Services: data resources

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.

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

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

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. 

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

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

An integrative platform for the analysis of transcriptomics, proteomics and genomic data

with advanced functional profiling.

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. 

 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.

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.

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

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

COPO is a portal for scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results. COPO can link your outputs to your ORCiD profile.

A data resource for Quercus suber.