Library: Finding and reusing research datasets: Biosciences

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Model organism data repositories

The Arabidoposis Information Resources (TAIR)
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
Eukaryotic Pathogen Database Resources (EuPathDB)
EuPathDB (formerly ApiDB) is an integrated database covering the eukaryotic pathogens.
FlyBase
FlyBase is a database of genetic, genomic and functional data for Drosophila species.
Mouse Genome Informatics
MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.
Rat Genome Database
The goal of the database is to establishment of a Rat Genome Database, to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community.
VectorBase
VectorBase provides data on arthropod vectors of human pathogens. Sequence data, gene expression data, images, population data, and insecticide resistance data for arthropod vectors are available for download.
WormBase
International collaboration to provide accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and some related nematodes.
XenBase
Database providing access the diverse and rich genomic, expression and functional data available from Xenopus research.
Zebrafish Model Organism Database (ZFIN)
Model organism database for the Zebrafish research community.

Sequencing data archives

Database of Genomic Variants (DGVa)
Data archive of genomic structural variants.
dbSNP
NCBI Short Genetic Variations database (dbSNP) contains data on short variations in nucleotide sequences from a wide range of organisms.
dbVar
NCBI database of genomic structural variation with data from multiple gene studies using a variety of organisms and techniques.
DNA Databank of Japan
The sole nucleotide sequence databank for Asia containing international data on nucleotide sequences.
MGNify (formerly EBI Metagenomics)
Archive of microbiome data to help determine taxonomic diversity and functional and metabolic potential.
European Nucleotide Archive (ENA)
Data repository for experimental workflows based around nucleotide sequencing.
European Variation Archive
Database of genetic variation data from all species with highly detailed, granular raw data from human genetic data.
GenBank
Annotated collection of publicly-available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. These three organizations exchange data on a daily basis.
MIRBase
Searchable database of published annotated miRNA sequences.
NCBI Sequence Read Archive
Raw sequencing data from platforms including the Roche 454 GS system, the Illumina Genome analyser, the Applied Biosystems SOLiD System, the Helicos Helicoscope and the Complete Genomics.
NCBI Trace Archive
Archive of DNA sequence chromatograms, base calls and quality estimates for single pass reads from various large-scale sequencing projects.
Universal Protein Resource (UniProt)
Data archive of annotated protein sequence data.

Biochemical data archives

Beilstein-Institut STRENDA
Data archive and sharing platform for enzymology data.
CaNanoLab
Data sharing portal for biomedical nanotechnology datasets.
Mass Spectrometry Interactive Virtual Environment (MassIVE)
MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry.

Ecological and environmental data archives

British Ecological Survey
Over 400 datasets of environmental monitoring data, digital database and physical collections (e.g. borehole core, rocks, minerals and fossils).
Environmental Data Initiative Repository
Data from studies on ecological processes that play out on timescales spanning decades to centuries.
The Knowledge Network for Biocomplexity
International repository to support ecological, environmental and earth science research.
AEKOS-TERN Ecoinformatics
Data portal for Australian ecology data for land dwelling plants, animals and their environments.

Structural data repositories

The Binding Database
Database of measured binding affinities, focusing chiefly on the interactions of proteins considered to be candidate drug-targets with ligands that are small, drug-like molecules.
Biological Magnetic Resonance Data Bank (BMRB)
BMRB collects, annotates, archives, and disseminates spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites.
Cambridge Structural Database
Web access to the Cambridge Structural Database, with access to over 900,000 organic and organometallic crystal structures.
eCrystals
Archive for crystal structures generated by the Southampton Chemical Crystallography Group and the EPSRC UK National Crystallography Service.
Electron Microscopy Data Bank (EMDB)
Electron microscopy density maps of macromolecular complexes and subcelluar structures covering single-particle analysis, electronic tomography and electron crystallography.
IntAct Molecular Interaction Database
Database and analysis tool for molecular interaction data curated from the literature or direct deposits.
Protein Circular Dicronism Databank (PCDDB)
The Protein Circular Dicronism Data Bank (PCDDB) provides and accepts a circular dichroism spectra data.
Structural Biology Data Grid
Open access to macromolecular X-ray diffraction and MicroED datasets. The repository complements the Worldwide Protein Data Bank.
WorldWide Protein Data Bank
The data contained in the archive include atomic coordinates, crystallographic structure factors and NMR experimental data.

'Omics' databases

ArrayExpress
Major international repository for data from high-throughput functional genomics data from both microarray and high-throughput sequencing studies.
BioGrid: Biological General Repository for Interaction Datasets
Genetic and protein interaction data from human proteins and model organisms.
Database of Interacting Proteins (DIP)
Data on interactions between proteins.
European Genome-Phenome Archive
The European Genome-phenome Archive (EGA) is designed to be a repository for all types of sequence and genotype experiments, including case-control, population, and family studies.
Gene Expression Omnibus
NCBI genomics data repository array and sequence-based data.
GenomeRNAi
Data archive for phenotypes from RNA interference screens in Drosophila and Homo sapiens.
Japanese Genome-Phenome Archive
Individual-level genetic and de-identified phenotypic data resulting from biomedical research projects.
Mass Spectrometry Interactive Virtual Environment (MassIVE)
MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry.
MetaboLights
Database for metabolomics cross-species, cross-technique experimental data.
Metabolomics Workbench
Raw data and biological and analytical metadata for metabolomics research.
NCBI dbGAP
Database of interactions between Genotypes and Phenotypes including data from GWA studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits.
Peptide Atlas
Proteomic data from high-throughput processes.
Proteomics Identifications (PRIDE)
Repository of shotgun mass spectrometry proteomics data.

Finding and reusing research datasets: Biosciences

Finding published research datasets for biology and biochemistry research

University of Bath Library Subject Homepages

Model organism data repositories

Sequencing data archives

Biochemical data archives

Ecological and environmental data archives

Structural data repositories

'Omics' databases

Attribution