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Suggested Data Repositories (NIDDK)
Where can I deposit my data?
We have organized a list of data repositories that are recommended by the following sources: NIDDK domain experts, Nature Scientific Data, PlosOne, NLM NIH Data Sharing Repositories, Science. It is generally best practice to deposit data into a discipline-specific and community recognized repository if one is available, or into an institutional or generalist repository if no suitable specialist repository is available.
- NIDDK-specific repositories
- NIH-supported repositories
- Institutional repository
- Other NIDDK Project-specific or consortium-specific data or sample repositories
By scientific disciplines
- Nucleic acid sequence
- Protein sequence
- Molecular and supramolecular structure
- Functional Genomics
- Metabolomics
- Proteomics
- Cytometry and Immunology
- Chemistry and chemical biology, biochemistry
- Imaging
- Neuroscience
- All research data types
- Other domain-specific repositories
De-identified human clinical research data
Clinical trial data is encouraged to be submitted to the ClinicalTrials.gov even if it is not required. For studies include human genomic and associate phenotypic data, you can consider NIH database of Genotypes and Phenotypes (dbGaP). Another repository that you can consider is ICPSR, which hosts a variety of human data, including many demographic and social science studies. Information on uploading data to ICPSR can be found here. Before uploading data, please note that the data should be de-identified, and you should follow all your institutional IRB's requirements and receive approvals. For completed phase I-IV interventional studies, you can also share anonymized data at Vivli.
NIDDK-specific repositories
| Respository Name | RRID | Description | Type of Data | Submitting Data | Accessing Data | Guidelines/Standards | Recommended by |
|---|---|---|---|---|---|---|---|
| NIDDK Central Repository | RRID:SCR_006542 | The NIDDK Central Repository stores biosamples, genetic and other data collected in designated NIDDK-funded clinical studies. The purpose of the NIDDK Central Repository is to expand the usefulness of these studies by allowing a wider research community to access data and materials beyond the end of the study | Genetic and other data collected in designated NIDDK-funded clinical studies | How to submit data to NIDDK Central Repository | How to access NIDDK Central Repository data | NIDDK, NLM/NIH | |
| The AMP-T2D Knowledge Portal | RRID:SCR_003743 | The AMP-T2D Knowledge Portal is the NIDDK-designated repository being developed as part of the Accelerating Medicines Partnership (AMP), a public-private partnership between the National Institutes of Health (NIH), the U.S. Food and Drug Administration (FDA), 10 biopharmaceutical companies, and multiple non-profit organizations that is managed through the Foundation for the NIH (FNIH) for collection of various types of molecular data such as DNA sequences, functional and epigenomic information, and clinical data from studies on type 2 diabetes and its macro- and microvascular complications from human, cell-based and animal model biosamples, analytical results and research tools towards improving current efforts to develop new therapies for complex, heterogeneous diseases, including type 2 diabetes. | Array, exome sequencing, whole genome sequencing data | How to submit data to the AMP-T2D Knowledge Portal | How to access AMP-T2D Knowledge Portal data | NIDDK |
NIH-supported repositories (for complete and current list of NIH repositories click here)
| Respository Name | RRID | Description | Type of Data | Submitting Data | Accessing Data | Guidelines/Standards | Recommended by |
|---|---|---|---|---|---|---|---|
| Analysis, Visualization, and Informatics Lab-space (AnVIL) (Coming soon) | The AnVIL is a scalable and interoperable resource for the genomic scientific community, that leverages a cloud-based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic-related data sets. The AnVIL will facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health (NIH), or by other agencies that support human genomics research. The AnVIL will be a component of the emerging NIH Data Commons, and is expected to collaborate and integrate with other genomic data resources through the adoption of the FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from the scientific community. | Genomic data | |||||
| Biological General Repository for Interaction Datasets (BioGRID) | RRID:SCR_007393 | BioGRID is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications from major model organism species. All interaction data are freely provided through our search index and available via download in a wide variety of standardized formats. | Molecular interaction data | How to submit data to BioGRID | How to access BioGRID data | Molecular interaction data should be deposited with a member of the International Molecular Exchange Consortium (IMEx), following the MIMIx recommendations | NIDDK; NLM/NIH |
| Cell Image Library | RRID:SCR_003510 | The Cell Image Library, accepts image data sets that are too large for publishers to store, and provides access to the biomedical community. There are 10,000 datasets in 20TB of uploaded data as of mid-2018. The library inherits data from the Cell Centered Database at UCSD. Since its launch in 2010, the site has had 721,00 visitors and was cited by 175 research publications. | Microscopic imaging data | How to submit data to Cell Image Library | How to access Cell Image Library data | NIDDK; NLM/NIH | |
| ClinicalTrials.gov | RRID:SCR_002309 | A database of privately and publicly funded clinical studies conducted around the world. | Clinical trial | How to submit clinicl trials | How to access clinical trials | NIDDK; NLM/NIH; Nature Scientific Data | |
| Database of Interacting Proteins (DIP) | RRID:SCR_003167 | The DIP database, a founding member of the International Molecular Exchange Consortium (IMEx: https://www.imexconsortium.org), catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database are manually curated and include, when available, detailed information on the interacting regions, mutations and post-translational modifications that affect each interaction. | Protein interaction data | How to submit data to DIP | How to access DIP 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 | NIDDK; NLM/NIH; Nature Scientific Data; PLOS |
| FlyBase: A Drosophila Genomic and Genetic Database | RRID:SCR_006549 | Drosophila Genomic and Genetic database that includes proteomics data, microarrays and Tiling BAC's. | How to submit data to Flybase | How to access Flybase data | NIDDK; NLM/NIH | ||
| International Mouse Phenotyping Consortium (IMPC) | RRID:SCR_006158 | Phenotype data on knockout mouse lines. | How to submit data to IMPC | How to access IMPC data | NIDDK | ||
| Metabolomics Workbench (MetWB) | RRID:SCR_013794 | The Metabolomics Program's Data Repository and Coordinating Center (DRCC), housed at the San Diego Supercomputer Center (SDSC), University of California, San Diego, has developed the Metabolomics Workbench. MetWB will serve as a national and international repository for metabolomics data and metadata and will provide analysis tools and access to metabolite standards, protocols, tutorials, training, and more | Metabolomics data and metadata | How to submit data to MetWB | How to access MetWB data | NIDDK; NLM/NIH: PLOS | |
| Mouse Genome Informatics (MGI) | RRID:SCR_006460 | 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. | How to submit data to MGI | How to access MGI data | NIDDK; NLM/NIH | ||
| PeptideAtlas | RRID:SCR_006783 | PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. | Tandem mass spectrometry proteomics data of peptides | How to submit data to PeptideAtlas | How to access Peptide Atlas data | Submit proteomics data to members of ProteomeXchange consortium (listed below), following the MIAPE recommendations | NIDDK; Nature Scientific Data; PLOS |
| PhysioNet | RRID:SCR_007345 | The PhysioNet Resource is intended to stimulate current research and new investigations in the study of complex biomedical and physiologic signals. It offers free web access to large collections of recorded physiologic signals (PhysioBank) and related open-source software (PhysioToolkit). | Physiological data | How to submit data to PhysioNet | How to access PhysioNet data | NIDDK; NLM/NIH; PLOS | |
| Protein Data Bank (PDB) | RRID:SCR_012820 | The mission of the RCSB Protein Data Bank (PDB) is to Sustain a unique data resource of three-dimensional biomolecular structure | How to submit data to PDB | How to access PDB data | NIDDK; NLM/NIH | ||
| The Network Data Exchange (NDEx) | RRID:SCR_003943 | NDEx is an online commons where scientists can upload, share, and publicly distribute biological networks and pathway models. The NDEx Project maintains a web-accessible public server, a documentation website, provides seamless connectivity to Cytoscape as well as programmatic access using a variety of languages including Python and Java. NDEx users can easily create accounts or sign in using their Google credentials thanks to the supported open authentication (OAUTH2) method and mint DOIs for their networks to use in publications or include in other resources for long term access. | How to submit data to NDEx | How to access NDEx data | NIDDK; NLM/NIH | ||
| The Universal Protein Resource (UniProt) | RRID:SCR_002380 | 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). | How to submit data to UniProt | How to access UniProt data | NIDDK; NLM/NIH | ||
| The Zebrafish Information Network (ZFIN) | RRID:SCR_002560 | ZFIN serves as the zebrafish model organism database. It aims to: a) be the community database resource for the laboratory use of zebrafish, b) develop and support integrated zebrafish genetic, genomic and developmental information, c) maintain the definitive reference data sets of zebrafish research information, d) to link this information extensively to corresponding data in other model organism and human databases, e) facilitate the use of zebrafish as a model for human biology, and f) serve the needs of the research community. | How to submit data to ZFIN | How to access ZFIN data | NIDDK; NLM/NIH | ||
| WormBase | RRID:SCR_003098 | WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes. | How to submit data to WormBase | How to access WormBase data | NIDDK; NLM/NIH |
Institutional repository
| 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. |
Nucleic acid sequence
| Respository Name | RRID | Description | Type of Data | Submitting Data | Accessing Data | Guidelines/Standards | Recommended by |
|---|---|---|---|---|---|---|---|
| Database of Genomic Variants Archive (DGVa) | RRID:SCR_004896 | The Database of Genomic Variants archive (DGVa) is a repository that provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. | Genomic structural variants | How to submit data to DGVa | How to access DGVa data | NIDDK; Nature Scientific Data; PLOS; Science | |
| dbSNP | RRID:SCR_002338 | dbSNP is a general public archive of all short sequence variation, not just single nucleotide substitutions that occur frequently enough in a population to be termed polymorphic, but also rare variants, including those with clinical assertions in ClinVar. dbSNP includes a broad collection of simple genetic variations such as single-base nucleotide substitutions, small-scale multi-base deletions or insertions, and microsatellite repeats. | Simple genetic polymorphism or structural variations | How to submit data to dbSNP | How to access dbSNP data | NIDDK; Nature Scientific Data; PLOS | |
| dbVar | RRID:SCR_003219 | dbVar is a NCBI database of genomic structural variation. | Simple genetic polymorphism or structural variations | How to submit data to dbVar | How to access dbVar data | NIDDK; Nature Scientific Data; PLOS | |
| DNA DataBank of Japan (DDBJ) | RRID:SCR_002359 | DDBJ Center provides sharing and analysis services for data from life science researches and advances science. | Gene sequence | How to submit data to DDBJ | How to access DDBJ data | Minimum Information about any (x) Sequence (MIxS) | NIDDK; Nature Scientific Data; PLOS; Science |
| EBI Metagenomics | RRID:SCR_016429 | Submit, analyze, discover and compare microbiome data (now called MGnify) | metagonomics sequence data and associate metadata | How to submit data to MGnify | How to access MGnify data | Minimum Information about a (Meta)Genome Sequence; Minimum Information about any (x) Sequence | NIDDK; Nature Scientific Data; PLOS; Science |
| European Nucleotide Archive (ENA) | RRID:SCR_006515 | A comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. | Sequence reads, genome assemblies, targeted assembled and annotated sequences | How to submit data to ENA | How to access ENA data | 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 | NIDDK; Nature Scientific Data; PLOS; Science |
| European Variation Archive (EVA) | RRID:SCR_017425 | The European Variation Archive is an open-access database of all types of genetic variation data from all species. | Gene sequence | how to submit data to EVA | How to access EVA data | NIDDK; Nature Scientific Data; PLOS; Science | |
| GenBank | RRID:SCR_002760 | GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is designed to provide and encourage access within the scientific community to the most up to date and comprehensive DNA sequence information. | Gene sequence | How to submit data to GenBank | How to access GenBank data | Minimum Information about any (x) Sequence (MIxS) | NIDDK; Nature Scientific Data; PLOS; Science |
| Gene Expression Omnibus (GEO) | RRID:SCR_007303 | A public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles. | microarray; next-generation sequencing (NGS) | How to submit to GEO | How to access GEO data | MIAME standard for microarray data. | NIDDK; Nature Scientific Data; PLOS; Science |
| miRBase | RRID:SCR_003152 | The miRBase database is a searchable database of published miRNA sequences and annotation. | miRNA sequences and annotation | How to submit to miRBase | How to access miRBase data | NIDDK; PLOS | |
| NCBI Assembly | RRID:SCR_012917 | A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. | Genome assemblies (collection of genomic sequences that are used to represent the genome of an organism) | How to submit to Assembly | How to access Assembly data | NIDDK; Nature Scientific Data | |
| NCBI Sequence Read Archive (SRA) | RRID:SCR_004891 | The SRA is NIH's primary archive of high-throughput sequencing data and is part of the International Nucleotide Sequence Database Collaboration (INSDC) that includes at the NCBI Sequence Read Archive (SRA), the European Bioinformatics Institute (EBI), and the DNA Database of Japan (DDBJ). Data submitted to any of the three organizations are shared among them. | NGS data only; Multiple sequence alignment | How to submit data to SRA | How to access SRA data | Minimum Information about a MARKer gene Sequence; Minimal Information about a high throughput SEQuencing Experiment | NIDDK; Nature Scientific Data; PLOS; Science |
| NCBI Trace Archive | RRID:SCR_013788 | The Trace Archive serves as the repository of sequencing data from gel/capillary platforms such as Applied Biosystems ABI 3730®. | Capillary electrophoresis data | How to submit to NCBI Trace Archive | How to access NCBI Trace Archive data | Nature Scientific Data; PLOS |
Protein sequence
| Respository Name | RRID | Description | Type of Data | Submitting Data | Accessing Data | Guidelines/Standards | Recommended by |
|---|---|---|---|---|---|---|---|
| UniProtKB | RRID:SCR_004426 | 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 UniProt Knowledgebase consists of two sections: a section containing manually-annotated records with information extracted from literature and curator-evaluated computational analysis, and a section with computationally analyzed records that await full manual annotation. For the sake of continuity and name recognition, the two sections are referred to as "UniProtKB/Swiss-Prot" (reviewed, manually annotated) and "UniProtKB/TrEMBL" (unreviewed, automatically annotated), respectively. | Amino acid sequence and annotation | How to submit to UniProtKB | How to access UniProKB data | Nature Scientific Data; Science; PLOS |
Molecular and supramolecular structure
| Respository Name | RRID | Description | Type of Data | Submitting Data | Accessing Data | Guidelines/Standards | Recommended by |
|---|---|---|---|---|---|---|---|
| Biological Magnetic Resonance Data Bank (BMRB) (BioMag Res Bank) | RRID:SCR_002296 | A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules | Peptides and proteins; NMR spectroscopy data | How to submit to BMRB | How to access BMRB data | NIDDK; Nature Scientific Data; PLOS; Science | |
| Cambridge Crystallographic Data Centre (CCDC) | RRID:SCR_014707 | The world's comprehensive and up-to-date database of crystal structures with over 900,000 curated entries. | small-molecule crystal structure | How to submit to CCDC | How to access CCDC data | NIDDK; PLOS; Science | |
| Coherent X-ray Imaging Data Bank (CXIDB) | RRID:SCR_014722 | Database which offers scientists from all over the world a unique opportunity to access data from Coherent X-ray Imaging (CXI) experiments. | Peptides and proteins; Coherent X-ray Imaging (CXI) data | How to submit to CXIDB | How to access CXIDB data | NIDDK; Nature Scientific Data; PLOS | |
| Crystallography Open Database (COD) | RRID:SCR_005874 | Open-access collection of crystal structures of organic, inorganic, metal-organics compounds and minerals, excluding biopolymers. | Structural data for small molecules; peptides and proteins | How to submit to COD | How to access COD data | NIDDK; Nature Scientific Data; PLOS | |
| Electron Microscopy Data Bank (MSD-EBI) | RRID:SCR_006506 | 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. | Peptides and proteins; Electron microscopy density maps | How to access MSD-EBI data | NIDDK; Science | ||
| EMDataBank (EMDB) | RRID:SCR_003207 | A unified global portal for deposition and retrieval of 3DEM density maps, atomic models, and associated metadata, as well as a resource for news, events, software tools, data standards, validation methods for the 3DEM community. | Peptides and proteins; larger assemblies; 3-Dimensional Electron Microscopy (3DEM) | How to submit to EMBD | How to access EMDB data | NIDDK; Nature Scientific Data; PLOS | |
| Inorganic Crystal Structure Database (ICSD) | RRID:SCR_017429 | The world's largest database for completely identified inorganic crystal structures, ICSD. | Inorganic crystal structure | How to access ICSD data | NIDDK; Science | ||
| Macromolecular Structure Database (*becoming the PDBe) | RRID:SCR_004312 | European resource for the collection, organisation and dissemination of data on biological macromolecular structures | Macromolecular structure data | How to submit to PDBe | How to access PDBe data | NIDDK; Science | |
| Protein Circular Dichroism Data Bank (PCDDB) | RRID:SCR_017428 | The protein circular dichroism data bank is a repository for circular dichroism spectral and metadata. | Peptides and proteins | How to submit to PCDDB | How to access PCDDB data | NIDDK; Nature Scientific Data; PLOS | |
| Protein Data Bank Japan | RRID:SCR_008912 | Maintains a centralized PDB archive of macromolecular structures and provides integrated tools. | Macromolecular structure data | How to submit to PDB | How to access PDB data | NIDDK; Science | |
| Structural Biology Data Grid | RRID:SCR_003511 | Provides support for the publication of X-ray diffraction, MicroED, LLSM datasets, as well as structural models | Peptides and proteins | How to submit to SBDG | How to access SBDG data | NIDDK; Nature Scientific Data | |
| Worldwide Protein Data Bank (wwPDB) | RRID:SCR_006555 | A repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies. | Peptides and proteins | How to submit to wwPDB | How to access wwPDB data | NIDDK; Nature Scientific Data; PLOS; Science |
Functional Genomics
| Respository Name | RRID | Description | Type of Data | Submitting Data | Accessing Data | Guidelines/Standards | Recommended by |
|---|---|---|---|---|---|---|---|
| ArrayExpress | RRID:SCR_002964 | Archive of Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data for reuse to the research community. | Microarray; next-generation sequencing (NGS) | How to submit to ArrayExpress | How to access ArrayExpress Data | MIAME standard for microarray data. | NIDDK; Nature Scientific Data; PLOS; Science |
| Biological General Repository for Interaction Datasets (BioGRID) | RRID:SCR_007393 | BioGRID is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications from major model organism species. All interaction data are freely provided through our search index and available via download in a wide variety of standardized formats. | Molecular interaction data | How to submit data to BioGRID | How to access BioGRID data | Molecular interaction data should be deposited with a member of the International Molecular Exchange Consortium (IMEx), following the MIMIx recommendations. | NIDDK; Nature Scientific Data; PLOS |
| database of Genotypes and Phenotypes (dbGaP) | RRID:SCR_002709 | The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in Humans. | Genotyping and phenotyping information in human subjects | How to submit data to dbGaP | How to access dbGaP data | NIDDK; Nature Scientific Data; PLOS | |
| Database of Interacting Proteins (DIP) | RRID:SCR_003167 | DIP catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. | Protein interaction data | How to submit data to DIP | How to access DIP 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. | NIDDK; Nature Scientific Data; PLOS |
| Gene Expression Omnibus (GEO) | RRID:SCR_007303 | Gene Expression Omnibus is a public functional genomics data repository supporting MIAME-compliant submissions of array- and sequence-based data. Tools are provided to help users query and download experiments and curated gene expression profiles. | Microarray; next-generation sequencing (NGS) | How to submit to GEO | How to access GEO data | MIAME standard for microarray data. | NIDDK; Nature Scientific Data; PLOS; Science |
| GenomeRNAi | RRID:SCR_013088 | 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. | RNAi screening data (phenotype and/or reagent) | How to access GenomeRNAi database | NIDDK; Nature Scientific Data; PLOS | ||
| IntAct | RRID:SCR_006944 | Provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available. | Molecular interaction data | How to submit data to IntAct | How to access IntAct 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. | NIDDK; Nature Scientific Data; PLOS |
| Japanese Genotype-phenotype Archive (JGA) | RRID:SCR_003118 | A service for permanent archiving and sharing of all types of individual-level genetic and de-identified phenotypic data resulting from biomedical research projects. | Data linking genotyping and phenotyping information in human subjects; all types of individual-level genetic and de-identified phenotypic data | How to submit data to JGA | How to access JGA data | NIDDK; Nature Scientific Data | |
| NCBI PubChem BioAssay | RRID:SCR_010734 | Contains small-molecule and RNAi screening data along with associated annotation information from contributing organizations. BioAssay contains a collection of bioactivity and toxicity data that has greatly supported research in fields such as medicinal chemistry, drug discovery, pharmaceutical genomics and informatics research. | Small-molecule and RNAi screening data; bioactibity and toxicity data | How to submit data to PubChem BioAssay | How to access PubChem BioAssay data | Minimum Information About a RNAi Experiment | NIDDK; Nature Scientific Data |
| The European Genome-phenome Archive (EGA) | RRID:SCR_004944 | A service for the permanent archiving and distribution of personally identifiable genetic and phenotypic data resulting from biomedical research projects. | Data linking genotyping and phenotyping information in human subjects, including sequence data, array based data, and phenotype data. | How to submit data to EGA | How to access EGA data | The minimum information about any (x) sequence (MIxS) | NIDDK; Nature Scientific Data; PLOS; Science |
Metabolomics
| Respository Name | RRID | Description | Type of Data | Submitting Data | Accessing Data | Guidelines/Standards | Recommended by |
|---|---|---|---|---|---|---|---|
| MetaboLights | RRID:SCR_014663 | A database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. | Metabolite structure | How to submit data to MetaboLights | How to access MetaboLights data | MSI guidelines | NIDDK; Nature Scientific Data; PLOS |
| Metabolomics Workbench (MetWB) | RRID:SCR_013794 | The Metabolomics Program's Data Repository and Coordinating Center (DRCC), housed at the San Diego Supercomputer Center (SDSC), University of California, San Diego, has developed the Metabolomics Workbench. MetWB will serve as a national and international repository for metabolomics data and metadata and will provide analysis tools and access to metabolite standards, protocols, tutorials, training, and more | Metabolomics data and metadata | How to submit data to MetWB | How to access MetWB data | NIDDK; NLM/NIH: PLOS |
Proteomics
| Respository Name | RRID | Description | Type of Data | Submitting Data | Accessing Data | Guidelines/Standards | Recommended by |
|---|---|---|---|---|---|---|---|
| Global Proteome Machine Database (GPM DB) | RRID:SCR_006617 | The GPM is an experimental project to create knowledge from proteomics data and reuse it to solve biomedical research problems. The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. | Protein and peptides; Mass spectrometry | How to access data | NIDDK; PLOS | ||
| Mass Spectrometry Interactive Virtual Environment (MassIVE) | RRID:SCR_013665 | MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. MassIVE datasets can be assigned ProteomeXchange accessions to satisfy publication requirements. | Protein and peptides; Mass spectrometry | How to submit data | How to access data | ProteomeXchange identifiers can be requested to meet publication guidelines of proteomics datasets. Peak List Files – Processed mass spectrum files in a standardized format:mzXML, mzML, and MGF. Result Files – Spectrum identifications in a standardized format: mzIdentML and mzTab. | Nature Scientific Data |
| PeptideAtlas | RRID:SCR_006783 | A multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. | Tandem mass spectrometry proteomics data of peptides | How to submit data to PeptideAtlas | How to access PeptideAtlas data | Submit proteomics data to members of the ProteomeXchange consortium (listed below), following the MIAPE recommendations | NIDDK; Nature Scientific Data; PLOS |
| ProteomeXchange | RRID:SCR_004055 | Provide globally coordinated standard data submission and dissemination pipelines involving the main proteomics repositories | Proteomics | How to submit data to ProteomeXchange | How to access data in ProteomeXchange | MIAPE: Mass Spectrometry; Minimum Information About a Proteomics Experiment; MIAPE: Mass Spectrometry Informatics | NIDDK; PLOS |
| Proteomics Identifications (PRIDE) | RRID:SCR_003411 | A centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. | Protein and peptide identification/quantification data from mass spectrometry | How to submit data to PRIDE | How to access PRIDE data | Submit proteomics data to members of the ProteomeXchange consortium (listed below), following the MIAPE recommendations | NIDDK; Nature Scientific Data; PLOS |
| Worldwide Protein Data Bank (wwPDB) | RRID:SCR_006555 | The single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies. | Peptides and proteins | How to submit data to wwPDB | How to access wwPDB data | NIDDK; Nature Scientific Data; PLOS; Science |
Cytometry and Immunology
| Respository Name | RRID | Description | Type of Data | Submitting Data | Accessing Data | Guidelines/Standards | Recommended by |
|---|---|---|---|---|---|---|---|
| FlowRepository | RRID:SCR_013779 | FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field. | Flow cytometry data | How to submit data to FlowRepository | How to access FlowRepository data | MIFlowCyt standard | NIDDK; Nature Scientific Data; PLOS |
| ImmPort | RRID:SCR_012804 | The ImmPort system serves as a long-term, sustainable archive of immunology research data generated by investigators mainly funded through the NIAID/DAIT. The core component of the ImmPort system is an extensive data warehouse containing an integration of experimental data and clinical trial data. | Immunology research data including experimental data and clinical trial data | How to access ImmPort 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 | NIDDK; Nature Scientific Data; PLOS |
Chemistry and chemical biology, biochemistry
| Respository Name | RRID | Description | Type of Data | Submitting Data | Accessing Data | Guidelines/Standards | Recommended by |
|---|---|---|---|---|---|---|---|
| Beilstein-Institut, STRENDA | RRID:SCR_017422 | STRENDA DB is a storage and search platform supported by the Beilstein-Institut that incorporates the STRENDA Guidelines in a user-friendly, web-based system. If you are an author who is preparing a manuscript containing functional enzymology data, STRENDA DB provides you the means to ensure that your data sets are complete and valid before you submit them as part of a publication to a journal. | Functional enzymology data | How to submit data to STRENDA | How to access STRENDA data | NIDDK; Nature Scientific Data; PLOS | |
| caNanoLab | RRID:SCR_013717 | 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 | Nature Scientific Data; PLOS | ||||
| ChEMBL* | RRID:SCR_014042 | ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data). | 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 | How to access ChEMBL data | NIDDK; Nature Scientific Data | ||
| Kinetic Models of Biological Systems (KiMoSys) | RRID:SCR_017423 | A web application for quantitative KInetic MOdels of biological SYStems. | Kinetic models | How to submit data to KiMoSys | How to access KiMoSys data | NIDDK; PLOS | |
| Mass spectrometry Interactive Virtual Environment (MassIVE) | RRID:SCR_013665 | MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. MassIVE datasets can be assigned ProteomeXchange accessions to satisfy publication requirements. | Mass spectrometry data | How to submit data to MassIVE | How to access MassIVE data | NIDDK; PLOS | |
| NCBI PubChem Substance | RRID:SCR_004742 | The PubChem Substance Database contains descriptions of samples, from a variety of sources, and links to biological screening results that are available in PubChem BioAssay. If the chemical contents of a sample are known, the description includes links to PubChem Compound. | Community-provided information about chemical entities | How to submit data to PubChem Substance | How to access PubChem Substance data | NIDDK; Nature Scientific Data; PLOS |
Imaging
| Respository Name | RRID | Description | Type of Data | Submitting Data | Accessing Data | Guidelines/Standards | Recommended by |
|---|---|---|---|---|---|---|---|
| Cell Image Library | RRID:SCR_003510 | Images of all cell types from all organisms, including intracellular structures and movies or animations demonstrating functions. | Microscopic imaging data | How to submit data to Cell Image Library | How to access data in Cell Image Library | NIDDK | |
| Coherent X-ray Imaging Data Bank (CXIDB) | RRID:SCR_014722 | A database which offers scientists from all over the world a unique opportunity to access data from Coherent X-ray Imaging (CXI) experiments. | Peptides and proteins; Coherent X-ray Imaging (CXI) data | How to submit data to CXIDB | How to access CXIDB data | NIDDK; Nature Scientific Data; PLOS | |
| Image Data Resource | RRID:SCR_017421 | This online, public data repository seeks to store, integrate and serve image datasets from published scientific studies. | Reference image datasets supporting an original scientific publication | How to submit data to IDR | How to access IDR data | NIDDK; Nature Scientific Data | |
| SICAS Medical Image Repository | RRID:SCR_017420 | SICAS offers a unique combination of competence in acquiring and storing medical images, in processing and visualising data for research and applications in medicine. | Brain images, Segmentations, SSM, Dicom, ITK based images and statistical models | How to access SMIR data | NIDDK; Nature Scientific Data; PLOS | ||
| The Cancer Imaging Archive (TCIA) | RRID:SCR_008927 | TCIA is a service which de-identifies and hosts a large archive of medical images of cancer accessible for public download. The data are organized as “Collections”, typically patients related by a common disease (e.g. lung cancer), image modality (MRI, CT, etc) or research focus. DICOM is the primary file format used by TCIA for image storage. Supporting data related to the images such as patient outcomes, treatment details, genomics, pathology, and expert analyses are also provided when available. | Primary DICOM image datasets from cancer patients and analysis datasets | How to submit data to TCIA | How to access TCIA data | NIDDK; Nature Scientific Data; PLOS |
Neuroscience
| Respository Name | RRID | Description | Type of Data | Submitting Data | Accessing Data | Guidelines/Standards | Recommended by |
|---|---|---|---|---|---|---|---|
| Functional Connectomes Project International Neuroimaging Data-Sharing Initiative (FCP/INDI) | RRID:SCR_015771 | Over 1200 resting state fMRI (R-fMRI) datasets collected from 33 sites around the world | Resting-state functional Magnetic Resonance Imaging (fMRI) and DTI images | How to access FCP/INDI data | NIDDK; Nature Scientific Data; PLOS | ||
| G-Node | RRID:SCR_007279 | A free data management system designed for comprehensive and reproducible management of scientific data | Neuroscience research data | How to submit data to G-Node | How to access G-Node data | NIDDK; Nature Scientific Data; PLOS | |
| NeuroMorpho.org | RRID:SCR_002145 | A centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications. | 3D neuronal reconstructions and associated metadata | How to access NeuroMorpho data | NIDDK; Nature Scientific Data; PLOS | ||
| OpenNeuro (formerly OpenfMRI) | RRID:SCR_005031 | Neuroimaging data; Magnetic Resonance Imaging (MRI) | How to submit data to OpenNeuro | How to access OpenNeuro data | NIDDK; Nature Scientific Data; PLOS |
All research data types
| Respository Name | RRID | Description | Type of Data | Submitting Data | Accessing Data | Guidelines/Standards | Recommended by |
|---|---|---|---|---|---|---|---|
| Dryad Digital Repository | RRID:SCR_005910 | A curated resource that makes the data underlying scientific publications discoverable, freely reusable, and citable. Dryad provides a general-purpose home for a wide diversity of datatypes. | Data underlying scientific publications | How to submit data to Dryad | How to access Dryad data | Common Metadata Elements for Cataloging Biomedical Datasets | NIDDK; Nature Scientific Data; PLOS; Science |
| NIH Figshare | RRID:SCR_017580 | An NIH instance of Figshare that stores, shares and manages all types of NIH-funded research datasets underlying publication figures and tables, as well as data not associated with publications, to enhance the rigor and reproducibility of research results and to make sure the datasets are in line with FAIR (Findable, Accessible, Interoperable, and Reusable) principles. | All research data, datasets and spreadsheet data, video, audio, code | How to submit data to NIH Figshare | How to access NIH Figshare data | NIDDK | |
| Figshare | RRID:SCR_004328 | Store, share and manage all types of research outputs | All research data | How to submit data to Figshare | How to access Figshare data | NIDDK; Nature Scientific Data; PLOS | |
| Harvard Dataverse | RRID:SCR_001997 | Share, archive, find and cite data across all research fields | All research data | How to submit data to Dataverse | How to access Dataverse data | NIDDK; Nature Scientific Data; PLOS | |
| Mendeley Data | RRID:SCR_015671 | Store, share, publish and find all types of research data | All research data | How to submit data to Mendeley | How to access Mendeley data | ||
| Open Science Framework | RRID:SCR_017419 | A scholarly commons to connect the entire research cycle | Research data in all domain areas | How to submit to OSF | How to access OSF | NIDDK; Nature Scientific Data; PLOS | |
| Zenodo | RRID:SCR_004129 | Multidisciplinary research results including text, spreadsheet, audio, video, images and source code | Multidisciplinary research results inculding text, spreadsheet, zudio, video, images, source code | How to submit to Zenodo | How to access Zenodo data | NIDDK; Nature Scientific Data; PLOS |
Other domain-specific repositories
| Respository Name | RRID | Description | Type of Data | Submitting Data | Accessing Data | Guidelines/Standards | Recommended by |
|---|---|---|---|---|---|---|---|
| Influenza Research Database | RRID:SCR_006641 | The Influenza Research Database (IRD) serves as a public repository and analysis platform for flu sequence, experiment, surveillance and related data. | Flu sequence, experiment and surveillance data | How to submit data to IRD | How to access IRD data | PLOS | |
| National Addiction & HIV DATA Archive Program (NAHDAP) | RRID:SCR_000636 | Archive that acquires, preserves and disseminates data relevant to drug addiction and HIV research. This library of electronic data on drug addiction and HIV infection in the United States offers scholars the opportunity to conduct secondary analysis on major issues of social and behavioral sciences and public policy. Most of the datasets are raw data from surveys, interviews, and administrative records. They were originally gathered in research projects and for administrative purposes. Some datasets have been used in published studies. Bibliographies of these studies are available under the view related literature link on each study's home page. In addition to providing access to research data, NAHDAP provides technical assistance for data depositors and e-workshops on data preparation and data systems of interest to the addiction / HIV research community. | Wide variety of data related to drug abuse | How to submit data to NAHDAP | How to access NAHDAP data | PLOS | |
| National Database for Autism Research (NDAR) | RRID:SCR_004434 | Research data repository for data sharing and collaboration among autism spectrum disorder investigators. Used to accelerate scientific discovery through data sharing, data harmonization and reporting of research results. | Imaging data; neurosignal recordings data; austism spectrum disorder-relevant data (all data types) | How to submit data to NDA | How to access NDA data | Data Standards | 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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