precise biodiversity spatial data collected in early times. Biological collections certainly play a key role in our knowledge of biodiversity in the past. However, digitisation of historical literature is underway, being a modern trend in biodiversity data mining. The grid dataset for the flora of Vladimir Oblast, Russia, includes many historical records borrowed from the "Flora des Gouvernements Wladimir" by Alexander F. Fleroff (also known as Flerov or Flerow). Intensive study of Fleroff's collections and field surveys exactly in the same localities where he worked, showed that the quality of his data is superb. Species lists collected across hundreds of localities form a unique source of reliable information on the floristic diversity of Vladimir Oblast and adjacent areas for the period from 1894 to 1901. Since the grid dataset holds generalised data, we made precise georeferencing of Fleroff's literature records and published them in the form of a GBIF-mediated dataset.A dataset, based on "Flora des Gouvernements Wladimir. I. Pflanzengeographische Beschreibung des Gouvernements Wladimir" by Fleroff (1902), includes 8,889 records of 654 taxa (mainly species) from 366 localities. The majority of records originate from Vladimir Oblast (4,611 records of 534 taxa from 195 localities) and Yaroslavl Oblast (2,013 records of 409 taxa from 66 localities), but also from Nizhny Novgorod Oblast (942 records), Ivanovo Oblast (667 records) and Moscow Oblast (656 records). The leading second-level administrative units by the number of records are Pereslavsky District (2,013 records), Aleksandrovsky District (1,318 records) and Sergievo-Posadsky District (599 records). Georeferencing was carried out, based on the expert knowledge of the area, analysis of modern satellite images and old topographic maps. For 2,460 records, the georeferencing accuracy is 1,000 m or less (28%), whereas for 6,070 records it is 2,000 m or less (68%). The mean accuracy of records of the entire dataset is 2,447 m. That accuracy is unattainable for most herbarium collections of the late 19th century. Some localities of rare plants discovered by Fleroff and included into the dataset were completely lost in the 20th century due to either peat mining or development of urban areas.

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Data Paper Wed, 20 Oct 2021 09:45:00 +0300
Infrastructure and Population of the OpenBiodiv Biodiversity Knowledge Graph https://bdj.pensoft.net/article/67671/ Biodiversity Data Journal 9: e67671

DOI: 10.3897/BDJ.9.e67671

Authors: Mariya Dimitrova, Viktor Senderov, Teodor Georgiev, Georgi Zhelezov, Lyubomir Penev

Abstract: OpenBiodiv is a biodiversity knowledge graph containing a synthetic linked open dataset, OpenBiodiv-LOD, which combines knowledge extracted from academic literature with the taxonomic backbone used by the Global Biodiversity Information Facility. The linked open data is modelled according to the OpenBiodiv-O ontology integrating semantic resource types from recognised biodiversity and publishing ontologies with OpenBiodiv-O resource types, introduced to capture the semantics of resources not modelled before.We introduce the new release of the OpenBiodiv-LOD attained through information extraction and modelling of additional biodiversity entities. It was achieved by further developments to OpenBiodiv-O, the data storage infrastructure and the workflow and accompanying R software packages used for transformation of academic literature into Resource Description Framework (RDF). We discuss how to utilise the LOD in biodiversity informatics and give examples by providing solutions to several competency questions. We investigate performance issues that arise due to the large amount of inferred statements in the graph and conclude that OWL-full inference is impractical for the project and that unnecessary inference should be avoided.

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Software Description Fri, 24 Sep 2021 19:00:00 +0300
"Flora of Russia" on iNaturalist: a dataset https://bdj.pensoft.net/article/59249/ Biodiversity Data Journal 8: e59249

DOI: 10.3897/BDJ.8.e59249

Authors: Alexey Seregin, Dmitriy Bochkov, Julia Shner, Eduard Garin, Igor Pospelov, Vadim Prokhorov, Pavel Golyakov, Sergey Mayorov, Sergey Svirin, Alexander Khimin, Marina Gorbunova, Ekaterina Kashirina, Olga Kuryakova, Boris Bolshakov, Aleksandr Ebel, Anatoliy Khapugin, Maxim Mallaliev, Sergey Mirvoda, Sergey Lednev, Dina Nesterkova, Nadezhda Zelenova, Svetlana Nesterova, Viktoriya Zelenkova, Georgy Vinogradov, Olga Biryukova, Alla Verkhozina, Alexey Zyrianov, Sergey Gerasimov, Ramazan Murtazaliev, Yurii Basov, Kira Marchenkova, Dmitry Vladimirov, Dina Safina, Sergey Dudov, Nikolai Degtyarev, Diana Tretyakova, Daba Chimitov, Evgenij Sklyar, Alesya Kandaurova, Svetlana Bogdanovich, Alexander Dubynin, Olga Chernyagina, Aleksandr Lebedev, Mikhail Knyazev, Irina Mitjushina, Nina Filippova, Kseniia Dudova, Igor Kuzmin, Tatyana Svetasheva, Vladimir Zakharov, Vladimir Travkin, Yaroslav Magazov, Vladimir Teploukhov, Andrey Efremov, Olesya Deineko, Viktor Stepanov, Eugene Popov, Dmitry Kuzmenckin, Tatiana Strus, Tatyana Zarubo, Konstantin Romanov, Alexei Ebel, Denis Tishin, Vladimir Arkhipov, Vladimir Korotkov, Svetlana Kutueva, Vladimir Gostev, Mikhail Krivosheev, Natalia Gamova, Veronica Belova, Oleg Kosterin, Sergey Prokopenko, Rinat Sultanov, Irina Kobuzeva, Nikolay Dorofeev, Alexander Yakovlev, Yuriy Danilevsky, Irina Zolotukhina, Damir Yumagulov, Valerii Glazunov, Vladimir Bakutov, Andrey Danilin, Igor Pavlov, Elena Pushay, Elena Tikhonova, Konstantin Samodurov, Dmitrii Epikhin, Tatyana Silaeva, Andrei Pyak, Yulia Fedorova, Evgeniy Samarin, Denis Shilov, Valentina Borodulina, Ekaterina Kropocheva, Gennadiy Kosenkov, Uladzimir Bury, Anna Mitroshenkova, Tatiana Karpenko, Ruslan Osmanov, Maria Kozlova, Tatiana Gavrilova, Stepan Senator, Maxim Khomutovskiy, Eugene Borovichev, Ilya Filippov, Serguei Ponomarenko, Elena Shumikhina, Dmitry Lyskov, Evgeny Belyakov, Mikhail Kozhin, Leonid Poryadin, Artem Leostrin

Abstract: The "Flora of Russia" project on iNaturalist brought together professional scientists and amateur naturalists from all over the country. Over 10,000 people are involved in the data collection.Within 20 months the participants accumulated over 750,000 photo observations of 6,853 species of the Russian flora. This constitutes the largest dataset of open spatial data on the country’s biodiversity and a leading source of data on the current state of the national flora. About 85% of all project data are available under free licenses (CC0, CC-BY, CC-BY-NC) and can be freely used in scientific, educational and environmental activities.

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Data Paper Tue, 17 Nov 2020 17:15:00 +0200
Analysis of Chagas disease vectors occurrence data: the Argentinean triatomine species database https://bdj.pensoft.net/article/58076/ Biodiversity Data Journal 8: e58076

DOI: 10.3897/BDJ.8.e58076

Authors: Soledad Ceccarelli, Agustín Balsalobre, Maria Cano, Delmi Canale, Patricia Lobbia, Raúl Stariolo, Jorge Rabinovich, Gerardo Marti

Abstract: Chagas disease is a neglected tropical disease and Trypanosoma cruzi (its etiological agent) is mainly transmitted by triatomines (Hemiptera: Reduviidae). All triatomine species are considered as potential vectors; thus, their geographic distribution and habitat information should be a fundamental guide for the surveillance and control of Chagas disease. Currently, of the 137 species distributed in the Americas (Justi and Galvão 2017), 17 species are cited for Argentina: Panstrongylus geniculatus, P. guentheri, P. megistus, P. rufotuberculatus, Psammolestes coreodes, Triatoma breyeri, T. delpontei, T. eratyrusiformis, T. garciabesi, T. guasayana, T. infestans, T. limai, T. patagonica, T. platensis, T. rubrofasciata, T. rubrovaria and T. sordida. Almost 20 years have passed since the publication of the “Atlas of the Triatominae” by Carcavallo et al. (1998), and no work has been done to provide an updated complete integration and analysis of the existing information for Argentinean triatomine species. Here we provided a detailed temporal, spatial and ecological analysis of updated occurrence data for triatomines present in Argentina.This is the first database of the 17 triatomine species present in Argentina (15917 records), with a critical analysis of the temporal, spatial and ecological characteristics of 9788 records. The information spans for the last 100 years (1918–2019) and it was mostly obtained from the DataTri database and from the Argentinean Vector Reference Center. As 70% of the occurrences corresponded to the last 20 years, the information was split into two broad periods (pre-2000 and post-2000). Occurrence data for most species show distribution ranges contractions, which from the pre-2000 to post-2000 period became restricted mainly to the dry and humid Chaco ecoregions. Concurrently, the highest species richness foci occurred within those ecoregions. The species T. infestans, T. sordida, T. garciabesi and T. guasayana mostly colonize human dwelling habitats. This study provides the most comprehensive picture available for Argentinean triatomine species, and we hope that any knowledge gaps will encourage others to keep this information updated to assist health policy makers to make decisions based on the best evidence.

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Data Paper Thu, 12 Nov 2020 15:15:00 +0200
Biodiversidata: A novel dataset for the vascular plant species diversity in Uruguay https://bdj.pensoft.net/article/56850/ Biodiversity Data Journal 8: e56850

DOI: 10.3897/BDJ.8.e56850

Authors: Florencia Grattarola, Andrés González, Patricia Mai, Laura Cappuccio, César Fagúndez-Pachón, Florencia Rossi, Franco Teixeira de Mello, Lucía Urtado, Daniel Pincheira-Donoso

Abstract: South America hosts some of the world’s most prominent biodiversity hotspots. Yet, Uruguay – a country where multiple major ecosystems converge – ranks amongst the countries with the lowest levels of available digital biodiversity data in the continent. Such prevalent data scarcity has significantly undermined our ability to progress towards evidence-based conservation actions – a critical limitation for a country with a strong focus on agricultural industries and only 1.3% of the land surface guarded by protected areas. Under today’s rapid biodiversity loss and environmental changes, the need for open-access biodiversity data is more pressing than ever before. To address this national issue, Biodiversidata – Uruguay’s first Consortium of Biodiversity Data – has recently emerged with the aim of assembling a constantly growing database for the biodiversity of this country. While the first phase of the project targeted vertebrate biodiversity, the second phase presented in this paper spans the biodiversity of plants.As part of the second phase of the Biodiversidata initiative, we present the first comprehensive open-access species-level database of the vascular plant diversity recorded in Uruguay to date (i.e. all species for which data are currently available and species presence has been confirmed). It contains 12,470 occurrence records from across 1,648 species and 160 families, which roughly represents 60% of the total recorded flora of Uruguay. The primary biodiversity data include extant native and introduced species from the lycophytes, ferns, gymnosperms and angiosperms groups. Records were collated from multiple sources, including data available in peer-reviewed scientific literature, institutional scientific collections and datasets contributed by members of the Biodiversidata initiative. The complete database can be accessed at the Zenodo repository: doi.org/10.5281/zenodo.3954406

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Data Paper Mon, 26 Oct 2020 13:10:09 +0200
Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature https://bdj.pensoft.net/article/28737/ Biodiversity Data Journal 7: e28737

DOI: 10.3897/BDJ.7.e28737

Authors: Gabriel Muñoz, W. Daniel Kissling, E. Emiel van Loon

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Software Description Wed, 16 Jan 2019 09:26:22 +0200
A story of data won, data lost and data re-found: the realities of ecological data preservation https://bdj.pensoft.net/article/28073/ Biodiversity Data Journal 6: e28073

DOI: 10.3897/BDJ.6.e28073

Authors: Alison Specht, Matthew Bolton, Bryn Kingsford, Raymond Specht, Lee Belbin

Abstract: This paper discusses the process of retrieval and updating legacy data to allow on-line discovery and delivery. There are many pitfalls of institutional and non-institutional ecological data conservation over the long term. Interruptions to custodianship, old media, lost knowledge and the continuous evolution of species names makes resurrection of old data challenging. We caution against technological arrogance and emphasise the importance of international standards. We use a case study of a compiled set of continent-wide vegetation survey data for which, although the analyses had been published, the raw data had not. In the original study, publications containing plot data collected from the 1880s onwards had been collected, interpreted, digitised and integrated for the classification of vegetation and analysis of its conservation status across Australia. These compiled data are an extremely valuable national collection that demanded publishing in open, readily accessible online repositories, such as the Terrestrial Ecosystem Research Network (http://www.tern.org.au) and the Atlas of Living Australia (ALA: http://www.ala.org.au), the Australian node of the Global Biodiversity Information Facility (GBIF: http://www.gbif.org). It is hoped that the lessons learnt from this project may trigger a sober review of the value of endangered data, the cost of retrieval and the importance of suitable and timely archiving through the vicissitudes of technological change, so the initial unique collection investment enables multiple re-use in perpetuity.

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Research Article Wed, 7 Nov 2018 10:05:09 +0200
Liberating links between datasets using lightweight data publishing: an example using plant names and the taxonomic literature https://bdj.pensoft.net/article/27539/ Biodiversity Data Journal 6: e27539

DOI: 10.3897/BDJ.6.e27539

Authors: Roderic Page

Abstract: Constructing a biodiversity knowledge graph will require making millions of cross links between diversity entities in different datasets. Researchers trying to bootstrap the growth of the biodiversity knowledge graph by constructing databases of links between these entities lack obvious ways to publish these sets of links. One appealing and lightweight approach is to create a "datasette", a database that is wrapped together with a simple web server that enables users to query the data. Datasettes can be packaged into Docker containers and hosted online with minimal effort. This approach is illustrated using a dataset of links between globally unique identifiers for plant taxonomic namesand identifiers for the taxonomic articles that published those names.

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Forum Paper Mon, 23 Jul 2018 16:45:18 +0300
The taxlist package: managing plant taxonomic lists in R https://bdj.pensoft.net/article/23635/ Biodiversity Data Journal 6: e23635

DOI: 10.3897/BDJ.6.e23635

Authors: Miguel Alvarez, Federico Luebert

Abstract: Taxonomic lists are crucial elements of vegetation-plot databases and provide the links between original entries, reference taxon views and different taxon concepts. We introduce the R package taxlist in the context of object-oriented modelling for taxonomic lists. This package provides a data structure based on species lists in Turboveg, which is a software broadly used for the storage of vegetation-plot databases and implements functions for importing and handling them prior to statistical analysis. We also present a schema for relational databases, compatible with taxlist objects and recommend its use for handling diversity records.

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R Package Wed, 2 May 2018 09:03:40 +0300
A crowdsourcing approach to collecting photo-based insect and plant observation records https://bdj.pensoft.net/article/21271/ Biodiversity Data Journal 5: e21271

DOI: 10.3897/BDJ.5.e21271

Authors: Takeshi Osawa, Takehiko Yamanaka, Yukinobu Nakatani, Jun Nishihiro, Shiori Takahashi, Suzuki Mahoro, Hironobu Sasaki

Abstract:

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Data Paper Mon, 6 Nov 2017 08:53:43 +0200
iCollections methodology: workflow, results and lessons learned https://bdj.pensoft.net/article/21277/ Biodiversity Data Journal 5: e21277

DOI: 10.3897/BDJ.5.e21277

Authors: Vladimir Blagoderov, Malcolm Penn, Mike Sadka, Adrian Hine, Stephen Brooks, Darrell Siebert, Chris Sleep, Steve Cafferty, Elisa Cane, Geoff Martin, Flavia Toloni, Peter Wing, John Chainey, Liz Duffell, Rob Huxley, Sophie Ledger, Caitlin McLaughlin, Gerardo Mazzetta, Jasmin Perera, Robyn Crowther, Lyndsey Douglas, Joanna Durant, Elisabetta Scialabba, Martin Honey, Blanca Huertas, Theresa Howard, Victoria Carter, Sara Albuquerque, Gordon Paterson, Ian Kitching

Abstract: The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections. The first phase of this programme was to undertake a series of pilot projects to develop the workflows and infrastructure needed to support mass digitisation of very large scientific collections. This paper presents the results of one of the pilot projects – iCollections. This project digitised all the lepidopteran specimens usually considered as butterflies, 181,545 specimens representing 89 species from the British Isles and Ireland. The data digitised includes, species name, georeferenced location, collector and collection date - the what, where, who and when of specimen data. In addition, a digital image of each specimen was taken. A previous paper explained the way the data were obtained and the background to the collections that made up the project. The present paper describes the technical, logistical, and economic aspects of managing the project.

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Research Article Thu, 28 Sep 2017 14:03:45 +0300
iCollections methodology: workflow, results and lessons learned https://bdj.pensoft.net/article/19893/ Biodiversity Data Journal 5: e19893

DOI: 10.3897/BDJ.5.e19893

Authors: Vladimir Blagoderov, Malcolm Penn, Mike Sadka, Adrian Hine, Stephen Brooks, Darrell Siebert, Chris Sleep, Steve Cafferty, Elisa Cane, Geoff Martin, Flavia Toloni, Peter Wing, John Chainey, Liz Duffell, Rob Huxley, Sophie Ledger, Caitlin McLaughlin, Gerardo Mazzetta, Jasmin Perera, Robyn Crowther, Lyndsey Douglas, Joanna Durant, Martin Honey, Blanca Huertas, Theresa Howard, Victoria Carter, Sara Albuquerque, Gordon Paterson, Ian Kitching

Abstract: The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections. The first phase of this programme was to undertake a series of pilot projects to develop the workflows and infrastructure needed to support mass digitisation of very large scientific collections. This paper presents the results of one of the pilot projects – iCollections. This project digitised all the lepidopteran specimens usually considered as butterflies, 181,545 specimens representing 89 species from the British Isles and Ireland. The data digitised includes, species name, georeferenced location, collector and collection date - the what, where, who and when of specimen data. In addition, a digital image of each specimen was taken. A previous paper explained the way the data were obtained and the background to the collections that made up the project. The present paper describes the technical, logistical, and economic aspects of managing the project.

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Research Article Mon, 25 Sep 2017 12:03:52 +0300
Fauna Europaea: Hymenoptera – Symphyta & Ichneumonoidea https://bdj.pensoft.net/article/14650/ Biodiversity Data Journal 5: e14650

DOI: 10.3897/BDJ.5.e14650

Authors: Kees van Achterberg, Andreas Taeger, Stephan Blank, Kees Zwakhals, Matti Viitasaari, Dicky Yu, Yde de Jong

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.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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Data Paper Thu, 27 Jul 2017 09:20:43 +0300
Building a database for long-term monitoring of benthic macrofauna in the Pertuis-Charentais (2004-2014) https://bdj.pensoft.net/article/10288/ Biodiversity Data Journal 5: e10288

DOI: 10.3897/BDJ.5.e10288

Authors: Anne Philippe, Christine Plumejeaud-Perreau, Jérôme Jourde, Philippe Pineau, Nicolas Lachaussée, Emmanuel Joyeux, Frédéric Corre, Philippe Delaporte, Pierrick Bocher

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Data Paper Thu, 12 Jan 2017 14:52:21 +0200
Toward a new data standard for combined marine biological and environmental datasets - expanding OBIS beyond species occurrences https://bdj.pensoft.net/article/10989/ Biodiversity Data Journal 5: e10989

DOI: 10.3897/BDJ.5.e10989

Authors: Daphnis De Pooter, Ward Appeltans, Nicolas Bailly, Sky Bristol, Klaas Deneudt, Menashè Eliezer, Ei Fujioka, Alessandra Giorgetti, Philip Goldstein, Mirtha Lewis, Marina Lipizer, Kevin Mackay, Maria Marin, Gwenaëlle Moncoiffé, Stamatina Nikolopoulou, Pieter Provoost, Shannon Rauch, Andres Roubicek, Carlos Torres, Anton van de Putte, Leen Vandepitte, Bart Vanhoorne, Matteo Vinci, Nina Wambiji, David Watts, Eduardo Klein Salas, Francisco Hernandez

Abstract: The Ocean Biogeographic Information System (OBIS) is the world’s most comprehensive online, open-access database of marine species distributions. OBIS grows with millions of new species observations every year. Contributions come from a network of hundreds of institutions, projects and individuals with common goals: to build a scientific knowledge base that is open to the public for scientific discovery and exploration and to detect trends and changes that inform society as essential elements in conservation management and sustainable development. Until now, OBIS has focused solely on the collection of biogeographic data (the presence of marine species in space and time) and operated with optimized data flows, quality control procedures and data standards specifically targeted to these data. Based on requirements from the growing OBIS community to manage datasets that combine biological, physical and chemical measurements, the OBIS-ENV-DATA pilot project was launched to develop a proposed standard and guidelines to make sure these combined datasets can stay together and are not, as is often the case, split and sent to different repositories. The proposal in this paper allows for the management of sampling methodology, animal tracking and telemetry data, biological measurements (e.g., body length, percent live cover, ...) as well as environmental measurements such as nutrient concentrations, sediment characteristics or other abiotic parameters measured during sampling to characterize the environment from which biogeographic data was collected. The recommended practice builds on the Darwin Core Archive (DwC-A) standard and on practices adopted by the Global Biodiversity Information Facility (GBIF). It consists of a DwC Event Core in combination with a DwC Occurrence Extension and a proposed enhancement to the DwC MeasurementOrFact Extension. This new structure enables the linkage of measurements or facts - quantitative and qualitative properties - to both sampling events and species occurrences, and includes additional fields for property standardization. We also embrace the use of the new parentEventID DwC term, which enables the creation of a sampling event hierarchy. We believe that the adoption of this recommended practice as a new data standard for managing and sharing biological and associated environmental datasets by IODE and the wider international scientific community would be key to improving the effectiveness of the knowledge base, and will enhance integration and management of critical data needed to understand ecological and biological processes in the ocean, and on land.

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Research Article Mon, 9 Jan 2017 12:19:04 +0200
Rescuing biogeographic legacy data: The "Thor" Expedition, a historical oceanographic expedition to the Mediterranean Sea https://bdj.pensoft.net/article/11054/ Biodiversity Data Journal 4: e11054

DOI: 10.3897/BDJ.4.e11054

Authors: Dimitra Mavraki, Lucia Fanini, Marilena Tsompanou, Vasilis Gerovasileiou, Stamatina Nikolopoulou, Eva Chatzinikolaou, Wanda Plaitis, Sarah Faulwetter

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Data Paper Thu, 22 Dec 2016 14:13:35 +0200
iCollections – Digitising the British and Irish Butterflies in the Natural History Museum, London https://bdj.pensoft.net/article/9559/ Biodiversity Data Journal 4: e9559

DOI: 10.3897/BDJ.4.e9559

Authors: Gordon Paterson, Sara Albuquerque, Vladimir Blagoderov, Stephen Brooks, Steve Cafferty, Elisa Cane, Victoria Carter, John Chainey, Robyn Crowther, Lyndsey Douglas, Joanna Durant, Liz Duffell, Adrian Hine, Martin Honey, Blanca Huertas, Theresa Howard, Rob Huxley, Ian Kitching, Sophie Ledger, Caitlin McLaughlin, Geoff Martin, Gerardo Mazzetta, Malcolm Penn, Jasmin Perera, Mike Sadka, Elisabetta Scialabba, Angela Self, Darrell Siebert, Chris Sleep, Flavia Toloni, Peter Wing

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Data Paper Tue, 13 Sep 2016 17:49:34 +0300
Fauna Europaea – Orthopteroid orders https://bdj.pensoft.net/article/8905/ Biodiversity Data Journal 4: e8905

DOI: 10.3897/BDJ.4.e8905

Authors: Klaus-Gerhard Heller, Horst Bohn, Fabian Haas, Fer Willemse, Yde de Jong

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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Data Paper Wed, 29 Jun 2016 11:22:09 +0300
The Analysis Portal and the Swedish LifeWatch e-infrastructure for biodiversity research https://bdj.pensoft.net/article/7644/ Biodiversity Data Journal 4: e7644

DOI: 10.3897/BDJ.4.e7644

Authors: Sonja Leidenberger, Martin Käck, Björn Karlsson, Oskar Kindvall

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Software Description Wed, 23 Mar 2016 10:10:17 +0200
Fauna Europaea: Annelida - Terrestrial Oligochaeta (Enchytraeidae and Megadrili), Aphanoneura and Polychaeta https://bdj.pensoft.net/article/5737/ Biodiversity Data Journal 3: e5737

DOI: 10.3897/BDJ.3.e5737

Authors: Emilia Rota, Yde de Jong

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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Data Paper Fri, 11 Sep 2015 11:23:41 +0300
Fauna Europaea: Gastrotricha https://bdj.pensoft.net/article/5800/ Biodiversity Data Journal 3: e5800

DOI: 10.3897/BDJ.3.e5800

Authors: Maria Balsamo, Jean-Loup d`Hondt, Jacek Kisielewski, M. Todaro, Paolo Tongiorgi, Loretta Guidi, Paolo Grilli, Yde de Jong

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 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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Data Paper Fri, 14 Aug 2015 10:05:42 +0300
A Preliminary Investigation of Reversing RML: From an RDF dataset to its Column-Based data source https://bdj.pensoft.net/article/5464/ Biodiversity Data Journal 3: e5464

DOI: 10.3897/BDJ.3.e5464

Authors: Carlo Allocca, Alexandros Gougousis

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Software Description Wed, 29 Jul 2015 16:34:01 +0300
Displaying bias in sampling effort of data accessed from biodiversity databases using ignorance maps https://bdj.pensoft.net/article/5361/ Biodiversity Data Journal 3: e5361

DOI: 10.3897/BDJ.3.e5361

Authors: Alejandro Ruete

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Software Description Tue, 28 Jul 2015 12:59:43 +0300
Fauna Europaea: Mollusca – Bivalvia https://bdj.pensoft.net/article/5211/ Biodiversity Data Journal 3: e5211

DOI: 10.3897/BDJ.3.e5211

Authors: Rafael Araujo, Yde de Jong

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 (Corbicula fluminea) and the Dreissenoidea the famous invasive zebra mussel (Dreissena polymorpha). 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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Data Paper Fri, 17 Jul 2015 13:40:39 +0300
Extending Marine Species Distribution Maps Using Non-Traditional Sources https://bdj.pensoft.net/article/4900/ Biodiversity Data Journal 3: e4900

DOI: 10.3897/BDJ.3.e4900

Authors: John Wood, Fabio Moretzsohn, James Gibeaut

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Editorial Fri, 17 Apr 2015 08:30:59 +0300
Fauna Europaea: Neuropterida (Raphidioptera, Megaloptera, Neuroptera) https://bdj.pensoft.net/article/4830/ Biodiversity Data Journal 3: e4830

DOI: 10.3897/BDJ.3.e4830

Authors: Ulrike Aspöck, Horst Aspöck, Agostino Letardi, Yde de Jong

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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Data Paper Fri, 17 Apr 2015 08:30:47 +0300
Fauna Europaea: Coleoptera 2 (excl. series Elateriformia, Scarabaeiformia, Staphyliniformia and superfamily Curculionoidea) https://bdj.pensoft.net/article/4750/ Biodiversity Data Journal 3: e4750

DOI: 10.3897/BDJ.3.e4750

Authors: Paolo Audisio, Miguel-Angel Alonso Zarazaga, Adam Slipinski, Anders Nilsson, Josef Jelínek, Augusto Taglianti, Federica Turco, Carlos Otero, Claudio Canepari, David Kral, Gianfranco Liberti, Gianfranco Sama, Gianluca Nardi, Ivan Löbl, Jan Horak, Jiri Kolibac, Jirí Háva, Maciej Sapiejewski, Manfred Jäch, Marco Bologna, Maurizio Biondi, Nikolai Nikitsky, Paolo Mazzoldi, Petr Zahradnik, Piotr Wegrzynowicz, Robert Constantin, Roland Gerstmeier, Rustem Zhantiev, Simone Fattorini, Wioletta Tomaszewska, Wolfgang Rücker, Xavier Vazquez-Albalate, Fabio Cassola, Fernando Angelini, Colin Johnson, Wolfgang Schawaller, Renato Regalin, Cosimo Baviera, Saverio Rocchi, Fabio Cianferoni, Ron Beenen, Michael Schmitt, David Sassi, Horst Kippenberg, Marcello Zampetti, Marco Trizzino, Stefano Chiari, Giuseppe Maria Carpaneto, Simone Sabatelli, Yde de Jong

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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Data Paper Thu, 9 Apr 2015 09:01:11 +0300
Fauna Europaea: Hymenoptera – Apocrita (excl. Ichneumonoidea) https://bdj.pensoft.net/article/4186/ Biodiversity Data Journal 3: e4186

DOI: 10.3897/BDJ.3.e4186

Authors: Mircea-Dan Mitroiu, John Noyes, Aleksandar Cetkovic, Guido Nonveiller, Alexander Radchenko, Andrew Polaszek, Fredrick Ronquist, Mattias Forshage, Guido Pagliano, Josef Gusenleitner, Mario Bartalucci, Massimo Olmi, Lucian Fusu, Michael Madl, Norman Johnson, Petr Jansta, Raymond Wahis, Villu Soon, Paolo Rosa, Till Osten, Yvan Barbier, Yde de Jong

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. 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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Data Paper Fri, 20 Mar 2015 08:27:05 +0200
Fauna Europaea: Diptera – Brachycera https://bdj.pensoft.net/article/4187/ Biodiversity Data Journal 3: e4187

DOI: 10.3897/BDJ.3.e4187

Authors: Thomas Pape, Paul Beuk, Adrian Pont, Anatole Shatalkin, Andrey Ozerov, Andrzej Woźnica, Bernhard Merz, Cezary Bystrowski, Chris Raper, Christer Bergström, Christian Kehlmaier, David Clements, David Greathead, Elena Kameneva, Emilia Nartshuk, Frederik Petersen, Gisela Weber, Gerhard Bächli, Fritz Geller-Grimm, Guy Van de Weyer, Hans-Peter Tschorsnig, Herman de Jong, Jan-Willem van Zuijlen, Jaromír Vaňhara, Jindřich Roháček, Joachim Ziegler, József Majer, Karel Hůrka, Kevin Holston, Knut Rognes, Lita Greve-Jensen, Lorenzo Munari, Marc de Meyer, Marc Pollet, Martin Speight, Martin Ebejer, Michel Martinez, Miguel Carles-Tolrá, Mihály Földvári, Milan Chvála, Miroslav Barták, Neal Evenhuis, Peter Chandler, Pierfilippo Cerretti, Rudolf Meier, Rudolf Rozkosny, Sabine Prescher, Stephen Gaimari, Tadeusz Zatwarnicki, Theo Zeegers, Torsten Dikow, Valery Korneyev, Vera Richter, Verner Michelsen, Vitali Tanasijtshuk, Wayne Mathis, Zdravko Hubenov, Yde de Jong

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 Thyreophora cynophila (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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Data Paper Fri, 20 Feb 2015 10:39:33 +0200
Corrected data re-harvested: curating literature in the era of networked biodiversity informatics https://bdj.pensoft.net/article/4552/ Biodiversity Data Journal 3: e4552

DOI: 10.3897/BDJ.3.e4552

Authors: Jeremy Miller, Teodor Georgiev, Pavel Stoev, Guido Sautter, Lyubomir Penev

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Editorial Wed, 21 Jan 2015 11:01:56 +0200
A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control https://bdj.pensoft.net/article/4221/ Biodiversity Data Journal 2: e4221

DOI: 10.3897/BDJ.2.e4221

Authors: Cherian Mathew, Anton Güntsch, Matthias Obst, Saverio Vicario, Robert Haines, Alan Williams, Yde de Jong, Carole Goble

Abstract: 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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Software Description Thu, 11 Dec 2014 15:57:33 +0200
Fauna Europaea: Annelida – Hirudinea, incl. Acanthobdellea and Branchiobdellea https://bdj.pensoft.net/article/4015/ Biodiversity Data Journal 2: e4015

DOI: 10.3897/BDJ.2.e4015

Authors: Alessandro Minelli, Boris Sket, Yde de Jong

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. 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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Data Paper Fri, 14 Nov 2014 19:32:11 +0200
Trends in access of plant biodiversity data revealed by Google Analytics https://bdj.pensoft.net/article/1558/ Biodiversity Data Journal 2: e1558

DOI: 10.3897/BDJ.2.e1558

Authors: Timothy Jones, David Baxter, Gregor Hagedorn, Ben Legler, Edward Gilbert, Kevin Thiele, Yalma Vargas-Rodriguez, Lowell Urbatsch

Abstract: The amount of plant biodiversity data available via the web has exploded in the last decade, but making these data available requires a considerable investment of time and work, both vital considerations for organizations and institutions looking to validate the impact factors of these online works. Here we used Google Analytics (GA), to measure the value of this digital presence. In this paper we examine usage trends using 15 different GA accounts, spread across 451 institutions or botanical projects that comprise over five percent of the world's herbaria. They were studied at both one year and total years. User data from the sample reveal: 1) over 17 million web sessions, 2) on five primary operating systems, 3) search and direct traffic dominates with minimal impact from social media, 4) mobile and new device types have doubled each year for the past three years, 5) and web browsers, the tools we use to interact with the web, are changing. Server-side analytics differ from site to site making the comparison of their data sets difficult. However, use of Google Analytics erases the reporting heterogeneity of unique server-side analytics, as they can now be examined with a standard that provides a clarity for data-driven decisions. The knowledge gained here empowers any collection-based environment regardless of size, with metrics about usability, design, and possible directions for future development.

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Research Article Tue, 11 Nov 2014 18:31:55 +0200
Fauna Europaea: Helminths (Animal Parasitic) https://bdj.pensoft.net/article/1060/ Biodiversity Data Journal 2: e1060

DOI: 10.3897/BDJ.2.e1060

Authors: David Gibson, Rodney Bray, David Hunt, Boyko Georgiev, Tomaš Scholz, Philip Harris, Tor Bakke, Teresa Pojmanska, Katarzyna Niewiadomska, Aneta Kostadinova, Vasyl Tkach, Odile Bain, Marie-Claude Durette-Desset, Lynda Gibbons, František Moravec, Annie Petter, Zlatka Dimitrova, Kurt Buchmann, E. Valtonen, Yde de Jong

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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Data Paper Wed, 17 Sep 2014 17:25:10 +0300
Fauna Europaea – all European animal species on the web https://bdj.pensoft.net/article/4034/ Biodiversity Data Journal 2: e4034

DOI: 10.3897/BDJ.2.e4034

Authors: Yde de Jong, Melina Verbeek, Verner Michelsen, Per de Place Bjørn, Wouter Los, Fedor Steeman, Nicolas Bailly, Claire Basire, Przemek Chylarecki, Eduard Stloukal, Gregor Hagedorn, Florian Wetzel, Falko Glöckler, Alexander Kroupa, Günther Korb, Anke Hoffmann, Christoph Häuser, Andreas Kohlbecker, Andreas Müller, Anton Güntsch, Pavel Stoev, Lyubomir Penev

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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Research Article Wed, 17 Sep 2014 16:28:32 +0300
Usage patterns of blue flower color representation by Encyclopedia of Life content providers https://bdj.pensoft.net/article/1143/ Biodiversity Data Journal 2: e1143

DOI: 10.3897/BDJ.2.e1143

Authors: Chantal-Marie Wright, Katja Seltmann

Abstract: Encyclopedia of Life (EOL) is a resource for community-driven biodiversity data, focusing on species information and images. Research into blue flowers to compare color ('blueness') at different elevations revealed that data content providers describe flowers as blue for any color hue in the range from blue to magenta. We propose methods for standardizing color values and color searching within EOL by means of an expanded color vocabulary and improved access to image metadata, in order to improve the research capacity of this valuable resource.

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Research Article Mon, 11 Aug 2014 09:45:36 +0300
Symbiota – A virtual platform for creating voucher-based biodiversity information communities https://bdj.pensoft.net/article/1114/ Biodiversity Data Journal 2: e1114

DOI: 10.3897/BDJ.2.e1114

Authors: Corinna Gries, Edward Gilbert, Nico Franz

Abstract: We review the Symbiota software platform for creating voucher-based biodiversity information portals and communities. Symbiota was originally conceived to promote small- to medium-sized, regionally and/or taxonomically themed collaborations of natural history collections. Over the past eight years the taxonomically diverse portals have grown into an important resource in North America and beyond for mobilizing, integrating, and using specimen- and observation-based occurrence records and derivative biodiversity information products. Designed to mirror the conceptual structure of traditional floras and faunas, Symbiota is exclusively web-based and employs a novel data model, information linking, and algorithms to provide highly dynamic customization. The themed portals enable meaningful access to biodiversity data for anyone from specialist to high school student. Symbiota emulates functionality of modern Content Management Systems, providing highly sophisticated yet intuitive user interfaces for data entry, batch processes, and editing. Each kind of content provision may be selectively accessed by authenticated information providers. Occupying a fairly specific niche in the biodiversity informatics arena, Symbiota provides extensive data exchange facilities and collaborates with other development projects to incorporate and not duplicate functionality as appropriate.

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Software Description Tue, 24 Jun 2014 08:44:39 +0300
The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth https://bdj.pensoft.net/article/1079/ Biodiversity Data Journal 2: e1079

DOI: 10.3897/BDJ.2.e1079

Authors: Cynthia S. Parr, Nathan Wilson, Patrick Leary, Katja Schulz, Kristen Lans, Lisa Walley, Jennifer Hammock, Anthony Goddard, Jeremy Rice, Marie Studer, Jeffrey Holmes, Robert Corrigan, Jr.

Abstract: The Encyclopedia of Life (EOL, http://eol.org) aims to provide unprecedented global access to a broad range of information about life on Earth. It currently contains 3.5 million distinct pages for taxa and provides content for 1.3 million of those pages. The content is primarily contributed by EOL content partners (providers) that have a more limited geographic, taxonomic or topical scope. EOL aggregates these data and automatically integrates them based on associated scientific names and other classification information. EOL also provides interfaces for curation and direct content addition. All materials in EOL are either in the public domain or licensed under a Creative Commons license. In addition to the web interface, EOL is also accessible through an Application Programming Interface. In this paper, we review recent developments added for Version 2 of the web site and subsequent releases through Version 2.2, which have made EOL more engaging, personal, accessible and internationalizable. We outline the core features and technical architecture of the system. We summarize milestones achieved so far by EOL to present results of the current system implementation and establish benchmarks upon which to judge future improvements. We have shown that it is possible to successfully integrate large amounts of descriptive biodiversity data from diverse sources into a robust, standards-based, dynamic, and scalable infrastructure. Increasing global participation and the emergence of EOL-powered applications demonstrate that EOL is becoming a significant resource for anyone interested in biological diversity.

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Software Description Tue, 29 Apr 2014 19:20:04 +0300
Open source data logger for low-cost environmental monitoring https://bdj.pensoft.net/article/1059/ Biodiversity Data Journal 2: e1059

DOI: 10.3897/BDJ.2.e1059

Authors: Ed Baker

Abstract: The increasing transformation of biodiversity into a data-intensive science has seen numerous independent systems linked and aggregated into the current landscape of biodiversity informatics. This paper outlines how we can move forward with this programme, incorporating real time environmental monitoring into our methodology using low-power and low-cost computing platforms.

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Software Description Tue, 11 Feb 2014 12:25:29 +0200
New records of Microgaster deductor Nixon, 1968 (Hymenoptera: Braconidae: Microgastrinae) for the Holarctic region, with comments on its historical distribution https://bdj.pensoft.net/article/1040/ Biodiversity Data Journal 2: e1040

DOI: 10.3897/BDJ.2.e1040

Authors: Jose Fernandez-Triana

Abstract: Four new localities for the species Microgaster deductor Nixon (1968) are recorded from the Nearctic (Canada and the United States) and the Palaearctic (Sweden), expanding significantly the range of the species. M. deductor seems to be widely distributed in boreal areas of the Holarctic, and it is characterized by unique morphological (tarsal claw structure) and molecular (COI) traits. Preliminary evidence, to be corroborated when more data is available, suggests that the species might have shifted northwards between 1950 and the present day.

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Taxonomy & Inventories Fri, 3 Jan 2014 13:31:00 +0200
Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data https://bdj.pensoft.net/article/1013/ Biodiversity Data Journal 1: e1013

DOI: 10.3897/BDJ.1.e1013

Authors: Pavel Stoev, Ana Komerički, Nesrine Akkari, Shanlin Liu, Xin Zhou, Alexander Weigand, Jeroen Hostens, Christopher Hunter, Scott Edmunds, David Porco, Marzio Zapparoli, Teodor Georgiev, Daniel Mietchen, David Roberts, Sarah Faulwetter, Vincent Smith, Lyubomir Penev

Abstract: We demonstrate how a classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. A cave-dwelling centipede, Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae), found in a remote karst region in Knin, Croatia, is the first eukaryotic species for which, in addition to the traditional morphological description, we provide a fully sequenced transcriptome, a DNA barcode, detailed anatomical X-ray microtomography (micro-CT) scans, and a movie of the living specimen to document important traits of its ex-situ behaviour. By employing micro-CT scanning in a new species for the first time, we create a high-resolution morphological and anatomical dataset that allows virtual reconstructions of the specimen and subsequent interactive manipulation to test the recently introduced ‘cybertype’ notion. In addition, the transcriptome was recorded with a total of 67,785 scaffolds, having an average length of 812 bp and N50 of 1,448 bp (see GigaDB). Subsequent annotation of 22,866 scaffolds was conducted by tracing homologs against current available databases, including Nr, SwissProt and COG. This pilot project illustrates a workflow of producing, storing, publishing and disseminating large data sets associated with a description of a new taxon. All data have been deposited in publicly accessible repositories, such as GigaScience GigaDB, NCBI, BOLD, Morphbank and Morphosource, and the respective open licenses used ensure their accessibility and re-usability.

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Taxonomy & Inventories Mon, 28 Oct 2013 06:30:00 +0200
EXIF Custom: Automatic image metadata extraction for Scratchpads and Drupal https://bdj.pensoft.net/article/973/ Biodiversity Data Journal 1: e973

DOI: 10.3897/BDJ.1.e973

Authors: Ed Baker

Abstract: Many institutions and individuals use embedded metadata to aid in the management of their image collections. Many deskop image management solutions such as Adobe Bridge and online tools such as Flickr also make use of embedded metadata to describe, categorise and license images. Until now Scratchpads (a data management system and virtual research environment for biodiversity)  have not made use of these metadata, and users have had to manually re-enter this information if they have wanted to display it on their Scratchpad site. The Drupal described here allows users to map metadata embedded in their images to the associated field in the Scratchpads image form using one or more customised mappings. The module works seamlessly with the bulk image uploader used on Scratchpads and it is therefore possible to upload hundreds of images easily with automatic metadata (EXIF, XMP and IPTC) extraction and mapping.

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Software Description Mon, 16 Sep 2013 09:00:00 +0300