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Suggested Data Repositories  

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  2. 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.

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 - 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

 

Community repositories or projects - NIDDK funded (accept data from collaborators)

Respository Name Type of Data Guidelines/Standards Recommended by
Type 2 Diabetes Knowledge Portal (T2DK) Array, exome sequencing, whole genome sequencing data    
Vitamin D to Prevent Type 2 Diabetes (D2d) Clinical data    
Human Islet Research Network (HIRN) Epigenomics, genomics, metabolomics, proteomics, transcriptomics data    
JDRF Artificial Pancreas Project Consortium Clinical data    
Diabetic Complications Consortium      
NIDDKInflammatory Bowel Disease Genetics Consortium Clinical data    
Collaborative Islet Transplant Registry Clinical data    
Teen-Longitudinal Assessment of Bariatric Surgery Clinical data    
SEARCH for Diabetes in Youth Clinical data    
SEARCH for Diabetes in Youth Clinical data    
Intestinal Stem Cell Consortium RNA seq    
Chronic Renal Insufficiency Cohort Study Clinical data    
GenitoUrinary Development Molecular Anatomy Project RNA-Seq, Histological Images, Immunofluorescence Images, Section In Situ Images and Data    
ReBuilding a Kidney RNA-Seq, Histological Images, Immunofluorescence Images, Section In Situ Images and Data    
nPOD TCR/BCR Search      



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

Respository Name Type of Data Guidelines/Standards Recommended by
Protein Circular Dichroism Data Bank (PCDDB) Peptides and proteins   Natural Scientific Data; PLOS
Crystallography Open Database (COD) Structural data for small molecules; peptides and proteins   Natural Scientific Data; PLOS
Coherent X-ray Imaging Data Bank (CXIDB) Peptides and proteins; Coherent X-ray Imaging (CXI) data   Natural Scientific Data; PLOS; Science
Biological Magnetic Resonance Data Bank (BMRB) (BioMag Res Bank) Peptides and proteins; NMR spectroscopy data   Natural Scientific Data; PLOS; Science
EMDataBank (EMDB) Peptides and proteins; larger assemblies; 3-Dimensional Electron Miscroscopy (3DEM)   Nature Scientific Data; PLOS
Worldwide Protein Data Bank (wwPDB) Peptides and proteins   Nature Scientific Data; PLOS; Science
Structural Biology Data Grid Peptides and proteins   Nature Scientific Data
Cambridge Crystallographic Data Centre (CCDC) Small-molecule crystal structure   PLOS; Science
Electron Microscopy Data Bank (MSD-EBI) Peptides and proteins; Electron density maps   Science
Inorganic Crystal Structure Database (ICSD) Inorganic crystal structure   Science
Protein Data Bank Japan Macromolecular structure data   Science
Macromolecular Structure Database ("becoming the PDBe") Macromolecular structure data   Science



Omics - Functional Genomics

Respository Name Type of Data Guidelines/Standards Recommended by
ArrayExpress Microarray; next-generation sequencing (NGS) MIAME standard for microarray data Natural Scientific Data; PLOS; Science
Gene Expression Omnibus (GEO) Microarray; next-generation sequencing (NGS) MIAME standard for microarray data Natural Scientific Data; PLOS; Science
GenomeRNAi RNAi screening data (phenotype and/pr reagent)   Natural Scientific Data; PLOS
dbGAP Genotyping and phenotyping information in human subjects   Nature Scientific Datal PLOS
The European Genome-phenome Archive (EGA) Data linking genotyping and phenotyping information in human subjects, including sequence data, array based data, and phenotype data. The minimum information about any (x) sequence (MlxS) Natural Scientific Data; PLOS; Science
Database of Interacting Proteins (DIP) Protein interaction data Molecular interaction data should be deposited with a member of the International Molecular Exchange Consortium (IMEx), following the Minimum Information about a Molecular Interaction Experiment (MIMIx) recommendations Nature Scientific Data; PLOS
Japanese Genotype-phenotype Archive (JGA) Data linking genotyping and phenotyping information in human subjects; all types of individual-level genetic and de-identified phenotypic data   Nature Scientific Data
Biological General Repository for Interaction Datasets (BioGRID) Molecular interaction data Molecular interaction data should be deposited with a member of the International Molecular Exchange Consortium (IMEx), following the MIMIx recommendations Nature Scientific Data; PLOS
NCBI PubChem BioAssay Small-molecule and RNAi screening data; bioactibity and toxicity data Minimum information About a RNAi Experiment Nature Scientific Data



Omics - Metabolomics

Respository Name Type of Data Guidelines/Standards Recommended by
MetaboLights Metabolite structure MSI guidelines Nature Scientific Data; PLOS







Chemistry and chemical biology, biochemistry

Respository Name Type of Data Guidelines/Standards Recommended by
caNanoLab Physico-chemical, in vitro and in vivo assays data that characterize nanomaterials. *This is a curated resource which may not accept direct submission of data. Contact the database directly for further information   Natural Scientific Data; PLOS
ChEMBL Bioactivity data containing information mannually extracted from the medicinal chemistry literature. *This is a curated resource which may not accept direct submission of data. Contact the database directly for further information   Natural Scientific Data
NCBI PubChem BioAssay Small-molecule and RNAi screening data; bioactibity and toxicity data Minimum Information About a RNAi Experiment Natural Scientific Data
NCBI PubChem Substance Community-provided information about chemical entities   Natural Scientific Data; PLOS
Beilstein-Institut, STRENDA Functional enzymology data STRENDA Guidelines Nature Scientific Data; PLOS
Kinetic Models of Biological Systems (KiMoSys) Kinetic models   PLOS
Mass spectrometry Interactive Virtual Environment (MassIVE) Mass spectrometry data   PLOS
Cambridge Crystallographic Data Centre (CCDC) Small-molecule crystal structure   PLOS; Science
Electron Microscopy Data Bank (MSD-EBI) Peptides and proteins; Electron density maps   Science
Inorganic Crystal Structure Database (ICSD) Inorganic crystal structure   Science
Protein Data Bank Japan Macromolecular structure data   Science
Macromolecular Structure Database ("becoming the PDBe") Macromolecular structure data   Science





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 U24DK097771.

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