Suchergebnisse

The Open Biodiversity Knowledge Management System (OBKMS) is an end-to-end, eXtensible Markup Language (XML)- and Linked Open Data (LOD)-based ecosystem of tools and services that encompasses the entire process of authoring, submission, review, publication, dissemination, and archiving of biodiversity literature, as well as the text mining of published biodiversity literature (Fig. 1). These capabilities lead to the creation of interoperable, computable, and reusable biodiversity data with provenance linking facts to publications. OBKMS is the result of a joint endeavour by Plazi and Pensoft lasting many years. The system was developed with the support of several biodiversity informatics projects - initially (Virtual Biodiversity Research and Access Network for Taxonomy) ViBRANT, and then followed by pro-iBiosphere, European Biodiversity Observation Network (EU BON), and Biosystematics, informatics and genomics of the big 4 insect groups (BIG4). The system includes the following key components: ARPHA Journal Publishing Platform: a journal publishing platform based on the TaxPub XML extension for National Library of Medicine (NLM)'s Journal Publishing Document Type Definition (DTD) (Version 3.0). Its advanced ARPHA-BioDiv component deals with integrated biodiversity data and narrative publishing (Penev et al. 2017). GoldenGATE Imagine: an environment for marking up, enhancing, and extracting text and data from PDF files, supporting the TaxonX XML schema. It has specific enhancements for articles containing descriptions of taxa ("taxonomic treatments") in the field of biological systematics, but its core features may be used for general purposes as well. Biodiversity Literature repository (BLR): a public repository hosted at Zenodo (CERN) for published articles (PDF and XML) and images extracted from articles. Ocellus/Zenodeo: a search interface for the images stored at BLR. TreatmentBank: an XML-based repository for taxonomic treatments and data therein extracted from literature. The OpenBiodiv knowledge graph: a biodiversity knowledge graph built according to the Linked Open Data (LOD) principles. Uses the RDF data model, the SPARQL Protocol and RDF Query Language (SPARQL) query language, is open to the public, and is powered by the OpenBiodiv-O ontology (Senderov et al. 2018). OpenBiodiv portal: Semantic search and browser for the biodiversity knowledge graph. Multiple semantic apps packaging specific views of the biodiviersity knowledge graph. Supporting tools: Pensoft Markup Tool (PMT) ARPHA Writing Tool (AWT) ReFindit R libraries for working with RDF and for converting XML to RDF (ropenbio, RDF4R). Plazi RDF converter, web services and APIs. As part of OBKMS, Plazi and Pensoft offer the following services beyond supplying the software toolkit: Digitization through imaging and text capture of paper-based or digitally born (PDF) legacy literature. XML markup of both legacy and newly published literature (journals and books). Data extraction and markup of taxonomic names, literature references, taxonomic treatments and organism occurrence records. Export and storage of text, images, and structured data in data repositories. Linking and semantic enhancement of text and data, bibliographic references, taxonomic treatments, illustrations, organism occurrences and organism traits. Re-packaging of extracted information into new, user-demanded outputs via semantic apps at the OpenBiodiv portal. Re-publishing of legacy literature (e.g., Flora, Fauna, and Mycota series, important biodiversity monographs, etc.). Semantic open access publishing (including data publishing) of journal and books. Integration of biodiversity information from legacy and newly published literature into interoperable biodiversity repositories and platforms (Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EOL), Species-ID, Plazi, Wikidata, and others). In this presentation we make the case for why OpenBiodiv is an essential tool for advancing biodiversity science. Our argument is that through OpenBiodiv, biodiversity science makes a step towards the ideals of open science (Senderov and Penev 2016). Furthermore, by linking data from various silos, OpenBiodiv allows for the discovery of hidden facts. A particular example of how OpenBiodiv can advance biodiversity science is demonstrated by the OpenBiodiv's solution to "taxonomic anarchy" (Garnett and Christidis 2017). "Taxonomic anarchy" is a term coined by Garnett and Christidis to denote the instability of taxonomic names as symbols for taxonomic meaning. They propose an "authoritarian" top-down approach to stablize the naming of species. OpenBiodiv, on the other hand, relies on taxonomic concepts as integrative units and therefore integration can occur through alignment of taxonomic concepts via Region Connection Calculus (RCC-5) (Franz and Peet 2009). The alignment is "democratically" created by the users of system but no consensus is forced and "anarchy" is avoided by using unambiguous taxonomic concept labels (Franz et al. 2016) in addition to Linnean names.

Nature-based solutions (NbS) have the potential to build climate resilience and tackle key societal challenges while also providing multiple co-benefits to biodiversity and human well-being. The demand for nature-based innovation is strongly felt in Malta – a small island state, with the highest population density in the European Union. Against this background, the Horizon 2020 project ReNature (Promoting research excellence in nature-based solutions for innovation, economic growth and human well-being in Malta) has the goal to enhance research excellence of the Malta College of Arts, Science and Technology (MCAST), as well as the national research, policy, business and stakeholder community. The six strategically designed training activities fostering capacity-building and research excellence, delivered during the first half of the project, resulted in useful learning outputs. These are twelve presentations, available as attachments to this article, which cover a large scope of topics related to the implementation of NbS. At a later stage, ReNature will publish another round of learning outputs, resulting from the rest of the training activities planned within the scope of the project.

Nature-based solutions (NBS) is a term often used to refer to adequate green infrastructure that provides multiple benefits to society whilst addressing societal challenges. They are defined as actions to protect, sustainably manage and restore natural or modified ecosystems that address societal challenges effectively and adaptively, simultaneously providing human well-being and biodiversity benefits. Malta, the smallest member state of the EU, has been characterised by rapid economic growth and urbanisation and Maltese citizens had the highest rate of exposure to pollution, grime or other environmental problems, in the EU. The project ReNature aims to establish and implement a nature-based solutions research strategy for Malta with a vision to promote research and innovation and develop sustainable solutions whilst improving human well-being and tackling environmental challenges. Here, we introduce the opening of ReNature collection of research articles in the Open Access Research Ideas and Outcomes (RIO) journal to publish unconventional research outputs and training materials. It will host key outputs relating to the sustainable use of biodiversity, biodiversity – ecosystem functioning, green infrastructure and ecosystem service assessments across rural-urban gradients, equitable access to the benefits derived from nature in cities and socio-environmental justice, payments for ecosystem services, and designing nature-based solutions.

The present paper describes policies and guidelines for scholarly publishing of biodiversity and biodiversity-related data, elaborated and updated during the Framework Program 7 EU BON project, on the basis of an earlier version published on Pensoft's website in 2011. The document discusses some general concepts, including a definition of datasets, incentives to publish data and licenses for data publishing. Further, it defines and compares several routes for data publishing, namely as (1) supplementary files to research articles, which may be made available directly by the publisher, or (2) published in a specialized open data repository with a link to it from the research article, or (3) as a data paper, i.e., a specific, stand-alone publication describing a particular dataset or a collection of datasets, or (4) integrated narrative and data publishing through online import/download of data into/from manuscripts, as provided by the Biodiversity Data Journal. The paper also contains detailed instructions on how to prepare and peer review data intended for publication, listed under the Guidelines for Authors and Reviewers, respectively. Special attention is given to existing standards, protocols and tools to facilitate data publishing, such as the Integrated Publishing Toolkit of the Global Biodiversity Information Facility (GBIF IPT) and the DarwinCore Archive (DwC-A). A separate section describes most leading data hosting/indexing infrastructures and repositories for biodiversity and ecological data.

Half of the European Union (EU) land and the livelihood of 10 million farmers is threatened by unsustainable land-use intensification, land abandonment and climate change. Policy instruments, including the EU Common Agricultural Policy (CAP) have so far failed to stop this environmental degradation. BESTMAP will: 1) Develop a behavioural theoretical modelling framework to take into account complexity of farmers' decision-making; 2) Develop, adapt and customize a suite of opensource, flexible, interoperable and customisable computer models linked to existing data e.g. LPIS/IACS and remote sensing e.g. Sentinel-2; 3) Link economic, individual-farm agent-based, biophysical ecosystem services and biodiversity and geostatistical socio-economic models; 4) Produce a simple-to-use dashboard to compare scenarios of Agri-Environmental Schemes adoption; 5) Improve the effectiveness of future EU rural policies' design, monitoring and implementation.

QC 20191128 ; EU Horizon 2020 ESMERALDA Project, Grant agreement No. 642007

Biodiversity is threatened on a global scale and the losses are ongoing. In order to stop further losses and maintain important ecosystem services, programmes have been put into place to reduce and ideally halt these processes. A whole suite of different approaches is needed to meet these goals. One major scientific contribution is to collate, integrate and analyse the large amounts of fragmented and diverse biodiversity data to determine the current status and trends of biodiversity in order to inform the relevant decision makers. To contribute towards the achievement of these challenging tasks, the project EU BON was developed. The project is focusing mainly on the European continent but contributes at the same time to a much wider global initiative the Group on Earth Observations Biodiversity Observation Network (GEO BON), which itself is a part of the Group of Earth Observation System of Systems (GEOSS). EU BON will build on existing infrastructures such as GBIF, LifeWatch and national biodiversity data centres in Europe and will integrate relevant biodiversity data from on-ground observations to remote sensing information, covering terrestrial, freshwater and marine habitats.A key feature of EU BON will be the delivery of relevant, fully integrated data to multiple and different stakeholders and end users ranging from local to global levels. Through development and application of new standards and protocols, EU BON will enable greater interoperability of different data layers and systems, provide access to improved analytical tools and services, and will provide better harmonized biodiversity recording and monitoring schemes from citizen science efforts to long-term research programs to mainstream future data collecting. Furthermore EU BON will support biodiversity science-policy interfaces, and facilitate political decisions for sound environmental management, also to help conserve biodiversity for human well-being at different levels, ranging from communal park management to the Intergovernmental Platform ...

Biodiversity is threatened on a global scale and the losses are ongoing. In order to stop further losses and maintain important ecosystem services, programmes have been put into place to reduce and ideally halt these processes. A whole suite of different approaches is needed to meet these goals. One major scientific contribution is to collate, integrate and analyse the large amounts of fragmented and diverse biodiversity data to determine the current status and trends of biodiversity in order to inform the relevant decision makers. To contribute towards the achievement of these challenging tasks, the project EU BON was developed. The project is focusing mainly on the European continent but contributes at the same time to a much wider global initiative the Group on Earth Observations Biodiversity Observation Network (GEO BON), which itself is a part of the Group of Earth Observation System of Systems (GEOSS). EU BON will build on existing infrastructures such as GBIF, LifeWatch and national biodiversity data centres in Europe and will integrate relevant biodiversity data from on-ground observations to remote sensing information, covering terrestrial, freshwater and marine habitats.A key feature of EU BON will be the delivery of relevant, fully integrated data to multiple and different stakeholders and end users ranging from local to global levels. Through development and application of new standards and protocols, EU BON will enable greater interoperability of different data layers and systems, provide access to improved analytical tools and services, and will provide better harmonized biodiversity recording and monitoring schemes from citizen science efforts to long-term research programs to mainstream future data collecting. Furthermore EU BON will support biodiversity science-policy interfaces, and facilitate political decisions for sound environmental management, also to help conserve biodiversity for human well-being at different levels, ranging from communal park management to the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES). Additionally, the project will strengthen European capacities and infrastructures for environmental information management and sustainable development. The following paper outlines the framework and the approach that is pursued.

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.

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.

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.

The world's forests have never been more threatened by invasions of exotic pests and pathogens, whose causes and impacts are reinforced by global change. However, forest entomologists and pathologists have, for too long, worked independently, used different concepts and proposed specific management methods without recognising parallels and synergies between their respective fields. Instead, we advocate increased collaboration between these two scientific communities to improve the long-term health of forests. Our arguments are that the pathways of entry of exotic pests and pathogens are often the same and that insects and fungi often coexist in the same affected trees. Innovative methods for preventing invasions, early detection and identification of non-native species, modelling of their impact and spread and prevention of damage by increasing the resistance of ecosystems can be shared for the management of both pests and diseases. We, therefore, make recommendations to foster this convergence, proposing in particular the development of interdisciplinary research programmes, the development of generic tools or methods for pest and pathogen management and capacity building for the education and training of students, managers, decision-makers and citizens concerned with forest health. ; The European Union's Horizon 2020 research and innovation programme ; http://neobiota.pensoft.net ; am2021 ; Biochemistry ; Forestry and Agricultural Biotechnology Institute (FABI) ; Genetics ; Microbiology and Plant Pathology

This Editorial presents the focus, scope and policies of the inaugural issue of Nature Conservation, a new open access, peer-reviewed journal bridging natural sciences, social sciences and hands-on applications in conservation management. The journal covers all aspects of nature conservation and aims particularly at facilitating better interaction between scientists and practitioners. The journal will impose no restrictions on manuscript size or the use of colour. We will use an XML-based editorial workflow and several cutting-edge innovations in publishing and information dissemination. These include semantic mark-up of, and enhancements to published text, data, and extensive cross-linking within the journal and to external sources. We believe the journal will make an important contribution to better linking science and practice, offers rapid, peer-reviewed and flexible publication for authors and unrestricted access to content. ; The journal Nature Conservation was established within the framework of the European Union's Framework Program 7 large-integrated project SCALES: Securing the Conservation of biodiversity across Administrative Levels and spatial, temporal, and Ecological Scales, www.scales-project.net (grant 226852; Henle et al. 2010).

The European Union (EU) Horizon 2020 Coordination and Support Action ESMERALDA aimed at developing guidance and a flexible methodology for Mapping and Assessment of Ecosystems and their Services (MAES) to support the EU member states in the implementation of the EU Biodiversity Strategy's Target 2 Action 5. ESMERALDA's key tasks included network creation, stakeholder engagement, enhancing ecosystem services mapping and assessment methods across various spatial scales and value domains, work in case studies and support of EU member states in MAES implementation. Thus ESMERALDA aimed at integrating various project outcomes around four major strands: i) Networking, ii) Policy, iii) Research and iv) Application. The objective was to provide guidance for integrated ecosystem service mapping and assessment that can be used for sustainable decision-making in policy, business, society, practice and science at EU, national and regional levels. This article presents the overall ESMERALDA approach of integrating the above-mentioned project components and outcomes and provides an overview of how the enhanced methods were applied and how they can be used to support MAES implementation in the EU member states. Experiences with implementing such a large pan-European Coordination and Support Action in the context of EU policy are discussed and recommendations for future actions are given.

The European Union (EU) Horizon 2020 Coordination and Support Action ESMERALDA aimed at developing guidance and a flexible methodology for Mapping and Assessment of Ecosystems and their Services (MAES) to support the EU member states in the implementation of the EU Biodiversity Strategy's Target 2 Action 5. ESMERALDA's key tasks included network creation, stakeholder engagement, enhancing ecosystem services mapping and assessment methods across various spatial scales and value domains, work in case studies and support of EU member states in MAES implementation. Thus ESMERALDA aimed at integrating various project outcomes around four major strands: i) Networking, ii) Policy, iii) Research and iv) Application. The objective was to provide guidance for integrated ecosystem service mapping and assessment that can be used for sustainable decision-making in policy, business, society, practice and science at EU, national and regional levels. This article presents the overall ESMERALDA approach of integrating the above-mentioned project components and outcomes and provides an overview of how the enhanced methods were applied and how they can be used to support MAES implementation in the EU member states. Experiences with implementing such a large pan-European Coordination and Support Action in the context of EU policy are discussed and recommendations for future actions are given. ; QC 20191008