Biodiversity services
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This study is divided into four Work Packages (WP). The first three aim to survey the biodiversity data domain and catalogue and assess relevant research data management elements (WP1), analysis tools, services, and infrastructures (WP2), as well as active and planned projects and stakeholders (WP3). WP4 aims to grow the ELIXIR Biodiversity Community by collating resources and materials for training and knowledge transfer amongst ELIXIR members and the wider research community. WP1: Research data management and data interoperabilityThe aim of WP1 is to survey and catalogue Research Data Management (RDM) elements relevant to the biodiversity domain, with a focus on molecular data but not excluding other relevant data collection activities. By focusing on data management and not data analysis it remains distinct from WP2. It is aligned with WP3 through the mapping of RDM-related activities being performed as part of ongoing projects (e.g. BGE, BiCIKL, TETTRIs), and will provide some of the substrate for discussions as part of WP3’s planned network event, contributing to creating connections with the wider community (particularly active ELIXIR Nodes). It will also highlight current capacities and gaps in RDM practices that will feed into WP4’s activities. Development and adoption of best practices in RDM for the biodiversity research domain remain extremely variable, hence the focus here on assessing the current status and collating existing best practices. This will strengthen ELIXIR’s position in the biodiversity domain by leveraging ELIXIR’s RDM-related strengths in other research domains including other ELIXIR Communities. LeadJosie Burgin (EMBL-EBI) Tasks
Milestones and deliverables
WP2: Services, tools, and analysisThe main aims of WP2 are to catalogue, review, and categorise tools, services, and analytical workflows currently in use by ELIXIR Nodes and the wider community, that process and analyse biodiversity-related data, with an emphasis on molecular data. This will include ELIXIR and non-ELIXIR tools. It remains distinct from WP1 by focusing on data analysis tools, services, and infrastructures and not on data management in research. It will benefit from WP3’s surveys of stakeholders/projects to help identify key tools and services that should be prioritised for review and cataloguing. These priorities can feed into WP4’s training activities by identifying community needs with respect to the usability of important tools and services. The outputs will ensure that ELIXIR is playing a leading role in identifying and exposing high-quality biodiversity-related analysis tools and services to the wider community of users, as well as fostering the development of such tools and services through connecting ELIXIR Nodes which are active in the domain. LeadToni Gabaldón and Matúš Kalaš Tasks
Milestones and deliverables
WP3: Outreach, networking, and communicationsBiodiversity is a very broad and diverse domain of research, in which many networks of infrastructures and initiatives are involved. The main aims of WP3 are to better describe the landscape of stakeholders ELIXIR is working with or needs to better engage with and to establish a “network of networks” for biodiversity research. It will feed into WP1 and WP2 by identifying ongoing or planned work directly relevant for improving RDM practices, and by exposing tools, services, and analysis workflows that the wider community are developing. It will also help to link training and knowledge transfer activities of various projects and stakeholders to the ELIXIR Training Platform and WP4. By leveraging ELIXIR’s federated structure, these network growing activities will support biodiversity research by improving connections between existing projects and communities, as well as by promoting synergies and aligning data and tools to the needs of researchers. This will also strengthen ELIXIR’s position as a partner in the planning and development of new projects and initiatives in the biodiversity data/research domain. LeadHenrik Lantz Tasks
Milestones and deliverables
WP4: Training and knowledge transferThe overarching aim of WP4 is to leverage the strengths of ELIXIR’s training experience to help support the growth of the ELIXIR Biodiversity Community through network-driven sharing of training experiences and knowledge transfer and materials. The work will be developed in close collaboration with the ELIXIR Training Platform and extensively use the methods already developed. Activities in Work Packages 1, 2, and 3 will help to connect to a wide range of relevant stakeholders and thereby feed WP4 with information about ongoing or planned training-related activities on the broader biodiversity community. LeadPatricia Palagi and Anne-Françoise Adam-Blondon Tasks
Milestones and deliverables
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ELIXIR France, ELIXIR Greece, ELIXIR Italy, ELIXIR Germany, ELIXIR Portugal, ELIXIR Ireland, ELIXIR Norway, ELIXIR Spain, ELIXIR UK, ELIXIR Switzerland, ELIXIR Hungary, ELIXIR Sweden, EMBL-EBI, ELIXIR Czech Republic | |
Over the coming decade, Europe will face critical challenges in maintaining biodiversity, ensuring food security and combating pathogens. Our 2024–28 Programme will address these issues by mobilising and integrating molecular data, using successful coordination models from human genomics. Through strategic investments and collaboration in externally-funded projects, ELIXIR will enhance scientific services and support transnational research in these essential areas. The following projects have been selected as part of the ELIXIR 2024–28 Programme’s Biodiversity, food security and pathogens Science tier:
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ELIXIR Belgium, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR UK, EMBL-EBI, ELIXIR Italy | |
Cellular and molecular biology are fundamental to ELIXIR's mission. As part of our 2024–28 Programme, we are committed to advancing data services and software for research on nucleic acids, proteins and other biomolecules. This initiative will address new demands for multi-omics and multi-modal analyses, including imaging, by developing methods and partnerships. We will also expand expertise in reusable data and software to incorporate FAIR models, ensuring robust solutions for modelling at all scales. The following projects are key to connecting the latest developments with established data resources, unlocking the potential of cellular and molecular biology:
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ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR France, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR UK, EMBL-EBI | |
This project aims to strengthen the basis for a one-stop shop connecting databases, datasets and tools for the deployment of the engineering Design-Build-Test-Learn (DBTL) framework in biotechnology. It will do so by surveying the tools and data landscape, pinpointing gaps and opportunities, and establishing design patterns for task-specific workflows for analysis, integration and sharing of multimodal data. It will provide a resource that will allow users to navigate the complex landscape of biotechnology tooling and data, as well as to establish solutions that fit their specific DBTL requirements. Use cases from ongoing programmes in various communities will be used to ascertain and establish the pragmatic value of the solutions. The work will be carried out through hands-on activities, dedicated workshops and hackathons, providing training and resources, as well as fostering industrial engagement. The experience of the communities and platforms involved in systems biology, industrial biotechnology, metabolic modelling, metabolomics, enzymes, bioprospecting and data management will be particularly valuable in this respect, as well as their respective industrial relations. Accordingly, the project engages participants from seven ELIXIR nodes and connects researchers and their activities from six communities. The project outcomes will contribute to advancing the ambition of connecting the latest developments and established data resources across ELIXIR to realise the potential of cellular and molecular biology, particularly in the fields of industrial biotechnology and biomanufacturing. |
ELIXIR Spain, ELIXIR Greece, ELIXIR France, ELIXIR Netherlands, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR UK | |
Project objectivesUnderstanding molecular biodiversity is essential for ecological conservation and sustainable development. While a vast array of molecular data awaits exploration, its lack of connectivity with other sources of data and metadata such as geographical reference, habitat, population size and phenotypic data often pose significant barriers to biodiversity research. This project proposal is about developing Odyssey, a web portal in the form of a user-friendly interface that will allow researchers, educators and citizens to navigate the world of molecular biodiversity using Greece and Norway as case studies – two countries with a characteristic and unique wealth of biodiversity, representative for Mediterranean and Nordic types of ecosystems respectively. Based on existing sources of information and prototype applications available for specific regions and taxa, this project aims to link actual efforts and develop a new interface to offer diverse functionalities for data exploration and analysis, such as descriptive statistics, graphs, maps, customisable data filters and dynamic visualisations. Through modular design, the application will ensure flexibility and scalability, enabling easy integration of new data sets and analytical tools in the future. This approach will be used for training and communication, inviting traditional biodiversity research groups to utilise new information concerning the spatial patterns of biodiversity and their connection with features that are important for designing conservation measures, such as habitat connectivity, representativity, population demographics, dynamics of adaptation and migration. Odyssey’s outcome will be a valuable tool for studying and, ultimately, offering a basis for managing and conserving the rich molecular biodiversity of Greece and Norway, as well as supporting the activities of the ELIXIR Biodiversity Community in the two Nodes and in Europe. This will promote collaboration, innovation and knowledge exchange in biodiversity research and beyond. This new tool will be developed and offered under an open-source licence, encouraging community participation and contribution to further enhance its capabilities and broaden its applications, fostering a robust network for biodiversity research in Greece and Norway. Project outcomesOdyssey: An Interactive R Shiny App to Explore Molecular Biodiversity in Greece Highlighted outcome (in progress) Co-leads
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ELIXIR Greece, ELIXIR Norway | |
Project objectivesUnderstanding molecular biodiversity is essential for ecological conservation and sustainable development. While a vast array of molecular data awaits exploration, its lack of connectivity with other sources of data and metadata such as geographical reference, habitat, population size and phenotypic data often pose significant barriers to biodiversity research. This project proposal is about developing Odyssey, a web portal in the form of a user-friendly interface that will allow researchers, educators and citizens to navigate the world of molecular biodiversity using Greece and Norway as case studies – two countries with a characteristic and unique wealth of biodiversity, representative for Mediterranean and Nordic types of ecosystems respectively. Based on existing sources of information and prototype applications available for specific regions and taxa, this project aims to link actual efforts and develop a new interface to offer diverse functionalities for data exploration and analysis, such as descriptive statistics, graphs, maps, customisable data filters and dynamic visualisations. Through modular design, the application will ensure flexibility and scalability, enabling easy integration of new data sets and analytical tools in the future. This approach will be used for training and communication, inviting traditional biodiversity research groups to utilise new information concerning the spatial patterns of biodiversity and their connection with features that are important for designing conservation measures, such as habitat connectivity, representativity, population demographics, dynamics of adaptation and migration. Odyssey’s outcome will be a valuable tool for studying and, ultimately, offering a basis for managing and conserving the rich molecular biodiversity of Greece and Norway, as well as supporting the activities of the ELIXIR Biodiversity Community in the two Nodes and in Europe. This will promote collaboration, innovation and knowledge exchange in biodiversity research and beyond. This new tool will be developed and offered under an open-source licence, encouraging community participation and contribution to further enhance its capabilities and broaden its applications, fostering a robust network for biodiversity research in Greece and Norway. Project outcomesOdyssey: An Interactive R Shiny App to Explore Molecular Biodiversity in Greece Highlighted outcome (in progress) Co-leads
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ELIXIR Greece, ELIXIR Norway |