Research Data Management services

Name	Description	ELIXIR Node
Building FAIR metadata standards for non-human pathogen genomic and phenotypic data	This project will develop a harmonised, FAIR-aligned metadata standard for non-human pathogen genomic and phenotypic data. By reviewing existing frameworks and performing gap analyses, the project will produce community-validated templates aligned with international ontologies and repository requirements. Pilot datasets will demonstrate interoperability through ENA, BioSamples and BioStudies. The work supports One Health approaches to surveillance and research across food, veterinary, agricultural and plant pathogen domains. Predicted outcomes: FAIR metadata standard for non-human pathogen genomic and phenotypic data Human- and machine-readable templates with clear implementation guidance Pilot submissions to ENA, BioSamples and BioStudies Open training materials (TeSS/Zenodo) Sustainability and adoption plan across ELIXIR Nodes	ELIXIR Germany, ELIXIR Norway, ELIXIR Portugal, ELIXIR Spain, ELIXIR Switzerland
Cellular and molecular research	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: Advancing structural and functional ontologies of disordered proteins DBTLHub: Towards a one-stop shop for connecting databases, datasets and tools for the Design-Build-Test-Learn cycle in biotechnology FAIR annotation workflows for PDBe-KB via community-driven Nextflow development and training FRET-IDP Community Resource: Integrating and standardising FRET data for disordered proteins Next level of reproducible, comparable and integrable metabolomics (RCI-M) Spatial2Galaxy: There is no Galaxy without Space TELLME: LLM-based narratives to explain and empower systems biology research	ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Israel, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR UK, EMBL-EBI
Creation of a virtual assistant guiding plant researchers in making their datasets FAIR-compliant	Plant phenotyping datasets are highly heterogeneous and difficult to annotate consistently. This project will develop a conversational AI 'virtual assistant' that extracts structured metadata from natural-language descriptions and produces ISA-JSON and RO-Crate outputs. The assistant integrates with ISA tools and reduces the burden of metadata creation, improving FAIR compliance across plant research communities. Predicted outcomes: Conversational AI service for extracting structured metadata MetaBuddy web app and integration into ISA Wizard Standards-compliant metadata outputs (ISA-JSON, RO-Crate) Improved metadata quality for plant phenotyping datasets Sustainable, open-source software for long-term community use	ELIXIR Belgium, ELIXIR Germany, ELIXIR Netherlands
DATAREX - Data Management for Research in ELIXIR	Research Data Management (RDM) is crucial for implementing FAIR and Open Science principles. ELIXIR Platforms, Nodes, and other structures have invested in RDM, resulting in valuable tools and resources. The RDM Community aims to bring together RDM professionals to coordinate ELIXIR's activities and develop its vision. The short-term objectives include: creating a knowledge exchange forum, coordinating the RDM ecosystem, focusing on RDM training and data brokering. To achieve these goals, DATAREX will facilitate knowledge sharing, develop resources for RDM service providers, coordinate RDM training and content, and make recommendations for enhancing data brokering services. This project will empower RDM professionals and contribute to improving research data management practices.	ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Greece, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK
DBTLHub: Towards a one-stop shop for connecting databases, datasets and tools for the Design-Build-Test-Learn cycle in biotechnology	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
Developing Learning Paths for the ELIXIR RDM Community
ELIXIR Biodiversity, Food Security, & Pathogens Cross-Community Workshop
ELIXIR Federated Human Data Community Day
ELIXIR IDP Community meeting
ELIXIR Outreach webinar with India - Data management, human data and infectious diseases: Opportunities for engagement
ELIXIR Outreach webinar with Latin America - Data management and training: Opportunities for engagement
ELIXIR RDM Community meeting
ELIXIR Single-Cell Omics Community meeting
ELIXIR Webinar: Research Data Management Kit (RDMKit)		ELIXIR Belgium, ELIXIR UK
ELIXIR-CONVERGE releases the RDMkit to make research data management simple		ELIXIR Belgium, ELIXIR Germany, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Portugal, ELIXIR Spain, ELIXIR Sweden, ELIXIR UK
KYBELΕ: Knowledge Yield from BiodivΕrsity Literature through Large Language Model (LLM) Extraction	KYBELE develops an AI-powered, FAIR-compliant system to unlock biodiversity knowledge hidden in scientific literature. By harvesting species data, ecological traits and habitat information, and annotating BiodiversityPMC with domain-specific vocabularies, the project creates structured datasets for reuse. A fine-tuned LLM will power an interactive literature-exploration chatbox deployed via ELIXIR and LifeWatch ERIC. KYBELE directly advances BFSP priorities by enabling scalable, automated extraction of biodiversity knowledge. Predicted outcomes: FAIR-aligned catalogues of species, traits and habitats Annotated BiodiversityPMC enriched with domain vocabularies Public LLM-powered biodiversity literature exploration service Containerised extraction workflows integrated with ELIXIR/LifeWatch ERIC FAIR training materials and documentation for adoption	ELIXIR Greece, ELIXIR Italy, ELIXIR Switzerland
Next level of reproducible, comparable and integrable metabolomics (RCI-M)	The ELIXIR Metabolomics Community relies on standards, formats and data treatment solutions development and adoption, but it remains challenging to ensure high-quality reported metadata, sufficiently contextualised results, interoperable and reusable datasets and to integrate these metabolomics data with other omics or studies. This project is designed to address these issues and aims to connect key international standards with ELIXIR resources, as well as creating associated community guidelines and training materials. Based on the FAIRification framework, activities in the project will: Increase interoperability and reuse of public metabolomics datasets and workflows through enhanced and extended open data standards, resources and new semantic annotations Define, ensure and establish quality control for study baselines in Metabolomics and Exposomics Facilitate metabolomic data interpretation and meta-analysis integration with multi-omics and systems biology studies As a first necessary step, the project will create a Semantic Metabolomics Data Model to standardise metadata, ensuring unambiguous reuse of metabolomics projects. This model will focus on integrating key ontologies, providing open training initiative and enhancing the interoperability of metabolomics data through the production of open guidelines for annotation steps. By linking with ELIXIR’s Deposition databases, ISA Framework and other services, the project seeks to boost interconnection with ELIXIR platforms, other ELIXIR communities (Systems Biology, Food and Nutrition, Galaxy, Proteomics, Toxicology, Research Data Alliance Focus Group, etc.), the FAIR Cookbook and BioSchemas.org communities. Project outcomes are expected to promote the emergence of ambitious and innovative semantic-based solutions for inter-comparison of studies in healthcare, clinical and plant domains.	ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Italy, ELIXIR Spain, ELIXIR France, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR UK, EMBL-EBI
Research data management guide illustrates user journeys through ELIXIR resources		ELIXIR Luxembourg, ELIXIR Norway
Training and RDM collaboration activities in Brazil (SEP 2025-11)	The ELIXIR Belgium and ELIXIR Switzerland Nodes will work together to strengthen collaboration between ELIXIR and Brazilian research organisations through a programme of events and training activities in Brazil. The Staff Exchange will support the delivery of ELIXIR training courses in both the northeast and southeast regions. Activities will include presentations at the Natal Bioinformatics Forum, as well as engagements at Fiocruz and the Universidade Federal do Rio de Janeiro (UFRJ). Training will align with ongoing work in the ELIXIR Training Platform, the ELIXIR FAIR Training Focus Group and the Research Data Management (RDM) Community. Topics will include research data management, reproducible analysis, the ELIXIR-GOBLET Train-the-Trainer programme and FAIR training materials. A dedicated RDM workshop will also explore approaches to international collaboration and sensitive data sharing, supported by a hands-on Git session focused on reproducible workflows. The exchange will increase awareness of ELIXIR resources, support capacity building and strengthen long-term collaboration with Brazilian partners.	ELIXIR Belgium, ELIXIR Switzerland