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Trans-NIH BioMedical Informatics Coordinating Committee (BMIC)

NIH Data Sharing Repositories

This table lists NIH-supported data repositories that make data accessible for reuse. Most accept submissions of appropriate data from NIH-funded investigators (and others), but some restrict data submission to only those researchers involved in a specific research network. Also included are resources that aggregate information about biomedical data and information sharing systems. The table can be sorted according by name and by NIH Institute or Center and may be searched using keywords so that you can find repositories more relevant to your data. Links are provided to information about submitting data to and accessing data from the listed repositories. Additional information about the repositories and points-of-contact for further information or inquiries can be found on the websites of the individual repositories.

ICRepository NameRepository DescriptionData Submission PolicyAccess to Data
NCI The Cancer Imaging Archive (TCIA) The Cancer Imaging Archive (TCIA) is a large archive of medical images of cancer accessible for public download. All images are stored in DICOM file format. The images are organized as "Collections", typically patients related by a common disease (e.g. lung cancer), image modality (MRI, CT, etc) or research focus. How to Submit Data to TCIA How to Access TCIA Data
NCI (NHGRI, NIGMS) PeptideAtlas 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. How to Submit Data to PeptideAtlas How to Access TCIA Data
NHGRI FlyBase: A Drosophila Genomic and Genetic Database 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
NHGRI The Zebrafish Model Organism Database (ZFIN) 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
NHGRI WormBase 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
NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) The goal of BioLINCC is to facilitate and coordinate the existing activities of the NHLBI Biorepository and the Data Repository and to expand their scope and usability to the scientific community through a single web-based user interface. How to Submit Data to BioLINCC How to Access BioLINCC Data
NHLBI Rat Genome Database (RGD) The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research 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. How to Submit Data to RGD How to Access RGD Data
NHLBI Integrating Data for Analysis, Anonymization, and Sharing (iDASH) iDASH, the newest Common Fund National Center for Biomedical Computing, addresses fundamental challenges to research progress and enables global collaborations anywhere and anytime. iDASH offers a secure cyberinfrastructure and tools to support a privacy-preserving data repository and open source software. iDASH also is active in research and training in its mission area. How to Submit Data to iDASH How to Access iDASH Data
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NHLBI The Cardiovascular Research Grid (CVRG) The CardioVascular Research Grid (CVRG) project is creating an infrastructure for sharing cardiovascular data and data analysis tools. CVRG tools are developed using the Software as a Service model, allowing users to access tools through their browser, thus eliminating the need to install and maintain complex software. How to Submit Data to CVRG How to Access CVRG Data
NIAAA (NIDA, NIMH) GeneNetwork GeneNetwork is a group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. GeneNetwork combines more than 25 years of legacy data generated by hundreds of scientists together with sequence data (SNPs) and massive transcriptome data sets (expression genetic or eQTL data sets). How to Submit Data to GeneNetwork How to Access GeneNetwork Data
NIAID BEI Resource Repository BEI Resources provides reagents, tools and information for studying Category A, B, and C priority pathogens, emerging infectious disease agents, non-pathogenic microbes and other microbiological materials of relevance to the research community. How to Submit Data to BEI How to Access BEI Data
NIAID Eukaryotic Pathogen Database Resources (EuPathDB) EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with the eukaryotic pathogens. How to Submit Data to EuPathDB How to Access EuPathDB Data
NIAID The Immunology Database and Analysis Portal (ImmPort) 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. The ImmPort system also provides data analysis tools and an immunology-focused ontology. The analytical tools created and integrated as part of the ImmPort system are available to any researcher within ImmPort after registration and approval by DAIT. Additionally, the data provided mainly by NIAID/DAIT funded researchers in ImmPort will be available to all registered users after the appropriate embargo time. How to Submit ImmPort Data[PDF] How to Access ImmPort Data
NIAID Influenza Research Database (IRD) The Influenza Research Database (IRD) serves as a public repository and analysis platform for flu sequence, experiment, surveillance and related data. How to Submit Data to IRD How to Access IRD Data
NIAID TrialShare The immune tolerance data management and visualization portal for studies sponsored by the Immune Tolerance Network (ITN) and collaborating investigators. Data from published studies are accessible to any user; data from current in-progress studies are accessible to study investigators and collaborators. Includes links to published Figures, tools for visualization and analysis of data, and ability to query study data by subject, group, or any other study parameter. TrialShare data are submitted by the Immune Tolerance Network How to Access TrialShare Data[PDF]
NIAID VectorBase VectorBase is a Bioinformatics Resource Center for invertebrate vectors. It is one of four Bioinformatics Resource Centers funded by NIAID to provide web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases. How to Submit Data to VectorBase How to Access VectorBase Data
NIBIB LONI Database The LONI Image Data Archive (IDA) is a user-friendly environment for archiving, searching, sharing, tracking and disseminating neuroimaging and related clinical data. The IDA is utilized for dozens of neuroimaging research projects across North America and Europe and accommodates MRI, PET, MRA, DTI and other imaging modalities. How to Submit Data to LONI[PDF] How to Access LONI data[PDF]
NIBIB Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) The objective of this Bioengineering Research Partnership is to focus the resources of a powerful interdisciplinary team from academia (MIT), industry (Philips Medical Systems) and clinical medicine (Beth Israel Deaconess Medical Center) to develop and evaluate advanced ICU patient monitoring systems that will substantially improve the efficiency, accuracy and timeliness of clinical decision making in intensive care. How to Access MIMIC-II data[PDF] How to Access MIMIC-II data[PDF]
NIBIB Nanomaterial Registry By leveraging and developing a set of Minimal Information About Nanomaterials (MIAN), ontology and standards through a community effort, it has developed a data model for data collection and sharing in the nanotechnology field. It facilitates data validation and data quality improvement. It is a data-driven tool aimed at enabling researchers to close knowledge gap. How to Submit Data to MIAN How to Access MIAN data
NIBIB (NIMH, NIDA) Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) facilitates finding and comparing neuroimaging resources for functional and structural neuroimaging analyses—including popular tools as well as those that once might have been hidden in another researcher's laboratory or some obscure corner of cyberspace. How to Submit Data to NITRC How to Access NITRC Data
NICHD Xenbase Xenbase is a Xenopus laevis and Xenopus tropicalis biology and genomics resource. How to Submit Data to Xenbase How to Access Xenbase Data
NIDA Mouse Phenome Database (MPD) The Mouse Phenome Database (MPD) has characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. How to Submit Data to MPD How to Access MPD Data
NIDA National Addiction & HIV Data Archive Program (NAHDAP) NAHDAP acquires, preserves and disseminates data relevant to drug addiction and HIV research. By preserving and making available an easily accessible library of electronic data on drug addiction and HIV infection in the United States, NAHDAP offers scholars the opportunity to conduct secondary analysis on major issues of social and behavioral sciences and public policy. How to Submit Data to NAHDAP How to Access NAHDAP Data
NIDA CTN Data Share A repository of data from completed CTN clinical trials to be distributed to investigators in order to promote new research, encourage further analyses, and disseminate information to the community. Secondary analyses produced from data sharing multiply the scientific contribution of the original research. How to Submit Data to CTN How to Access CTN Data Share Data
NIDA NIDA Center on Genetics Studies Blood and other biospecimens along with phenotypic data collected, archived and stored. How to Submit Data to NIDA Center How to Access NIDA Center Data
NIDA Neuroscience Information Framework (NIF) NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. How to Submit Data to NIF How to Access NIF Data
NIDA, NIMH The 1000 Functional Connectomes Project (FCP) / International Neuroimaging Data-Sharing Initiative (INDI) This project is a follow on to the 1000 Functional Connectome Project. Imaging data, of all types, and in some cases related phenotype data can be deposited by any researcher. The project is supported by NIMH, but is open to all researchers. More than 5,000 resting state fMRI data sets are available through the FCP and INDI efforts combined as well as a growing number of diffusion MRI data sets. How to submit data to FCP[PDF] How to Access FCP data[PDF]
NIDA, NINDS NeuroMorpho.org NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications. It contains contributions from over 80 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. How to Submit Data to NeuroMorpho How to Access NeuroMorpho Data
NIDDK NIDDK Central Repository 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. How to Submit Data to NIDDK Central Repository How to Access NIDDK CR data
NIDDK NIDDK Information Network (DKnet) The NIDDK Information Network serves the needs of basic and clinical investigators by providing seamless access to large pools of data relevant to the mission of NIDDK. The goal of DKnet is to develop a community-based network for integration across disciplines to include the larger DK universe of diseases, investigators, and potential users. How to Submit Data to DKnet How to Access DKnet data
NIDDK Nuclear Receptor Signaling Atlas (NURSA) The Nuclear Receptor Signaling Atlas (NURSA) was created to foster the development of a comprehensive understanding of the structure, function, and role in disease of nuclear receptors (NRs) and coregulators. NURSA seeks to elucidate the roles played by NRs and coregulators in metabolism and the development of metabolic disorders (including type 2 diabetes, obesity, osteoporosis, and lipid dysregulation), as well as in cardiovascular disease, oncology, regenerative medicine and the effects of environmental agents on their actions. How to Submit Data to NURSA How to Access NURSA Data
NIEHS/NTP Chemical Effects in Biological Systems (CEBS) CEBS stores data of interest to environmental health science, including microarray, histopathology, genetic toxicology and high-throughput sequencing data. Submit to CEBS How to Access CEBS Data
NIGMS Cell Centred Database (CCDB) The Cell Centered Database (CCDB) is a web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging. How to Submit Data to CCDB How to Access CCDB Data
NIGMS PhysioNet 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). How to Submit Data to PhysioNet How to Access PhysioNet Data
NIGMS Transporter Classification Database (TCDB) The Transporter Classification Database details a comprehensive classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. How to Submit Data to TCDB How to Access TCDB Data
NIGMS Database of Interacting Proteins (DIP) The DIP database 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 curated both manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. How to Submit Data to DIP How to Access DIP Data
NIGMS Quantitative Trait Loci (QTL) Archive This site provides access to raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data. How to Submit Data to QTL How to Access QTL Data
NIGMS (NLM, NCI, NINS, NIDDK) Protein Data Bank (PDB) The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids found in all organisms including bacteria, yeast, plants, flies, other animals, and humans. How to Submit Data to PDB How to Access PDB Data
NIH Biological General Repository for Interaction Datasets (BioGRID) BioGRID is an online interaction repository with data on raw protein and genetic interactions 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. How to Submit Data to BioGRID How to Access BioGRID Data
NIH (NIA, NICHD, NIDA) Inter-university Consortium for Political and Social Research (ICPSR) ICPSR maintains a data archive of more than 500,000 files of research in the social sciences. It hosts 16 specialized collections of data in education, aging, criminal justice, substance abuse, terrorism, and other fields. How to Submit Data to ICPSR How to Access ICPSR Data
NIHGRI (NICHD, NCI) Mouse Genome Informatics (MGI) 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
NIMH Human Connectome Project The Human Connectome Project is comprehensively mapping human brain circuitry in 1200 healthy adults using cutting-edge methods of noninvasive neuroimaging. Imaging, behavioral data, and genomic data are all made freely available to the research community as the data is collected. In addition, other laboratories using similar data collection techniques are releasing their data via this web site. Coming soon How to Access Human Connectome Project data
NIMH National Database for Autism Research (NDAR) National Database for Autism Research (NDAR) is an extensible, scalable informatics platform for austism spectrum disorder-relevant data at all levels of biological and behavioral organization (molecules, genes, neural tissue, behavioral, social and environmental interactions) and for all data types (text, numeric, image, time series, etc.). NDAR was developed to share data across the entire ASD field and to facilitate collaboration across laboratories, as well as interconnectivity with other informatics platforms. How to Submit Data to NDAR How to Access MGI Data
NIMH NIMH Limited Access Clinical Trial Datasets The NIMH makes a variety of data available from clinical studies supported by the institute. It is the view of NIMH that the full value of the data can only be realized if they are made available, under appropriate terms and conditions, in a timely manner to the wider scientific community, provided that the confidentiality and privacy of study participants are protected. Coming soon How to Access NIMH data
NIMH OpenfMRI OpenfMRI.org is a project dedicated to the free and open sharing of functional magnetic resonance imaging (fMRI) datasets, including raw data. The focus of the database is on task fMRI data. How to Submit Data to OpenfMRI Access Open fMRI data
NIMH Parkinson’s Progression Markers Initiative The Parkinson’s Progression Markers Initiative (PPMI is ), a landmark observational clinical study to comprehensively evaluate cohorts of significant interest using advanced imaging, biologic sampling and clinical and behavioral assessments to identify biomarkers of Parkinson’s disease progression. PPMI is taking place at clinical sites in the United States, Europe, and Australia. Data and samples acquired from study participants will enable the development of a comprehensive Parkinson’s database and biorepository, which is currently available to the scientific community to conduct field-changing research. Coming soon How to Access PPMI data
NINDS Federal Interagency Traumatic Brain Injury Research (FITBIR) Informatics System The Federal Interagency Traumatic Brain Injury Research (FITBIR) informatics system is an extensible, scalable informatics platform for TBI relevant imaging, assessment, genomics, and other data types. It was developed to share data across the entire TBI research field and to facilitate collaboration between laboratories, as well as interconnectivity with other informatics platforms. How to Submit Data to FITBIR How to Access FITBIR Data
NINDS Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) The NINDS Parkinson’s Disease (PD) Biomarkers Program Data Management Resource enables web-based data entry for clinical studies supporting PD biomarker development, as well as broad data sharing (imaging, clinical, genetic, and biospecimen analysis) across the entire PD research community. The PDBP DMR coordinates information and access to PD biospecimens distributed through the NINDS Human Genetics, DNA, iPSC , Cell Line and Biospecimen Repository and the Harvard Neurodiscovery Initiative. How to Submit Data to PDBPDMR How to Access PDBPDMR Data
NLM database of Genotypes and Phenotypes (dbGaP) The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. How to Submit Data to dbGaP How to Access dbGaP Data
NLM PubChem PubChem provides information on the biological activities of small molecules. PubChem is organized as three linked databases (bioassay, compound, and substance data) within the NCBI's Entrez information retrieval system. How to Submit Data to PubChem How to Access PubChem Data
NLM ClinicalTrials.gov ClinicalTrials.gov is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world. How to Submit Data to ClinicalTrials.gov How to Access ClinicalTrials.gov Data
NLM GenBank 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. How to Submit Data to GenBank How to Access GenBank Data
NLM Gene Expression Omnibus (GEO) 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. How to Submit Data to GEO How to Access GEO Data
NLM dbSNP dbSNP is a database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants. How to Submit Data to dbSNP How to Access dbSNP Data
NLM dbVar dbVar is a database of genomic structural variation. It accepts data from all species and includes clinical data. It can accept diverse types of events, including inversions, insertions and translocations. Additionally, both germline and somatic variants are accepted. How to Submit Data to dbVar How to Access dbVar Data
NLM Sequence Read Archive (SRA) The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD® System, Helicos Heliscope®, Complete Genomics®, and Pacific Biosciences SMRT®. How to Submit Data to SRA How to Access SRA Data
NCATS, ORDR Biospecimens/Biorepositories: Rare Disease Hub (RD-HUB) The Biospecimens/Biorepositories Database: Rare Disease-HUB (RD-HUB) contains a searchable database of biospecimens and is designed to assist interested parties and investigators search, locate, and identify desired biospecimens needed for the research and to facilitate collaboration and sharing of material and data among investigators across the globe. RD-HUB links to the Global Rare Diseases Patient Registry and Data Repository (GRDR) via the GRDR Global Unique Identifier (GUID). How to Submit Data to RD-HUB How to Access RD-HUB Data

 

This table lists NIH-supported d