A5060220259- Species Distribution and Climate Change
- Research Data Management Practices
- Scientific Computing and Data Management
- Semantic Web and Ontologies
- Biomedical Text Mining and Ontologies
- Smart Agriculture and AI
- Remote Sensing in Agriculture
- Plant Pathogens and Fungal Diseases
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Phylogenetic Studies
- Genomics and Rare Diseases
- Bryophyte Studies and Records
- Environmental DNA in Biodiversity Studies
- Soil Carbon and Nitrogen Dynamics
- Bioinformatics and Genomic Networks
- linguistics and terminology studies
- Image Processing and 3D Reconstruction
- Geographic Information Systems Studies
- Horticultural and Viticultural Research
- Leaf Properties and Growth Measurement
- Stellar, planetary, and galactic studies
- Zoonotic diseases and public health
- Evolution and Paleontology Studies
- Animal and Plant Science Education
- Advanced Aircraft Design and Technologies
University of Manchester
2024
ZB MED - Information Centre for Life Sciences
2024
University of Oslo
2024
Senckenberg Society for Nature Research
2014-2024
Deutsche Gesellschaft für Information und Wissen
2023-2024
Senckenberg Research Institute and Natural History Museum Frankfurt/M
2020-2024
Global Biodiversity Information Facility
2024
Netherlands Organisation for Applied Scientific Research
2024
Helmholtz Centre for Environmental Research
2024
VSB - Technical University of Ostrava
2024
Herbaria worldwide are housing a treasure of 100s millions herbarium specimens, which increasingly being digitized in recent years and thereby made more easily accessible to the scientific community. At same time, deep learning algorithms rapidly improving pattern recognition from images these techniques applied biological objects. We using digital specimens order identify taxa traits collection objects by applying convolutional neural networks (CNN). Images 1000 species most frequently...
Amidst population growth and climate-driven crop stresses such as drought, extreme weather, fungal insect pests, well various diseases, ensuring food security demands innovative strategies. Crop wild relatives (CWR), plants in the same genus populations belonging to species crop, offer novel genetic resources crucial for enhancing resilience against these stress factors. Here, we introduce a prototype digital twin (pDT) aid searching utilising CWR resources. Using MoDGP (Modelling Germplasm...
As part of the BioHackathon Europe 2023, we here report from progress hackathon project #15: "Enabling FAIR Digital Objects with RO-Crate, Signposting and Bioschemas". We added to three existing resources, made a Chrome browser extension show headers. RO-Crate two explored making hybrid FDO using both Handle PID Record Signposting/RO-Crate approach.
The Horizon Europe project “Biodiversity Digital Twin for Advanced Modelling, Simulation and Prediction Capabilities” (biodt.eu) combines state-of-the-art supercomputing resources with FAIR data practices to address biodiversity grand challenges such as the loss of diversity at genetic, species ecosystem levels driven by factors anthropogenic climate change, intensified land use spreading alien invasive species.Key tools integration assessment information in BioDT are...
The reputation of data providers and the accuracy geodata sources are critical factors for trustworthiness environmental metrics indicators to support policy making. In this context, possibility user-specific assessment quality input composite indicator calculations using data-fitness-for-use data-fitness-for-purpose approaches has gained importance. Data-fitness-for-use criteria describe general suitability a set further use thus refer intrinsic such as completeness, accuracy, consistency,...
The mapping.bio platform for the curation of FAIR semantic mappings is presented and implementation storage as “webby” Digital Objects based on established standards described.
Research Object Crate (RO-Crate) is a lightweight method to package research outputs along with their metadata. Signposting provides simple yet powerful approach navigate scholarly objects on the Web. Combining these technologies form "webby" implementation of FAIR Digital principles which suitable for retrofitting existing data infrastructures or even ad-hoc using regular Web hosting platforms. Here we give an update recent community development and adoption RO-Crate Signposting. It notable...
We developed the WildLIVE platform to enable curation, analysis and mobilization of data from high-throughput biodiversity monitoring for European global cross-domain space pro-grams. The implements “webby” FAIR Digital Objects leveraging on RO-Crate Signposting foster self-contained operation machines contained digital resources (machine actionability).
The systematic analysis of a large number comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, the functioning ecosystems. Floras, i.e., books collecting information on all known species found within region, are potentially rich source such data. Floras describe traits focus morphology other relevant for identification addition to characteristics species, as affinities,...
As herbarium specimens are increasingly becoming digitised and accessible in online repositories, advanced computer vision techniques being used to extract information from them. The presence of certain plant organs on sheets is useful various scientific contexts automatic recognition these will help mobilise such information. In our study, we use deep learning detect with Faster R-CNN. For experiment, manually annotated hundreds scans thousands bounding boxes for six types them training...
Abstract Phylogenetic inference is done regularly in many biological studies not focussed on the phylogeny itself, but which use as a tool to infer hypotheses for interpretation of laboratory experiments. However, phylogenetic often performed at low standards these studies, can result wrong interpretations. Using high-standard tools usually requires substantial methodological knowledge or only possible with paid tools. To enable beginners, researchers just one many, and scientists...
In this paper we describe with the help of two examples how FAIR Digital Objects can be used to bridge between different dataspaces, repositories using technologies, and model worlds. The first example is digital specimen as defined by DiSSCO which offers access a variety information from in persistent way. second results collaboration I4.0 Asset Administration Shell experts where integrate domains Product Pass an example. also show FDOs implement secure on shared data it occurs almost all...
African swine fever is a transmissible virus impacting wild and domestic populations. In Europe, it non-native the recently introduced genotype affects boar populations with occasional outbreaks in pigs. The ability to predict short-term spatial dynamics of this disease will greatly improve our control limit future spread virus. BioDT prototype, currently development, implements an individual-based landscape-level mechanistic model as digital twin aimed at providing informed support for...
Persistent identifiers (PID) to identify digital representations of physical specimens in natural science collections (i.e., specimens) unambiguously and uniquely on the Internet are one mechanisms for digitally transforming collections-based science. Digital Specimen PIDs contribute building maintaining long-term community trust accuracy authenticity scientific data be managed presented by Distributed System Scientific Collections (DiSSCo) research infrastructure planned Europe commence...
Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source "data enrichment" workflows, they are increasingly being represented variety standards-compliant interchange formats. Here, we report on an initiative which software developers and taxonomists came together address the challenges highlight opportunities enrichment such engaging intensive, collaborative...
Abstract Biodiversity research studies the variability and diversity of organisms, including within between species with particular focus on functional traits their relationship to environment. Managing biodiversity data implies dealing its heterogeneous nature using semantics tailored ontologies. These are themselves differently conceived, combining them in semantically enabled applications necessitates an effective alignment concepts. This paper describes ontology matching biodiversity-...
Abstract Despite great strides in the development and wide acceptance of standards for exchanging structured information about genomic variants, there is no corresponding standard phenotypic data, this has impeded sharing computational analysis. Here, we introduce Global Alliance Genomics Health (GA4GH) Phenopacket schema, which supports exchange computable longitudinal case-level diagnosis research all types disease including Mendelian complex genetic diseases, cancer, infectious diseases....
The Distributed System of Scientific Collections (DiSSCo) is a pan-European Research Infrastructure (RI) initiative. DiSSCo aims to bring together natural science collections from 175 museums, botanical gardens, universities and research institutes across 23 countries in distributed infrastructure that makes these physically digitally open accessible for all forms innovation. RI entered the ESFRI roadmap 2018 successfully concluded its Preparatory Phase early 2023. now transitioning towards...
The growing public interest in biodiversity monitoring has led to a significant increase initiatives that unite citizen scientists, researchers, and machine learning technologies. In this context, we introduce WildLIVE!, dynamic biomonitoring science project. participants analyze vast array of images from long-term camera trapping project Bolivia investigate the impacts shifting environmental factors on wildlife. From 2020 2023, more than 850 registered for contributing nearly 9,000 hours...
Amidst population growth and climate-driven crop stresses, ensuring food security demands innovative strategies. Crop wild relatives (CWR), plants in the same genus as crop, offer novel genetic resources crucial for enhancing resilience. Here, we introduce a prototype digital twin (pDT) to aid searching utilising CWR resources. Leveraging MoDGP (Modeling Germplasm of Interest) tool, pDT enables mapping geographic areas where stress-tolerant populations can be found. With its graphical user...
Biodiversity data are substantially increasing, spurred by technological advances and community (citizen) science initiatives. To integrate is, likewise, becoming more commonplace. Open promotes open sharing usage. Data standardization is an instrument for the organization integration of biodiversity data, which required complex research projects digital twins. However, just like with actual instrument, there a learning curve to understanding standards field. Here we provide guide, providers...
Camera traps and passive acoustic devices are particularly useful in providing non-invasive methods to document wildlife diversity, ecology, behavior, conservation. The application of autonomous Internet Things (IoT) sensors is constantly developing opens up new possibilities for research nature conservation such as taxon identification based on real-time audio processing the field (Höchst et al. 2022). Furthermore, amount associated recorded digital photos, videos, files growing at a rapid...
Biodiversity research has a strong focus on the links between environment and functional traits, e.g., to assess how anthropogenic drivers of change impact ecological systems (Díaz et al. 2013). Interoperable exchange integration such data is enabled through use ontologies that provide ”meaning” enable downstream processing involving learning inference over graph-structured models these (Kulmanov 2020). However, development thematically similar semantic artifacts, Environmental Ontology...