Services: Data resources
Name of service | Tag | ELIXIR Node | Key collection | |
---|---|---|---|---|
ArrayExpress |
ArrayExpress is a MIAME-standard compliant resource that stores functional genomics experiments performed using RNA-Seq/ChIP-Seq and array-based technologies. |
EMBL-EBI | CDR EDD | |
arrayMap |
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 | ||
BEGDB |
Benchmark Energy and geometry DataBase is available through web interface with integrated analytical tools. |
ELIXIR Czech Republic | ||
Bgee |
Database to retrieve and compare gene expression patterns between animal species. |
ELIXIR Switzerland | ||
BioModels |
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 | EDD | |
Biosamples |
BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. |
EMBL-EBI | EDD | |
BioStudies |
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. |
EMBL-EBI | EDD | |
BRENDA |
Database of enzyme and enzyme-ligand information, across all taxonomic groups, manually extracted from primary literature and extended by text mining procedures, integration of external data and prediction algorithms. |
ELIXIR Germany | CDR | |
CAMEO |
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 | ||
CATH/Gene3D |
A classification of protein structures and sequences that groups protein domains into superfamilies. |
ELIXIR UK | CDR | |
CAZy |
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 | ||
Cellosaurus |
A knowledge resource on cell lines. |
ELIXIR Switzerland | ||
ChEBI |
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 | CDR | |
ChEMBL |
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 | CDR | |
Collections and registries from the Finnish population: SISU data resource |
Supports Finnish national data custodians (biobanks) in building a data resource for Sequence Initiative Suomi and affiliated projects. |
ELIXIR Finland | ||
CorkOakDB |
A data resource for Quercus suber. |
ELIXIR Portugal | ||
CRISPRdb |
The CRISPRdb database and services are leading international resources for CRISPR sequence analysis. |
ELIXIR France | ||
Dolbico (formely DOLCE) |
Database Of Local Biomolecumal COnfromers. |
ELIXIR Czech Republic | ||
EMDB | EMBL-EBI | EDD | ||
Ensembl |
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 | CDR | |
Ensembl Farmed and Domesticated Animals |
Provides annotated genomes of farmed and domesticated animals in an easily viewable format via the Ensembl system. |
ELIXIR UK | ||
Ensembl Genomes |
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 | CDR | |
ENZYME |
ENZYME is a repository of information on enzyme nomenclature based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). ENZYME describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided. |
ELIXIR Switzerland | ||
Enzyme Portal |
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 | ||
EPD |
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 | ||
EuropePMC |
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 | CDR | |
EVA |
European Variation Archive |
EMBL-EBI | EDD | |
Expression Atlas |
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 | ||
Expression atlases |
These include the Human Developmental Studies Network (HuDSeN), emouseatlas.org, echickatlas.org, and macrophages.com, a gene expression atlas of the domestic pig. |
ELIXIR UK | ||
GnpIS |
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 |