DOI: 10.3897/arphapreprints.e197166

Authors: Martin Jung, Maximilian Wolschlager, Louise O'Connor, Matea Osti, Carla Freund, Kyle J Brumm, Piero Visconti

Abstract: Ambitious commitments under the European Biodiversity Strategy for 2030, including protecting at least 30% of land area and restoring 20% of ecosystems, are an opportunity to halt and reverse biodiversity loss. Achieving these objectives would benefit from coordinated, integrated and biodiversity-inclusive spatial planning approaches to identify where conservation and restoration actions will be most effective and resilient. Systematic conservation planning (SCP) provides such a framework, but its outputs are often complex and need to be translated into actionable and interpretable information for decision makers. Here in the context of the NaturaConnect project, we developed stand-alone policy support tools designed to bridge this gap between science, policy and practice, specifically tailored to the implementation of the EU Biodiversity Strategy in the terrestrial realm. Specifically, we developed two interactive platforms, described in this deliverable: NaturaConnector and PriorityCheck. Both tools are web-based and enable to visualise spatially explicit prioritisation outputs generated using the prioritizr R-package. We produced multiple spatial scenarios reflecting different objectives and planning assumptions, allowing exploration of trade-offs and synergies across different scenarios. NaturaConnector provides a web-based interface that enables users to explore our prioritisation outputs interactively and to better understand the implications of alternative planning strategies. It allows users to compare different scenarios, adjust planning criteria, and visualise how priorities shift under different objectives, assumptions, and implications in terms of performance across a range of ecological, geographic and socio-economic indicators. To facilitate uptake and dissemination, the platform also includes a link to downloadable infosheets for 39 countries and 10 biogeographic regions. The infosheets showcase consensus prioritization outputs as well as an assessment of the performance of the spatial planning solutions with some key takeaways specific to each country or geographic region. PriorityCheck is an online tool that enables users (stakeholders, practitioners, and experts) to engage directly with the prioritisation outputs, including querying the species and habitats composition at each site, and provide spatially explicit feedback to the research team on selected priority areas, regarding their implementation challenges, feasibility, and local relevance and value for conservation or restoration. Based on this spatially-explicit feedback entered by stakeholders and regional experts on PriorityCheck, we then further refined and improved the spatial prioritisation outputs.

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DOI: 10.3897/rio.12.e176590

Authors: Beatrice Bock

Abstract: Fungi exhibit diverse trophic strategies, ranging from obligate symbiosis to saprotrophy, with some taxa capable of occupying multiple ecological roles. Manually identifying trophic versatility from literature is time-consuming and difficult to scale. Here, we present a pilot workflow that automates the classification of fungal trophic modes using transformer-based language models. A curated dataset of 56 fungal ecology abstracts was manually labelled as dual (occupying multiple trophic modes) or solo (restricted to one mode) and used to fine-tune four models: BioBERT, BERT-base-cased, BERT-base-uncased and BiodivBERT. Stratified 5-fold cross-validation revealed that BioBERT and BERT-base-cased performed equally well (~ 89% accuracy, balanced precision and recall), highlighting the importance of case sensitivity in taxonomic text. BiodivBERT and uncased BERT models underperformed, indicating that domain adaptation alone is not sufficient. This pilot study emphasises reproducibility, transparency and open data integration, offering a generalisable proof-of-concept for linking literature-derived ecological information to existing fungal trait databases such as FUNGuild and FungalTraits. All code and data are openly available to support reuse and scaling to larger datasets.

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DOI: 10.3897/rio.11.e160367

Authors: Rajapreethi Rajendran, Claus Weiland, Jonas Grieb, Soulaine Theocharides, Sam Leeflang, Wouter Addink, Sharif Islam

Abstract: The Distributed System for Scientific Collections (DiSSCo) is a research infrastructure to integrate European natural science collections (NSCs) digitally. The aim is to facilitate and enhance the access, management and analysis of collection assets in one unified digital collection. The Machine Annotation Services (MAS) are essential components of DiSSCo’s Digital Specimen Architecture (DSArch). These services automate the annotation of digital objects to enable labelling and categorisation of NSC's digital assets.To further advance this, a Machine Learning as a Service (MLaaS) approach was developed which provides researchers with the access to pre-trained machine-learning models for complex tasks, such as instance segmentation and morphological analysis of datasets. MLaaS enhances the DiSSCo’s scalability and flexibility and allows the integration of machine-learning tools in close alignment with the FAIR (Findable, Accessible, Interoperable, Reusable) principles.This study employs DiSSCO's MLaaS framework for the quantitative analysis of herbarium specimens. Machine-learning models, such as Mask R-CNN and YOLO11, are comparatively applied to detect and generate the pixel-level masks of plant organs in herbarium sheets. Subsequently, these models are used to reconstruct the scale in the herbarium sheet and to calculate the surface area of identified plant organs. The determination of quantitative characteristics of plant specimens, such as measuring leaf area or the timestamp of the floral transition, opens up herbarium data for reuse in the large prognosis platforms currently developed in the framework of the Common European Data Spaces. In this way, plant trait data mobilised from natural science collections can improve the predictive capability of the vegetation model components of climate-related data spaces.

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DOI: 10.3897/arphapreprints.e180864

Authors: Sara Si-Moussi, Marianne Tzivanopoulos, Gabrielle Deschamps, Maxime Hoareau, Julien Renaud, Rémi LEMAIRE-PATIN, Wilfried Thuiller

Abstract: This deliverable outlines the creation of high-resolution (1km²) distribution maps for species and habitats across Europe, crucial for biodiversity conservation, policy compliance, and ecosystem management. Employing advanced Species Distribution Models (SDMs) and Habitat Distribution Models (HDMs), the task addressed plants, vertebrates, invertebrates, and all EUNIS Level 3 habitats.Species distribution modeling involved machine learning algorithms, carefully selected environmental variables, and spatially comprehensive occurrence datasets from GBIF, EVA, and other databases. Ensemble modeling techniques, spatial block cross-validation, and pseudo-absence generation ensured robust, reliable predictions, validated with metrics like True Skill Statistic (TSS).Habitat modeling similarly utilized environmental predictors (climate, topography, hydrography, geology, soil properties) alongside vegetation plot data from EVA and additional regional databases. Multi-class classification and ensemble forecasting methods provided high-quality predictive habitat maps validated externally and through cross-validation.Current and future scenarios (2050) were developed under varying climate and land-use trajectories (SSP1-RCP2.6, SSP3-RCP7.0), incorporating model uncertainty and expert-informed constraints. These maps support targeted conservation planning, monitoring programs, and decision-making, guiding efforts to enhance Europe's protected area network and biodiversity management.

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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/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.11.e156185

Authors: Denis Michez, Michel Bocquet, Philippe Bulet, Marie-Pierre Chauzat, Pilar De la Rúa, Reet Karise, Tomasz Kiljanek, Alexandra Klein, Marion Laurent, Elli Leadbeater, Marika Mänd, Anne-Claire Martel, Teodor Metodiev, Marija Miličić, Julia Osterman, Robert Paxton, Simon Potts, Sara Reverte, Marie-Pierre Rivière, Oliver Schweiger, Deepa Senapathi, Olga Tcheremenskaia, Simone Tosi, Ante Vujic, Dimitry Wintermantel, Mark Brown

Abstract: Wild fauna and flora are facing variable and challenging environmental disturbances. One of the animal groups that is most impacted by this, concerns pollinators. Pollinators face multiple threats, but the spread of anthropogenic chemicals (i.e. pesticides) form a major potential driver of these threats. WildPosh is a multi-actor, transdisciplinary project whose overarching mission and ambition are to significantly improve the evaluation of risk to pesticide exposure of wild pollinators, and enhance the sustainable health of pollinators and pollination services in Europe. As chemical exposure varies geographically, across cropping systems, inside the crop system and among pollinators, we will characterise exposure by doing fieldwork in 4 countries representing the four main climatic European regions, Mediterranean, Atlantic, Continental and Boreal climate in Germany, England, Estonia and Spain. We will also develop experiments in controlled conditions on different species of bees, syrphid flies, moths and butterflies, and collect in silico data on their traits and on toxicity of pesticides. With WildPosh, we aim to achieve the following objectives:1. Determining the real-world agrochemical exposure profile of wild pollinators at landscape level, within and among sites;2. Using integrated and controlled laboratory and semi-field experiments to characterise causal relationships between pesticides and pollinator health;3. Building an open database on pollinator traits/distribution and chemicals to define exposure and toxicity scenarios by developing databases on ecological traits and the spatial distribution of pollinators in relation to their potential exposure to pesticide;4. Proposing integrated systems-based risk assessment tools for risk assessment for wild pollinators; and5. Driving policy and practice through interactive innovation, meeting the need for monitoring tools, novel and innovative screening protocols for practice and policymaker use.

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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/rio.10.e129578

Authors: Zoe Ryan, Emily Clark, Beatrice Cundiff, Joslyn Nichols, Maya Mahoney, Nkosi Evans, Thomas Campbell, Danny Kreider, Matt von Konrat

Abstract: Over the last decade, access to global data has become increasingly critical for research, allowing insights into diverse biological, environmental and societal questions at a macro scale. Digitisation has greatly enhanced the use of herbarium data in the analysis of species distributions and ecological niche modelling. Yet, sources on modelling and mapping methodology using open-source software is greatly lacking for beginners. We have created a replicable and thorough tutorial to visualise species occurrence data and exploratory analysis that was developed by undergraduates with broad backgrounds and levels of experience. This tutorial integrates the open-source programmes QGIS, MaxEnt and R to develop distribution maps, using bryophytes as a case study, to promote the accessibility of open-source software and remote access learning. This tutorial has already set the foundation for further research into distribution modelling of rare Illinois bryophytes to better understand the potential impact of climate change.

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DOI: 10.3897/rio.10.e124579

Authors: Taimur Khan, Ahmed El-Gabbas, Marina Golivets, Allan Souza, Julian Gordillo, Dylan Kierans, Ingolf Kühn

Abstract: Invasive alien species (IAS) threaten biodiversity and human well-being. These threats may increase in the future, necessitating accurate projections of potential locations and the extent of invasions. The main aim of the IAS prototype Digital Twin (IAS pDT) is to dynamically project the level of plant invasion at habitat level across Europe under current and future climates using joint species distribution models. The pDT detects updates in data sources and versions of the datasets and model outputs, implementing the FAIR principles. The pDT’s outputs will be available via an interactive dashboard. All input and output data will be freely accessible.

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DOI: 10.3897/rio.10.e125192

Authors: Desalegn Chala, Erik Kusch, Claus Weiland, Carrie Andrew, Jonas Grieb, Tuomas Rossi, Tomas Martinovic, Dag Endresen

Abstract: Amidst population growth and climate-driven crop stresses such as drought, extreme weather, fungal and insect pests, as well as various crop diseases, ensuring food security demands innovative strategies. Crop wild relatives (CWR), wild plants in the same genus as the crop as well as wild populations belonging to the same species as the crop, offer novel genetic resources crucial for enhancing crop resilience against these stress factors. Here, we introduce a prototype digital twin (pDT) to aid in searching and utilising CWR genetic resources. Using the MoDGP (Modelling the Germplasm of Interest) tool, the pDT enables mapping geographic areas where stress-tolerant CWR populations can be found. With its graphical user interface, it offers flexibility in selecting genetic resources from CWR tailored to enhance resilience of various crops against diverse stress factors.

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DOI: 10.3897/arphapreprints.e114920

Authors: Mathias Dillen, Andreas Plank

Abstract: In this task, the aim is to develop a workflow that should facilitate the linking process of collector name strings to PIDs for those collectors. Such a workflow should help scale up the number of links being made, make the process more efficient and should take advantage as much as possible of existing work and infrastructures, so as not to reinvent the wheel. As such, the work can be roughly split into a few subtasks:- Make existing linking workflows more easily implementable in other contexts and by other infrastructures. This includes finding ways for such workflows to produce links that can easily be published, i.e. in a standardised format compatible with existing infrastructure. The suitability of different infrastructures for making established links available should also be assessed.- Establish, document and improve the comprehensiveness, findability and interoperability of the content in PID-minting resources, in particular Wikidata as it can be edited openly.- Refine the decision making process of establishing links, by implementing and improving the methods that can be used to validate potential links.In this document, the focus lies on linking people. We will propose a workflow to 'roundtrip' links established through the Bionomia platform back to the collections holding the attributed specimens, as well as making them available for use by other BiCIKL infrastructures. We will also refine existing automated linking workflows and pilot the new functionalities on the (botanical) collections of the task partners. These refinements will be influenced by an assessment of the current state of Wikidata, investigated through shape expressions constructed from commonly used queries and from Wikidata records which have been linked in previous efforts such as the Botany Pilot, Bionomia and published specimen data to GBIF.

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DOI: 10.3897/arphapreprints.e114048

Authors: Maëlle Wannier

Abstract: The Digital Botanical Gardens Initiative (DBGI) embarks on an innovative journey to curate, manage, and disseminate digital data from living botanical collections, with an emphasis on mass spectrometric evaluations of chemodiversity. Using semantic web technology, this data is linked with relevant metadata, propelling ecosystem research and guiding biodiversity conservation efforts. Central to the success of DBGI is the creation of an interactive platform for both humans and machines to assimilate this knowledge. This report outlines our efforts to design the prototype of a data visualization portal intended to evolve into the DBGI dashboard. Starting with a Plotly Dash application, the project transitioned to a Node.js application leveraging Javascript, HTML, and CSS for enhanced customization. This provides a basis for future improvements, some of which are proposed in the report.

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DOI: 10.3897/arphapreprints.e107169

Authors: Wouter Addink, Niki Kyriakopoulou, Lyubomir Penev, David Fichtmueller, Ben Norton, David Shorthouse

Abstract: 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.

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DOI: 10.3897/arphapreprints.e107168

Authors: Wouter Addink, Sharif Islam, Mathias Dillen, Anton Güntsch, Soulaine Theocharides

Abstract: 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.

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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

Abstract: 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.

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DOI: 10.3897/arphapreprints.e107166

Authors: Soulaine Theocharides, Niki Kyriakopoulou

Abstract: 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.

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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.e25742

Authors: Lilliana Sancho-Chavarria, Fabian Beck, Daniel Weiskopf, Erick Mata-Montero

Abstract: Maintenance and curation of large-sized biological taxonomies are complex and laborious activities. Information visualization systems use interactive visual interfaces to facilitate analytical reasoning on complex information. Several approaches such as treemaps, indented lists, cone trees, radial trees, and many others have been used to visualize and analyze a single taxonomy. In addition, methods such as edge drawing, animation, and matrix representations have been used for comparing trees. Visualizing similarities and differences between two or more large taxonomies is harder than the visualization of a single taxonomy. On one hand, less space is available on the screen to display each tree; on the other hand, differences should be highlighted. The comparison of two alternative taxonomies and the analysis of a taxonomy as it evolves over time provide fundamental information to taxonomists and global initiatives that promote standardization and integration of taxonomic databases to better document biodiversity and support its conservation. In this work we assess how ten user visualization tasks for the curation of biological taxonomies are supported by several visualization tools. Tasks include the identification of conditions such as congruent taxa, splits, merges, and new species added to a taxonomy. We consider tools that have gone beyond the prototype stage, that have been described in peer-reviewed publications, or are in current use. We conclude with the identification of challenges for future development of taxonomy comparison tools.

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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.e14944

Authors: W. Daniel Kissling

Abstract: Seed dispersal by fruit-eating animals is a pivotal ecosystem function in tropical forests, but the role that frugivores have played in the biogeography and macroevolution of species-rich tropical plant families remains largely unexplored. This project investigates how frugivory-relevant plant traits (e.g. fruit size, fruit color, fruit shape etc.) are distributed within the angiosperm family of palms (Arecaceae), how this relates to diversification rates, and whether and how it coincides with the global biogeographic distribution of vertebrate frugivores (birds, bats, primates, other frugivorous mammals) and their ecological traits (e.g. diet specialization, body size, flight ability, color vision etc.). Palms are particularly suitable because they are well studied, species-rich, characteristic of tropical rainforests, and dispersed by all groups of vertebrate seed dispersers. Using newly compiled data on species distributions and ecological traits in combination with phylogenies we will test (1) how fruit trait variability relates to palm phylogeny and other aspects of plant morphology (e.g. leaf size, plant height, growth form), (2) whether geographic variability in fruit traits correlates with geographic distributions of animal consumers and their traits, and (3) to what extent interaction-relevant plant traits are related to palm diversification rates. This combined macroecological and macroevolutionary approach allows novel insights into the global ecology and the evolution of a tropical keystone plant family. This is important for the conservation and sustainable management of tropical rainforests because palms are often key components of subsistence economies, ecosystem dynamics and carbon storage and therefore help to enhance nature’s goods, benefits and services to humanity.

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DOI: 10.3897/rio.3.e14013

Authors: Katherine Despot-Belmonte, Michel Doudin, Quentin Groom, Florian Wetzel, Donat Agosti, Kim Jacobsen, Larissa Smirnova, Lauren V. Weatherdon, Tim Robertson, Lyubomir Penev, Eugenie Regan, Anke Hoffmann, Brian MacSharry, Yara Shennan-Farpon, Corinne S. Martin

Abstract: The EU BON (“Building the European Biodiversity Observation Network”) project has made important contributions towards the achievement of global conservation targets. This infographic illustrates EU BON's contributions towards the achievement of Aichi Biodiversity Target 19 "By 2020, knowledge, the science base and technologies relating to biodiversity, its values, functioning, status and trends, and the consequences of its loss, are improved, widely shared and transferred, and applied.”

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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

Abstract:

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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.e10708

Authors: Ethan White

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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

Abstract:

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