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Trans-NIH BioMedical Informatics Coordinating Committee (BMIC)

Other NIH Data Resources

This table lists NIH-supported domain-specific data resources that do not meet the full criteria for inclusion on the Open Repositories list. This list includes repositories that restrict data submission to a specific set of researchers, as well as those that limit who may access the data. This list also includes knowledgebases, which  the NIH Strategic Plan for Data Science defines as resources that “accumulate, organize, and link growing bodies of information related to core datasets.” The table provides links to information about submitting data to and accessing data from the listed repositories, as well as further information provided by the repository about funding and data availability. This non-exhaustive list is also available in a downloadable Excel version.

Are we missing a knowledgebase that should be included in this list? Do you have comments or feedback on this list or the website? Contact us.

 

ICO Repository Name Repository Description Data Submission Policy Access to Data Current NIH funding support Open data submission Open data access Open time frame for data deposit Sustained support
Common Fund Epigenomics Epigenomic, 6 histone modification marks, DNAse I, DNA methylation, transcriptome for wide variety of cell types and tissues. Not applicable How to access Epigenomics data No No Yes No Yes
Common Fund exRNA Atlas Includes exRNA profiles derived from various biofluids and conditions and currently stores data profiled from small RNA sequencing assays. Not applicable How to access exRNA Atlas data Yes No Yes No Yes
Common Fund GTEx The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. This project will collect and analyze multiple human tissues from donors who are also densely genotyped, to assess genetic variation within their genomes. By analyzing global RNA expression within individual tissues and treating the expression levels of genes as quantitative traits, variations in gene expression that are highly correlated with genetic variation can be identified as expression quantitative trait loci, or eQTLs. Project data only How to access GTEx data Yes No Yes No Yes
Common Fund HMP DACC The HMP DACC is a common repository for diverse human microbiome datsets and minimum reporting standards for the Common Fund Human Microbiome Project (HMP). Project data only How to access HMP DACC data No No Yes No Yes
Common Fund Illuminating Druggable Genome The goal of the Illuminating the Druggable Genome (IDG) program is to improve our understanding of the properties and functions of proteins that are currently unannotated within the three most commonly drug-targeted protein families: G-protein coupled receptors, ion channels, and protein kinases. Project data only How to access IDG data Yes No Yes Yes Yes
Common Fund International Mouse Phenotyping Consortium (IMPC) Phenotype data on knockout mouse lines. Not applicable How to access IMPC data Yes No Yes Yes Yes
Common Fund Kids First Data Resource The Common Fund’s Gabriella Miller Kids First Pediatric Research Program (Kids First) is developing a large-scale data resource to help researchers uncover new insights into the biology of childhood cancer and structural birth defects, including the discovery of shared genetic pathways between these disorders. Childhood cancers and structural birth defects have profound, lifelong effects on patients and their families. The Kids First program will stimulate research in these areas and work towards providing a better understanding of how genetics plays a role in these conditions that will lead to early detection, therapeutic interventions, and toward more effective prevention. Project data only How to access Kids First data Yes No Yes No Yes
Common Fund LINCS The Library of Integrated Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. Project data only How to access LINCS data Yes No Yes Yes Yes
Common Fund SOBC Measures Repository The SOBC measures repository is the source for behavioral science measures that have been validated (or are in the process of being validated) in accordance with the SOBC Experimental Medicine Approach. How to submit data to SOBC How to access SOBC data Yes No Yes No No
Common Fund Stimulating Peripheral Activity to Relieve Conditions Portal (SPARC) The SPARC Portal provides interactive access to a growing collection of data, maps, and computational studies that focus on the role of the autonomic nervous system in controlling organ function. These resources are made available to the public with the intent of advancing bioelectronic medicine towards more precise treatment of diseases and conditions. Project data only How to access SPARC data Yes No Yes Yes Yes
Common Fund (NCCIH, NCI, NHLBI, NIA, NIAMS, NIDA, NIDCD, NIDDK, NIMH, NINDS, NINR, & OD) PROMIS The Patient-Reported Outcomes Measurment Informmation System (PROMIS) is a set of person-centered measures that evaluates and monitors physical, mental, and social health in adults and children.  Project data only How to access PROMIS data Yes No Yes No No
NCI Human Cancer Models Initiative (HCMI) Searchable Catalog HCMI Searchable Catalog is a continuously updated resource for querying the next-generation models developed by HCMI and their available associated data. The HCMI Searchable Catalog contains data elements extracted from the quality-checked clinical and molecular characterization data for each model. Within the catalog, users can search by patient demographics, tumor, and model elements including age at diagnosis, sex, treatment information, clinical tumor diagnosis, primary site, clinical stage, and type of model (e.g. 3D-organoid, 2D-conditionally reprogrammed cells), etc. Not applicable How to access HCMI data Yes No Yes No Yes
NCI NCI CSSI Data Coordinating Center (CSSI DCC) The CSSI DCC stores and manages access to diverse NCI-supported cancer reserarch data, such as advanced imaging, pre-analytical variable studies, and cell characterizations. This data is in the standard Investigation-Study-Assay tab-delimited format (ISA-TAB) format, which describes a scientific investigation, its study or studies, and each study's assay(s). How to submit data to CSSI DCC How to access CSSI DCC data Yes No Yes Yes Yes
NCI The Cancer Genomic Characterization Initiative (CGCI) Data Matrix The CGCI Data Matrix  hosts genomic profiles (molecular characterization and sequence data) and clinical data for rare adult and pediatric tumor types generated by CGCI projects. The data are organized in the tabular format; the rows being each project and the columns being research method employed. New data from ongoing projects gets incorporated into the Data Matrix as it becomes available. Not applicable How to access CGCI data Yes No Yes No Yes
NCI The Cancer Target Discovery and Development (CTD2) Dashboard The CTD2 Dashboard compiles the Network-generated conclusions, or “observations,” associated with a specific gene, cell line, animal model, or perturbagen. It provides supporting evidence with links to data, references, and to the validation strength of the evidence. Data is generated from multiple types of biological and analytical approaches used by CTD2 centers. The dashboard allows easy navigation to a broad range of computational and non-computational scientists. Not applicable How to access CTD2 Dashboard data Yes No Yes No Yes
NCI The Cancer Target Discovery and Development (CTD2) Network Data Portal  The CTD2 Data Portal provides access to raw/analyzed primary data generated from different types of approaches e.g. chemical genetics (small-molecules, natural products); genome-wide gain-of-function (cDNA expression libraries, CRISPRa); genome-wide loss-of-function (siRNA, shRNA, CRISPR/Cas9, CRISPRi); protein-protein interactions; and in vivo gain and loss-of function studies. Not applicable How to access CTD2 Network Data Portal data Yes No Yes No Yes
NCI The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) Data Matrix TARGET is a comprehensive molecular characterization initiative that utilizes state-of-the-art genomics tools to identify molecular changes that drive childhood cancers, including hematologic and solid tumors. The TARGET Data Matrix contains whole-genome and transcriptomic sequencing of acute lymphoblastic leukemia, acute myeloid leukemia, kidney tumors, neuroblastomas, and osteosarcoma pediatric cancer types. Researchers can access up to four levels of data, from primary through higher level summary data for the molecular platform employed. To protect the privacy of patients, some clinical and genetic data require approval to access through NCBI’s database for Genotypes and Phenotypes (dbGAP; https://www.ncbi.nlm.nih.gov/gap/). Not applicable How to access TARGET data Yes No Yes No Yes
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 Peptide Atlas data No yes Yes Yes No
NHLBI The Cardiovascular Research Grid (CVRG) The CardioVascular Research Grid (CVRG) project is creating an infrastructure for secure seamless access to study data and 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. The CVRG project is supported by the National Heart Lung & Blood Institute. The project is based at the Institute for Computational Medicine at the Johns Hopkins University, Department of Biomedical Informatics at Vanderbilt University Medical Center, The College of Computing and Informatics at UNC Charlotte, The Center for Comprehensive Informatics at Emory University, The College of Engineering and Applied Sciences at Stony Brook University, and the Computation Institute at The University of Chicago. No new data submission, but one could submit new tools.   How to access CVRG data No No Yes No No
NICHD Biospecimen Repository Access and Data Sharing (BRADS) The Division of Intramural Population Health Research (DIPHR) of the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) maintains an extensive repository of datasets from completed studies, including biospecimens and ancillary data. Not applicable How to access BRADS data Yes No No No Yes
NICHD (NINDS, & NIBIB) Archive of Data on Disability to Enable Policy (ADDEP) ADDEP provides access to data including a wide range of topics related to disability. ADDEP data can be used to better understand and inform the implementation of the Americans with Disabilities Act and other disability policies. How to submit data to ADDEP How to access ADDEP data Yes Yes Yes Yes No
NIDA NIDA Center for Genetics Studies Blood and other biospecimens along with phenotypic data collected, archived and stored. How to submit data to the NIDA Center for Genetics Studies How to access NIDA Center for Genetics Studies data Yes Yes No Yes Yes
NIDA NIDA Data Share The NIDA Data Share web site is an electronic environment that allows data from completed clinical trials to be distributed to investigators and the public in order to promote new research, encourage further analyses, and disseminate information to the community.  Data download only.  Data is submitted through NIDA POC How to access NIDA Data Share data Yes No Yes No Yes
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. Not applicable How to access TCDB data Yes No Yes No Yes
NIGMS (NCI, NSF, DOE-BER) Protein Data Bank (PDB) The mission of the RCSB Protein Data Bank (PDB) is to Sustain a unique data resource of three-dimensional  biomolecular structure information. How to submit data to PDB How to access PDB data Yes Yes Yes Yes No
NIMH NIMH Data Archive The National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains. The NDA provides infrastructure for sharing research data, tools, methods, and analyses enabling collaborative science and discovery. De-identified human subjects data, harmonized to a common standard, are available to qualified researchers.  Summary data is available to all. How to submit data to the NIMH Data Archive How to access NIMH Data Archive data Yes No Yes Yes Yes
NINDS Federal Interagency Traumatic Brain Injury Research (FITBIR) Informatics System The Federal Interagency Traumatic Brain Injury Research (FITBIR) informatics system 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. Sharing data, methodologies, and associated tools, rather than summaries or interpretations of this information, can accelerate research progress by allowing re-analysis of data, as well as re-aggregation, integration, and rigorous comparison with other data, tools, and methods. This community-wide sharing requires common data definitions and standards, as well as comprehensive and coherent informatics approaches. How to submit data to FITBIR How to access FITBIR data Yes No Yes Yes Yes
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 PDBP DMR How to access PDBP DMR data          
NINDS The NINDS Human Cell and Data Repository (NHCDR) Cell sources currently include fibroblasts and/or induced pluripotent stem cells for Alzheimer’s Disease, Amyotrophic Lateral Sclerosis (ALS), Ataxia-telangiectasia, Frontotemporal Lobar Degeneration (FTD), Huntington’s Disease, Parkinson’s Disease, and healthy controls. Cell sources, including isogenic cell lines for current and new diseases covered by the NINDS will be added over the next several years. How to submit data to NHCDR How to access NHCDR data          
NINR Common Data Repository for Nursing Science (cdRNS) The NINR, part of the National Institutes of Health (NIH), is a leading supporter of clinical studies in symptom science and self-management research. To harmonize and share data collected from clinical studies, NINR is spearheading the collection of data consistent with common data elements (CDEs). The cdRNS, a Biomedical Research Informatic Computing System (BRICS), strongly supports making NINR data findable, accessible, interoperable, and reusable (FAIR). How to submit data to cdRNS How to access cdRNS data Yes No No Yes Yes

 

 

Last Reviewed: August 31, 2020