Service list

The BioImage Archive is a free, publicly available online resource which stores and distributes biological images. It accepts submissions of data from any imaging modality, as long as the data are either associated with a peer-reviewed publication, or of value beyond a single experiment.

The BioModels Database is a repository of computational models of biological processes. Models described from literature are manually curated and enriched with cross-references.

BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. 

The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI.

ChEBI (Chemical Entities of Biological Interest) is a dictionary of small molecular entities. It is manually annotated and provides a chemical ontology to describe small molecules, including their biological and chemical roles.

ChEMBL is a database of bioactive compounds that focuses on interactions between small molecules and their macromolecular targets, including medicinal chemistry, clinical development and therapeutics data.

EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images: it allows users to upload, and download and reprocess the thousands of raw, 2D images used to build a 3D structure.

This is an OpenStack platform co-located with EMBL-EBI’s services and data resources. Access to the Embassy Cloud is available for researchers outside EMBL if they have a collaboration with staff at EMBL.

The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.

Produces and maintains automatic and manually curated annotation on eukaryotic genomes. It is integrated with important molecular resources, for example UniProt, and can be accessed programmatically or through a web browser.

Provides access to genome-scale data from bacteria, protists, fungi, plants and invertebrate metazoa, through a unified set of interactive and programmatic interfaces based on the Ensembl software platform.

The European Genome-phenome Archive (EGA) allows users to explore datasets from numerous genotype experiments, including case-control, population and family studies, that are supplied by a range of data providers. 

Europe PubMedCentral (EuropePMC) contains over 3 million full text life science research articles, of which over 900 000 are open access, and combines these with 30 million abstracts from PubMed and other sources. 

European Variation Archive

The Expression Atlas allows users to search for gene expression changes measured in various cell types, organism parts, and disease states. It represents a curated subset of the ArrayExpress and GEO Archive experiments.

FAIRtracks is a set of JSON Schemas defining a draft minimal standard used to consolidate genomic track metadata from various sources, which can be queried by downstream clients through the TrackFind webtool/API.

The Gene Ontology (GO) project addresses the need for consistent descriptions of gene products across databases. It has developed three structured, controlled vocabularies (ontologies) that describe gene products.

The UniProt  GO annotation program (GOA) aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB).

The NHGRI-EBI GWAS Catalog is a quality-controlled, manually curated, literature-derived collection of all published genome-wide association studies.
 

Identifiers.org is a system providing resolvable persistent URIs used to identify data for the scientific community, with a current focus on the Life Sciences domain.

IntAct provides a freely available, open source database system and analysis tools for molecular interaction data.

InterPro classifies proteins into families and predicts the presence of important domains and sites.

MetaboLights is a database for metabolomics experiments and derived information. 

Formerly called EBI Metagenomics, MGnify is an automated pipeline for the analysis and archiving of metagenomic data.

The Omics Discovery Index provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics). It indexes metadata from more than 20 omics resources across four continents.

PRIDE (The Proteomics Identifications Database) is a standards-compliant, public repository for proteomics data. It contains protein and peptide identifications and their associated supporting evidence.

The Protein Data Bank in Europe (PDBe) is the European part of the wwPDB for the collection, organisation and dissemination of data on biological macromolecular structures.

An open-source, curated and peer reviewed pathway database. Its goal is to provide tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling and systems biology.

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).

RNAcentral is a free, public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases representing a broad range of organisms and RNA types.