ELIXIR has announced the life science data and interoperability resources joining its prestigious list of Core Data Resources, ELIXIR Deposition Databases, and Recommended Interoperability Resources.
ELIXIR Core Data Resources are European life science data resources (deposition archives and knowledge bases) that are of fundamental importance to biological and biomedical research and long-term preservation of biological data. In this selection round, 10 new Core Data Resources have been added, bringing the total to 32.
ELIXIR Deposition Databases are European databases recommended for the deposition of experimental data. Some meet the technical quality and governance criteria expected of Core Data Resources but others may be at an earlier stage of development, address an emerging scientific area or are narrower in scope. Consequently some, but not all, of the Deposition Databases also appear in the Core Data Resources list. There are now 16 Deposition Databases, 10 of which are also Core Data Resources.
ELIXIR Recommended Interoperability Resources are European tools and registries that help make scientific research findable, accessible, interoperable and reusable (FAIR). Following the selection process, there are now 21 Recommended Interoperability Resources, an increase of seven.
Core Data Resources, ELIXIR Deposition Databases and Recommended Interoperability Resources form a well-respected set of trustworthy resources, which help raise resource visibility and provide guidance to users and organisations such as research journals and funders. Since 2018, the European Research Council has encouraged grantees to make use of all three categories of ELIXIR recommended resources.
ELIXIR’s European resources complement the Global Core Biodata Resources (GCBRs), as defined by the Global Biodata Coalition (GBC).
Two independent panels of international reviewers, one for ELIXIR Core Data Resources and ELIXIR Deposition Databases, the other for ELIXIR Recommended Interoperability Resources, evaluated all candidate resources. The evaluation was based on a selection of excellence indicators which are given below. Full details of the two selections processes are in the Find out more section,
- Scientific focus and quality of science
- Community served by the resource
- Quality of service
- Legal and funding infrastructure, and governance
- Impact and translational stories
- Resource facilitation to scientific research
Peter Maccallum, ELIXIR Chief Technical Officer, said “Today’s announcement of new Core Data Resources and Recommended Interoperability Resources is the culmination of a detailed and collaborative process with independent experts and data resource representatives. This initiative not only identifies high-quality and trustworthy data and interoperability resources for the user community but supports our progress towards sustainable funding of the resources, which together form the backbone of the life science data ecosystem in Europe."
The new resources are listed below.
New ELIXIR Core Data Resources and ELIXIR Deposition Databases
|
Resource |
Status |
Description |
|
CDR |
BacDive is a bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity. Bacterial diversity includes information on taxonomy, morphology, physiology, and ecology of bacterial strains with genome and other molecular data. |
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|
CDR & existing EDD |
BioStudies holds descriptions of biological studies, linking to the underlying data, including data that do not fit in the structured archives at EMBL-EBI. It accepts a wide range of study types via a simple format. |
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|
CDR & existing EDD |
The Electron Microscopy Data Bank (EMDB) is a public repository for electron cryo-microscopy maps and tomograms of macromolecular complexes and subcellular structures. It covers a range of techniques, from single-particle analysis to electron tomography. |
|
|
EDD only |
The Electron Microscopy Public Image Archive (EMPIAR) repository is a public resource for raw images underpinning 3D cryo-EM maps and tomograms. It also accommodates 3D datasets obtained with volume EM techniques and soft and hard X-ray tomography. |
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CDR & EDD |
The NHGRI-EBI GWAS Catalog is a curated collection of all human genome-wide association studies, produced by a collaboration between EMBL-EBI and NHGRI. |
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|
CDR |
The HGNC (HUGO Gene Nomenclature Committee) is a resource for approved human gene nomenclature containing ~42,000 gene symbols and names and 1,300+ gene families and sets. |
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|
CDR & EDD |
LIPID MAPS is designed to be an open, systematic and standardised lipidomics resource. Providing information on Lipids and their structures, properties and functions in biological processes. |
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|
CDR |
The MGnify platform facilitates the assembly, analysis and archiving of microbiome-derived nucleic acid sequences. It provides access to taxonomic assignments and functional annotations for nearly half a million analyses covering metagenomic data from a wide range of environments. |
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EDD only |
ModelArchive stores theoretical models of macromolecular structures and provides unique stable accessions (DOI) for referencing. It also supports the storage of assumptions, parameters and constraints applied in the simulation to make models more reproducible. |
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|
CDR |
PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets. |
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CDR |
SWISS-MODEL is a fully automated protein structure homology-modelling server, making protein modelling accessible to all life science researchers worldwide. It is also a repository for models of all the protein sequences for thirteen core species, which are generated every week, based on the latest UniProtKB proteome. |
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|
CDR |
VEuPathDB provides a single point of access to diverse genomic and other large scale datasets related to eukaryotic pathogens and invertebrate vectors of disease. Organisms supported by this resource include (but are not limited to) the US-based NIAID list of emerging and re-emerging infectious diseases. |
New ELIXIR Recommended Interoperability Resources
|
Resource |
Description |
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The Bgee Knowledge Graph provides access to gene expression patterns in multiple animal species and tissue types via a SPARQL endpoint that understands a number of controlled vocabularies and identifiers. The underlying database results from the integration and harmonisation of several data sources. |
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|
The Data Stewardship Wizard is a tool designed to assist researchers and data stewards in creating smart Data Management Plans (DMPs) for FAIR (Findable, Accessible, Interoperable, and Reusable) Science. It uses a unique and modular question-based approach to help users to create, plan, and collaborate on DMPs. |
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|
The FAIR Cookbook is an online, open, and live resource for the life sciences, providing “recipes” to help users make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR). Each recipe covers a particular set of steps towards FAIRer data and are indexed according to a particular dataset “maturity” level. |
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Galaxy is an interoperable open-source platform for scientific data analysis and sharing, covering diverse research fields such as omics, machine learning, and climate science. |
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Jalview is a free, cross-platform (inc. web app) system that connects across different resources, providing visualisation and analysis of biological data. It allows users to conduct integrated analyses of their own data in combination with a variety of public data resources through interoperation, including ENA, Ensembl, PDBe, UniProt, InterPro, and AlphafoldDB. It supports reproducible science by supporting project files that capture the state of a Jalview session. |
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OpenEBench is a multifaceted platform for evaluating life sciences tools from two critical perspectives: scientific performance through community-based benchmarking and software quality through the Software Quality Observatory. It helps ensure the reliability, reproducibility, and effectiveness of tools used for analysis and processing of life science data. |
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The RDMkit is an open-source, online toolkit for researchers and data stewards, providing Research Data Management (RDM) best practices in line with the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. It encompasses the entire research data lifecycle, from planning and collecting data to storing, preserving, and sharing. |
Find out more
- Full list of Core Data Resources, ELIXIR Deposition Databases and Recommended Interoperability Resources
- About Core Data Resource selection and Recommended Interoperability Resource selection
- Identifying ELIXIR Core Data Resources (2017)
- The Annual Indicator Monitoring and Periodic Review Processes: ELIXIR Core Data Resources and Deposition Databases (2020)
- The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences (2020)
- Global Core Biodata Resources