Abstract: Research Ideas and Outcomes 9: e107220 DOI : 10.3897/rio.9.e107220 Authors : Dimitrios Koureas, Laurence Livermore, Eva Alonso, Wouter Addink, Ana Casino : The Distributed System of Scientific Collections (DiSSCo) is a new world-class Research Infrastructure (RI) for Natural Science Collections. The DiSSCo RI aims to create a new business model for one European collection that digitally unifies all European natural science assets under common access, curation, policies and practices that ensure that all the data is easily Findable, Accessible, Interoperable and Reusable (FAIR principles). DiSSCo represents the largest ever formal agreement between natural history museums, botanic gardens and collection-holding institutions in the world.DiSSCo entered the European Roadmap for Research Infrastructures in 2018 and launched its main preparatory phase project (DiSSCo Prepare) in 2020. DiSSCo Prepare is the primary vehicle through which DiSSCo reaches the overall maturity necessary for its construction and eventual operation. DiSSCo Prepare raises DiSSCo’s implementation readiness level (IRL) across the five dimensions: technical, scientific, data, organisational and financial. Each dimension of implementation readiness is separately addressed by specific Work Packages (WP) with distinct targets, actions and tasks that will deliver DiSSCo’s Construction Masterplan. This comprehensive and integrated Masterplan will be the product of the outputs of all of its content related tasks and will be the project’s final output. It will serve as the blueprint for construction of the DiSSCo RI, including establishing it as a legal entity.DiSSCo Prepare builds on the successful completion of DiSSCo’s design study, ICEDIG and the outcomes of other DiSSCo-linked projects such as SYNTHESYS+ and MOBILISE.This paper is an abridged version of the original DiSSCo Prepare grant proposal. It contains the overarching scientific case for DiSSCo Prepare, alongside a description of our major activities. HTML XML PDF PubDate: Thu, 1 Jun 2023 17:46:22 +0300
Abstract: DOI : 10.3897/arphapreprints.e107169 Authors : Wouter Addink, Niki Kyriakopoulou, Lyubomir Penev, David Fichtmueller, Ben Norton, David Shorthouse : United and coordinated efforts of biodiversity data infrastructures are needed to bring together various data forms from many different scientific areas. Biodiversity data are considered of great importance and use when they form a network of knowledge that can be seamlessly integrated and presented to various audiences, promoting both research and education. The Biodiversity Community Integrated Knowledge Library (BiCIKL) project seeks to maximise the potential of integrated data sources by striving to connect fragmented data derived from biological, paleontological, and geological specimens and collections, as well as all derived information such as literature in the form of taxonomic treatments, research papers etc., taxonomic information and molecular sequences provided by these infrastructures, under the umbrella of common digital practices and policies in curation, data sharing and open data access over different scientific fields. One of the main goals of BiCIKL is to create bi-directional links between various data types, a process enabled by: a) the adoption of globally unique and persistent identifiers upon agreement among all stakeholders, that link to digital specimen objects, collections, taxonomic treatments, people, sequence data and taxa, and b) implementation of the best practices for the generation, management and curation of interlinked data by the host infrastructures. At the same time, infrastructures should be readily discoverable and accessible by end users, providing data that enable re-usability. In this manual we give an overview of the best practices and their associated recommendations for infrastructures on making the most out of their services and data, for establishing a network of knowledge with other infrastructures, for servicing researchers, data providers and other end users. These guidelines have been developed in collaboration with the infrastructures through Technical RI Forum meetings organised in the context of the BiCIKL project. Practices and recommendations were divided into six categories: 1) modalities of access, 2) building communities and trust, 3) technology and standards, 4) versioning of APIs and their data, 5) bi-directional linking between infrastructures and 6) API design patterns and naming conventions. A second division into three user groups (Infrastructures, Data providers, Users e.g. Researchers, Developers and Citizen scientists) is presented in Appendix I. HTML XML PDF PubDate: Tue, 30 May 2023 09:51:32 +030
Abstract: DOI : 10.3897/arphapreprints.e107168 Authors : Wouter Addink, Sharif Islam, Mathias Dillen, Anton Güntsch, Soulaine Theocharides : Persistent Identifier (PID) systems are the foundation for achieving the FAIR Guiding Principles (“findable, accessible, interoperable and reusable”). As FAIR data and connecting different data classes (i.e. specimens, genomics, observations, taxonomy and publications) are essential aspects of the BiCIKL project, we need a PID system at least at the European level to create and maintain identifiers for the digital representation of specimens and samples, called Digital Specimens (DS) (Hardisty et al. 2022). The PID system provides the mechanism to ensure that identifiers are globally unique, persistent and resolvable. This system should also manage associated metadata, facilitate provenance, enable discovery, manage states and the life cycle of the PID, link to other derived data and digital content, and allow content providers to enforce metadata constraints. For the successful provision of a PID system, this design document has been created to guide us during the implementation and operation phases. The document is based on an earlier milestone (MS28) that was used for discussion and evaluation with potential end-users. HTML XML PDF PubDate: Tue, 30 May 2023 09:50:12 +030
Abstract: DOI : 10.3897/arphapreprints.e107167 Authors : Kessy Abarenkov, Allan Zirk, Guy Cochrane, Vishnukumar Kadhirvelu, Joana Pauperio, Olaf Bánki, Jerry Lanfear, Filipp Ivanov, Timo Piirmann, Raivo Pöhönen, Urmas Kõljalg : This deliverable report includes description of the work steps towards building a web interface for the reporting of errors and gaps in sequenced material source annotations as part of the Task 8.3 of BiCIKL. Beta version of the web interface has been published and is available for the registered users of PlutoF platform. HTML XML PDF PubDate: Tue, 30 May 2023 09:49:52 +030
Abstract: DOI : 10.3897/arphapreprints.e107166 Authors : Soulaine Theocharides, Niki Kyriakopoulou : Work package 11 of the BiCIKL project involves developing software tools to support a FAIR experience for members of the biodiversity research community. The package overall focuses on Findability, by providing tools to search and answer questions, and Accessibility, through developing links across various biodiversity data sources and research tools. Task 11.2 specifically involves prediction of new links using machine learning. We chose to demonstrate the functionality of machine learning link prediction with plant-pollinator interactions. This type of interaction was chosen due to the wealth of data available, particularly on the Global Biotic Interactions (GloBI) database, as well as this kind of interaction’s ecological and economic significance. The result was a RESTful API capable of predicting plant-pollinator interactions among a predefined set of species. Predictions are made on-the-fly, at the time of the request. The GitHub repository for the API can be found here: https://github.com/DiSSCo/BiCIKL_Linkages_APIThe API takes either a plant or a pollinator as inputs, and outputs potential matches based on a user-defined confidence score. The API’s prediction is powered by a random forest classifier stored on disk. The classifier was trained on the taxonomic hierarchy of observed plant-pollinator pairs obtained from the GloBI database. When evaluating the likelihood of an interaction, the trained classifier looks at the taxonomic hierarchy of both the plant and pollinator and outputs a confidence score. What pairs are returned is determined by the minimum confidence score set by the user. HTML XML PDF PubDate: Tue, 30 May 2023 09:39:22 +030
Abstract: Research Ideas and Outcomes 9: e105155 DOI : 10.3897/rio.9.e105155 Authors : Mathilde Bessert-Nettelbeck, Andreas Bischof, Ulrike Sturm, Emilia Nagy, Martina Schraudner, Julia Backhaus, Till Bruckermann, Susanne Hecker, Justus Henke, Karola Köpferl, Sabrina Kirschke, Christin Liedtke, Felix Mahr, Arne Maibaum, Audrey Podann, Wiebke Rössig, Martina Schäfer, Carolin Schröder, Philipp Schrögel, Victoria Shennan, Norbert Steinhaus, Mhairi Stewart, Vanessa van den Bogaert, Silke Voigt-Heucke : Citizen science, transdisciplinary research, dialogic forms of science communication or public engagement: these and other research approaches and fields, often subsumed under participatory research, have in common that they enable people outside of academia to actively engage in the production of scientific knowledge. However, each of these fields sets its own goals, uses different formats and has a different scope and impact. The conference 'Opportunities and Limitations of Participation in Academia' held in September 2022 as part of the German Science Year 'Participate!' aimed to connect the various participation communities in Germany and to explore commonalities and success factors. Through intensive discussions in four working groups, a keynote speech and a panel discussion, the conference initiated an exchange of ideas and experiences amongst researchers in a converging field. This report is a summary of the key questions and outcomes of the conference. HTML XML PDF PubDate: Mon, 29 May 2023 09:35:50 +030
Abstract: DOI : 10.3897/arphapreprints.e106475 Authors : Christos Arvanitidis, Alberto Basset, Thierry Carval, Katrina Exter, Nicola Fiore, Alessandra Giorgetti, Juan Miguel González-Aranda, Mark Hebden, Georgios Kotoulas, Joaquín López Lérida, Rory Meyer, Nikos Minadakis, Matthias Obst, Nicolas Pade, Christina Pavloudi, Marc Portier, Ioulia Santi, Dick Schaap, Peter Thijsse, Lucia Vaira, Cristina Huertas Olivares : This Science Project (SP) contributes to the estimation of the impacts of the invasive species on the European Biodiversity and Ecosystems. This topic is important for European Green Deal and the new European Biodiversity Strategy. The SP is also linked with the socio-economic issues because of the NIS implications to the local ecosystems and their services, and their societal goods and services. Since many of the above impacts may be of local scale, they may alter common practices in circular economies. The SP is implemented by: (a) Combining different sources of data and information; (b) Using a dual workflow to analyse the data; (c) Integrating its resources with core EOSC services and potentially horizontal services available; (d) Engaging the relevant scientific communities. The users will be able to: (a) Analyse distribution patterns of invasive species from different sources of data; (b) Compare the above patterns; (c) Provide managerial suggestions to relevant authorities; (d) Build on the existing infrastructure to address more complex questions (e.g. future scenarios). HTML XML PDF PubDate: Tue, 16 May 2023 10:15:00 +030
Abstract: DOI : 10.3897/arphapreprints.e106369 Authors : Christos Arvanitidis, Ron Dekker, Andreas Petzold, Niklas Blomberg, Giovanni Lamanna, Rudolf Dimper, Cristina Isabel Huertas Olivares, Ana Mellado, Matthew Viljoen, Sally Chambers, Montserrat González, Sophie Viscido : The Special Collection of articles on the Science Projects of the EOSC Future project, funded by the European Commission, refers to one of the essential components of the project. This editorial article explains how the Science Projects fit to the EOSC Future, the way their concept has been developed and evolved during the preparation and the implementation of the project and it also makes an introduction to the templates developed by the Science Projects as a plan to carry out their activities. HTML XML PDF PubDate: Mon, 15 May 2023 17:03:13 +030
Abstract: DOI : 10.3897/arphapreprints.e105599 Authors : Tom Breeze, Miguel Fernandez, Ian McCallum, Alejandra Morán-Ordóñez, Henrique Pereira, Jessi Junker : Financial factors are among the most widely cited bottlenecks around biodiversity monitoring but are relatively poorly studied, compared to monitoring methodologies. The existing body of literature on the cost-effectiveness of monitoring focuses heavily on the hypothetical costs of generating data rather than the practical realities of undertaking and managing monitoring. To address this we used a combination of surveys and semi-structured interviews with 67 biodiversity monitoring managers to provide an in-depth exploration of 1) what are the main rivers of their costs, 2) how different factors affect their cost-effectiveness in generating biodiversity monitoring data, 3) What is the scale and economic value of volunteer labor and 4) what are the main cost bottlenecks and spending priorities. Analysis of these responses demonstrates that monitoring efforts are able to generate more data at a lower cost when they have a) higher numbers of volunteers, b) greater densities of sites and c) monitor a wider range of taxa and habitats. Volunteer labour was worth millions of Euros to these organizations, sometimes more than their total costs. Total budgets and volunteer recruitment and retention were the main cost related bottlenecks among respondents, while staff recruitment was the highest priority for new spending. The results and discussion around them highlight the challenges faced by biodiversity monitoring organizations, particularly in recruiting and retaining qualified staff for the long-term. We produce a series of nine key messages and six recommendations for policy-markers and funders going forward. HTML XML PDF PubDate: Tue, 2 May 2023 12:30:00 +0300
Abstract: DOI : 10.3897/arphapreprints.e105600 Authors : Maria Dornelas, Cher Chow, Robert Patchett, Tom Breeze, Lluís Brotons, Pedro Beja, Laurence Carvalho, Ute Jandt, Jessi Junker, W. Daniel Kissling, Ingolf Kühn, Maria Lumbierres, Anne Lyche Solheim, Marit Mjelde, Francisco Moreira, Martin Musche, Henrique Pereira, Leonard Sandin, Roy Van Grunsven : The goal of this task was to identify and characterise novel methods for biodiversity monitoring, and to assess their suitability for large scale deployment across Europe. To address this goal we combined extensive literature searches with expert consultation, namely using a survey and through an online workshop. The outcome of our searches is summarised in a metadatabase, which includes 282 methods or method components, which have been classified according to EBV classes addressed, target taxa, and broad method type the method relates to. We then consulted experts within the EuropaBON network and beyond, on the advantages and challenges associated with each of these novel methods, as well as their technology readiness level. In combination, our approaches revealed a wealth of novel methods and a highly active research field, with extensive emerging innovation on several fronts. However, it also revealed high variability in technology readiness, with lack of validation being a prevalent hurdle yet to be overcome for many applications of these methods (i.e. for some taxa and in some environments). Moreover, the opportunities for expansion in observations created by these novel approaches open new challenges associated to the standardisation, integration and storage of biodiversity monitoring data. Finally, the expansion of observations should take a designed approach, in order to deliver on its potential to improve representation and resolution of biodiversity monitoring, and should aim to complement rather than replace human observations. HTML XML PDF PubDate: Tue, 2 May 2023 10:40:00 +0300
Abstract: Research Ideas and Outcomes 9: e99607 DOI : 10.3897/rio.9.e99607 Authors : Michael Boehmler, David DeMay, Adriane Rogers, Heidi Murray, Lawrence Hribar : The Florida Keys Mosquito Control District utilises dry ice-baited light traps to monitor mosquito populations on Key Largo, Florida. This paper describes the methodology of trapping, habitat description and dataset of adult mosquito populations from 18 years of weekly monitoring from a single site on Key Largo, Monroe County, Florida, USA.This paper details a previously unreported dataset derived from trap collections made on Key Largo, Florida at a site designated as “Gun Club Road.” HTML XML PDF PubDate: Mon, 24 Apr 2023 15:46:07 +030
Abstract: DOI : 10.3897/arphapreprints.e104881 Authors : David Kleijn, Ignasi Bartomeus, Vincent Bretagnolle, Kati Häfner, Felix Herzog, Jochen Kantelhardt, Erik Öckinger, Simon Potts, Giulia Riedo, Anna Sapundzhieva, Lena Luise Schaller, Nikol Yovcheva : Agricultural expansion and intensification are key drivers of biodiversity decline. There is mounting evidence that modern farming impacts the effectiveness of protected areas as one of the key instruments of biodiversity conservation through, for example, eutrophication, pesticide emissions or increasing access to remote areas [1]. This is increasingly acknowledged and in many countries conservation efforts now include farmed lands and engage farmers to enhance biodiversity on their lands. This benefits farmland biodiversity which, especially in Eurasia, supports some highly threatened species groups [2]. However, farmland biodiversity is also functionally important as it provides a wide range of ecosystem services. Examples are natural pest regulation, pollination, carbon sequestration, human well-being, water purification and cultural services. Agricultural management influences the provision of a wide range of ecosystem services and therefore, contributes to food security and mankind’s ability to sustain itself in the mid to long term. There is clear evidence that enhancing farmland biodiversity promotes the delivery of specific ecosystem services [3]. For example, enhancing wild pollinators and natural enemies through the provision of semi-natural habitat enhances productivity of many crops [4, 5]. However, only a few ecosystem services, such as pollination, pest control and nutrient cycling, may provide private benefits to farmers. Other services, such as carbon sequestration, biodiversity conservation, health benefits and water purification, are public goods which are poorly captured by markets [6]. HTML XML PDF PubDate: Thu, 13 Apr 2023 09:47:11 +030
Abstract: Research Ideas and Outcomes 9: e96576 DOI : 10.3897/rio.9.e96576 Authors : Osamudiamen Obasuyi : The sustainable development goals (SDGs) of providing universal health coverage for all and ending poverty by 2030 aim to make healthcare accessible and available for all, irrespective of status, gender or race. Unfortunately, access to universal healthcare is still hampered by preventable inequalities, especially amongst the Low-Middle income countries (LMICs).Cataracts are the leading cause of preventable blindness globally, affecting over 17 million people; 80% of these people reside in the LMICs and cost-effective cataract surgery is the only way to treat it. However, barriers exist that prevent access to cataract surgery amongst these people. Despite widespread reports of these barriers to cataract surgical access, the complex relationships between the barriers and cataract surgical access have yet to be fully explored by researchers or policy-makers.A randomised control trial involving three groups is proposed and presented in this paper to test the relationship between well-known barriers to cataract surgical access in resource-poor communities and programmes designed to overcome them. HTML XML PDF PubDate: Mon, 10 Apr 2023 09:16:19 +030
Abstract: Research Ideas and Outcomes 9: e101286 DOI : 10.3897/rio.9.e101286 Authors : Michael Boehmler, Heidi Murray, David DeMay, Adriane Rogers, Lawrence Hribar : The Florida Keys Mosquito Control District has used dry ice-baited light traps to monitor mosquito populations on Key Largo since 2003. This paper describes the methodology of trapping, the habitat and the dataset of adult mosquito populations from 18 years of weekly monitoring from a single site on Key Largo, Monroe County, FL, USA.This data paper provides previously unpublished data from a single trapping location in Key Largo, Florida. Two new species have been added to previously-published data from this trapping site. HTML XML PDF PubDate: Tue, 4 Apr 2023 17:16:06 +0300
Abstract: DOI : 10.3897/arphapreprints.e104251 Authors : Hannah Moersberger, Juliette G. C. Martin, Jessi Junker, Ivelina Georgieva, Joachim Maes, Ian McCallum, Henrique M. Pereira, Aletta Bonn : In order to assess user and policy needs related to biodiversity monitoring and data, the EuropaBON project invited national experts to fill in this survey in August 2021. The survey was tailored to the national level and aimed at identifying current monitoring efforts, data flows from collection to reporting, data uptake by policymaking, challenges and roadblocks, as well as biodiversity variables and indicators for a desirable future. On behalf of the European Commission (DG Environment) and EuropaBON, the surveys were sent out to all national focal points of the European Environment Information and Observation Network (Eionet) as well as key national agencies. Eionet is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries to gather and develop data, knowledge, and advice to policy makers about Europe's environment. The results of our surveys form the basis for the analysis of the EuropaBON User and Policy Needs Assessment ( DOI ) and inform the design of the Europa Biodiversity Observation Network and its work programme. We published the original responses of survey sections A and B in the annex of the User and Policy Needs Assessment. Responses of section C were synthesised in the assessment. HTML XML PDF PubDate: Tue, 4 Apr 2023 10:16:24 +0300
Abstract: DOI : 10.3897/arphapreprints.e104168 Authors : Hannah Moersberger, Juliette G. C. Martin, Jessi Junker, Ivelina Georgieva, Joachim Maes, Ian McCallum, Henrique M. Pereira, Aletta Bonn : In order to assess user and policy needs related to biodiversity monitoring and data, the EuropaBON project invited European experts to fill in this survey in August 2021. The survey was tailored to the European level and aimed at identifying current monitoring efforts, data flows from collection to reporting, data uptake by policymaking, challenges and roadblocks, as well as biodiversity variables and indicators for a desirable future. On behalf of the European Commission (DG Environment) and EuropaBON, the surveys were sent out to key European agencies (e.g., DG ENV, DG AGRI, DG CLIMA, EEA, Eurostat, Biodiversa+). The results of our surveys form the basis for the analysis of the EuropaBON User and Policy Needs Assessment ( DOI ) and inform the design of the Europa Biodiversity Observation Network and its work programme. We published the original responses of survey sections A and B in the annex of the User and Policy Needs Assessment. Responses of section C were synthesised in the assessment. HTML XML PDF PubDate: Fri, 31 Mar 2023 18:01:35 +030
Abstract: DOI : 10.3897/arphapreprints.e103765 Authors : Alejandra Morán-Ordóñez, Pedro Beja, Sara Fraixedas, Sergi Herrando, Jessi Junker, W. Daniel Kissling, Maria Lumbierres, Anne Lyche Solheim, Gabriel Miret, Jannicke Moe, Francisco Moreira, Henrique Pereira, Joana Santana, Dani Villero, Lluís Brotons : The EuropaBON project seeks to design a European Biodiversity Observation Network to monitor the status and trends of European biodiversity and ecosystems in the coming years. To accomplish this, the project has brought together biodiversity monitoring experts and other relevant stakeholders from various sectors (policy, NGO, academia, business, citizen science) from all over Europe. These have agreed on a list of 70 Essential Biodiversity Variables (Deliverable 4.1) that should enable tracking the progress of biodiversity-oriented policy instruments and provide information on changes in biodiversity at different levels. HTML XML PDF PubDate: Wed, 22 Mar 2023 09:46:21 +020
Abstract: DOI : 10.3897/arphapreprints.e103657 Authors : Joana Santana, Miguel Porto, Lluís Brotons, Jessi Junker, W. Daniel Kissling, Maria Lumbierres, Jannicke Moe, Alejandra Morán-Ordóñez, Henrique Pereira, Anne Lyche Solheim, Dani Villero, Francisco Moreira, Pedro Beja : The co-design of a European Observatory Observation Network requires information on the existing monitoring capacity in Europe, including the quantity and quality of the data available to generate the Essential Biodiversity Variables (EBVs) identified in Task 4.1 at the spatial- and temporal resolutions desired by users and policy. In this document, we provide a framework to identify the main monitoring gaps to produce European-wide EBVs. Specifically, we provide a detailed and spatially explicit information (country-level) on monitoring gaps for the production of 44 EBVs by analyzing the data flowing to current and past monitoring integration initiatives according to the defined criteria (country coverage; taxonomic/ecosystem coverage; standardized monitoring; time-series data; long-term monitoring; ongoing monitoring; sampling frequency; spatial coverage density; minimum sampling unit; raw data available). Results are presented in factsheets for each EBV and summarized across EBV classes and realms. HTML XML PDF PubDate: Tue, 21 Mar 2023 16:36:19 +020
Abstract: Research Ideas and Outcomes 9: e103675 DOI : 10.3897/rio.9.e103675 Authors : Tamara Heck, Isabel Steinhardt, Rima-Maria Rahal, Moritz Schubotz, Dominik Scholl, Sarah Behrens : HTML XML PDF PubDate: Tue, 21 Mar 2023 15:18:27 +020
Abstract: Research Ideas and Outcomes 9: e101006 DOI : 10.3897/rio.9.e101006 Authors : Anton Andreev, Grégoire Cattan, Sylvain Chevallier, Quentin Barthélemy : Quantum computing is a promising technology for machine learning, in terms of computational costs and outcomes. In this work, we intend to provide a framework that facilitates the use of quantum machine learning in the domain of brain-computer interfaces – where biomedical signals, such as brain waves, are processed.To this end, we integrated Qiskit, a well-known quantum library, with pyRiemann, a framework for the analysis of biomedical signals using Riemannian Geometry. In this paper, we describe our approach, the main elements of our implementation and our research directions. A key result is the creation of a standardised pipeline (QuantumClassifierWithDefaultRiemannianPipeline) for the binary classification of brain waves. The git repository reported in this paper also contains a complete test suite and examples to guide practitioners. We believe that this software will enable further research on the joint field of brain-computer interfaces and quantum computing. HTML XML PDF PubDate: Mon, 20 Mar 2023 09:46:20 +020
Abstract: Research Ideas and Outcomes 9: e102908 DOI : 10.3897/rio.9.e102908 Authors : Astrid de Mestier, Daniel Mulcahy, David J. Harris, Nadja Korotkova, Sarah Long, Eva Häffner, Alan Paton, Edmund Schiller, Frederik Leliaert, Jacqueline Mackenzie-Dodds, Tim Fulcher, Gunilla Stahls, Thomas von Rintelen, María P. Martín, Robert Lücking, China Williams, Christopher Lyal, Anton Güntsch, Heléne Aronsson, Magalie Castelin, Anna Pielach, Peter Poczai, Yolanda Ruiz-León, Isabel Sanmartin Bastida, Marco Thines, Gabriele Droege : The access to molecular collections worldwide greatly improves the quality of scientific research by making a growing number of data available for investigation. The efforts on digitisation also aim at facilitating the exchange of material between institutions and researchers that must follow regulations in place and respect best practice. The handbook presented here proposes a workflow to follow to safely exchange materials, in accordance with international laws and legislation. We make numerous recommendations here to help the institutions and researchers to navigate the legal and administrative procedures, in order to manage molecular collections in the best way possible. HTML XML PDF PubDate: Tue, 14 Mar 2023 15:09:30 +020
Abstract: DOI : 10.3897/arphapreprints.e103105 Authors : Carolina Corrales, Samantha Luciano, Jonas J. Astrin : Biobanks are curated collections of biological samples that are preserved at the molecular level, usually frozen, along with associated data, and managed to high scientific standards. We conducted a 'landscape analysis'—based both on a community survey and a literature review—to determine commonalities, information gaps, and challenges in the various workflows of biodiversity and environmental biobanks. The survey was completed by 55 institutions from more than 20 countries. Its results were compared to other collection-based surveys and complemented by literature research in the areas of general biobank management, staffing, sample handling, storage, (cryo-/)preservation, policies, databases, and networking. We illustrate the strengths and weaknesses of biodiversity and environmental biobanks and provide some basic recommendations for improving biobank procedures. In general, we found that increased efforts are needed to standardise biobank workflows or individual workflow components. While general, organism-independent biobanking guidelines already exist, more detailed guidance documents to date mostly address only human biobanking, or a narrow range of biodiversity. We hope to start closing that gap by providing an overview of current protocols and practices in biodiversity and environmental biobanking in form of a handbook, to which the present work is directly related. The handbook is available open-access under https://doi.org/10.3897/ab.e101876. HTML XML PDF PubDate: Tue, 14 Mar 2023 14:16:27 +020
Abstract: Research Ideas and Outcomes 9: e93859 DOI : 10.3897/rio.9.e93859 Authors : Alberto Bucciero, Emanuel Demetrescu, Bruno Fanini, Alessandra Chirivì, Francesco Taurino : In this article, we present an approach designed to extend the metadata schema of the Zenodo data management platform to strengthen the FAIRness of the published dataset. We focus on a bottom-up approach starting from a series of datasets ranging from the 3D digitalisation of monuments and sites to the creation of reconstructive records (including the scientific documentation they are based on), to the implementation of digital storytelling and to the development of open source-based web-apps. We propose the simplest possible set of metadata to be included in the Zenodo platform with the possibility, for the community, to adopt and further develop/modify them. This article will describe in detail the formalisation and the digital formats adopted providing the related metadata templates developed within the projects. HTML XML PDF PubDate: Fri, 10 Mar 2023 09:33:34 +020
Abstract: Research Ideas and Outcomes 9: e96744 DOI : 10.3897/rio.9.e96744 Authors : Duccio Migliorini, Marie-Anne Auger-Rozenberg, Andrea Battisti, Eckehard Brockerhoff, René Eschen, Jian-ting Fan, Hervé Jactel, Christophe Orazio, Trudy Paap, Simone Prospero, Lili Ren, Marc Kenis, Alain Roques, Alberto Santini : The use of sentinel woody plants in experimental plantings, Botanical Gardens and Arboreta has been experimentally validated as a tool for identifying possible unknown future threats prior to their introduction into new countries. Sentinel Plantings were recently established in Italy, France, Switzerland, China and South Africa, using a common experimental design. The plantings included various tree and shrub species of broadleaves and conifers. Two planting types were established, each with different objectives. In-patria plantings using native plants aim to estimate, in absence of any phytosanitary treatments, the associations and infestation rates of native insects susceptible to be exported to other countries with that particular commodity. Ex-patria plantings using non-native plants are relevant to identify native insect species capable of switching to the non-native plant that would otherwise be impossible to predict prior to its introduction. In the frame of the EU project HOMED, we have implemented this concept, widening the use of this tool simultaneously to many different countries and continents HTML XML PDF PubDate: Tue, 7 Mar 2023 08:21:44 +0200
Abstract: Research Ideas and Outcomes 9: e94851 DOI : 10.3897/rio.9.e94851 Authors : Gabriele Fahrenkrog, Lambert Heller, Ina Blümel : This paper aims to provide a structured overview of four open, participatory formats that are particularly applicable in inquiry-based teaching and learning contexts: hackathons, book sprints, barcamps, and learning circles. Using examples, mostly from the work and experience context of the Open Science Lab at TIB Hannover, we address concrete processes, working methods, possible outcomes and challenges.The compilation offers an introduction to the topic and is intended to provide tools for testing in practice. HTML XML PDF PubDate: Wed, 1 Mar 2023 09:46:37 +0200
Abstract: DOI : 10.3897/arphapreprints.e102613 Authors : Slavena Peneva, Kristina Hristova, Anna Sapundzhieva, Boris Barov, Pavel Stoev, Margarita Grudova, Iva Kostadinova : This document presents BiCIKL’s recognizable visual identity, including the project logo, visual identity guide, brochure, poster, document, presentation templates and website design and functionality developed in the first three months. These materials will ensure that BiCIKL is communicated effectively and professionally with the aim to raise awareness and build a community from the start of the project.The modern and user-friendly public website (bicikl-project.eu) provides an easy-to-navigate, continuously updated platform allowing fast access to general information about BiCIKL and its activities, operating on several levels. It also prominently features the participating project partners and Research Infrastructures and their extensive service portfolio. HTML XML PDF PubDate: Fri, 24 Feb 2023 16:50:06 +020
Abstract: DOI : 10.3897/arphapreprints.e102612 Authors : Lyubomir Penev, Mariya Dimitrova, Georgi Zhelezov, Teodor Georgiev : To the best of our knowledge, OpenBiodiv is the first production-stage semantic system running on top of a reasonably-sized biodiversity knowledge graph. It stores biodiversity data in a semantic interlinked format and offers facilities for working with it (Senderov et Penev 2016, Senderov et al. 2018, Penev et al. 2019, Dimitrova et al. 2021). It is a dynamic system that continuously updates its database as new biodiversity information becomes available by several international biodiversity publishers. It also allows its users to ask complex queries via SPARQL (a query language for semantic graph databases) and a simplified semantic search interface.OpenBiodiv was created during two EU-funded Marie Sklodowska-Curie PhD projects: BIG4 (Grant Agreement No 642241) and IGNITE (Grant Agreement No 764840). During those projects, the backend Ontology-0, the first versions of RDF converters and the basic website functionalities have been created (see Dimitrova et al. 2021 for overview).After the start of the BiCIKL project, the entire workflow for processing and RDF conversion of full-text articles in XML and Plazi’s treatments in XML has been re-built using up-to-date technological solutions (such as Apache Kaka and Elasticsearch) to fully automatise and speed up the conversion process and to make it trackable and efficient. As a result, the entire graph content has been re-processed and indexed. New user applications described in Milestone MS27 App specifications have been discussed and implemented.The present deliverable describes the newly built workflow and tools for data extraction, conversion and indexing and the user applications, created in the BiCIKL project. HTML XML PDF PubDate: Fri, 24 Feb 2023 16:49:01 +020
Abstract: DOI : 10.3897/arphapreprints.e102609 Authors : Lyubomir Penev, Teodor Georgiev, Boris Barov, Pavel Stoev, Kristina Hristova : The main goal of the BiCIKL project is to improve, for the first time, seamless access, linking and usage tracking of data within a network of Research Infrastructures managing different data classes (literature, specimens, samples, occurrences, sequences, taxon names and Operational Taxonomic Units (OTU)), ultimately represented also in a biodiversity knowledge graph. To achieve this, the consortium members will operate with huge amount of data during and after the end of the project.As a Horizon 2020 project, BiCIKL conforms to the Open Research Data Pilot (ORDP)1 and Article 29.3 of the H2020 Model Grant Agreement by default, hence the consortium aims to improve and maximise access, sharing, linking and reuse of FAIR Open Research Data (ORD), generated or managed by the project. A detailed Data Management Plan is a critical part of the ORDP. The DMP described in the present document is developed in BiCIKL within the first six months of the project and it will evolve as a “living document” during the lifetime of the project and beyond in order to present the status of the project's reflections on data management.The BiCIKL DMP outlines the handling of research data and provides the basis of the project consortium’s data management life cycle for the data collected, generated and processed by the participants in the project. The DMP also covers the methodologies and standards previously developed for data sharing and open access, curation and preservation. The subject of the DMP is the management of research data. Personal data management is covered by deliverable D9.1 Protection of Personal Data.The BiCIKL DMP was developed in close collaboration with all project partners and involved Research Infrastructures (RI) who provided information on their data management practices and policies in a questionnaire and planned generation, collection, and processing of data for the purposes of building a resilient data management strategy of the project which meets all criteria for open research.This DMP aims to adhere to the FAIR (Findable, Accessible, Interoperable, Reusable) data management criteria of Horizon 20202. HTML XML PDF PubDate: Fri, 24 Feb 2023 16:46:45 +020
Abstract: DOI : 10.3897/arphapreprints.e102530 Authors : Jessi Junker, Pedro Beja, Lluís Brotons, Miguel Fernandez, Néstor Fernández, W. Daniel Kissling, Maria Lumbierres, Anne Lyche Solheim, Joachim Maes, Alejandra Morán-Ordóñez, Francisco Moreira, Martin Musche, Joana Santana, Jose Valdez, Henrique Pereira : EuropaBON harnesses the power of modelling Essential Biodiversity Variables (EBVs) to integrate different reporting streams, data sources, and monitoring schemes, and measure biodiversity change across multiple dimensions in space and time. Therefore, EBVs are at the core of the project and form the basis for several of the tasks feeding into the co-design of a biodiversity monitoring system for Europe. In this document, we describe the stepwise process of identifying and specifying the EBVs in the EBV list presented in this deliverable. We further provide a summary of the characteristics of the EBVs identified for EuropaBON, in terms of their desired spatial- and temporal resolutions, as well as the taxonomic/ ecosystem scope to be measured. HTML XML PDF PubDate: Fri, 24 Feb 2023 16:31:19 +020
Abstract: Research Ideas and Outcomes 9: e101455 DOI : 10.3897/rio.9.e101455 Authors : Per Gundersen, Т. Martijn Bezemer, Sebastian Rojas, Leho Tedersoo, Lars Vesterdal, Inger Schmidt : Afforestation is proposed as one of the most effective climate solutions for carbon sequestration. As a majority of threatened species are linked to forests, afforestation can also contribute to mitigate the biodiversity crisis. There is however a caveat: the agricultural legacy (high nutrient availability, altered soil biota structure and function) of new forests constrains the development of forest-adapted species, affects tree growth and stability, and delays environmental benefits from afforestation.We hypothesize that inoculation of former arable land with soil (including microbiome, fauna and seeds/rhizomes of understory vegetation) from old forests along with targeted tree species mixtures will improve productivity and more rapidly restore forest-adapted communities. This will ultimately result in diverse, stable and resilient multifunctional forests.We will test this hypothesis and develop applied inoculation methods by: i) exploring soil biota and benchmarking biodiversity in existing afforestation research Chronosequence platforms (chronosequences and sites with increasing distance to other forests); ii) conducting inoculation experiments in mesocosms to measure seedling performance and, above- and belowground linkages; iii) establishing field-scale inoculation experiments in new and existing afforestations to test short- and long-term inoculation success on forest productivity, biodiversity and soil functioning at the ecosystem scale; iv) incorporating the landscape context into guidelines and tools for spatially explicit prioritization of areas for assisted dispersal.The aims are to resolve barriers for successful restoration and develop landscape-scale afforestation strategies that optimize productivity and biodiversity for the planning and implementation of green infrastructure; and produce basic knowledge on the tree, understory vegetation, soil fauna and microbiome nexus and its effect on forest productivity, biodiversity and soil functions (N-retention, C-sequestration, methane uptake). HTML XML PDF PubDate: Mon, 20 Feb 2023 15:18:21 +020
Abstract: DOI : 10.3897/arphapreprints.e102047 Authors : Serena Rasconi : The fist hybrid meeting and workshop of the COST Action “Applications for zoosporic parasites in aquatic systems” was held from 4th to 7th of July 2022 at the Multifunctional Center for Social Activities and Welfare of the Larnaka Municipality in Larnaca, Cyprus. 22 participants from 11 countries and 15 institutions attended on site, 26 participants from 9 countries and 26 institutions attended online. The activities included presentations, open discussions and collaborative work.This report presents the results of the feedback survey send to participants after the event. The survey was anonymous and included multiple choice responses (checkboxes) and short answers to complete and provide arguments to the checkboxes answers. 16 surveys were collected from the 54 participants, 13 from onsite and 3 from virtual attendees. Based on feedbacks and comments from the participants, the report will also include some considerations on challenges and advantages of mixed events.The report will contribute to set-up an active network and effective communication strategy for ParAqua, by describing advantages and limitations of different settings based on the Action experience and provide tips and hints to foster collaboration and effective work in hybrid mode. HTML XML PDF PubDate: Mon, 20 Feb 2023 12:04:15 +020
Abstract: DOI : 10.3897/arphapreprints.e101949 Authors : W. Daniel Kissling, Maria Lumbierres : This document will form the basis for the EuropaBON virtual workshop on EBV workflows (22-24 February 2023) and for developing the co-design of the European Biodiversity Observation Network. HTML XML PDF PubDate: Tue, 14 Feb 2023 15:09:24 +020
Abstract: DOI : 10.3897/arphapreprints.e101543 Authors : Oliver Barić : Since the creation of ParAqua social media pages, the number of page likes and follows has been tracked. After reaching a sufficient number of followers, an analysis was performed to begin the tracking of meaningful metrics. For Facebook and Instagram, an integrated analytics tool was used, and for Twitter and LinkedIn the metrics are analyzed in less detail since no integrated analytics tools were available. The role of each social media platform was discussed depending on the platform`s characteristics, dominant groups among the followers, and strategies applied by other organizations.A list was made containing conferences and workshops in the near future. The scientific interests of the Action members have been taken into consideration while creating the list, so it contains a somewhat broad specter of events, but is still related to the Action`s mission. Only those events whose deadline for submission hasn’t passed were selected. The conferences are divided into two tables depending on whether they are taking place in or outside of Europe and arranged in chronological order. HTML XML PDF PubDate: Wed, 8 Feb 2023 11:46:45 +0200
Abstract: DOI : 10.3897/arphapreprints.e101323 Authors : Matthew J Allan, Robin Dean, Alexandra-Maria Klein, Dimitry Wintermantel, Matthias Albrecht, Janine Schwarz, Anina Knauer : Under the terms of the PoshBee agreement, the members tasked with delivering Work Package 7 carried out semi-field and field studies on honey bees, bumble bees and solitary bees. These studies involved the exposure of the bees to more than one stressor, for example a fungicide and an insecticide or a fungicide and a nutritional deficiency. This is in contrast to the conventional study design where one stressor or product alone is assessed.These studies built upon recommendations by the European and Mediterranean Plant Protection Organisation (EPPO), European Food Safety Authority (EFSA), Prevention of Honeybee Colony Losses (COLOSS), and the Organisation of Economic Co-operation and Development (OECD). The team of researchers incorporated several innovative approaches in designing and carrying out the studies. In the authors’ view both the quality and quantity of data required for ecotoxicology studies can be improved by adoption of novel methods, including electronic means and artificial intelligence, and the design, manufacture and use of equipment specifically for such studies. Several examples are described.It is the intention of the team to include in this document practical advice for workers who are not familiar with such studies. HTML XML PDF PubDate: Mon, 6 Feb 2023 10:31:16 +0200
Abstract: Research Ideas and Outcomes 9: e96476 DOI : 10.3897/rio.9.e96476 Authors : Étienne Serbe-Kamp, Jens Bemme, Daniel Pollak, Katja Mayer : Citizen Science or community science has been around for a long time. The scope of community involvement in Citizen Science initiatives ranges from short-term data collection to intensive engagement to delve into a research topic together with scientists and/or other volunteers. Although many volunteer researchers have academic training, it is not a prerequisite for participation in research projects. It is important to adhere to scientific standards, which include, above all, transparency with regard to the methodology of data collection and public discussion of the results, and open educational resources (OER). Hereby, Citizen Science is closely linked to Open Science. In our contribution, we will introduce two projects, both developed within the Wikimedia Fellowship Freies Wissen.The top-down approach: ERGo! An Entomology Research Tool to raise awareness of biodiversity protection.Inclusion in academia and pressing social problems such as climate change are fundamentally social justice issues. To facilitate early participation in the scientific process on the part of people holding underrepresented identities in science, we develop a Citizen Science initiative based on a low-cost open-source platform (ERGo!) to perform a technique for electrical recordings from insect eyes known as electroretinograms (ERGs) while presenting visual stimuli. Pasadena Unified School District High School students pilot ERG experiments to test the feasibility of this technique as a large-scale Citizen Science initiative. With ERGo!, future Citizen Scientists contribute data to cutting-edge research that monitors insect biodiversity, adaptation, and health in rapidly changing environments caused by monocultures, pesticides, and climate change.The bottom-up approach: Open cultural data collection. A Citizen Science initiative for regional knowledge curation.We catalogued the 18th century German magazine ‘Die Gartenlaube’ (in Wikisource) with bibliographic metadata in Wikidata in a project called ‘Die Datenlaube’. We develop collaborative approaches for linked open data methods to produce data sets about historical knowledge. The concept of ‘Open Citizen Science’ offers a methodological baseline for Open Science practises in fields of digital humanities. Scanned documents and structured open metadata revealed open access to historic collections. Through the Wikimedia platforms 'Die Datenlaube' creates possibilities to edit entries, to design own investigations, and to contribute to OER.Based on the elaboration of the two rather different projects (natural and social sciences, involvement of pupils vs citizens, top-down vs bottom-up), we will discuss similarities and hence the challenges and lessons learned for using and developing Open Science elements in Citizen Science and mutual learning. Furthermore, we will conclude by focusing on the opportunities resulting from the integration of societal expectations in science and vice versa. HTML XML PDF PubDate: Mon, 23 Jan 2023 09:49:48 +020
Abstract: DOI : 10.3897/arphapreprints.e99679 Authors : Elena Velado-Alonso, Ignasi Bartomeus, Kira Keini, Suresh Chithathur, Anna Sapundzhieva, Alexandra Korcheva, David Kleijn : Communication and dissemination are key elements to maximise SHOWCASE project impact and ensure long‐term effects. For that, an effective communication strategy is essential to convey the principles and best practices to integrate biodiversity in farm management to favour farmers’ livelihoods while promoting conservation in agricultural landscapes. Current discourses around biodiversity, nature conservation and farming are contradictory with each other and not always engaging for SHOWCASE stakeholders. Thus, an inspirational narrative has been developed in the first months of the project by WP4 “Communicating the benefits of agrobiodiversity through multistakeholder knowledge exchange”, task 4.1. SHOWCASE narrative explains in an effective manner 1) why people care about biodiversity; 2) what we can do, and; 3) how we can do it better. HTML XML PDF PubDate: Mon, 16 Jan 2023 10:38:37 +020
Abstract: Research Ideas and Outcomes 9: e85860 DOI : 10.3897/rio.9.e85860 Authors : Felicitas Kruschick, Kerstin Schoch : Knowledge equity is a broad concept. Although it is linked to the goals of Open Science, it is rarely discussed in the scientific community. The term refers to a variety of aspects such as epistemology, research methods, data analysis, inclusive education, equal representation, participation, and science communication. It is reflected on individual, institutional, and structural levels.In this article, we attempt to outline the field theoretically against the background of a power-theoretical perspective and discuss what knowledge is in the first place. In a second step, we explore the question of what is hidden behind the terms equality and equity and to what extent these concepts can be linked to the underlying concept of knowledge. When can we speak of equity, why, and to what extent' Finally, the article links the overall social development of increasing sensitivity to diversity, which is discussed in conjunction with inclusive education and inclusion in general. Herein we refer to concepts of intersectional feminist research, the principles of Open Science, and a critical perspective on the concept of diversity.For illustration, exemplary projects associated with the Open Science Fellow Program, which address the issue of marginalized groups in the research process, are described. Among others, these relate to the following focal points: Data collection of non-binary gender, awareness of adultism, collaborative interpretation with interviewees, queer narratives, diversity in editorial boards, research in the context of North-South relations, participatory science communication using art, and exclusion factors of science communication.The overarching question we ask in this article is the extent to which knowledge equity is relevant to marginalized groups and exclusive dynamics in terms of an inclusive rationale and how those dynamics can be identified by using critical perspectives and self-reflexive considerations. HTML XML PDF PubDate: Mon, 16 Jan 2023 09:38:07 +020
Abstract: Research Ideas and Outcomes 9: e95174 DOI : 10.3897/rio.9.e95174 Authors : Oliver Keller, Stefan Appelhoff, Benjamin Paffhausen, Tobias Wenzel : The promise of open hardware as a branch of open science is a sustainable change of research instrumentation towards more openly documented and licensed designs. Methods, code, and data are already valued by journal editors and peer-reviews to judge if a study's result can be replicated with the information provided in a manuscript. The open hardware movement seeks to include laboratory tools and research instrumentation into the same category. Availability of and access to open hardware equipment are set to democratize professional lab work and field studies as well as enhance the transferability of methods to civic science settings. Here, we report four case studies from the first five years of the Wikimedia Program "Free Knowledge", an open science fellowship funded by Wikimedia Germany and partners. The project developers discuss and evaluate the impact related to key aspects typically attributed with open hardware: costs, availability, adaptability, community and educational value. The open hardware projects covered in this review span from natural sciences to life sciences to education. HTML XML PDF PubDate: Wed, 4 Jan 2023 11:07:22 +0200
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