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Research Ideas and Outcomes
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  This is an Open Access Journal Open Access journal
ISSN (Online) 2367-7163
Published by Pensoft Homepage  [58 journals]
  • Ant-plant symbioses trade-offs and its role in forest restoration projects

    • Abstract: Research Ideas and Outcomes 8: e94784
      DOI : 10.3897/rio.8.e94784
      Authors : Sze Huei Yek : Ant-plant symbioses are complex between-species interactions found only in the tropical environment. Typically, in such symbioses, plants provide housing structures and food to their ant symbionts. In return, the ants protect their plants' host against herbivore attack and additional nutrients to help with plants' growth. These win-win interactions range from facultative to obligate mutualism. This proposal aims to test the three main mechanisms: (1) by-product benefits, (2) partner fidelity feedback and (3) partner choice in stabilising the ant-plant mutualism. Understanding the mechanisms are crucial as they form the foundation of the ant-plant distribution and growth, in other words - the health of the myrmecophyte (ants-loving) trees in the forest ecosystem. Hence, ant-plant symbioses are an ideal model system for investigating the effects of anthropogenic changes, such as deforestation and climate change on the outcome of ant-plant mutualistic interactions. This project attempts to identify the mechanisms regulating the mutualistic interactions and, in particular, identify the context in which such mutualistic interactions evolved and adapt to the changing environment. We hypothesise that there will be a higher diversity of obligate mutualistic ant-plant interactions in the undisturbed environment compared to degraded habitat. Furthermore, we expect there are different complexity of symbioses, involving multiple partners (ants-hemipteran insects-bacteria-fungi-plants) that deepen our understanding of how such symbioses can be stabilised. Finally, the deforestation combined with climate change in Southeast Asia will have a detrimental effect on ant-plant symbioses, causing breakdown of mutualistic partners and invasion of cheater ant species that do not confer a protective advantage to their plants' host. HTML XML PDF
      PubDate: Tue, 27 Sep 2022 09:01:31 +030
       
  • Scholia for Software

    • Abstract: Research Ideas and Outcomes 8: e94771
      DOI : 10.3897/rio.8.e94771
      Authors : Lane Rasberry, Daniel Mietchen : Scholia for Software is a project to add software profiling features to Scholia, which is a scholarly profiling service from the Wikimedia ecosystem and integrated with Wikipedia and Wikidata. This document is an adaptation of the funded grant proposal. We are sharing it for several reasons, including research transparency, our wish to encourage the sharing of research proposals for reuse and remixing in general, to assist others specifically in making proposals that would complement our activities, and because sharing this proposal helps us to tell the story of the project to community stakeholders.A "scholarly profiling service" is a tool which assists the user in accessing data on some aspect of scholarship, usually in relation to research. Typical features of such services include returning the biography of academic publications for any given researcher, or providing a list of publications by topic. Scholia already exists as a Wikimedia platform tool built upon Wikidata and capable of serving these functions. This project will additionally add software-related data to Wikidata, develop Scholia's own code, and address some ethical issues in diversity and representation around these activities. The end result will be that Scholia will have the ability to report what software a given researcher has described using in their publications, what software is most used among authors publishing on a given topic or in a given journal, what papers describe projects which use some given software, and what software is most often co-used in projects which use a given software. HTML XML PDF
      PubDate: Thu, 15 Sep 2022 16:16:40 +030
       
  • Applications for zoosporic parasites in aquatic systems (ParAqua)

    • Abstract:
      DOI : 10.3897/arphapreprints.e94590
      Authors : Serena Rasconi, Hans-Peter Grossart, Alena Gsell, Bastiaan Willem Ibelings, Dedmer van de Waal, Ramsy Agha, Ariola Bacu, Maija Balode, Meryem Beklioğlu, Maja Berden Zrimec, Florina Botez, Tom Butler, Slawomir Cerbin, Angela Cortina, Michael Cunliffe, Thijs Frenken, Esther Garcés, Laura Gjyli, Yonatan Golan, Tiago Guerra, Ayis Iacovides, Antonio Idà, Maiko Kagami, Veljo Kisand, Jovica Leshoski, Pini Marco, Natasa Mazalica, Takeshi Miki, Maria Iasmina Moza, Sigrid Neuhauser, Deniz Özkundakci, Kristel Panksep, Suzana Patcheva, Branka Pestoric, Maya Petrova Stoyneva, Diogo Pinto, Juergen Polle, Carmen Postolache, Joaquín Pozo Dengra, Albert Reñé, Pavel Rychtecky, Dirk S. Schmeller, Bettina Scholz, Géza Selmeczy, Télesphore Sime-Ngando, Kálmán Tapolczai, Orhideja Tasevska, Ivana Trbojevic, Blagoy Uzunov, Silke Van den Wyngaert, Ellen van Donk, Marieke Vanthoor, Elizabeta Veljanoska Sarafiloska, Susie Wood, Petr Znachor : Zoosporic parasites (i.e. fungi and fungi-like aquatic microorganisms) constitute important drivers of natural populations, causing severe host mortality. Economic impacts of parasitic diseases are notable in the microalgae biotech industry, affecting production of food ingredients, biofuels, pharma- and nutraceuticals.While scientific research on this topic is gaining traction by increasing studies elucidating the functional role of zoosporic parasites in natural ecosystems, we are currently lacking integrated and interdisciplinary efforts for effectively detecting and controlling parasites in the microalgae industry. To fill this gap we propose to establish an innovative, dynamic European network connecting scientists, industries and stakeholders to optimize information exchange, equalize access to resources and to develop a joint research agenda. ParAqua aims at compiling and making available all information on the occurrence of zoosporic parasites and their relationship with hosts, elucidate drivers and evaluate impacts of parasitism in natural and man-made aquatic environments. We aim to implement new tools for monitoring and prevention of infections, and to create protocols and a Decision Support Tool for detecting and controlling parasites in the microalgae biotech production. Applied knowledge on zoosporic parasites can feed back from industry to ecology, and we therefore will explore whether the developed tools can be applied for monitoring lakes and reservoirs. Short-Term Scientific Missions and Training Schools will be organised specifically for early stage scientists and managers – with a specific focus on ITC – with the aim to share and integrate both scientific and applied expertise and increase exchange between basic and applied researchers and stakeholders. HTML XML PDF
      PubDate: Fri, 9 Sep 2022 17:40:00 +0300
       
  • Joint statement on best practices for the citation of authorities of
           scientific names in taxonomy by CETAF, SPNHC and BHL

    • Abstract: Research Ideas and Outcomes 8: e94338
      DOI : 10.3897/rio.8.e94338
      Authors : Laurence Benichou, Jutta Buschbom, Mariel Campbell, Elisa Hermann, Jiří Kvaček, Patricia Mergen, Lorna Mitchell, Constance Rinaldo, Donat Agosti : This joint statement aims at encouraging all authors, publishers and editors involved in scientific publishing to give the bibliographic source of the authorities of taxonomic names. This initiative, written by members of the three communities, has been approved by the executive boards of the SPNHC (Society for the Preservation of Natural History Collections), CETAF (Consortium of European Taxonomic Facilities) and BHL (Biodiversity Heritage Library). HTML XML PDF
      PubDate: Fri, 9 Sep 2022 10:15:03 +0300
       
  • Illuminating biodiversity changes in the ‘Black Box’

    • Abstract: Research Ideas and Outcomes 8: e87143
      DOI : 10.3897/rio.8.e87143
      Authors : Helen Phillips, Erin Cameron, Nico Eisenhauer : Soil is often described as a ‘black box’, as surprisingly little is known about the high levels of biodiversity that reside there. For aboveground organisms, we have good knowledge of the distribution of the species and how they might change under future human impacts. Yet despite the fact that soil organisms provide a wide variety of ecosystem functions, we have very limited knowledge of their distribution and how their diversity might change in the future. In order to create accurate and generalisable models of biodiversity, the underlying data need to be representative of the entire globe. Yet even with our recently compiled global earthworm dataset of over 11000 sites, there are gaps across large regions. These gaps are consistent across many other datasets of both above- and belowground diversity. In order to fill the gaps we propose a sampling network (SoilFaUNa), to create a comprehensive database of soil macrofauna diversity and soil functions (e.g. decomposition rates). Building on the existing dataset of earthworm diversity and early data from the SoilFaUNa project, we will investigate changes in earthworm diversity. From our current work, we know that both climate and land use are main drivers in predicting earthworm diversity, but both will change under future scenarios and may alter ecosystem functions. We will, using space-for-time substitution models, estimate how earthworm diversity and their functions might change in the future, modelling earthworm diversity as a function of climate, land use and soil properties and predicting based on future scenarios. Previous studies of aboveground diversity changes over time using time-series analysis have found no-net-loss in richness, but analyses have criticisms. We aim to use time-series data on earthworms to move this debate forward, by using data and statistical methods that would address the criticisms, whilst increasing our knowledge on this understudied soil group. Field experiments and micro-/mesocosm experiments have been used to investigate the link between a number of soil organisms and ecosystem functions under few environmental conditions. Meta-analyses, which can produce generalisable results can only answer questions for which there are data. Thus, we have been lacking on information on the link between the entire community of soil fauna and ecosystem functions and impact of changes to the soil fauna community across environmental contexts. Using data collected from the SoilFaUNa project, we will, for the first time, synthesise globally distributed specifically-sampled data to model how changes in the community composition of soil macrofauna (due to changes in land use, climate or soil properties) impact the ecosystem functions in the soil. HTML XML PDF
      PubDate: Wed, 31 Aug 2022 08:15:39 +030
       
  • Taxonomic Treatments as Open FAIR Digital Objects

    • Abstract: Research Ideas and Outcomes 8: e93709
      DOI : 10.3897/rio.8.e93709
      Authors : Donat Agosti, Alexandros Ioannidis-Pantopikos : Taxonomy is the science of charting and describing the worlds biodiversity. Organisms are grouped into taxa which are given a given rank building the taxonomic hierarchy. The taxa are described in taxonomic treatments, well defined sections of scientific publications (Catapano 2019). They include a nomenclatural section and one or more sections including descriptions, material citations referring to studied specimens, or notes ecology and behavior. In case the treatment does not describe a new discovered taxon, previous treatments are cited in the form of treatment citations. This citation can refer to a previous treatment and add additional data, or it can be a statement synonymizing the taxon with another taxon. This allows building a citation network, and ultimately is a constituent part of the catalogue of life. Thus treatments play an important role to understand the diversity of life on Earth by providing the scientific argument why group of organism is a new species, or a synonym, and the data provided will increasingly be important to analyze and compare whole genomes of individual genomes.Treatments have been extracted by Plazi since 2008 (Agosti and Egloff 2009), and the TaxPub schema has been described by Catapano (Catapano 2019) to complement existing vocabularies to allow annotation of legacy literature and to produce new publications including the respective annotations (Penev et al. 2010). Today, more than 750,000 treatments have been annotated by Plazi’s TreatmenBank and over 400,000 have been made FAIR digital objects in the Biodiversity Literature Repository in a collaboration of Plazi, Zenodo and Pensoft (Ioannidis-Pantopikos and Agosti 2021, Agosti et al. 2019), and are reused by the Global Biodiversity Information Facility (GBIF), Global Biotic Interaction (GloBI), and the Library System of the Swiss Institute of Bioinformatics (SIBiLS).Each treatment on the Zenodo repository is findable through its rich metadata. The insertion of custom metadata in Zenodo provides metadata referring to domain specific vocabularies such as Darwin Core (Ioannidis-Pantopikos and Agosti 2021). The treatment are accessible through its DataCite Digital Object Identifier (
      DOI ) for the taxonomic treatment as subtype of a publication. The data is interoperable by machine actionable JSON version of the treatment. A license is provided to assure it is reusable.The richness of data and citations within a treatment provide a stepping stone to add treatments not only to knowledge systems such as Wikidata or openBioDiv, but to provide links to many of the cited objects, such as specimens through the material citations, and thus a well curated assemblage of links. Being a FAIR digital object, treatments can be cited and should ultimately linked to from a taxonomic name used in an identification of an organism. HTML XML PDF
      PubDate: Thu, 25 Aug 2022 12:09:04 +030
       
  • From Green Deal to Cultural Heritage: FAIR Digital Objects and European
           Common Data Spaces

    • Abstract: Research Ideas and Outcomes 8: e93815
      DOI : 10.3897/rio.8.e93815
      Authors : Sharif Islam, Andreas Weber, Erzsébet Tóth-Czifra : This talk outlines a vision for Common European Data Spaces, proposed by the European Commission, where FAIR principles (Wilkinson et al. 2016) and FAIR Digital Objects (FDOs) (De Smedt et al. 2020, Schwardmann 2020) can play a role in bringing together research infrastructures, data aggregators and other stakeholders working with curated objects in museums, herbaria, libraries and archives. The organisations and stakeholders involved represent a wide range of disciplines and data types including biodiversity, ecology, anthropology, archaeology, cultural history, digital storytelling, art conservation, and history of science among others (ICEDIG 2020, Ortolja-Baird and Nyhan 2021). The context and the history of the curated objects also span the natural sciences and cultural heritage domains (Nadim 2021, Weber 2021). Despite this heterogeneity, various common themes in the area of digital curation, open access, and data usage (Tasovac et al. 2020) appear where FDOs and Common European Data Spaces can be a useful venue for supporting the European Strategy for Data. In particular, FDOs, as an abstraction mechanism to structure and describe digital artefacts from a specific domain yet at the same time provide interoperability (De Smedt et al. 2020), can help realise the vision behind a common data space to “bring together relevant data infrastructures and governance frameworks in order to facilitate data pooling and sharing” (European Commission 2022:2).A May 2022 report on the challenges and opportunities of European Common Data Spaces highlights the following points:Open data holders have extensive experience in data publishing, metadata management, data quality, dataset discovery, data federation, as well as tried-and-tested standards (e.g. DCAT) and technologies. There seems to be very little knowledge/technology transfer from the open data community to the data spaces community, which is a missed opportunity. Data space implementations should not reinvent wheels that the open data community has already developed, tested, and used extensively.Whether the data is private, shared, or open, using data from multiple sources requires interoperability at several levels, from identifiers to vocabularies. The question of which data intermediaries will act as neutral agents to ensure interoperability is underexplored in the data space context. Public administrations, building on their experience of publishing open data, are best placed to take on such rolesBuilding on previous conversations facilitated by DiSSCo, DARIAH, Europeana, and Archives Portal Europe Foundation, (Europeana Conference 2021, DARIAH Annual Event 2022), this talk will address the above points from the perspective of bringing together the domains of natural history museums, cultural heritage, and digital humanities. Within our collaboration, we have identified several common areas such as data discoverability, linking, and providing contextual information, which align with the goal of FDO implementation. DiSSCo and DARIAH as European infrastructures, on the one hand, and Europeana and Archives Portal as data aggregators, on the other hand, are involved in improving access to data and the researchers' capacity to work with heterogeneous data sources. One of the biggest shared challenges across the diverse workflows in the arts and humanities and natural history domains is that the data curation processes form a natural continuum between a range of different actors working either in cultural heritage institutions or in academia. In reality, these different layers of curation, enrichment and analysis are separated by legal, institutional, infrastructural and even funding silos (as in many countries, these institutions belong to different ministries, and fall under different legislative frameworks). How can this continuum, from a scholarly point of view, be supported within common data space and FDO framework' At the same time, implementing a common data space requires not just interoperability but stewardship and strategy for sharing resources (Keller 2021).The data infrastructure and FAIR related activities explored in our collaboration are of strategic importance to help Europe and the rest of the world deal with important societal issues. Therefore, bringing this collaboration within the context of FDO provides an ideal avenue to explore potential data, policy, and implementation matters, in order to address the two gaps outlined above for Common Data Spaces. Furthermore, the ideas expressed in Common European Data Space for Cultural Heritage (with Europeana as the core stakeholder) and Green Deal Data Spaces need further clarification concerning implementation planning and most importantly, how multiple commons would work together. With DARIAH coming from the humanities and DiSSCo from the natural sciences side, such collaborations and synergy should align with the Common Data Spaces vision. The philosophy and ideas behind data and digital commons are not new (Fuchs 2020, Kashwan et al. 2021). However, it is crucial to contextualise the implementation strategy and benefits within data intensive, multidisciplinary research and FAIR principles.Given that curated objects are informational resources for the researchers, but can also provide contexts, and make visible the relationships between artefacts, people, publications, organisations, provenance, and events, it is important to think of them as much more than just records in a database. Additionally, FDOs as the digital representations of the curated objects have the potential of fostering cross-disciplinary collaborations (such as between biology, history, art or anthropology) and of providing a wider lens for understanding materiality and the role of data (Ribes 2019). As interdisciplin...
      PubDate: Thu, 25 Aug 2022 12:08:54 +030
       
  • From data pipelines to FAIR data infrastructures: A vision for the new
           horizons of bio- and geodiversity data for scientific research

    • Abstract: Research Ideas and Outcomes 8: e93816
      DOI : 10.3897/rio.8.e93816
      Authors : Sharif Islam, Claus Weiland, Wouter Addink : Natural science collections are vast repositories of bio- and geodiversity specimens. These collections, originating from natural history cabinets or expeditions, are increasingly becoming unparalleled sources of data facilitating multidisciplinary research (Meineke et al. 2018, Heberling et al. 2019, Cook et al. 2020, Thompson et al. 2021). Due to various global data mobilization and digitisation efforts (Blagoderov et al. 2012,Nelson and Ellis 2018), this digitised information about specimens includes database records along with two/three-dimensional images, sonograms, sound or video recordings, computerised tomography scans, machine-readable texts from labels on the specimens as well as media items and notes related to the discovery sites and acquisition (Hedrick et al. 2020,Phillipson 2022).The scope and practice of specimen gathering are also evolving. The term extended specimen was coined to refer to the specimen and associated data extending beyond the singular physical object to other physical or digital entities such as chemical composition, genetic sequence data or species data. Thus the specimen becomes an interconnected network of data resources that have incredible potential to enhance integrative and data-driven research (Webster 2017,Lendemer et al. 2019,Hardisty et al. 2022). These practices also reflect the role of data and the curatorial data life-cycle starting from the initial material sampling process to the downstream analysis. We are also seeing growing acknowledgement that disparate and domain specific data elements prevent interdisciplinarity which is crucial for a holistic understanding of biodiversity and climate crisis (Hicks et al. 2010, Craven et al. 2019, Folk and Siniscalchi 2021). Thus the data elements are not just records or rows in a database or data pipelines going from one repository to another. They have the potential to become self-describing digital artefacts that can revolutionise how machines interpret and work with specimen data. Within this context, the Distributed System of Scientific Collections (DiSSCo), a new European Research Infrastructure for natural science collections, envisions an infrastructure based on FAIR Digital Objects (FDO) that can unify more than 170 European natural science collections under common and FAIR-compliant (Findable, Accessible, Interoperable, Reusable) (Wilkinson et al. 2016) access and curation policies and practices. DiSSCo’s key element in achieving FAIR is the implementation of Digital Specimen (a domain specific FDO) that closely aligns with the extended specimen practices. The idea behind Digital Specimen – an FDO that acts as a digital surrogate for a specific physical specimen in a natural science collection – was influenced by global conversations around the implementation of the Digital Object Architecture for biodiversity data (De Smedt et al. 2020, Islam et al. 2020,Hardisty et al. 2020). The main purpose of this talk is to explain the vision of how FAIR and FDO can create a data infrastructure that can not only take advantage of existing databases and repositories but at the same time provide support for innovative services such as AI and digital twinning. With scientific use cases in mind, the talk will highlight a few key FAIR and FDO components (persistent identifiers, metadata, ontologies) within the collaborative modelling activity of Digital Specimen specification. These components provide the template for specifying how a Digital Specimen should look so DiSSCo can build a FAIR service ecosystem based on FDOs (Addink et al. 2021). We will also give examples of envisioned services that can help with image feature extraction, and model training (Grieb et al. 2021,Hardisty et al. 2022) and digital twinning (Schultes et al. 2022). We believe this is an exciting new paradigm powered by FAIR and FDO that can help both humans and machines to accelerate the use of specimen data. From physical objects curated over hundred years, we have developed data pipelines, aggregators and repositories (Barberousse 2021). Now is the time to look for solutions where these data records can become FAIR Digital Objects to enable wider access and multidisciplinary research. HTML XML PDF
      PubDate: Thu, 25 Aug 2022 12:08:41 +030
       
  • FAIR Research Objects for realizing Open Science with RELIANCE EOSC
           project

    • Abstract: Research Ideas and Outcomes 8: e93940
      DOI : 10.3897/rio.8.e93940
      Authors : Anne Fouilloux, Federica Foglini, Elisa Trasatti : The H2020 Reliance project delivers a suite of innovative and interconnected services that extend European Open Science Cloud (EOSC)’s capabilities to support the management of the research lifecycle within Earth Science Communities and Copernicus Users. The project has delivered 3 complementary  technologies: Research Objects (ROs), Data Cubes and AI-based Text Mining.RoHub is a Research Object management platform that implements these 3 technologies and enables researchers to collaboratively manage, share and preserve their research work.RoHub implements the full RO model and paradigm: resources associated to a particular research work are aggregated into a single FAIR digital object, and metadata relevant for understanding and interpreting the content is represented as semantic metadata that are user and machine readable. The development of RoHub is co-designed and validated through multidisciplinary and thematic real life use cases led by three different Earth Science communities: Geohazards, Sea Monitoring and Climate Change communities. A RO commonly starts its life as an empty Live RO. ROs aggregate new objects through their whole lifecycle. This means, a RO is filled incrementally by aggregating new relevant resources such as workflows, datasets, documents according to its typology that are being created, reused or repurposed. These resources can be modified at any point in time.We can copy and keep ROs in time through snapshots which reflect their status at a given point in time. Snapshots can have their own identifiers (
      DOI s) which facilitates tracking the evolution of a research. At some point in time, a RO can be published and archived (so called Archived RO) with a permanent identifier (
      DOI ). New Live ROs can be derived based on an existing Archived RO, for instance by forking it. To guide researchers, different types of Research Objects can be created:Bibliography-centric: includes manuals, anonymous interviews, publications, multimedia (video, songs) and/or other material that support research;Data-centric: refers to datasets which can be indexed, discovered and manipulated;Executable: includes the code, data and computational environment along with a description of the research object and in some cases a workflow. This type of ROs can be executed and is often used for scripts and/or Jupyter Notebooks;Software-centric: also known as “Code as a Research Object”. Software-centric ROs include source codes and associated documentation. They often include sample datasets for running tests.Workflow-centric: contains workflow specifications, provenance logs generated when executing the workflows, information about the evolution of the workflow (version) and its components elements, and additional annotations for the workflow as a whole.Basic: can contain anything and is used when the other types do not cover the need.To ease the understanding and the reuse of the ROs, each type of RO (except Basic RO) has a template folder structure that we recommend researchers to select. For instance an executable RO has 4 folders:'biblio' where  researchers can aggregate documentations, scientific papers that øed to the development of the software/tool that is aggregated in the tool folder;'input' where all the input datasets required for executing the RO are aggregated;'output' where some or all the results generated by executing the RO are aggregated;'tool' where the executable tool is aggregated. Typically, we aggregate Jupyter Notebook and/or executable workflows (Galaxy or snakemake workflows).In addition to the different types of ROs and associated template structures, researchers can select the type of resources that constitutes the main entity of a RO: for instance, a Jupyter Notebook can be selected as the main entity of an executable RO. As shown on Fig. 1, this additional metadata is then visible to everyone (and machine readable) to ease reuse. Examples of Bibliography-centric and Data-centric Research Objects are shown on Fig. 2: the overall overview of any types of Research Object is always the same with mandatory metadata information such as the title, description, authors & collaborators, sketch (featured plots/images), the content of the RO (with different structures depending on the type of ROs). Additional information is displayed on the right panel such as number of downloads, additional discovered metadata (automatically discovered from the Reliance text enrichment service), free keywords (added by end-users) and citation. The 'toolbox' and 'share' sections allows end-users to download, snapshot and archive the RO and/or share it.Any Research Object in RoHub is a FAIR digital object that is for instance findable in OpenAire, including Live ROs.In our presentation, we will showcase different types of ROs for the 3 Earth Science communities represented in Reliance to highlight how the scientists in our respective disciplines changed their working methodology towards Open Science. HTML XML PDF
      PubDate: Thu, 25 Aug 2022 12:08:31 +030
       
  • A Multi-omics Data Analysis Workflow Packaged as a FAIR Digital Object

    • Abstract: Research Ideas and Outcomes 8: e94042
      DOI : 10.3897/rio.8.e94042
      Authors : Anna Niehues, Casper de Visser, Fiona Hagenbeek, Naama Karu, Alida Kindt, Purva Kulkarni, René Pool, Dorret Boomsma, Jenny van Dongen, Alain van Gool, Peter 't Hoen : In current biomedical and complex trait research, increasing numbers of large molecular profiling (omics) data sets are being generated. At the same time, many studies fail to be reproduced (Baker 2016, Kim 2018). In order to improve study reproducibility and data reuse, including integration of data sets of different types and origins, it is imperative to work with omics data that is findable, accessible, interoperable, and reusable (FAIR, Wilkinson 2016) at the source. The data analysis, integration and stewardship pillar of the Netherlands X-omics Initiative aims to facilitate multi-omics research by providing tools to create, analyze and integrate FAIR omics data. We here report a joint activity of X-omics and the Netherlands Twin Register demonstrating the FAIRification of a multi-omics data set and the development of a FAIR multi-omics data analysis workflow.The implementation of FAIR principles (Wilkinson 2016) can improve scientific transparency and facilitate data reuse. However, Kim (2018) showed in a case study that the availability of data and code are required but not sufficient to reproduce data analyses. They highlighted the importance of interoperable and open formats, and structured metadata. In order to increase research reproducibility on the data analysis level, additional practices such as version-control, code licensing, and documentation have been proposed. These include recommendations for FAIR software by the Netherlands eScience Center and the Dutch Data Archiving and Networked Services (DANS), and FAIR principles for research software proposed by the Research Data Alliance (Chue Hong 2022). Data analysis in biomedical research usually comprises multiple steps often resulting in complex data analysis workflows and requiring additional practices, such as containerization, to ensure transparency and reproducibility (Goble 2020, Stoudt 2021).We apply these practices to a multi-omics data set that comprises genome-wide DNA methylation profiles, targeted metabolomics, and behavioral data of two cohorts that participated in the ACTION Biomarker Study (ACTION, Aggression in Children: Unraveling gene-environment interplay to inform Treatment and InterventiON strategies, see consortium members in Suppl. material 1) (Boomsma 2015, Bartels 2018, Hagenbeek 2020, van Dongen 2021, Hagenbeek 2022). The ACTION-NTR cohort consists of twins that are either longitudinally concordant or discordant for childhood aggression. The ACTION-Curium-LUMC cohort consists of children referred to the Dutch LUMC Curium academic center for child and youth psychiatry. With the joint analysis of multi-omics data and behavioral data, we aim to identify substructures in the ACTION-NTR cohort and link them to aggressive behavior. First, the individuals are clustered using Similarity Network Fusion (SNF, Wang 2014), and latent feature dimensions are uncovered using different unsupervised methods including Multi-Omics Factor Analysis (MOFA) (Argelaguet 2018) and Multiple Correspondence Analysis (MCA, Lê 2008, Husson 2017). In a second step, we determine correlations between -omics and phenotype dimensions, and use them to explain the subgroups of individuals from the ACTION-NTR cohort. In order to validate the results, we project data of the ACTION-Curium-LUMC cohort onto the latent dimensions and determine if correlations between omics and phenotype data can be reproduced.Integration of data across cohorts and across data types, requires interoperability. We applied different practices to make the data FAIR, including conversion of files to community-standard formats, and capturing experimental metadata using the ISA (Investigation, Study, Assay) metadata framework (Johnson 2021) and ontology-based annotations. All data analysis steps including pre-processing of different omics data types were implemented in either R or Python and combined in a modular Nextflow (Di Tommaso 2017) workflow, where the environment for each step is provided as a Singularity (Kurtzer 2017) container. The analysis workflow is packaged in a Research Object Crate (RO-Crate) (Soiland-Reyes 2022). The RO-Crate is a FAIR digital object that contains the Nextflow workflow including ontology-based annotations of each analysis step. Since omics data is considered to be potentially personally identifiable, the packaged workflow contains a minimal synthetic data set resembling the original data structure. Finally, the code is made available on GitHub and the workflow is registered at Workflowhub (Goble 2021). Since our Nextflow workflow is set up in a modular manner, the individual analysis steps can be reused in other workflows. We demonstrate this replicability by applying different sub-workflows to data from two different cohorts. HTML XML PDF
      PubDate: Thu, 25 Aug 2022 12:08:02 +030
       
  • Essential Biodiversity Variables: extracting plant phenological data from
           specimen labels using machine learning

    • Abstract: Research Ideas and Outcomes 8: e86012
      DOI : 10.3897/rio.8.e86012
      Authors : Maria Mora-Cross, Adriana Morales-Carmiol, Te Chen-Huang, María Barquero-Pérez : Essential Biodiversity Variables (EBVs) make it possible to evaluate and monitor the state of biodiversity over time at different spatial scales. Its development is led by the Group on Earth Observations Biodiversity Observation Network (GEO BON) to harmonize, consolidate and standardize biodiversity data from varied biodiversity sources. This document presents a mechanism to obtain baseline data to feed the Species Traits Variable Phenology or other biodiversity indicators by extracting species characters and structure names from morphological descriptions of specimens and classifying such descriptions using machine learning (ML).A workflow that performs Named Entity Recognition (NER) and Classification of morphological descriptions using ML algorithms was evaluated with excellent results. It was implemented using Python, Pytorch, Scikit-Learn, Pomegranate, Python-crfsuite, and other libraries applied to 106,804 herbarium records from the National Biodiversity Institute of Costa Rica (INBio). The text classification results were almost excellent (F1 score between 96% and 99%) using three traditional ML methods: Multinomial Naive Bayes (NB), Linear Support Vector Classification (SVC), and Logistic Regression (LR). Furthermore, results extracting names of species morphological structures (e.g., leaves, trichomes, flowers, petals, sepals) and character names (e.g., length, width, pigmentation patterns, and smell) using NER algorithms were competitive (F1 score between 95% and 98%) using Hidden Markov Models (HMM), Conditional Random Fields (CRFs), and Bidirectional Long Short Term Memory Networks with CRF (BI-LSTM-CRF). HTML XML PDF
      PubDate: Tue, 23 Aug 2022 11:16:05 +030
       
  • Deliverable D4.10 Plan for Exploitation and Dissemination of SHOWCASE
           results

    • Abstract:
      DOI : 10.3897/arphapreprints.e93509
      Authors : Anna Sapundzhieva, Alexandra Korcheva, Nikol Yovcheva : Communication, dissemination and exploitation play a vital role within SHOWCASE as the main means of ensuring knowledge transfer and uptake of results during the project lifetime and after the project is concluded. The project’s strategic objectives and target groups, as well as the key messages and narratives that the project aims to communicate serve as an orientation in the project’s actions in the relevant field. The current Plan for Exploitation and Dissemination of Results (PEDR) has been developed to define target-specific objectives and outline concrete implementation actions.The SHOWCASE PEDR represents a document that aims to guide the communication and dissemination efforts to target project-relevant audiences, convey clear, understandable, coordinated and effective messages, and reach out project results to all interested parties within the various stakeholder groups.The plan presents the different communication and dissemination tools, structured in an implementation plan according to the different target groups and different stage of development of the project. It also provides a list of tailored key performance indicators (KPI) for the project’s outreach activities that aim to provide a means to quantitatively monitor the effectiveness of dissemination activities. Indicative time schedule for implementation and updates is provided.In addition, this document will identify key project results, which will be a subject of exploitation. HTML XML PDF
      PubDate: Mon, 15 Aug 2022 17:30:00 +030
       
  • Deliverable D4.8 Data Management Plan

    • Abstract:
      DOI : 10.3897/arphapreprints.e93508
      Authors : Alexandra Korcheva, Anna Sapundzhieva, Ignasi Bartomeus : The SHOWCASE DMP is structured into five sections, which aim to establish the scope and terms of use of research data within the project in accordance with the Horizon 2020 requirements of data management.The first section provides an introduction to the plan, which outlines the main data management practices that SHOWCASE would implement throughout the five-year project duration, as well as aspects of sustainable management of results and data after the conclusion of the project period.The second section of the document provides an overview of the commitments that SHOWCASE has made in relation to handling data in a controlled and transparent way, and ensuring an open access to research data and results in line with the EU’s Open Research Data Pilot and FAIR data management.The third section describes the details of data management within the project, focusing on different aspects of the process - from data collection, through data processing, to storage and access provision. The section features information on personal data protection in accordance with the General Data Protection Regulation (GDPR), as well as a break-down of the research data usage into project work packages. Recommendations for relevant data management practices are described in the section.The fourth section includes an overview of the specific data management details for the project work packages. The specific data formats and data management requirements of work packages are described.The fifth section of the DMP features concluding remarks on the data management strategy adopted by the project, and it outlines future updates and additions to the plan, which are going to be presented at a later stage of the project’s development. HTML XML PDF
      PubDate: Mon, 15 Aug 2022 17:30:00 +030
       
  • Deliverable D1.1 Network of EBAs established across Europe

    • Abstract:
      DOI : 10.3897/arphapreprints.e93505
      Authors : Vincent Bretagnolle, Sabrina Gaba, Amelia Hood, Simon Potts : SHOWCASE’s first step is to create a European network of local Experimental Biodiversity Areas (EBAs), that will be used to co-develop (though to varying degrees) and test successful strategies for better integrating biodiversity into farming. EBAs are located across a wide range of agro-ecosystems and represent farming systems undergoing both intensification as well as agricultural abandonment. Rather than creating new sites for the network, the approach in SHOWCASE was that EBAs would be developed mostly from existing collaborations between scientists and practitioners. The first work Package of SHOWCASE, WP1, has built in the 10 countries an experimental and knowledge exchange network in agricultural landscapes across Europe. Existing collaborations include LTSER platforms from eLTER RI, farmer cooperatives, farming research organisations and conservation organisations. These are well-established multi-actor networks already undertaking knowledge exchange, participatory research and innovation activities. Then, participatory approaches with farmers, administrators and other stakeholders are defining operational biodiversity targets at field/farm/regional level by discussing the types and extents of biodiversity indicators that should be used. WP1 thus is building our EBA network, with each EBA serving both as a local testbed for developing and implementing novel interventions and as a knowledge exchange hub. This is a pan-European network of Experimental Biodiversity Areas. In these EBAs multi-actor communities (growers, extension workers, researchers, NGOs, citizens etc.) work together to co-develop, co-manage, co-monitor and co-evaluate biodiversity innovations to enhance farm production, wildlife protection, livelihood quality and resilience of social-ecological production systems. These multi-actor communities will i) identify and prioritise local or regional challenges of biodiversity-agricultural production trade-offs, and ii) co-formulate and test potential solutions. However, to add value at the European level and allow up- scaling and out-scaling of solutions, it is essential to have a common framework and set of core standardised methodologies and measures used by all EBAs. EBAs are expected to be somewhat representative of Europe, in terms of biogeography, farming system or agricultural intensification/abandonment. However, all EBAs are starting from different points. One main target was to develop the network of EBAs based on a core approach, though place-based, in order to provide local solutions to local challenges. A conceptual representation of an EBA is given below illustrating how each EBA will be the fundamental base and operational platform integrating the various Tasks of WP1. HTML XML PDF
      PubDate: Mon, 15 Aug 2022 17:30:00 +030
       
  • Deliverable D4.11 EIP abstract on the literature review of Task 2.1

    • Abstract:
      DOI : 10.3897/arphapreprints.e93510
      Authors : Lena Luise Schaller, Verena Scherfranz, Kati Häfner, Fabian Klebl, Jabier Ruiz, Jochen Kantelhardt, Annette Piorr : Regulatory and incentive instruments for biodiversity management on farms (Short summary for practitioners) HTML XML PDF
      PubDate: Mon, 15 Aug 2022 17:30:00 +030
       
  • Deliverable D2.1¬†Overview of regulatory and incentive instruments for
           biodiversity management on farms

    • Abstract:
      DOI : 10.3897/arphapreprints.e93506
      Authors : Lena Luise Schaller, Verena Scherfranz, Kati Häfner, Fabian Klebl, Jabier Ruiz, Jochen Kantelhardt, Annette Piorr : This document represents Deliverable 2.1 “Overview of regulatory and incentive instruments for biodiversity management on farms” within WP2 „Identifying incentives to promote biodiversity and ecosystem services in agricultural landscapes“ of the EU Horizon 2020 project SHOWCASE. It reports the outcomes of WP2 Task 2.1 “Evaluating regulatory and incentive instruments for biodiversity management on farms”.In the 1st and 2nd chapter, the report gives a short introduction of the deliverable’s objectives, the tasks addressed, the report’s outline and the main focus of the literature review.Chapter 3 gives an overview of the main laws governing biodiversity protection in the European Union. The main elements of the Birds and Habitats directives are presented, alongside other biodiversity laws and policies, with a focus on the obligations and requirements they set on agriculture in order to protect European native wildlife. Chapter 3 also covers the features of the EU’s Common Agricultural Policy that operate as a regulatory baseline for all beneficiaries of farm subsidies, i.e., cross-compliance and greening requirements under the current CAP and the new conditionality in the CAP 2023-2027.Chapter 4 gives an overview of economic and non-economic approaches potentially promoting farmers’ pro-biodiversity behaviour. Whereas economically oriented approaches imply positive or negative monetary flows – compensation payments or rewards vs. penalties – to motivate farmers to implement biodiversity-friendly management practices or to prevent them from harming biodiversity, partnerships and networks steer farmers’ behaviour through agreeing on a common goal and working towards it by sharing resources, skills and risk. With regards to the agricultural focus of SHOWCASE, Chapter 4 looks in more detail at the incentives provided by the Common Agricultural Policy (CAP) of the European Union. This covers both the current and future CAP, with an overview of how the novel eco-schemes can provide new incentives for farmers to adopt biodiversity friendly practices.Chapter 5 looks into how the combination of regulatory frameworks and incentives operate in practice for farmers in the EU. To this end, grey literature and European Commission publications related to farming for biodiversity have been reviewed. A specific focus is set on biodiversity-friendly farming in Natura 2000 sites, as central exemplary areas of continuous and long-lasting efforts in biodiversity conservation. This is followed by revising some of the main conclusions from very recent grey literature assessing the successes and failures of the CAP in relation to biodiversity.Chapter 6 provides an overview of approaches that have already been implemented to incentivize farmers’ pro-biodiversity behaviour. Based on grey literature, various types of approaches – i. e. focusing on plot or farm level, land tenure or the entire value chain, building on organic farming or including market-based, value-based or measure-based mechanisms – were identified within the EBA countries, further EU member states and selected western countries outside the EU. In sum, 62 examples of pro-biodiversity schemes were included in the further analysis representing highly divergent incentivizing mechanisms and the most important agricultural systems of the EBAs as well as in consequence serving as an information platform for further EBA scheme design activities.Based on the preceding chapters and their focus on result-based approaches, Chapter 7 casts a critical eye on their suitability with regards to various regulatory, policy, social and administrative contexts also considering potential national differences. On the international level, WTO requirements such as Green Box rules are a limiting factor with regards to result- based payment modalities and thus scheme design. On the national and regional level, issues to be considered include long-term availability of funding, guaranteeing additionality if requested, stakeholders’ and decision-makers’ attitudes towards agri-environment-climate measures in general as well as towards result-oriented approaches specifically, availability of suitable indicators and IT-systems, access to extension services and profound know-how of farmers and public authorities regarding the interlinkages between biodiversity and farming practices. On individual level, farmers’ trust in involved institutions and their willingness to participate are additionally discussed as highly relevant factors affecting the suitability of result- based approaches.In Chapter 8 a structured overview on factors influencing farmers’ willingness to promote biodiversity by implementing voluntary biodiversity measures is presented. Based on the review of scientific literature, the chapter describes several determinants which have been identified along three scales, i.e. 1) society, community and landscape, 2) farm scale, and 3) farmers’ intrinsic factors. The main influencing factors at the first scale range from the design of policies, to economic aspects, to socio-cultural norms. The second scale encompasses relevant farm characteristics, such as farm type and size to field conditions. For the farmers’ intrinsic factors age, education, experience, and self-identity play an important role. However, it is important to make a distinction between farmers’ willingness to participate in schemes and their actual behaviour, because the latter is determined by ...
      PubDate: Mon, 15 Aug 2022 17:30:00 +030
       
  • Deliverable D4.9 Project logo, marketing starter pack and website
           running

    • Abstract:
      DOI : 10.3897/arphapreprints.e93511
      Authors : Anna Sapundzhieva, Alexandra Korcheva, Georgi Zhelezov : The following report presents the initial project branding and marketing products that showcase the project’s visual identity and overall corporate appearance.As a foundation of the future effective communication activities, a sound set of working dissemination tools and materials is crucial to be established within the first months of the project. A project logo, project promotional materials, overall visual identity package, and a public website (www.showcase-project.eu) were developed in the first 4 months of the project duration in order to form the main tools of project public visibility and internal communication.The project is provided with a logo that has been communicated and coordinated with all project partners. Dissemination materials such as the SHOWCASE brochure and poster were produced for raising awareness and engaging stakeholders at events. A project brand manual was created and circulated among project partners in order to provide a consistent visual representation of the project. A set of corporate templates was also produced and made available to the consortium partners to facilitate future dissemination and reporting activities such as letters, milestones and deliverable reports, PowerPoint presentations, etc. The project website is developed as the main dissemination channel.The longer‐term impact of the project's results will be secured by maintaining the website for a minimum of 5 years after the end of the project. HTML XML PDF
      PubDate: Mon, 15 Aug 2022 17:30:00 +030
       
  • Deliverable D3.8¬†A review of existing citizen science approaches to
           monitoring farmland biodiversity

    • Abstract:
      DOI : 10.3897/arphapreprints.e93507
      Authors : Andrew Ruck, Erik Öckinger, Rene van der Wal, Alice Mauchline, Amelia Hood, Simon Potts, Michiel Wallis De Vries, Sabrina Gaba, Vincent Bretagnolle : This report was researched and written between April and December 2021 by researchers at the Swedish University of Agricultural Sciences (SLU), with support from partners at the University of Reading (UK), De Vlinderstichting (Netherlands), and Centre National de la Recherche Scientifique (CNRS, France). The report consists of a review of existing 'citizen science’ approaches to monitoring biodiversity on farmland, in which we introduce a typology of five different types of approach, and highlight the strengths and weaknesses of these. This forms part of the project “SHOWCASing synergies between agriculture, biodiversity and Ecosystem services to help farmers capitalising on native biodiversity” (SHOWCASE). SHOWCASE aims to encourage the widespread uptake of biodiversity-friendly farming practices across Europe, both through identifying effective incentives for farmers, and gathering further evidence of the ecosystem services provided by increased levels of biodiversity. The project receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No.862480. In particular, this report fulfils Deliverable 3.8 within SHOWCASE: “A review of existing citizen science approaches to monitoring farmland biodiversity, including an overview of the different statistical approaches to handling citizen science data”. We at SLU are grateful to all SHOWCASE partners for their contributions. HTML XML PDF
      PubDate: Mon, 15 Aug 2022 17:30:00 +030
       
  • Bio-photogrammetry: digitally archiving coloured 3D morphology data of
           creatures and associated challenges

    • Abstract: Research Ideas and Outcomes 8: e86985
      DOI : 10.3897/rio.8.e86985
      Authors : Yuichi Kano : Morphological data of life forms are fundamental for documenting and understanding biodiversity. I developed a photogrammetry technique for reconstructing the outer coloured morphology of various creatures and published more than 1000 models online (https://sketchfab.com/ffishAsia-and-floraZia). By suspending it with nylon fishing line(s), taking digital photos from multiple angles and analysing the photos with photogrammetry software, we can obtain a fine 3-dimensional (3D) model of a creature. I believe the challenge could contribute to various fields, such as taxonomy, museology, morphology, anatomy, ecology, education, artificial intelligence, virtual reality, metaverse and, eventually, open/citizen science. Herein, I report the idea and achievement, which I have termed “bio-photogrammetry.” HTML XML PDF
      PubDate: Mon, 8 Aug 2022 10:31:51 +0300
       
  • Situating social work within disaster governance. Assessing the agency of
           social work as a bridging agent and its professionalization in disaster
           governance

    • Abstract: Research Ideas and Outcomes 8: e81568
      DOI : 10.3897/rio.8.e81568
      Authors : Pia Hollenbach, Monika Goetzoe, Malith de Silva : The SARS-COV-2 pandemic created a serious shock and surprise to the disaster governance mechanisms in existence. Even the most advanced disaster governance systems in the world struggled to govern, respond, communicate risk and build resilience against the pandemic. The overall management – locally and globally- showed that relevant stakeholders such as social workers that work frontline but also within disaster management relevant fields, were not heart nor taken their potentials and knowledge into consideration to sustainably set up a disaster management and responds strategy. Applying a comparative multi-sited ethnographic approach, the study aims to highlight the potential agency of social work as a bridging agent to enhance the efficiency and effectiveness of existing disaster governance and communication architecture and improve the resilience of communities to cope with the socio-ecological complexity of future disasters, similar to SARS-COV-2. Impact will be created in four main areas: (1) Actors in disaster governance will be educated using the new knowledge produced on contextualized disaster governance and communication strategies and impacts on community resilience; (2) Enhanced capacity and awareness of professional social work practitioners on their role/s as bridging agents within the disaster governance architecture to enhance disaster risk communication and community resilience; (3) Improved capacity for decision and policy-making and strengthened agency of social work in the field of disaster governance through the introduction of professional development training and the ToolKit SW2BRIDGE; and (4) Improved social work education at the university level through the introduction of a post-graduate programme on the application of social work in disasters. HTML XML PDF
      PubDate: Mon, 1 Aug 2022 09:31:34 +0300
       
  • Language evolution is not limited to speech acquisition: a large study of
           language development in children with language deficits highlights the
           importance of the voluntary imagination component of language

    • Abstract: Research Ideas and Outcomes 8: e86401
      DOI : 10.3897/rio.8.e86401
      Authors : Andrey Vyshedskiy : Did the boy bite the cat or was it the other way around' When processing a sentence with several objects, one has to establish ‘who did what to whom’. When a sentence cannot be interpreted by recalling an image from memory, we rely on the special type of voluntary constructive imagination called Prefrontal synthesis (PFS). PFS is defined as the ability to juxtapose mental visuospatial objects at will. We hypothesised that PFS has fundamental importance for language acquisition. To test this hypothesis, we designed a PFS-targeting intervention and administered it to 6,454 children with language deficiencies (age 2 to 12 years). The results from the three-year-long study demonstrated that children who engaged with the PFS intervention showed 2.2-fold improvement in combinatorial language comprehension compared to children with similar initial evaluations. These findings suggest that language can be improved by training the PFS and exposes the importance of the visuospatial component of language. This manuscript reflects on the experimental findings from the point of view of human language evolution. When used as a proxy for evolutionary language acquisition, the study results suggest a dichotomy of language evolution, with its speech component and its visuospatial component developing in parallel. The study highlights the radical idea that evolutionary acquisition of language was driven primarily by improvements of voluntary imagination rather than by improvements in the speech apparatus. HTML XML PDF
      PubDate: Thu, 14 Jul 2022 11:59:19 +030
       
  • Anthropocenic Objects. Collecting Practices for the Age of Humans

    • Abstract: Research Ideas and Outcomes 8: e89446
      DOI : 10.3897/rio.8.e89446
      Authors : Ulrike Sturm, Elisabeth Heyne, Elisa Herrmann, Bergit Arends, Anna-Lisa Dieter, Eric Dorfman, Frank Drauschke, Nicole Heller, Rebecca Kahn, Katja Kaiser, Gerda Koch, Nicolas Kramar, Alicia Mansilla Sánchez, Franz Mauelshagen, Tahani Nadim, Richard Pell, Mareike Petersen, Katharina Schmidt-Loske, Henning Scholz, Colin Sterling, Helmuth Trischler, Sarah Wagner : The knowledge needed to tackle future environmental and societal challenges can only be generated through exchange between science and society. The conventional distinction made between natural and cultural heritage in museums and other institutions is no longer appropriate in the Anthropocene. Museums must rethink the social and cultural dimensions of existing museum collections and reinvent the organization of knowledge production for our present. In three workshops at the Museum für Naturkunde Berlin, practitioners and interdisciplinary theorists discussed the concept of “Anthropocenic objects” and considered how they create opportunities for the emergence of new collecting practices involving participatory research and open exchange between research, society, and conservation institutions. HTML XML PDF
      PubDate: Tue, 12 Jul 2022 14:31:59 +030
       
  • Showcasing synergies between agriculture, biodiversity and ecosystem
           services to help farmers capitalising on native biodiversity (SHOWCASE)

    • Abstract: Research Ideas and Outcomes 8: e90079
      DOI : 10.3897/rio.8.e90079
      Authors : David Kleijn, Simon Potts, Erik Öckinger, Felix Herzog, Lena Luise Schaller, Ignasi Bartomeus, Kati Häfner, Vincent Bretagnolle, Anna Sapundzhieva : The slow adoption by the agricultural sector of practices to promote biodiversity are thought to originate from three interrelated issues. First, we know little about which incentives effectively motivate farmers to integrate biodiversity into daily farm management. Second, few studies so far have produced evidence that biodiversity-based approaches produce benefits in terms of key variables for farmers (yield, profit). Third, there is a large communication gap between the scientists investigating biodiversity-based farming practices and the farmers who have to implement them. To overcome these barriers, SHOWCASE will review and test the effectiveness of a range of economic and societal incentives to implement biodiversity management in farming operations and examine farmer and public acceptance. Focus will be on three promising approaches: (i) result-based incentives, (ii) involvement in citizen science biodiversity monitoring and (iii) biodiversity-based business models. SHOWCASE will co-produce together with stakeholders solid interdisciplinary evidence for the agro-ecological and socio-economic benefits of biodiversity management in 10 contrasting farming systems across Europe. SHOWCASE will also design communication strategies that are tailor-made to farmers and other key stakeholders operating in different socio-economic and environmental conditions.SHOWCASE will develop a multi-actor network of 10 Experimental Biodiversity Areas in contrasting European farming systems that will be used for in-situ research on biodiversity incentives and evidence for benefits as well as knowledge exchange. This network will be used to identify and test biodiversity indicators and targets relevant to all stakeholders and use them in a learning-by-doing approach to improve benefits of biodiversity management on farms, both within the network and beyond. HTML XML PDF
      PubDate: Mon, 11 Jul 2022 10:16:31 +030
       
  • The Animal Landscape and Man Simulation System (ALMaSS): a history,
           design, and philosophy

    • Abstract: Research Ideas and Outcomes 8: e89919
      DOI : 10.3897/rio.8.e89919
      Authors : Christopher John Topping : This article is the first article in the new topical RIO journal collection for ALMaSS. This editorial introduces ALMaSS, its history, component parts and philosophy, and forms a first access point for those interested in knowing more. It is written from my own personal perspective as the instigator and main developer for the system, effectively as the ‘father’ of ALMaSS. HTML XML PDF
      PubDate: Thu, 7 Jul 2022 15:31:36 +0300
       
  • People-Powered Research and Experiential Learning: Unravelling Hidden
           Biodiversity

    • Abstract: Research Ideas and Outcomes 8: e83853
      DOI : 10.3897/rio.8.e83853
      Authors : Melanie Pivarski, Matt von Konrat, Thomas Campbell, Ayesha Qazi-Lampert, Laura Trouille, Heaven Wade, Aimee Davis, Selma Aburahmeh, Joseph Aguilar, Cosmin Alb, Ken Alferes, Ella Barker, Karl Bitikofer, Kelli Boulware, Carla Bruton, Sicong Cao, Arturo Corona Jr., Christine Christian, Kaltra Demiri, Daniel Evans, Nkosi Evans, Connor Flavin, Jasmine Gillis, Victoria Gogol, Elizabeth Heublein, Edward Huang, Jake Hutchinson, Cyrus Jackson, Odaliz Jackson, Lauren Johnson, Michi Kirihara, Henry Kivarkis, Annette Kowalczyk, Alex Labontu, Briajia Levi, Ian Lyu, Sylvie Martin-Eberhardt, Gaby Mata, Joann Martinec, Beth McDonald, Mariola Mira, Minh Nguyen, Pansy Nguyen, Sarah Nolimal, Victoria Reese, Will Ritchie, Joannie Rodriguez, Yarency Rodriguez, Jacob Shuler, Jasmine Silvestre, Glenn Simpson, Gabriel Somarriba, Rogers Ssozi, Tomomi Suwa, Cheyenne Syring, Nidhi Thirthamattur, Keith Thompson, Caitlin Vaughn, Mario Viramontes, Chak Shing Wong, Lauren Wszolek : Globally, thousands of institutions house nearly three billion scientific collections offering unparallelled resources that contribute to both science and society. For herbaria alone - facilities housing dried plant collections - there are over 3,000 herbaria worldwide with an estimated 350 million specimens that have been collected over the past four centuries. Digitisation has greatly enhanced the use of herbarium data in scientific research, impacting diverse research areas, including biodiversity informatics, global climate change, analyses using next-generation sequencing technologies and many others. Despite the entrance of herbaria into a new era with enhanced scientific, educational and societal relevance, museum specimens remain underused. Natural history museums can enhance learning and engagement in science, particularly for school-age and undergraduate students. Here, we outline a novel approach of a natural history museum using touchscreen technology that formed part of an interactive kiosk in a temporary museum exhibit on biological specimens. We provide some preliminary analysis investigating the efficacy of the tool, based on the Zooniverse platform, in an exhibit environment to engage patrons in the collection of biological data. We conclude there is great potential in using crowd‐sourced science, coupled with online technology to unlock data and information from digital images of natural history specimens themselves. Sixty percent of the records generated by community scientists (citizen scientists) were of high enough quality to be utilised by researchers. All age groups produced valid, high quality data that could be used by researchers, including children (10 and under), teens and adults. Significantly, the paper outlines the implementation of experiential learning through an undergraduate mathematics course that focuses on projects with actual data to gain a deep, practical knowledge of the subject, including observations, the collection of data, analysis and problem solving. We here promote an intergenerational model including children, high school students, undergraduate students, early career scientists and senior scientists, combining experiential learning, museum patrons, researchers and data derived from natural history collections. Natural history museums with their dual remit of education and collections-based research can play a significant role in the field of community engagement and people-powered research. There also remains much to investigate on the use of interactive displays to help learners interpret and appreciate authentic research. We conclude with a brief insight into the next phase of our ongoing people-powered research activities developed and designed by high school students using the Zooniverse platform. HTML XML PDF
      PubDate: Mon, 27 Jun 2022 17:01:37 +030
       
  • A price tag on species

    • Abstract: Research Ideas and Outcomes 8: e86741
      DOI : 10.3897/rio.8.e86741
      Authors : Urmas Kõljalg, R. Henrik Nilsson, Arnold Tobias Jansson, Allan Zirk, Kessy Abarenkov : Species have intrinsic value but also partake in a long range of ecosystem services of major economic value to humans. These values have proved hard to quantify precisely, making it all too easy to dismiss them altogether. We outline the concept of the species stock market (SSM), a system to provide a unified basis for valuation of all living species. The SSM amalgamates digitized information from natural history collections, occurrence data, and molecular sequence databases to quantify our knowledge of each species from scientific, societal, and economic points of view. The conceptual trading system will necessarily be very unlike that of the regular stock market, but the looming biodiversity crisis implores us to finally put an open and transparent price tag on symbiosis, deforestation, and pollution HTML XML PDF
      PubDate: Fri, 17 Jun 2022 13:46:14 +030
       
  • Biotic Interactions as Mediators of Context-Dependent
           Biodiversity-Ecosystem Functioning Relationships

    • Abstract: Research Ideas and Outcomes 8: e85873
      DOI : 10.3897/rio.8.e85873
      Authors : Nico Eisenhauer, Paola Bonfante, François Buscot, Simone Cesarz, Carlos Guerra, Anna Heintz-Buschart, Jes Hines, Guillaume Patoine, Matthias Rillig, Bernhard Schmid, Kris Verheyen, Christian Wirth, Olga Ferlian : Biodiversity drives the maintenance and stability of ecosystem functioning as well as many of nature’s benefits to people, yet people cause substantial biodiversity change. Despite broad consensus about a positive relationship between biodiversity and ecosystem functioning (BEF), the underlying mechanisms and their context-dependencies are not well understood. This proposal, submitted to the European Research Council (ERC), aims at filling this knowledge gap by providing a novel conceptual framework for integrating biotic interactions across guilds of organisms, i.e. plants and mycorrhizal fungi, to explain the ecosystem consequences of biodiversity change. The overarching hypothesis is that EF increases when more tree species associate with functionally dissimilar mycorrhizal fungi. Taking a whole-ecosystem perspective, we propose to explore the role of tree-mycorrhiza interactions in driving BEF across environmental contexts and how this relates to nutrient dynamics. Given the significant role that mycorrhizae play in soil nutrient and water uptake, BEF relationships will be investigated under normal and drought conditions. Resulting ecosystem consequences will be explored by studying main energy channels and ecosystem multifunctionality using food web energy fluxes and by assessing carbon storage. Synthesising drivers of biotic interactions will allow us to understand context-dependent BEF relationships. This interdisciplinary and integrative project spans the whole gradient from local-scale process assessments to global relationships by building on unique experimental infrastructures like the MyDiv Experiment, iDiv Ecotron and the global network TreeDivNet, to link ecological mechanisms to reforestation initiatives. This innovative combination of basic scientific research with real-world interventions links trait-based community ecology, global change research and ecosystem ecology, pioneering a new generation of BEF research and represents a significant step towards implementing BEF theory for human needs. HTML XML PDF
      PubDate: Tue, 7 Jun 2022 14:31:01 +0300
       
  • Current cave monitoring practices, their variation and recommendations for
           future improvement in Europe: A synopsis from the 6th EuroSpeleo
           Protection Symposium

    • Abstract: Research Ideas and Outcomes 8: e85859
      DOI : 10.3897/rio.8.e85859
      Authors : Alexander Weigand, Szilárd-Lehel Bücs, Stanimira Deleva, Lada Lukić Bilela, Pierrette Nyssen, Kaloust Paragamian, Axel Ssymank, Hannah Weigand, Valerija Zakšek, Maja Zagmajster, Gergely Balázs, Shalva Barjadze, Katharina Bürger, William Burn, Didier Cailhol, Amélie Decrolière, Ferdinando Didonna, Azdren Doli, Tvrtko Drazina, Joerg Dreybrodt, Lana Ðud, Csaba Egri, Markus Erhard, Sašo Finžgar, Dominik Fröhlich, Grant Gartrell, Suren Gazaryan, Michel Georges, Jean-Francois Godeau, Ralf Grunewald, John Gunn, Jeff Hajenga, Peter Hofmann, Lee Knight, Hannes Köble, Nikolina Kuharic, Christian Lüthi, Cristian Munteanu, Rudjer Novak, Dainis Ozols, Matija Petkovic, Fabio Stoch, Bärbel Vogel, Ines Vukovic, Meredith Hall Weberg, Christian Zaenker, Stefan Zaenker, Ute Feit, Jean-Claude Thies : This manuscript summarizes the outcomes of the 6th EuroSpeleo Protection Symposium. Special emphasis was laid on presenting and discussing monitoring activities under the umbrella of the Habitats Directive (EU Council Directive 92/43/EEC) for habitat type 8310 "Caves not open to the public" and the Emerald Network. The discussions revealed a high level of variation in the currently conducted underground monitoring activities: there is no uniform definition of what kind of underground environments the "cave" habitat should cover, how often a specific cave has to be monitored, and what parameters should be measured to evaluate the conservation status. The variation in spatial dimensions in national definitions of caves further affects the number of catalogued caves in a country and the number of caves to be monitored. Not always participants are aware of the complete national monitoring process and that data sets should be freely available or easily accessible. The discussions further showed an inherent dilemma between an anticipated uniform monitoring approach with a coherent assessment methodology and, on the contrary, the uniqueness of caves and subterranean biota to be assessed – combined with profound knowledge gaps and a lack of resources. Nevertheless, some good practices for future cave monitoring activities have been identified by the participants: (1) Cave monitoring should focus on bio- and geodiversity elements alike; (2) Local communities should be involved, and formal agreements envisaged; (3) Caves must be understood as windows into the subterranean realm; (4) Touristic caves should not be excluded ad-hoc from regular monitoring; (5) New digital tools and open FAIR data infrastructures should be implemented; (6) Cave biomonitoring should focus on a large(r) biological diversity; and (7) DNA-based tools should be integrated. Finally, the importance of the 'forgotten' Recommendation No. 36 from the Bern Convention as a guiding legal European document was highlighted. HTML XML PDF
      PubDate: Wed, 4 May 2022 12:46:42 +0300
       
  • An idea on Smart Farming: IoT monitoring of water production from
           dihydrogen combustion

    • Abstract: Research Ideas and Outcomes 8: e82995
      DOI : 10.3897/rio.8.e82995
      Authors : Radia Belkeziz : Smart Farming is a concept developing rapidly and gaining momentum. The management of livestock and farm products is done in an automated way thanks to IoT technology. The large field of data at hand offers the possibility of analysis for a better understanding of issues and more efficient decision-making. The management of water consumption is one of the most relevent Smart Farming use cases. In the event of drought, the pressure on water resources becomes increasingly strong. What if we produced water then' The idea of not worrying about the consequence of drought on agricultural production would be interesting.One of the first experiences you learn in a chemistry class is that the combustion of dihydrogen produces water. However, it is necessary to follow this experience closely because of the risk of explosion. Dihydrogen can be produced by the gasification of (agricultural) biomass. Here, the technology takes over, by the means of a supervising IoT system. This system will manage the overall process from biomass production, then dihydrogen production (biomass-to-hydrogen), to water production (dihydrogen-to-water).If the idea proves to be viable on a large scale, the result would be valuable in reducing the issue of water scarcity, in times of drought, in agricultural areas, and even in allowing energy autonomy on farms. HTML XML PDF
      PubDate: Mon, 18 Apr 2022 09:08:57 +030
       
  • FID Civil Engineering, Architecture and Urbanism digital - A platform for
           science (BAUdigital)

    • Abstract: Research Ideas and Outcomes 8: e82563
      DOI : 10.3897/rio.8.e82563
      Authors : Susanne Arndt, Anna Beer, Ina Blümel, Carsten Elsner, Christian Hauschke, Dagmar Holste, Benjamin Kampe, Micky Lindlar, Gelareh Mofakhamsanie, Andreas Noback, Hedda Saemann, Stephan Tittel, Friedmar Voormann, Katja Wermbter, Roger Winkler : University Library Braunschweig (UB Braunschweig), University and State Library Darmstadt (ULB Darmstadt), TIB – Leibniz Information Centre for Technology and Natural Sciences and the Fraunhofer Information Centre for Planning and Building (Fraunhofer IRB) are jointly establishing a specialised information service (FID, "Fachinformationsdienst") for the disciplines of civil engineering, architecture and urbanism. The FID BAUdigital, which is funded by the German Research Foundation (DFG, "Deutsche Forschungsgemeinschaft"), will provide researchers working on digital design, planning and production methods in construction engineering with a joint information, networking and data exchange platform and support them with innovative services for documentation, archiving and publication in their data-based research. HTML XML PDF
      PubDate: Wed, 6 Apr 2022 08:10:41 +0300
       
  • Europa Biodiversity Observation Network: User and Policy Needs Assessment

    • Abstract: Research Ideas and Outcomes 8: e84480
      DOI : 10.3897/arphapreprints.e84517
      Authors : Hannah Moersberger, Juliette G. C. Martin, Jessi Junker, Ivelina Georgieva, Silke Bauer, Pedro Beja, Tom Breeze, Lluís Brotons, Helge Bruelheide, Néstor Fernández, Miguel Fernandez, Ute Jandt, Christian Langer, Anne Lyche Solheim, Joachim Maes, Francisco Moreira, Guy Pe'er, Joana Santana, Judy Shamoun-Baranes, Bruno Smets, Jose Valdez, Ian McCallum, Henrique M. Pereira, Aletta Bonn : In this report, we present the analysis of the different available biodiversity data streams at the EU and national level, both baseline biodiversity data and monitoring data. We assess how these biodiversity data inform and trigger policy action and identify the related challenges the different European countries and relevant EU agencies face and the solutions to overcome them. To do this, we consulted with more than 350 expert stakeholders from policy, research and practice. The assessment identified a fragmented biodiversity data landscape that cannot currently easily answer all relevant policy questions. Quantity and quality of biodiversity baseline datasets differ for the different countries, ranging from non-existent biodiversity monitoring due to capacity issues, to regular monitoring of ecosystem processes and state. By engaging stakeholders and experts in both member states and non-member states and from several EU bodies, we identified key challenges and ways to address these with targeted solutions towards building a joint European Biodiversity Monitoring Network. Solutions include focussing on cooperation and coordination, enhanced data standardisation and sharing, as well as the use of models and new technologies. These solutions can however only be realised with dedicated funding and capacity building, in coordination with all stakeholders in partnership. HTML XML PDF
      PubDate: Wed, 30 Mar 2022 07:57:25 +030
       
  • The Ecological Observing System of the Adriatic Sea (ECOAdS): structure
           and perspectives within the main European biodiversity and environmental
           strategies

    • Abstract: Research Ideas and Outcomes 8: e82597
      DOI : 10.3897/rio.8.e82597
      Authors : Alessandra Pugnetti, Elisabetta Manea, Ivica Vilibić, Alessandro Sarretta, Lucilla Capotondi, Bruno Cataletto, Elisabeth De Maio, Carlo Franzosini, Ivana Golec, Marco Gottardi, Jelena Kurtović Mrčelić, Hrvoje Mihanovic, Alessandro Oggioni, Grgur Pleslic, Mariangela Ravaioli, Silvia Rova, Andrea Valentini, Caterina Bergami : This Policy Brief succinctly presents the Ecological Observing System of the Adriatic Sea (ECOAdS), aimed at integrating the ecological and oceanographic dimensions within the conservation strategy of the Natura 2000 network, and to propose a way to go for its future development and maintenance. After a definition of marine ecological observatories, we describe the current structure of ECOAdS, its key components and potential relevance in relation to the main European strategies for biodiversity and marine observation for the next decade. Finally, we suggest some actions that could be undertaken for the future development of ECOAdS, targeting possible perspectives in different regional, macro-regional, national and European strategic contexts. This Policy Brief is one of the outcomes of the Interreg Italy-Croatia Project ECOSS (ECological Observing System in the Adriatic Sea: oceanographic observations for biodiversity; https://www.italy-croatia.eu/web/ecoss), which had the main purpose to design and carry out the first steps for the establishment of ECOAdS. HTML XML PDF
      PubDate: Fri, 25 Mar 2022 09:08:20 +020
       
  • B-GOOD: Giving Beekeeping Guidance by cOmputatiOnal-assisted Decision
           making

    • Abstract: Research Ideas and Outcomes 8: e84129
      DOI : 10.3897/rio.8.e84129
      Authors : Dirk de Graaf, Martin Bencsik, Lina De Smet, Peter Neumann, Marten Schoonman, José Paulo Sousa, Christopher Topping, Wim Verbeke, James Williams, Coby van Dooremalen : A key to healthy beekeeping is the Health Status Index (HIS) inspired by EFSA’s Healthy-B toolbox which we will make fully operational, with the active collaboration of beekeepers, by facilitating the coordinated and harmonised flow of data from various sources and by testing and validating each component thoroughly. We envisage a step-by-step expansion of participating apiaries, and will eventually cover all EU biogeographic regions. The key to a sustainable beekeeping is a better understanding of its socio-economics, particularly within local value chains, its relationship with bee health and the human-ecosystem equilibrium of the beekeeping sector and to implement these insights into the data processing and decision making. We will fully integrate socio-economic analyses, identify viable business models tailored to different contexts for European beekeeping and determine the carrying capacity of the landscape. In close cooperation with the EU Bee Partnership, an EU-wide bee health and management data platform and affiliated project website will be created to enable sharing of knowledge and learning between scientists and stakeholders within and outside the consortium. We will utilise and further expand the classification of the open source IT-application for digital beekeeping, BEEP, to streamline the flow of data related to beekeeping management, the beehive and its environment (landscape, agricultural practices, weather and climate) from various sources. The dynamic bee health and management data platform will allow us to identify correlative relationships among factors impacting the HSI, assess the risk of emerging pests and predators, and enable beekeepers to develop adaptive management strategies that account for local and EU-wide issues. Reinforcing and establishing, where necessary, new multi-actor networks of collaboration will engender a lasting learning and innovation system to ensure social-ecological resilient and sustainable beekeeping. HTML XML PDF
      PubDate: Wed, 23 Mar 2022 08:49:02 +020
       
  • SKG4EOSC - Scholarly Knowledge Graphs for EOSC: Establishing a backbone of
           knowledge graphs for FAIR Scholarly Information in EOSC

    • Abstract: Research Ideas and Outcomes 8: e83789
      DOI : 10.3897/rio.8.e83789
      Authors : Markus Stocker, Tina Heger, Artur Schweidtmann, Hanna Ćwiek-Kupczyńska, Lyubomir Penev, Milan Dojchinovski, Egon Willighagen, Maria-Esther Vidal, Houcemeddine Turki, Daniel Balliet, Ilaria Tiddi, Tobias Kuhn, Daniel Mietchen, Oliver Karras, Lars Vogt, Sebastian Hellmann, Jonathan Jeschke, Paweł Krajewski, Sören Auer : In the age of advanced information systems powering fast-paced knowledge economies that face global societal challenges, it is no longer adequate to express scholarly information - an essential resource for modern economies - primarily as article narratives in document form. Despite being a well-established tradition in scholarly communication, PDF-based text publishing is hindering scientific progress as it buries scholarly information into non-machine-readable formats. The key objective of SKG4EOSC is to improve science productivity through development and implementation of services for text and data conversion, and production, curation, and re-use of FAIR scholarly information. This will be achieved by (1) establishing the Open Research Knowledge Graph (ORKG, orkg.org), a service operated by the SKG4EOSC coordinator, as a Hub for access to FAIR scholarly information in the EOSC; (2) lifting to EOSC of numerous and heterogeneous domain-specific research infrastructures through the ORKG Hub’s harmonized access facilities; and (3) leverage the Hub to support cross-disciplinary research and policy decisions addressing societal challenges. SKG4EOSC will pilot the devised approaches and technologies in four research domains: biodiversity crisis, precision oncology, circular processes, and human cooperation. With the aim to improve machine-based scholarly information use, SKG4EOSC addresses an important current and future need of researchers. It extends the application of the FAIR data principles to scholarly communication practices, hence a more comprehensive coverage of the entire research lifecycle. Through explicit, machine actionable provenance links between FAIR scholarly information, primary data and contextual entities, it will substantially contribute to reproducibility, validation and trust in science. The resulting advanced machine support will catalyse new discoveries in basic research and solutions in key application areas. HTML XML PDF
      PubDate: Tue, 15 Mar 2022 14:47:20 +020
       
  • The WIO Regional Benthic Imagery Workshop: Lessons from past IIOE-2
           expeditions

    • Abstract: Research Ideas and Outcomes 8: e81563
      DOI : 10.3897/rio.8.e81563
      Authors : Tanya Haupt, Jamie Ceasar, Paris Stefanoudis, Charles von der Meden, Robyn Payne, Luther Adams, Darrell Anders, Anthony Bernard, Willem Coetzer, Wayne Florence, Liesl Janson, Ashley Johnson, Roxanne Juby, Alison Kock, Daniel Langenkämper, Ahmed Nadjim, Denham Parker, Toufiek Samaai, Laurenne Snyders, Leshia Upfold, Grant van der Heever, Lauren Williams : Originating from the Second International Indian Ocean Expedition (IIOE-2), the main goal of the Western Indian Ocean (WIO) Regional Benthic Imagery Workshop, was to provide information and training on the use of various underwater imagery platforms in benthic research. To date, attempts made to explore the bottom of the ocean range from simple diving bells to more advanced camera systems, and the rapidly expanding field of underwater image-based research has supported marine exploration in many forms, from biodiversity surveys, spatial analyses and temporal studies, to monitoring schemes. Alongside the increasing use of underwater camera systems worldwide, there is an evident need to improve training and access to these techniques for students and researchers from institutes within the WIO. The week-long virtual event was conducted between 30 August and 3 September 2021 with 266 participants. Sessions consisted of lessons, practical demonstrations and interactive discussions which covered the steps required to conduct underwater imagery surveys, taking participants through elements of sampling design, data acquisition and processing, considerations for statistical analysis and, effective managment of data. The session recordings from the workshop are available online as a teaching aid which has the potential to reach marine researchers both regionally and globally. It is crucial that we build on this momentum by continuing to develop and strengthen the network established through this initiative for standardised benthic-image-based research within the WIO. HTML XML PDF
      PubDate: Tue, 8 Mar 2022 14:14:19 +0200
       
  • BridgeDb and Wikidata: a powerful combination generating interoperable
           open research (BridgeDb)

    • Abstract: Research Ideas and Outcomes 8: e83031
      DOI : 10.3897/rio.8.e83031
      Authors : Egon Willighagen, Martina Kutmon, Marvin Martens, Denise Slenter : Like humans have a unique social security number and different phone numbers from various providers, so do proteins and metabolites have a unique structure but different identifiers from various databases. BridgeDb is an interoperability platform that allows combining these databases, by matching database-specific identifiers. These matches are called identifier mappings, and they are indispensable when combining experimental (omics) data with knowledge in reference databases. BridgeDb takes care of this interoperability between gene, protein, metabolite, and other databases, thus enabling seamless integration of many knowledge bases and wet-lab results. Since databases get updated continuously, so should the Open Science BridgeDb project. HTML XML PDF
      PubDate: Mon, 7 Mar 2022 11:50:37 +0200
       
  • Sharing taxonomic expertise between natural history collections using
           image recognition

    • Abstract: Research Ideas and Outcomes 8: e79187
      DOI : 10.3897/rio.8.e79187
      Authors : Michael Greeff, Max Caspers, Vincent Kalkman, Luc Willemse, Barry Sunderland, Olaf Bánki, Laurens Hogeweg : Natural history collections play a vital role in biodiversity research and conservation by providing a window to the past. The usefulness of the vast amount of historical data depends on their quality, with correct taxonomic identifications being the most critical. The identification of many of the objects of natural history collections, however, is wanting, doubtful or outdated. Providing correct identifications is difficult given the sheer number of objects and the scarcity of expertise. Here we outline the construction of an ecosystem for the collaborative development and exchange of image recognition algorithms designed to support the identification of objects. Such an ecosystem will facilitate sharing taxonomic expertise among institutions by offering image datasets that are correctly identified by their in-house taxonomic experts. Together with openly accessible machine learning algorithms and easy to use workbenches, this will allow other institutes to train image recognition algorithms and thereby compensate for the lacking expertise. HTML XML PDF
      PubDate: Tue, 1 Mar 2022 10:02:21 +0200
       
  • D6.1 Analysis of needs and capacity of different audiences including
           policy makers, expert practitioners and other modellers

    • Abstract:
      DOI : 10.3897/arphapreprints.e82715
      Authors : Milica Trajković, Dajana Vujaklija, Guy Ziv, Arjan Gosal, Jiaqi Ge, Jodi Gunning, Birgit Mueller, Annabelle Williams, Elisabet Nadeu : This document has five main sections: the first one, “Developing the needs assessment protocol” which explains how we approached to different stakeholders in order to define and analyse their needs and capacities; the second section contains the report of of the interviews conducted by RISE and present the needs of Policy Makers; section three explains the needs of expert practitioners identified during the online workshop (14th and 15th of July 2020);  section four presents the needs of biophysical modeling community and section five explains the needs of ABM modellers identified from recent scholarly workshops. The results of this analysis will be taken under consideration and co-design and co-development processes. HTML XML PDF
      PubDate: Fri, 25 Feb 2022 16:30:00 +020
       
  • Deliverable D2.2 BESTMAP Conceptual Framework Design &
           Architecture 

    • Abstract:
      DOI : 10.3897/arphapreprints.e82404
      Authors : Guy Ziv, Jodi Gunning, Tomáš Václavík, Michael Beckmann, Anne Paulus, Birgit Mueller, Meike Will, Anna Cord, Stephanie Roilo, James Bullock, Paul Evans, Cristina Domingo-Marimon, Joan Masó Pau : This deliverable provides a General Framework for the BESTMAP Policy Impact Assessment Modelling (BESTMAP-PIAM) toolset. The BESTMAP-PIAM is based on the notion of defining (a) a typology of agricultural systems, with one (or more) representative case study (CS) in each major system; (b) mapping all individual farms within the case study to a Farm System Archetype (FSA) typology; (c) model the adoption of agri-environmental schemes (AES) within the spatially-mapped FSA population using Agent Based Models (ABM), based on literature and a survey with sufficient representative sample in each FSA of each CS, to elucidate the non-monetary drivers underpinning AES adoption and the relative importance of financial and non-financial/social/identity drivers; (d) linking AES adoption to a set of biophysical, ecological and socio-economic impact models; (e) upscaling the CS level results to EU scale; (f) linking the outputs of these models to indicators developed for the post-2020 CAP output, result and impact reports; (g) visualizing outputs and providing a dashboard for policy makers to explore a range of policy scenarios, focusing on cost-effectiveness of different AES. HTML XML PDF
      PubDate: Fri, 25 Feb 2022 15:30:00 +020
       
  • Use of Worksheet events in Excel to save solver objective cell value from
           each iteration

    • Abstract: Research Ideas and Outcomes 8: e79006
      DOI : 10.3897/rio.8.e79006
      Authors : Prasanth Sambaraju : Solver is a Microsoft Excel add-in program which is used to find an optimal value for a formula in the objective cell. Solver accomplishes this either by maximizing, minimizing or setting the objective cell value to a specific value. The article presents the utility of in built worksheet events in Excel VBA to save the value of objective cell from each iteration when solver is used for optimization. HTML XML PDF
      PubDate: Fri, 25 Feb 2022 08:43:38 +020
       
  • Unifying approaches to Functional Marine Connectivity for improved marine
           resource management: the European SEA-UNICORN COST Action

    • Abstract: Research Ideas and Outcomes 8: e80223
      DOI : 10.3897/rio.8.e80223
      Authors : Audrey Darnaude, Sophie Arnaud-Haond, Ewan Hunter, Oscar Gaggiotti, Anna Sturrock, Maria Beger, Filip Volckaert, Angel Pérez-Ruzafa, Lucía López-López, Susanne E. Tanner, Cemal Turan, Servet Ahmet Doğdu, Stelios Katsanevakis, Federica Costantini : Truly sustainable development in a human-altered, fragmented marine environment subject to unprecedented climate change, demands informed planning strategies in order to be successful. Beyond a simple understanding of the distribution of marine species, data describing how variations in spatio-temporal dynamics impact ecosystem functioning and the evolution of species are required. Marine Functional Connectivity (MFC) characterizes the flows of matter, genes and energy produced by organism movements and migrations across the seascape. As such, MFC determines the ecological and evolutionary interdependency of populations, and ultimately the fate of species and ecosystems. Gathering effective MFC knowledge can therefore improve predictions of the impacts of environmental change and help to refine management and conservation strategies for the seas and oceans. Gathering these data are challenging however, as access to, and survey of marine ecosystems still presents significant challenge. Over 50 European institutions currently investigate aspects of MFC using complementary methods across multiple research fields, to understand the ecology and evolution of marine species. The aim of SEA-UNICORN, a COST Action within the European Union Horizon 2020 framework programme, is to bring together this research effort, unite the multiple approaches to MFC, and to integrate these under a common conceptual and analytical framework. The consortium brings together a diverse group of scientists to collate existing MFC data, to identify knowledge gaps, to enhance complementarity among disciplines, and to devise common approaches to MFC. SEA-UNICORN will promote co-working between connectivity practitioners and ecosystem modelers to facilitate the incorporation of MFC data into the predictive models used to identify marine conservation priorities. Ultimately, SEA-UNICORN will forge strong forward-working links between scientists, policy-makers and stakeholders to facilitate the integration of MFC knowledge into decision support tools for marine management and environmental policies. HTML XML PDF
      PubDate: Tue, 22 Feb 2022 14:49:46 +020
       
  • Deliverable D3.4 Summaries of data, obstacles and challenges from
           interview campaigns

    • Abstract:
      DOI : 10.3897/arphapreprints.e81787
      Authors : Felix Wittstock, David Hötten, Sofia Biffi, Cristina Domingo, Bořivoj Šarapatka, Marek Bednář, Minučer Mesaroš : This deliverable presents a Summaries of data, obstacles and challenges from interview campaigns of the H2020 BESTMAP project. It covers a detailed description of methodology, reporting on the concrete steps taken to collect and analyze interview data. It also discusses obstacles and challenges to BESTMAP interview campaigns. Finally, the deliverable presents the main qualitative and quantitative findings of the interview analysis, with a focus on qualitative content analysis of open interview questions. HTML XML PDF
      PubDate: Mon, 7 Feb 2022 10:15:00 +0200
       
  • D1.3 Guidelines and protocols harmonizing activities across case
           studies

    • Abstract:
      DOI : 10.3897/arphapreprints.e81337
      Authors : Tomáš Václavík, Fanny Langerwisch, Guy Ziv, Jodi Gunning, Arjan Gosal, Michael Beckmann, Anne Paulus, Felix Wittstock, Anna Cord, Stephanie Roilo, Cristina Domingo-Marimon, Anabel Sanchez, Annelies Broekman, Dajana Vujaklija : This document is the first version of the Guidelines and protocols harmonizing activities across case studies of the H2020 BESTMAP project. It is intended to be updated in month 40 (D1.8). HTML XML PDF
      PubDate: Fri, 28 Jan 2022 10:00:00 +020
       
  • Europa Biodiversity Observation Network: integrating data streams to
           support policy

    • Abstract:
      DOI : 10.3897/arphapreprints.e81207
      Authors : Henrique M. Pereira, Jessi Junker, Néstor Fernández, Joachim Maes, Pedro Beja, Aletta Bonn, Tom Breeze, Lluís Brotons, Helge Bruelheide, Marcel Buchhorn, César Capinha, Cher Chow, Karolin Dietrich, Maria Dornelas, Grégoire Dubois, Miguel Fernandez, Mark Frenzel, Nikolai Friberg, Steffen Fritz, Ivelina Georgieva, Anne Gobin, Carlos Guerra, Sigrid Haande, Sergi Herrando, Ute Jandt, W. Daniel Kissling, Ingolf Kühn, Christian Langer, Camino Liquete, Anne Lyche Solheim, David Martí, Juliette G. C. Martin, Annett Masur, Ian McCallum, Marit Mjelde, Jannicke Moe, Hannah Moersberger, Alejandra Morán-Ordóñez, Francisco Moreira, Martin Musche, Laetitia M. Navarro, Alberto Orgiazzi, Robert Patchett, Lyubomir Penev, Joan Pino, Gabriela Popova, Simon Potts, Anna Ramon, Leonard Sandin, Joana Santana, Anna Sapundzhieva, Linda See, Judy Shamoun-Baranes, Bruno Smets, Pavel Stoev, Leho Tedersoo, Liis Tiimann, Jose Valdez, Sara Vallecillo, Roy H. A. Van Grunsven, Ruben Van De Kerchove, Dani Villero, Piero Visconti, Claudia Weinhold, Annika M. Zuleger : Observations are key to understand the drivers of biodiversity loss, and the impacts on ecosystem services and ultimately on people. Many EU policies and initiatives demand unbiased, integrated and regularly updated biodiversity and ecosystem service data. However, efforts to monitor biodiversity are spatially and temporally fragmented, taxonomically biased, and lack integration in Europe. EuropaBON aims to bridge this gap by designing an EU-wide framework for monitoring biodiversity and ecosystem services. EuropaBON harnesses the power of modelling essential variables to integrate different reporting streams, data sources, and monitoring schemes. These essential variables provide consistent knowledge about multiple dimensions of biodiversity change across space and time. They can then be analyzed and synthesized to support decision-making at different spatial scales, from the sub-national to the European scale, through the production of indicators and scenarios. To develop essential biodiversity and ecosystem variables workflows that are policy relevant, EuropaBON is built around stakeholder engagement and knowledge exchange (WP2). EuropaBON will work with stakeholders to identify user and policy needs for biodiversity monitoring and investigate the feasibility of setting up a center to coordinate monitoring activities across Europe (WP2). Together with stakeholders, EuropaBON will assess current monitoring efforts to identify gaps, data and workflow bottlenecks, and analyse cost-effectiveness of different schemes (WP3). This will be used to co-design improved monitoring schemes using novel technologies to become more representative temporally, spatially and taxonomically, delivering multiple benefits to users and society (WP4). Finally, EuropaBON will demonstrate in a set of showcases how workflows tailored to the Birds Directive, Habitats Directive, Water Framework Directive, Climate and Restoration Policy, and the Bioeconomy Strategy, can be implemented (WP5). HTML XML PDF
      PubDate: Wed, 26 Jan 2022 18:15:00 +020
       
  • Biodiversity Community Integrated Knowledge Library (BiCIKL)

    • Abstract: Research Ideas and Outcomes 8: e81136
      DOI : 10.3897/rio.8.e81136
      Authors : Lyubomir Penev, Dimitrios Koureas, Quentin Groom, Jerry Lanfear, Donat Agosti, Ana Casino, Joe Miller, Christos Arvanitidis, Guy Cochrane, Donald Hobern, Olaf Banki, Wouter Addink, Urmas Kõljalg, Kyle Copas, Patricia Mergen, Anton Güntsch, Laurence Benichou, Jose Benito Gonzalez Lopez, Patrick Ruch, Corinne Martin, Boris Barov, Kristina Hristova : BiCIKL is an European Union Horizon 2020 project that will initiate and build a new European starting community of key research infrastructures, establishing open science practices in the domain of biodiversity through provision of access to data, associated tools and services at each separate stage of and along the entire research cycle. BiCIKL will provide new methods and workflows for an integrated access to harvesting, liberating, linking, accessing and re-using of subarticle-level data (specimens, material citations, samples, sequences, taxonomic names, taxonomic treatments, figures, tables) extracted from literature. BiCIKL will provide for the first time access and tools for seamless linking and usage tracking of data along the line: specimens > sequences > species > analytics > publications > biodiversity knowledge graph > re-use. HTML XML PDF
      PubDate: Wed, 26 Jan 2022 17:00:00 +020
       
  • INAS: Interactive Argumentation Support for the Scientific Domain of
           Invasion Biology

    • Abstract: Research Ideas and Outcomes 8: e80457
      DOI : 10.3897/rio.8.e80457
      Authors : Tina Heger, Sina Zarrieß, Alsayed Algergawy, Jonathan Jeschke, Birgitta König-Ries : Developing a precise argument is not an easy task. In real-world argumentation scenarios, arguments presented in texts (e.g. scientific publications) often constitute the end result of a long and tedious process. A lot of work on computational argumentation has focused on analyzing and aggregating these products of argumentation processes, i.e. argumentative texts. In this project, we adopt a complementary perspective: we aim to develop an argumentation machine that supports users during the argumentation process in a scientific context, enabling them to follow ongoing argumentation in a scientific community and to develop their own arguments. To achieve this ambitious goal, we will focus on a particular phase of the scientific argumentation process, namely the initial phase of claim or hypothesis development. According to argumentation theory, the starting point of an argument is a claim, and also data that serves as a basis for the claim. In scientific argumentation, a carefully developed and thought-through hypothesis (which we see as Toulmin's "claim'' in a scientific context) is often crucial for researchers to be able to conduct a successful study and, in the end, present a new, high-quality finding or argument. Thus, an initial hypothesis needs to be specific enough that a researcher can test it based on data, but, at the same time, it should also relate to previous general claims made in the community. We investigate how argumentation machines can (i) represent concrete and more abstract knowledge on hypotheses and their underlying concepts, (ii) model the process of hypothesis refinement, including data as a basis of refinement, and (iii) interactively support a user in developing her own hypothesis based on these resources. This project will combine methods from different disciplines: natural language processing, knowledge representation and semantic web, philosophy of science and -- as an example for a scientific domain -- invasion biology. Our starting point is an existing resource in invasion biology that organizes and relates core hypotheses in the field and associates them to meta-data for more than 1000 scientific publications, which was developed over the course of several years based on manual analysis. This network, however, is currently static (i.e. needs substantial manual curation to be extended to incorporate new claims) and, moreover, is not easily accessible for users who miss specific background and domain knowledge in invasion biology. Our goal is to develop (i) a semantic model for representing knowledge on concepts and hypotheses, such that also non-expert users can use the network; (ii) a tool that automatically computes links from publication abstracts (and data) to these hypotheses; and (iii) an interactive system that supports users in refining their initial, potentially underdeveloped hypothesis. HTML XML PDF
      PubDate: Tue, 25 Jan 2022 10:00:00 +020
       
 
JournalTOCs
School of Mathematical and Computer Sciences
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