Services: Data Resources

A collection of high-resolution three-dimensional structural templates for domain-domain interactions. It contains templates for interactions between two globular domains as well as novel domain-peptide interactions, derived using a recently published method from our lab.

APID Interactomes provides a comprehensive collection of protein interactomes for more than 500 organisms based on the integration of known experimentally validated protein-protein physical interactions (PPIs). 

This is the place where you can find an updated list of the published mitochondrial sequences coming from the ancient DNA samples (aDNA). The main interest of our database lies in the anatomically modern Homo sapiens samples, ranging from the late Paleolithic to roughly Iron Age times, focusing on an Euroasian geographical area. We provide both the mtDNA sequences (in FASTA format), and the metadata for the samples (IDs, dates, geolocation, site, culture, mtDNA haplogroup etc., available to download in a tab-delimited text file).

ANISEED is the main model organism database for the worldwide community of scientists working on a class of marine invertebrates, the tunicates (sister-group of vertebrates). It integrates for each species: a main knowledge base with extended information on gene function, gene expression, phylogeny and embryonic anatomy at single cell resolution; a genomic browser and a Genomicus gene synteny browser.

Annotates variants with biological data such as protein structural information, functionally important residues, conservation of functional domains and evidence of cross-species conservation.

Web portal for the annotation of pathological protein variants.

Alternative splicing database of human genes and functional annotation of their isoforms using the ASPic algorithm.

BacDive represents a collection of organism-linked information covering the multifarious aspects of bacterial and archaeal biodiversity. The content encloses information on taxonomy, morphology, physiology, sampling and environmental conditions as well as molecular biology.

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

Online access to tools and databases related to miRNAs binding site predictions, RNA Binding protein binding sites, circular RNAs, CLIP data analysis and transcriptome analysis

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

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.

 BIII Bio Image informatics Index (www.biii.eu) is a knowledge database of software tools, test image databases and training materials for bio image analysis. Software tools are organized as full protocol of analysis (workflow), specific brick (component) to construct a workflow, or software platform or library (collection).  They are described using Edam Bio Imaging, which is iteratively defined using this website. All entries are exposed following FAIR principles and accessible for other usage with  (ODC-By) v1.0 license.

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

A biomarker database provides structured information on all biomarker candidates published in PubMed articles.

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.

A comprehensive enzyme information system. It is the world’s largest and most widely information system on all aspects of enzymes, including function, structure, mutants, properties like stability, purification. Data download is possible as an integrated text filed or via SOAP.

Mouse brain response to low-dose ionizing radiation (emerging service) 

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. 

A classification of protein structures and sequences that groups protein domains into superfamilies. 

A knowledge resource on cell lines.

A comprehensive resource of channels, pores and tunnels found in biomacromolecular structures deposited in the Protein Data Bank.

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.

ChIPSummitDB is a comprehensive database of transcription factor binding sites verified by human ChIP-seq experiments

A web tool for identifying CRISPR–Cas single guide RNA (sgRNA) targets

Collaborative Spanish Variant Server (CSVS) is a crowdsourcing initiative to provide information about the genomic variability of the Spanish population to the scientific/medical community.

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

Web based portal of organism-specific cross-platform expression compendia of bacterial organisms and grapevine