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Suggested Data Repositories
Where can I deposit my data?
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.
- Community repositories - NIDDK funded
- Community repositories - Specialized
- Community repositories: Domain specific
- Community repositories: General
- Institutional repository
- Community repositories or projects - NIDDK funded (accept data from collaborators)
By disciplines
- Nucleic acid sequence
- Protein sequence
- Molecular and supramolecular structure
- Omics - Functional Genomics
- Omics - Metabolomics
- Omics - Proteomics
- Cytometry and Immunology
- Chemistry and chemical biology, biochemistry
- Imaging
- Neuroscience
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 |
About
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
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