Database services

Name Description ELIXIR Node

ArrayExpress is a MIAME-standard compliant resource that stores functional genomics experiments performed using RNA-Seq/ChIP-Seq and array-based technologies.

EMBL-EBI

arrayMap is a reference database and bioinformatics resource targeting copy number profiling data in human cancer. The database provides an entry point for meta-analysis and data integration of high-resolution oncogenomic CNA data.

ELIXIR Switzerland

Benchmark Energy and geometry DataBase is available through web interface with integrated analytical tools.

ELIXIR Czech Republic

Database to retrieve and compare gene expression patterns between animal species. 

ELIXIR Switzerland

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

EMBL-EBI

Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. 

ELIXIR Switzerland

The CAZy platform performs the analysis of finished genomes in order to identify the encoded enzymes for the assembly and breakdown of complex carbohydrates. 

ELIXIR France

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.

EMBL-EBI

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.

EMBL-EBI

Supports Finnish national data custodians (biobanks) in building a data resource for Sequence Initiative Suomi and affiliated projects.

ELIXIR Finland

The CRISPRdb database and services are leading international resources for CRISPR sequence analysis. 

ELIXIR France

Database Of Local Biomolecumal COnfromers.

ELIXIR Czech Republic

EBI Metagenomics is an automated pipeline for the analysis and archiving of metagenomic data.

EMBL-EBI

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.

EMBL-EBI

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.

EMBL-EBI

The Enzyme Portal integrates publicly available information from the UniProt Knowledgebase, the Protein Data Bank in Europe, Rhea, Reactome, IntEnz, ChEBI, ChEMBL, Cofactor and MACiE.

EMBL-EBI

An annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Pointers to positions in nucleotide sequence entries provide access to promoter sequences.

ELIXIR Switzerland

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. 

EMBL-EBI

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.

EMBL-EBI

GnpIS is an interoperable Information System for plant and pest genomics. It is a powerful multispecies centralized information system with seven linked relational databases. 

ELIXIR France

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

EMBL-EBI

Human Endogenous RetroViruses Database.

ELIXIR Czech Republic

A database of homologous genes from fully sequenced organisms (bacteria, archeaea and eukarya). It allows you to select sets of homologous genes among species, and to visualize multiple alignments and phylogenetic trees. 

ELIXIR France

Database with millions of high-resolution images.

ELIXIR Sweden

An integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), and major histocompatibility (MH) of human and other vertebrate species. 

ELIXIR France

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

EMBL-EBI

IntEnz is a database of enzyme nomenclature that also provides enzyme classifications based on the nature of catalysed reactions. IntEnz is produced in collaboration with the SIB Swiss Institute of Bioinformatics.

EMBL-EBI

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

EMBL-EBI

International Reference Center for Prokaryotic Insertion Sequences (IS) is a public database and a research tool that provides a list of insertion sequences (IS) isolated from bacteria and archae.

ELIXIR France

Species focused genome data resource for sea lice, provides a genome browser, access to high-throughput data and LIMS.

ELIXIR Norway

MetaboLights is a database for metabolomics experiments and derived information. 

EMBL-EBI

MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. 

ELIXIR France

An innovative knowledge platform dedicated to human proteins. It contains a wealth of data on all the human proteins that are produced by the 20'000 protein- coding genes found in the human genome. 

ELIXIR Switzerland

OMA identifies orthologs among 2000 genomes from all domains of life. Other distinctive characteristics are the high quality of its inferences, the feature-rich web interface, and frequent update schedule of two releases per year.

ELIXIR Switzerland

Orphanet is the reference resource for information and data on rare diseases and orphan drugs. Orphanet derives from its knowledge base an ontology of rare diseases, information on rare diseases and data on rare diseases.

ELIXIR France

OrthoDB is a comprehensive catalog of evolutionary and functional annotations of orthologs, covering over 22 million genes from over 5000 species of animals, fungi, plants, archaea, bacteria, and viruses. 

ELIXIR Switzerland

Pfam is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). 

EMBL-EBI

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.

EMBL-EBI

This database contains families of homologous protein domains automatically constructed by sequence clustering of all sequences from the UniProt database, which allows for the most extensive coverage of the protein sequence space.

ELIXIR France

PROSITE consists of entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. PROSITE is a key element of the UniProt annotation pipeline “UniRule”.

ELIXIR Switzerland

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.

EMBL-EBI

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.

EMBL-EBI

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

EMBL-EBI

Rhea is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. 

ELIXIR Switzerland

STRING is a database of known and predicted protein-protein interactions. The database contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections.

ELIXIR Switzerland

SugarBind covers knowledge of glycan binding of human pathogen lectins and adhesins. Information is collected by experts from articles published in peer-reviewed scientific journals.

ELIXIR Switzerland

Database of protein expression time series for specific experiments on streptomyces, caulobacter, neiseria.

ELIXIR Czech Republic

SWISS-MODEL Repository is a continuously updated database of annotated protein structure homology models generated by the fully automated SWISS-MODEL modelling pipeline. 

ELIXIR Switzerland

A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form. 

ELIXIR Switzerland

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. 

EMBL-EBI

The European Nucleotide Archive (ENA) contains all the nucleotide sequences in the public domain and consolidates data from EMBL-Bank, the European Trace Archive and the Sequence Read Archive.

EMBL-EBI

UniProt produces and maintains automatic and manually curated annotation of all publicly available protein sequences and serves these to users through various interfaces. 

EMBL-EBI,, ELIXIR Switzerland

Collection of validation results for the entire Protein Data Bank.

ELIXIR Czech Republic

A resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries.

ELIXIR Switzerland