DOI: 10.3897/rio.11.e176476

Authors: Tina Heger, Stella Berger, Jonathan Jeschke, Chris Kittel, Peter Kraker, A. Makower, Daniel Mietchen, Jens Nejstgaard, Maxi Schramm

Abstract: Water is vital for life on Earth, but aquatic environments worldwide are facing critical challenges that cause severe problems for biodiversity and human well-being. These challenges include, for example, water pollution, habitat degradation, escalating water and air temperatures, salinisation of freshwaters, ocean acidification and invasive species. Since these stressors interact in complex ways, developing predictions and mitigation measures is difficult. Mesocosm experiments, offering controlled, yet realistic settings, are crucial for understanding and mitigating the impact of various stressors and their combinations on aquatic ecosystems. Mesocom facilities are key Research Infrastructures (RI), as they bridge the gap between laboratory experiments and natural systems allowing studies of highly complex environments comparable to natural ecosystems, while still offering controlled and replicated settings not available in natural systems.The AQUACOSM-RI consortium, comprising over 60 individual state-of-the-art mesocosm facilities at 28 host institutions across Europe, has therefore been instrumental in advancing aquatic environmental research across climate zones including marine, brackish and freshwater ecosystems. In addition, the EU H2020-INFRAIA projects AQUACOSM (CORDIS No. 731065) and AQUACOSM-plus (CORDIS No. 871081, www.aquacosm.eu) have developed a virtual network beyond Europe of presently > 85 host institutions with > 120 aquatic mesocosm facilities around the world, www.mesocosm.org. However, the rich, yet disconnected resources in aquatic mesocosm-based experimental research and mitigation approaches need to be combined in a modern, visible and accessible way.The project AQUANAVI (Navigating Grand Challenges and their Mitigation using Aquatic Experimental RIs) aims to enhance existing efforts by creating an interactive atlas of aquatic mesocosm facilities and related mesocosm-based experimental research. Integrating data, publications, reports and information on mesocosm facility capacities generated by the AQUACOSM consortium and other mesocosm facilities in Europe and beyond, AQUANAVI will facilitate fast discovery of resources and unused potentials of available mesocosm facilities in a modern, visible and accessible way that is presently not available. Such a multidimensional tool is expected to enable novel collaborations and a much faster setup and execution of connected and/or distributed experiments and efficient development of environmental mitigation strategies. Built upon the AQUACOSM-RIs and their encompassing data and information repository as well as scientific and technical competence, while also leveraging related infrastructures like AnaEE, EMBRC, JERICO-RI and eLTER, AQUANAVI will provide a comprehensive resource platform to more effectively explore available resources for aquatic experimental research.AQUANAVI will bridge this wealth of scientific data, expertise and mesocosm facility information through Hi Knowledge, an innovative analysis and visualisation platform that merges Wikidata, Open Knowledge Maps,and Scholia. Hi Knowledge harnesses the semantic capabilities of Wikidata to rapidly construct a FAIR and open corpus for a domain, based on a sophisticated conceptual classification system. Subsequently, Hi Knowledge incorporates visualisation components from Open Knowledge Maps and Scholia, allowing researchers to smoothly navigate information using cutting-edge visualisation techniques, artificial intelligence and knowledge synthesis methods.Open and collaborative by design, AQUANAVI’s architecture will engage a broad range of research communities. By consolidating data and information from diverse RIs, the platform will leverage and enhance the AQUACOSM and related research infrastructures, securing the reusability and interoperability of existing data collections and better exploration of existing RIs in the future. Compliant with FAIR principles and EOSC requirements, AQUANAVI will ensure the long-term sustainability and openness of its resources, enriching both the ENVRI services portfolio and the broader scientific community. In summary, AQUANAVI will empower researchers and stakeholders to implement measures to mitigate the effects of climate change and other Grand Challenges facing aquatic environments, serving as a key resource within and beyond the European research area.

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DOI: 10.3897/rio.11.e163815

Authors: Gonzalo Bravo, Gregorio Bigatti, Mariana Lozada, Luke Thompson, Juan Livore, María Mendez, Lorena Arribas, Lino Bigatti, Tyler Christian, Erasmo Macaya, Edgardo Londoño-Cruz, Nicolas Moity, Juan Cruz-Motta, Augusto Flores, Gabriela Vélez-Rubio, Maria Palomo, Cesar Cordeiro, Franciane Pellizzari, Maritza Cárdenas-Calle, La Daana Kanhai, Ivonne Vivar Linares, Patricia Gil-Kodaka, Linsey Martinez, Pablo Sugliano, Agostina Trigo, Juan Zottola, Dulce Blanco, Matias Tricase, Nadia Bravo, Mariana Degrati, Camila Tavano Formigo, Frank Muller-Karger, Enrique Montes

Abstract: The Marine Biodiversity Observation Network Pole to Pole of the Americas (MBON Pole to Pole) brought together 30 participants from 10 countries in Patagonia, Argentina, to strengthen observing capacity of coastal biodiversity across the Americas. The network held a five-day workshop focused on three core components: standardized rocky intertidal photo-quadrat surveys, low-cost environmental DNA (eDNA) sampling, and affordable plankton imaging tools. Participants included researchers, park rangers, and conservation practitioners fostering a collaborative and inclusive environment. Key outcomes included field validation of protocols, identification of context-specific methodological adaptations (e.g., for low tidal amplitude areas), adoption of novel tools for monitoring marine life, and strategies for broader participation and data harmonization. The workshop highlighted the potential of simple, replicable methods to support long-term monitoring, and emphasized the value of shared protocols, tools, and open data for building a more connected and resilient regional observation network.

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DOI: 10.3897/arphapreprints.e157339

Authors: Soulaine Theocharides, Sam Leeflang, Wouter Addink, Sharif Islam

Abstract: Biodiversity research relies on physical specimens stored in natural science collections, which serve as enduring reservoirs of data about organisms and their environments. However, these reservoirs remain siloed. The concept of Digital Specimen addresses the challenges posed by the vast amount of disconnected digital biodiversity data available today. The existing approach involves converting analogue records into digital replicas stored in local databases, leading to isolated and fragmented datasets that are difficult to integrate and utilise efficiently. The Digital Specimen aims to overcome this by establishing an interconnected network of digital objects on the Internet. Digital Specimens are FAIR Digital Objects (FDOs), structured digital entities that adhere to the FAIR principles: Findable, Accessible, Interoperable, and Reusable. FDOs have the potential to enhance the accessibility and interoperability of data from natural science collections by providing unique identifiers, descriptive metadata, and defined operations. DiSSCo utilises the FDO framework to enhance the accessibility and interoperability of biodiversity research data from natural science collections. FDOs facilitate seamless data exchange by providing structured digital objects with unique identifiers, descriptive metadata, and defined operations. As part of making Digital Specimens FDOs, DiSSCO implemented FDO records, metadata records associated with a Persistent Identifier, which further enable machine actionability. A Digital Object repository was developed for the purposes of storing and acting upon digital specimens. Three technological pillars compose the repository: a relational database stores the latest version of the digital specimen and is used for retrieving specimens by their identifier; an indexing solution provides full search capabilities on digital specimens; and a document store holds previous versions of a digital specimen for provenance purposes. There are three ways a user may interact with the digital object repository: a REST API; a user-friendly web portal; and a DOIP server.To ingest data from multiple source systems, a harmonised data model was developed, called OpenDS. Built upon existing international standards like DarwinCore and ABCD, OpenDs accommodates complex structures necessary to capture information about multiple taxonomic identifications, events, agents, and relationships to other data sources. DiSSCo has decided to adapt the GBIF Unified Model (UM) for specimen data, ensuring interoperability and avoiding the development of potentially competing standards. By aligning with the GBIF UM, DiSSCo enhances interoperability with GBIF and promotes the establishment of a unified data modelling standard within the biodiversity community, facilitating seamless data exchange and integration with data aggregators like GBIF.

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DOI: 10.3897/rio.10.e134825

Authors: Tom August, Mario Balzan, Paul Bodesheim, Gunnar Brehm, Lisette Cantú-Salazar, Sílvia Castro, Joseph Chipperfield, Guillaume Ghisbain, Alba Gomez-Segura, Jérémie Goulnik, Quentin Groom, Laurens Hogeweg, Chantal Huijbers, Andreas Kamilaris, Karolis Kazlauskis, Wouter Koch, Dimitri Korsch, João Loureiro, Youri Martin, Angeliki Martinou, Kent McFarland, Xavier Mestdagh, Denis Michez, Charlie Outhwaite, Luca Pegoraro, Nadja Pernat, Lars Pettersson, Pavel Pipek, Cristina Preda, David Rolnick, Tobias Roth, David Roy, Helen Roy, Veljo Runnel, Martina Sasic, Dmitry Schigel, Julie Sheard, Cecilie Svenningsen, Heliana Teixeira, Nicolas Titeux, Thomas Tscheulin, Elli Tzirkalli, Marijn van der Velde, Roel van Klink, Nicolas Vereecken, Sarah Vray, Toke Thomas Høye

Abstract: The InsectAI COST action will support insect monitoring and conservation at the national and continental scale in order to understand and counteract widespread insect declines. The Action will bring together a critical mass of researchers and stakeholders in image-based insect AI technologies to direct and drive the research agenda, build research capacity across Europe and support innovation and application.There is mounting evidence that populations of insects around the world are in sharp decline. Understanding trends in species and their drivers is key to knowing the size of the challenge, its causes and how to address it. To identify solutions that lead to sustainable biodiversity alongside economic prosperity, insect monitoring should be efficient and provide standardised and frequently updated status indicators to guide conservation actions.The EU Biodiversity Strategy 2030 identifies the critical challenge of delivering standardised information about the state of nature and image-based insect AI can contribute to this. Specifically, the EU Nature Restoration Law will likely set binding targets for the high resolution data that cameras can provide. Thus, outputs of the Action will contribute directly to EU policies implementation, where biodiversity monitoring is considered a key component.The InsectAI COST Action will organise workshops, conferences, short-term scientific missions, hackathons, design-sprints and much more, across four Working Groups. These groups will address how image-based insect AI technologies can best address Societal Needs, support innovation in Image Collection hardware, create standardised approaches for Image Processing and develop novel Data Analysis and Integration methods for turning data into actionable insights.

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DOI: 10.3897/arphapreprints.e138026

Authors: Andrea Tarallo, Giuseppe Turrisi, Davide Raho, Ilaria Rosati

Abstract: This paper presents the collaborative efforts of Working Group 1 (WG1 - Occurrence and detection of zoosporic parasites) and Working Group 2 (WG2 - Drivers underlying the dynamic of zoosporic diseases) within the ParAqua COST Action, a research initiative focused on understanding zoosporic parasites and their interactions with algae. Initially conceived as an interactive web page, one of the deliverables of WG1 has evolved into a centralised database for data gathered by the scientific community of ParAqua. In this paper we present a summary of our work, carried out from July 2022 to October 2023. After gathering and analysing community needs, we have harmonised data collection, designed and implemented the database structure. The upcoming steps involve the data upload and integration process into the database and creating a Graphical User Interface to query the database. The paper focuses on the methodology and discusses the challenges faced during the activity. As part of our commitment to promoting the practices of open science, we wrote this paper to document the entire process of the database development. Our aim is to provide a clear pathway for others to expand, challenge, and refine our database designing process, encouraging a dynamic exchange of ideas that propels the field forward. In a broad sense, this research contributes to the understanding of algae-parasite interactions, by providing a unique experience of data mobilisation and integration in the field of algae parasites research.

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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

Abstract: 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.

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DOI: 10.3897/rio.7.e67887

Authors: Felicitas Löffler, Andreas Schuldt, Birgitta König-Ries, Helge Bruelheide, Friederike Klan

Abstract: Searching for scientific datasets is a prominent task in scholars' daily research practice. A variety of data publishers, archives and data portals offer search applications that allow the discovery of datasets. The evaluation of such dataset retrieval systems requires proper test collections, including questions that reflect real world information needs of scholars, a set of datasets and human judgements assessing the relevance of the datasets to the questions in the benchmark corpus. Unfortunately, only very few test collections exist for a dataset search. In this paper, we introduce the BEF-China test collection, the very first test collection for dataset retrieval in biodiversity research, a research field with an increasing demand in data discovery services. The test collection consists of 14 questions, a corpus of 372 datasets from the BEF-China project and binary relevance judgements provided by a biodiversity expert.

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DOI: 10.3897/rio.4.e32449

Authors: Katja Seltmann, Sara Lafia, Deborah Paul, Shelley James, David Bloom, Nelson Rios, Shari Ellis, Una Farrell, Jessica Utrup, Michael Yost, Edward Davis, Rob Emery, Gary Motz, Julien Kimmig, Vaughn Shirey, Emily Sandall, Daniel Park, Christopher Tyrrell, R. Sean Thackurdeen, Matthew Collins, Vincent O'Leary, Heather Prestridge, Christopher Evelyn, Ben Nyberg

Abstract: Georeferencing is the process of aligning a text description of a geographic location with a spatial location based on a geographic coordinate system. Training aids are commonly created around the georeferencing process to disseminate community standards and ideas, guide accurate georeferencing, inform users about new tools, and help users evaluate existing geospatial data. The Georeferencing for Research Use (GRU) workshop was implemented as a training aid that focused on the creation and research use of geospatial coordinates, and included both data researchers and data providers, to facilitate communication between the groups. The workshop included 23 participants with a wide background of expertise ranging from students (undergraduate and graduate), professors, researchers and educators, scientific data managers, natural history collections personnel, and spatial analyst specialists. The conversations and survey results from this workshop demonstrate that it is important to provide opportunities for biocollections data providers to interact directly with the researchers using the data they produce and vice versa.

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DOI: 10.3897/rio.4.e24224

Authors: Annalisa Minelli, Alessandro Oggioni, Alessandra Pugnetti, Alessandro Sarretta, Mauro Bastianini, Caterina Bergami, Fabrizio Bernardi Aubry, Elisa Camatti, Tiziano Scovacricchi, Giorgio Socal

Abstract:

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DOI: 10.3897/rio.3.e21074

Authors: David Rose, Prue Addison, Malcolm Ausden, Leon Bennun, Craig Mills, Stephanie O’Donnell, Caroline Parker, Melanie Ryan, Lauren Weatherdon, Katherine Despot-Belmonte, William Sutherland, Rebecca Robertson

Abstract: A workshop held at the University of Cambridge in May 2017 brought developers, researchers, knowledge brokers, and users together to discuss user-centred design of decision support tools. Decision support tools are designed to take users through logical decision steps towards an evidence-informed final decision. Although they may exist in different forms, including on paper, decision support tools are generally considered to be computer- (online, software) or app-based. Studies have illustrated the potential value of decision support tools for conservation, and there are several papers describing the design of individual tools. Rather less attention, however, has been placed on the desirable characteristics for use, and even less on whether tools are actually being used in practice. This is concerning because if tools are not used by their intended end user, for example a policy-maker or practitioner, then its design will have wasted resources. Based on an analysis of papers on tool use in conservation, there is a lack of social science research on improving design, and relatively few examples where users have been incorporated into the design process. Evidence from other disciplines, particularly human-computer interaction research, illustrates that involving users throughout the design of decision support tools increases the relevance, usability, and impact of systems. User-centred design of tools is, however, seldom mentioned in the conservation literature. The workshop started the necessary process of bringing together developers and users to share knowledge about how to conduct good user-centred design of decision support tools. This will help to ensure that tools are usable and make an impact in conservation policy and practice.

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DOI: 10.3897/rio.3.e13820

Authors: Timm Schoening, Jennifer Durden, Inken Preuss, Alexandra Branzan Albu, Autun Purser, Bart De Smet, Carlos Dominguez-Carrió, Chris Yesson, Daniëlle de Jonge, Dhugal Lindsay, Jan Schulz, Klas Ove Möller, Kolja Beisiegel, Linda Kuhnz, Maia Hoeberechts, Nils Piechaud, Stephanie Sharuga, Tali Treibitz

Abstract: Marine optical imaging has become a major assessment tool in science, policy and public understanding of our seas and oceans. Methodology in this field is developing rapidly, including hardware, software and the ways of their application. The aim of the Marine Imaging Workshop (MIW) is to bring together academics, research scientists and engineers, as well as industrial partners to discuss these developments, along with applications, challenges and future directions. The first MIW was held in Southampton, UK in April 2014. The second MIW, held in Kiel, Germany, in 2017 involved more than 100 attendees, who shared the latest developments in marine imaging through a combination of traditional oral and poster presentations, interactive sessions and focused discussion sessions. This article summarises the topics addressed during the workshop, particularly the outcomes of these discussion sessions for future reference and to make the workshop results available to the open public.

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DOI: 10.3897/rio.3.e11825

Authors: John Chodacki, Thomas Lemberger, Jennifer Lin, Maryann Martone, Daniel Mietchen, Jessica Polka, Richard Sever, Carly Strasser

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DOI: 10.3897/rio.2.e11563

Authors: Veljo Runnel, Florian Wetzel, Quentin Groom, Wouter Koch, Israel Pe’er, Nils Valland, Emmanouela Panteri, Urmas Kõljalg

Abstract: Citizen science is an approach of public participation in scientific research which has gained significant momentum in recent years. This is particularly evident in biology and environmental sciences where input from citizen scientists has greatly increased the number of publicly available observation data. However, there are still challenges in effective networking, data sharing and securing data quality. EU BON project has analyzed the citizen science landscape in Europe with regards to biodiversity research and proposes several policy recommendations. One of the recommendations is a Pan-European citizen science gateway for biodiversity data with dedicated tools for data collection and management. The prototypes of the gateway components are part of the EU BON biodiversity portal and described in current report.

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DOI: 10.3897/rio.2.e10445

Authors: Sarah Faulwetter, Evangelos Pafilis, Lucia Fanini, Nicolas Bailly, Donat Agosti, Christos Arvanitidis, Laura Boicenco, Terry Catapano, Simon Claus, Stefanie Dekeyzer, Teodor Georgiev, Aglaia Legaki, Dimitra Mavraki, Anastasis Oulas, Gabriella Papastefanou, Lyubomir Penev, Guido Sautter, Dmitry Schigel, Viktor Senderov, Adrian Teaca, Marilena Tsompanou

Abstract: The objective of Workpackage 4 of the European Marine Observation and Data network (EMODnet) is to fill spatial and temporal gaps in European marine species occurrence data availability by carrying out data archaeology and rescue activities. To this end, a workshop was organised in the Hellenic Center for Marine Research Crete (HCMR), Heraklion Crete, (8–9 June 2015) to assess possible mechanisms and guidelines to mobilise legacy biodiversity data. Workshop participants were data managers who actually implement data archaeology and rescue activities, as well as external experts in data mobilisation and data publication. In particular, current problems associated with manual extraction of occurrence data from legacy literature were reviewed, tools and mechanisms which could support a semi-automated process of data extraction were explored and the re-publication of the data, including incentives for data curators and scientists were reflected upon.

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DOI: 10.3897/rio.2.e8827

Authors: Jennifer McWhorter, Darren Wright, Julie Thomas

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DOI: 10.3897/rio.2.e8767

Authors: Roderic Page

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