Filter
Reset all

Subjects

Content Types

Countries

AID systems

API

Certificates

Data access

Data access restrictions

Database access

Database access restrictions

Database licenses

Data licenses

Data upload

Data upload restrictions

Enhanced publication

Institution responsibility type

Institution type

Keywords

Metadata standards

PID systems

Provider types

Quality management

Repository languages

Software

Syndications

Repository types

Versioning

  • * at the end of a keyword allows wildcard searches
  • " quotes can be used for searching phrases
  • + represents an AND search (default)
  • | represents an OR search
  • - represents a NOT operation
  • ( and ) implies priority
  • ~N after a word specifies the desired edit distance (fuzziness)
  • ~N after a phrase specifies the desired slop amount
Found 47 result(s)

FlyReactome

a curated knowledgebase of drosophila melanogaster pathways

Subject(s)
Content type(s)
Country
<<<!!!<<< This repository is no longer available. This record is out dated >>>!!!>>>- eir fields, maintained by the FlyReactome staff.

Expression Atlas

Gene Expression Atlas

Subject(s)
Content type(s)
Country
The Expression Atlas provides information on gene expression patterns under different biological conditions such as a gene knock out, a plant treated with a compound, or in a particular organism part or cell. It includes both microarray and RNA-seq data. The data is re-analysed in-house to detect interesting expression patterns under the conditions of the original experiment. There are two components to the Expression Atlas, the Baseline Atlas and the Differential Atlas. The Baseline Atlas displays information about which gene products are present (and at what abundance) in "normal" conditions (e.g. tissue, cell type). It aims to answer questions such as "which genes are specifically expressed in human kidney?". This component of the Expression Atlas consists of highly-curated and quality-checked RNA-seq experiments from ArrayExpress. It has data for many different animal and plant species. New experiments are added as they become available. The Differential Atlas allows users to identify genes that are up- or down-regulated in a wide variety of different experimental conditions such as yeast mutants, cadmium treated plants, cystic fibrosis or the effect on gene expression of mind-body practice. Both microarray and RNA-seq experiments are included in the Differential Atlas. Experiments are selected from ArrayExpress and groups of samples are manually identified for comparison e.g. those with wild type genotype compared to those with a gene knock out. Each experiment is processed through our in-house differential expression statistical analysis pipeline to identify genes with a high probability of differential expression.

Reactome

a curated pathway database

Subject(s)
Content type(s)
Country
Reactome is a manually curated, peer-reviewed pathway database, annotated by expert biologists and cross-referenced to bioinformatics databases. Its aim is to share information in the visual representations of biological pathways in a computationally accessible format. Pathway annotations are authored by expert biologists, in collaboration with Reactome editorial staff and cross-referenced to many bioinformatics databases. These include NCBI Gene, Ensembl and UniProt databases, the UCSC and HapMap Genome Browsers, the KEGG Compound and ChEBI small molecule databases, PubMed, and Gene Ontology.

MGnify

formerly: EBI Metagenomics

Subject(s)
Content type(s)
Country
MGnify (formerly: EBI Metagenomics) offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.

Ensembl Metazoa

e!EnsemblMetazoa

Subject(s)
Content type(s)
Country
Ensembl Metazoa is a genome-centric portal for metazoan species of scientific interest.

UniProtKB

UniProtKnowledgebase

Subject(s)
Content type(s)
Country
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data. The UniProt Knowledgebase,is an expertly and richly curated protein database, consisting of two sections called UniProtKB/Swiss-Prot and UniProtKB/TrEMBL.

West African Vegetation

A vegetation data network for West Africa

Subject(s)
Content type(s)
Country
This is a database for vegetation data from West Africa, i.e. phytosociological and dendrometric relevés as well as floristic inventories. The West African Vegetation Database has been developed in the framework of the projects “SUN - Sustainable Use of Natural Vegetation in West Africa” and “Biodiversity Transect Analysis in Africa” (BIOTA, https://www.biota-africa.org/).

Golm Metabolome Database

GMD

Subject(s)
Content type(s)
Country
The Golm Metabolome Database (GMD) facilitates the search for and dissemination of reference mass spectra from biologically active metabolites quantified using gas chromatography (GC) coupled to mass spectrometry (MS)

Ensembl Plants

e!EnsemblPlants

Subject(s)
Content type(s)
Country
EnsemblPlants is a genome-centric portal for plant species. Ensembl Plants is developed in coordination with other plant genomics and bioinformatics groups via the EBI's role in the transPLANT consortium.

IMGT/LIGM-DBI

International ImMunoGeneTics information system / Laboratoire d'ImmunoGénétique Moléculaire-Database

Subject(s)
Content type(s)
Country
IMGT/LIGM-DB is a comprehensive database of Immunoglobulins (IG) and T cell Receptors (TR) from human and other vertebrates, with translation for fully annotated sequences.

COVID-19 Data Portal

Subject(s)
Content type(s)
Country
The COVID-19 Data Portal was launched in April 2020 to bring together relevant datasets for sharing and analysis in an effort to accelerate coronavirus research. It enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets as part of the wider European COVID-19 Data Platform.

ESRF Portal

European Synchrotron Radiation Facility Data Repository

Subject(s)
Content type(s)
Country
Explore, search, and download data and metadata from your experiments and from public Open Data. The ESRF data repository is intended to store and archive data from photon science experiments done at the ESRF and to store digital material like documents and scientific results which need a DOI and long term preservation. Data are made public after an embargo period of maximum 3 years.

MetabolomeXchange

Subject(s)
Content type(s)
Country
MetabolomeXchange.org delivers the mechanisms needed for disseminating the data to the metabolomics community at large (both metabolomics researchers and databases). The main objective is to make it easier for metabolomics researchers to become aware of newly released, publicly available, metabolomics datasets that may be useful for their research. MetabolomeXchange contains datasets from different data providers: MetaboLights, Metabolomic Repository Bordeaux, Metabolomics Workbench, and Metabolonote

AlphaFold

AlphaFold Protein Structure Database

Subject(s)
Content type(s)
Country
AlphaFold DB provides open access to protein structure predictions for the human proteome and 20 other key organisms to accelerate scientific research.

RADAM database portal

RADiation DAMage database

Subject(s)
Content type(s)
Country
RADAM portal is an interface to the network of RADAM (RADiation DAMage) Databases collecting data on interactions of ions, electrons, positrons and photons with biomolecular systems, on radiobiological effects and relevant phenomena occurring at different time, spatial and energy scales in irradiated targets during and after the irradiation. This networking system has been created by the Consortium of COST Action MP1002 (Nano-IBCT: Nano-scale insights into Ion Beam Cancer Therapy) during 2011-2014 using the Virtual Atomic and Molecular Data Center (VAMDC) standards.

European Variation Archive

EVA

Subject(s)
Content type(s)
Country
The European Variation Archive is an open-access database of all types of genetic variation data from all species. The EVA provides access to highly detailed, granular, raw variant data from human, with other species to follow. As of September 2017, EMBL-EBI will maintain reliable accessions for non-human genetic variation data through the European Variation Archive (EVA). NCBI's dbSNP database will continue to maintain stable identifiers for human genetic variation data only. This change will enable a more rapid turnaround for data sharing in this burgeoning field.

CERIC Data Portal

CERIC Metadata Catalogue

Subject(s)
Content type(s)
Country
CERIC Data Portal allows users to consult and manage data related to experiments carried out at CERIC (Central European Research Infrastructure Consortium) partner facilities. Data made available includes scientific datasets collected during experiments, experiment proposals, samples used and publications if any. Users can search for data based on related metadata (both their own data and other peoples' public data).

GenomeRNAi

Subject(s)
Content type(s)
Country
GenomeRNAi is a database containing phenotypes from RNA interference (RNAi) screens in Drosophila and Homo sapiens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality.

BioVel

Biodiversity Virtual e-Laboratory

Subject(s)
Content type(s)
Country
<<<!!!<<< This repository is no longer available. >>>!!!>>> BioVeL is a virtual e-laboratory that supports research on biodiversity issues using large amounts of data from cross-disciplinary sources. BioVeL supports the development and use of workflows to process data. It offers the possibility to either use already made workflows or create own. BioVeL workflows are stored in MyExperiment - Biovel Group http://www.myexperiment.org/groups/643/content. They are underpinned by a range of analytical and data processing functions (generally provided as Web Services or R scripts) to support common biodiversity analysis tasks. You can find the Web Services catalogued in the BiodiversityCatalogue.

IMGT/3Dstructure-DB and IMGT/2Dstructure-DB

International ImMunoGeneTics information system/3Dstructure-DB and IMGT/2Dstructure-DB

Subject(s)
Content type(s)
Country
IMGT/3Dstructure-DB is the IMGT three-dimensional (3D) structure database.

Array Express

functional genomics data

Subject(s)
Content type(s)
Country
ArrayExpress is one of the major international repositories for high-throughput functional genomics data from both microarray and high-throughput sequencing studies, many of which are supported by peer-reviewed publications. Data sets are submitted directly to ArrayExpress and curated by a team of specialist biological curators. In the past (until 2018) datasets from the NCBI Gene Expression Omnibus database were imported on a weekly basis. Data is collected to MIAME and MINSEQE standards.

ProteomeXchange

PX

Subject(s)
Content type(s)
Country
The ProteomeXchange consortium has been set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. Current members accepting submissions are: The PRIDE PRoteomics IDEntifications database at the European Bioinformatics Institute focusing mainly on shotgun mass spectrometry proteomics data PeptideAtlas/PASSEL focusing on SRM/MRM datasets.

European Nucleotide Archive

ENA

Subject(s)
Content type(s)
Country
The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources. These include submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centres and routine and comprehensive exchange with our partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature.

Electron Microscopy Data Bank

EMDB

Subject(s)
Content type(s)
Country
The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.

PhytoPath

Subject(s)
Content type(s)
Country
<<<!!!<<< This site is no longer maintained and is provided for reference only. Some functionality or links may not work. For all enquiries please contact the Ensembl Helpdesk http://www.ensembl.org/Help/Contact >>>!!!>>> PhytoPath is a new bioinformatics resource that integrates genome-scale data from important plant pathogen species with literature-curated information about the phenotypes of host infection. Using the Ensembl Genomes browser, it provides access to complete genome assembly and gene models of priority crop and model-fungal, oomycete and bacterial phytopathogens. PhytoPath also links genes to disease progression using data from the curated PHI-base resource. PhytoPath portal is a joint project bringing together Ensembl Genomes with PHI-base, a community-curated resource describing the role of genes in pathogenic infection. PhytoPath provides access to genomic and phentoypic data from fungal and oomycete plant pathogens, and has enabled a considerable increase in the coverage of phytopathogen genomes in Ensembl Fungi and Ensembl Protists. PhytoPath also provides enhanced searching of the PHI-base resource as well as the fungi and protists in Ensembl Genomes.