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 curated reference database and bioinformatics resource targeting copy number profiling data in human cancer. The arrayMap database provides an entry point for meta-analysis and...

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. Bgee first maps heterogeneous expression data (currently EST, Affymetrix, and in situ hybridization data) on...

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-...

ELIXIR Switzerland

The CAZy platform is based on the sequence-based families and curation efforts underlying the CAZy database (www.cazy.org), updated monthly since its launch in...

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...

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...

EMBL-EBI

Finland ELIXIR Node supports 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. The CRISPRdb database and tools are composed of 5 components, whose most important are...

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

Ensembl produces and maintains automatic and manually curated annotation on selected eukaryotic genomes. It is integrated with several other important molecular resources, for example UniProt, and...

EMBL-EBI

Ensembl Genomes is a portal providing access to genome-scale data from bacteria, protists, fungi, plants and invertebrate metazoa, through a unified set of interactive and programmatic interfaces...

EMBL-EBI

The Enzyme Portal integrates publicly available information from: the UniProt Knowledgebase; the Protein Data Bank in Europe; Rhea, a database of enzyme-catalyzed reactions; Reactome; IntEnz, a...

EMBL-EBI

The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Pointers to...

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...

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...

EMBL-EBI

GnpIS is a modular and interoperable Information System for plant and pest genomics (http://urgi.versailles.inra.fr/gnpis). It is a powerful...

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

HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeaea and eukarya). It allows to select sets of homologous genes among species, and to visualize multiple...

ELIXIR France

Database with millions of high-resolution images

ELIXIR Sweden

IDSM is an integrated database of small molecules. Available through web interface.

ELIXIR Czech Republic

IMGT® is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) of human and other vertebrate...

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...

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), ISfinder, is a public database (https://www-is.biotoul.fr) and a research tool...

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. Integration of new genomic data in...

ELIXIR France

neXtProt is an innovative knowledge platform dedicated to human proteins. This resource contains a wealth of high-quality data on all the human proteins that are produced by the 20'000 protein...

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...

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 (Orphanet Rare Disease Ontology...

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...

ELIXIR Switzerland

Pfam is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Proteins are generally composed of one or more functional regions...

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...

EMBL-EBI

The ProDom 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...

ELIXIR France

PROSITE consists of documentation 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...

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

Reactome is a free, open-source, curated and peer reviewed pathway database. Its goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway...

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...

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...

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

SwissRegulon is 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...

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...

EMBL-EBI

The European Nucleotide Archive (ENA), a member of the International Nucleotide Sequence Database Collaboration, contains all the nucleotide sequences in the public domain and consolidates data...

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. UniProt is the central...

EMBL-EBI,, ELIXIR Switzerland

Collection of validation results for the entire Protein Data Bank.

ELIXIR Czech Republic

ViralZone is a web 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...

ELIXIR Switzerland