Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
We have organized a list of data repositories that are recommended by the following sources: Nature Scientific Data, PlosOne, NLM NIH Data Sharing Repositories - NIDDK, Science. It is generally best practice to deposit data into a discipline-specific and community recognized repositories if one is available, or into an institutional or generalist repositories if no suitable specialist repository is available.
By disciplines
Community repositories - NIDDK funded
Respository Name | Type of Data | Guidelines/Standards | Recommended by |
---|---|---|---|
Metabolomics Workbench (MetWB) | Metabolomics data and metadata | NLMNIH-NIDDK: PLOS | |
NIDDK Central Repository | Genetic and other data collected in designated NIDDK-funded clinical studies | NLMNIH-NIDDK | |
NIDDK Information Network (dkNET) | Metadata on data sets | NLM/NIH-NIDDK | |
Nuclear Receptor Signaling Atlas (NURSA) | Metadata on Omics data sets contributed to community repositories, e.g., GEO, dbGAP, ENCODE | NLM/NIH-NIDDK; PLOS | |
dkNET - Signaling Pathways Project (SPP) | Curated omics data |
Community repositories - Specialized
Respository Name | Type of Data | Guidelines/Standards | Recommended by |
---|---|---|---|
ClinicalTrials.gov | Clinical trial | Nature Scientific Data | |
Cell Image Library | Microscopic imaging data | ||
Worldwide Protein Data Bank | Protein structure | Nature Scientific Data; PLOS; Science | |
PhysioNet | Physiological data | PLOS | |
Gene Expression Omnibus (GEO) | microarray; next-generation sequencing (NGS) | MIAME standard for microarray data | Nature Scientific Data; PLOS; Science |
ProteomeXchange | Proteomics | MIAPE: Mass Spectrometry; Minimum Information About a Proteomics Experiment; MIAPE: Mass Spectrometry Informatics | PLOS |
Electron Microscopy Data Bank | High resolution electron miscroscopic images and molecular maps | Science | |
EMDataBank (EMDB) | Peptides and proteins; large assemblies; 3-Dimensional Electron Microscopy (3DEM) | Nature Scientific Data; PLOS | |
dbGAP | Genotyping and phenotyping information in human subjects | Nature Scientific Data; PLOS |
Community repositories - domain specific
Community repositories - General
Respository Name | Type of Data | Guidelines/Standards | Recommended by |
---|---|---|---|
Zenodo | Multidisciplinary research results including text, spreadsheet, zudio, video, images, source code | Natural Scientific Data; PLOS | |
Open Science Framework | Research data in all domain areas | Natural Scientific Data; PLOS | |
Dyrad Digital Repository | Data underlying scientific publications | Common Metadata Elements for Cataloging Biomedical Datasets | Natural Scientific Data; PLOS |
Figshare | All research data | Natural Scientific Data; PLOS | |
Mendeley Data | All research data | ||
Harvard Dataverse | All research data | Natural Scientific Data; PLOS |
Institutional repository
Respository Name | Type of Data | Guidelines/Standards | Recommended by |
---|---|---|---|
Does your institution have a repository for managing and publishing your data? Usually, these services are provided by the library. The Directory of Open Access Resources provides a directory of institutional repositories |
Community repositories or projects - NIDDK funded (accept data from collaborators)
Nucleic acid sequence
Respository Name | Type of Data | Guidelines/Standards | Recommended by |
---|---|---|---|
dbSNP | Simple genetic polymorphism or structural variations | Natural Scientific Data; PLOS | |
dbVar | Simple genetic polymorphism or structural variations | Natural Scientific Data; PLOS | |
NCBI Trace Archive | Capillary electrophoresis data | Natural Scientific Data; PLOS | |
NCBI Sequence Read Archive (SRA) | NGS data only; Multiple sequence alignment | Minimum Information about a MARKer gene Sequence;Minimal Information about a high throughput SEQuencing Experiment | Natural Scientific Data; PLOS |
DNA DataBank of Japan (DDBJ) | Gene Sequence | Minimum Information about any (x) Sequence (MlxS) | Nature Scientific Data; PLOS; Science |
European Nucleotide Archive (ENA) | Sequence reads, genome assemblies, targeted assembled and annotated sequences | Minimum Information About Sample Preparation for a Phosphoproteomics Experiment;Minimum Information about any (x) Sequence;Marine Microbial Biodiversity, Bioinformatics and Biotechnology data reporting and service standards | Nature Scientific Data; PLOS; Science |
GenBank | Gene sequence | Minimum Information about any (x) Sequence (MlxS) | Nature Scientific Data; PLOS; Science |
European Variation Archive (EVA) | Gene sequence | Nature Scientific Data; PLOS; Science | |
Database of Genomic Variants Archive (DGVa) | Genomic structural variants | Nature Scientific Data; PLOS; Science | |
EBI Metagenomics | Metagonomics sequence data and associate metadata | Minimum Information about a (Meta)Genome Sequence;Minimum Information about any (x) Sequence | Nature Scientific Data; PLOS; Science |
NCBI Assembly | Genome assemblies (collection of genomic sequences that are used to represent the genome of an organism) | Nature Scientific Data | |
MiRBase | miRNA sequences and annotation | PLOS |
Protein sequence
Respository Name | Type of Data | Guidelines/Standards | Recommended by |
---|---|---|---|
UniProtKB | Amino acid sequence | Nature Scientific Data; Science; PLOS |
Molecular and supramolecular structure
Omics - Functional Genomics
Omics - Metabolomics
Respository Name | Type of Data | Guidelines/Standards | Recommended by |
---|---|---|---|
MetaboLights | Metabolite structure | MSI guidelines | Nature Scientific Data; PLOS |
Omics - Proteomics
Respository Name | Type of Data | Guidelines/Standards | Recommended by |
---|---|---|---|
PeptideAtlas | Tandem mass spectrometry proteomics data of peptides | Submit proteomics data to members of ProteomeXchange consortium (listed below), following the MIAPE recommendations | Nature Scientific Data; PLOS |
Proteomics Identifications (PRIDE) | Protein and peptide identification/quantification data from mass spectrometry | Submit proteomics data to members of the ProteomeXchange consortium (listed below), following the MIAPE recommendations | Nature Scientific Data; PLOS |
The Global Proteome Machine Database (GPM DB) | Protein and peptides; Mass spectrometry | PLOS |
Cytometry and Immunology
Respository Name | Type of Data | Guidelines/Standards | Recommended by |
---|---|---|---|
FlowRepository | Flow cytometry data | MIFlowCyt standard | Nature Scientific Data; PLOS |
ImmPort | Immunology research data including experimental data and clinical trial data | Minimum Information About a Microarray Experiment; Minimum Information about Flow Cytometry; Minimum Information About a Bioinformatics investigation; LINCS Pilot Phase 1 Metadata Standards: Antibody Reagents | Nature Scientific Data; PLOS |
Chemistry and chemical biology, biochemistry
Imaging
Respository Name | Type of Data | Guidelines/Standards | Recommended by |
---|---|---|---|
Image Data Resource | Reference image datasets supporting an original scientific publication | Nature Scientific Data | |
The Cancer Imaging Archive | Primary DICOM image datasets from cancer patients and analysis datasets | Nature Scientific Data; PLOS | |
SICAS Medical Image Repository | Brain images, Segmentations, SSM, Dicom, ITK based images and statistical models | Nature Scientific Data; PLOS | |
Coherent X-ray Imaging Data Bank (CXIDB) | Peptides and proteins; Coherent X-ray Imaging (CXI) data | Nature Scientific Data; PLOS |
Neuroscience
Respository Name | Type of Data | Guidelines/Standards | Recommended by |
---|---|---|---|
NeuroMorpho.org | 3D neuronal reconstructions and associated metadata | Nature Scientific Data; PLOS | |
Functional Connectomes Project International Neuroimaging Data-Sharing Initiative (FCP/INDI) | Primary DICOM image datasets from cancer patients and analysis datasets | Minimum Information about an fMRI Study | Nature Scientific Data; PLOS |
OpenNeuro (formerly OpenfMRI) | Neuroimaging data; Magnetic Resonance Imaging (MRI) | Nature Scientific Data; PLOS | |
G-Node | Neuroscience research data | Nature Scientific Data; PLOS |