"The NICHD Data and Specimen Hub (DASH) is a centralized resource that allows researchers to share and access de-identified data from studies funded by NICHD. DASH also serves as a portal for requesting biospecimens from selected DASH studies.". This dataset is associated with the following publication: Deluca, N., K. Thomas, A. Mullikin, R. Slover, L. Stanek, D. Pilant, and E. Hubal. Geographic and demographic variability in serum PFAS concentrations for pregnant women in the United States. Journal of Exposure Science and Environmental Epidemiology. Nature Publishing Group, London, UK, 33(1): 710-724, (2023).

A list of NIH-supported repositories that accept submissions of appropriate scientific research data from biomedical researchers. It includes resources that aggregate information about biomedical data and information sharing systems. 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.

A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

BRADS is a repository for data and biospecimens from population health research initiatives and clinical or interventional trials designed and implemented by NICHD’s Division of Intramural Population Health Research (DIPHR). Topics include human reproduction and development, pregnancy, child health and development, and women’s health. The website is maintained by DIPHR.

The NIH Common Data Elements (CDE) Repository has been designed to provide access to structured human and machine-readable definitions of data elements that have been recommended or required by NIH Institutes and Centers and other organizations for use in research and for other purposes. Visit the NIH CDE Resource Portal for contextual information about the repository.

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.

The BioProject database links to data that have been or will be deposited into archival databases maintained at members of the International Nucleotide Sequence Database Consortium (INSDC, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive at European Molecular Biology Laboratory (ENA), and GenBank at the National Center for Biotechnology Information (NCBI)).

The National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (NIAGADS) is a national genetics data repository facilitating access to genotypic and phenotypic data for Alzheimer's disease (AD). Data include GWAS, whole genome (WGS) and whole exome (WES), expression, RNA Seq, and CHIP Seq analyses. Data for the Alzheimer’s Disease Sequencing Project (ADSP) are available through a partnership with dbGaP (ADSP at dbGaP). Results are integrated and annotated in the searchable genomics database that also provides access to a variety of software packages, analytic pipelines, online resources, and web-based tools to facilitate analysis and interpretation of large-scale genomic data. Data are available as defined by the NIA Genomics of Alzheimer’s Disease Sharing Policy and the NIH Genomics Data Sharing Policy. Investigators return secondary analysis data to the database in keeping with the NIAGADS Data Distribution Agreement.

A database which contains longitudinal structural MRIs, spectroscopy, DTI and correlated clinical/behavioral data from approximately 500 healthy, normally developing children, ages newborn to young adult.

This dataset is a subset of the NIH (https://www.kaggle.com/datasets/nih-chest-xrays/data) dataset with a reduced imbalance and half the number of samples created by a stratified split. This also contains the localizations and samples provided in the original dataset, for explainability in ML purposes.

Created with this notebook: https://www.kaggle.com/code/abr1998/data-processor

Distribution:

https://www.googleapis.com/download/storage/v1/b/kaggle-user-content/o/inbox%2F3814934%2F9a64cce4f99f4278748e6b8002b00a66%2FSnip20251030_1.png?generation=1761819257824833&alt=media" alt="Distribution of diseases">

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.

DailyMed provides health information providers and the public with a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts, also known as Structured Product Labeling (SPL).

Database of Genotype and Phenotype (dbGaP) was developed to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in Humans.

Research projects funded by the National Institutes of Health (NIH), other DHHS Operating Divisions (ACF, AHRQ, CDC, FDA, HRSA), and the Department of Veterans Affairs. The ExPORTER files provide weekly and/or yearly snapshots of the data publicly accessible through the NIH Research Portfolio Online Reporting Tools, Expenditures and Results (RePORTER) system at https://reporter.nih.gov. The RePORTER database can also be queried using the user interface or the API. The RePORTER database contains information such as project title, abstract, principal investigator, funded organization, total awarded costs, categorization by area of research (NIH only), and project keywords. Also available is information on research publications and patents that have cited support from each project.

Dryad BioLINCC Survey Data 16-09-01This is the deidentified data from the 2015 cross-sectional survey of investigators who requested and received access to clinical research data from BioLINCC between 2007 and 2014.READ ME Dryad BioLINCC Survey 16-09-01.txtData Dictionary BioLINCC Survey 16-09-01This file lists and describes the variables from the 2015 cross-sectional BioLINCC survey.

Gene expression data from Gene Expression Omnibus (GEO) database.

UniVec and UniVec_Core databases in FASTA format.

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.

This is a database snapshot of the iCite web service (provided here as a single zipped CSV file, or compressed, tarred JSON files). In addition, citation links in the NIH Open Citation Collection are provided as a two-column CSV table in open_citation_collection.zip. iCite provides bibliometrics and metadata on publications indexed in PubMed, organized into three modules:

Influence: Delivers metrics of scientific influence, field-adjusted and benchmarked to NIH publications as the baseline.

Translation: Measures how Human, Animal, or Molecular/Cellular Biology-oriented each paper is; tracks and predicts citation by clinical articles

Open Cites: Disseminates link-level, public-domain citation data from the NIH Open Citation Collection

Definitions for individual data fields:

pmid: PubMed Identifier, an article ID as assigned in PubMed by the National Library of Medicine

doi: Digital Object Identifier, if available

year: Year the article was published

title: Title of the article

authors: List of author names

journal: Journal name (ISO abbreviation)

is_research_article: Flag indicating whether the Publication Type tags for this article are consistent with that of a primary research article

relative_citation_ratio: Relative Citation Ratio (RCR)--OPA's metric of scientific influence. Field-adjusted, time-adjusted and benchmarked against NIH-funded papers. The median RCR for NIH funded papers in any field is 1.0. An RCR of 2.0 means a paper is receiving twice as many citations per year than the median NIH funded paper in its field and year, while an RCR of 0.5 means that it is receiving half as many citations per year. Calculation details are documented in Hutchins et al., PLoS Biol. 2016;14(9):e1002541.

provisional: RCRs for papers published in the previous two years are flagged as "provisional", to reflect that citation metrics for newer articles are not necessarily as stable as they are for older articles. Provisional RCRs are provided for papers published previous year, if they have received with 5 citations or more, despite being, in many cases, less than a year old. All papers published the year before the previous year receive provisional RCRs. The current year is considered to be the NIH Fiscal Year which starts in October. For example, in July 2019 (NIH Fiscal Year 2019), papers from 2018 receive provisional RCRs if they have 5 citations or more, and all papers from 2017 receive provisional RCRs. In October 2019, at the start of NIH Fiscal Year 2020, papers from 2019 receive provisional RCRs if they have 5 citations or more and all papers from 2018 receive provisional RCRs.

citation_count: Number of unique articles that have cited this one

citations_per_year: Citations per year that this article has received since its publication. If this appeared as a preprint and a published article, the year from the published version is used as the primary publication date. This is the numerator for the Relative Citation Ratio.

field_citation_rate: Measure of the intrinsic citation rate of this paper's field, estimated using its co-citation network.

expected_citations_per_year: Citations per year that NIH-funded articles, with the same Field Citation Rate and published in the same year as this paper, receive. This is the denominator for the Relative Citation Ratio.

nih_percentile: Percentile rank of this paper's RCR compared to all NIH publications. For example, 95% indicates that this paper's RCR is higher than 95% of all NIH funded publications.

human: Fraction of MeSH terms that are in the Human category (out of this article's MeSH terms that fall into the Human, Animal, or Molecular/Cellular Biology categories)

animal: Fraction of MeSH terms that are in the Animal category (out of this article's MeSH terms that fall into the Human, Animal, or Molecular/Cellular Biology categories)

molecular_cellular: Fraction of MeSH terms that are in the Molecular/Cellular Biology category (out of this article's MeSH terms that fall into the Human, Animal, or Molecular/Cellular Biology categories)

x_coord: X coordinate of the article on the Triangle of Biomedicine

y_coord: Y Coordinate of the article on the Triangle of Biomedicine

is_clinical: Flag indicating that this paper meets the definition of a clinical article.

cited_by_clin: PMIDs of clinical articles that this article has been cited by.

apt: Approximate Potential to Translate is a machine learning-based estimate of the likelihood that this publication will be cited in later clinical trials or guidelines. Calculation details are documented in Hutchins et al., PLoS Biol. 2019;17(10):e3000416.

cited_by: PMIDs of articles that have cited this one.

references: PMIDs of articles in this article's reference list.

Large CSV files are zipped using zip version 4.5, which is more recent than the default unzip command line utility in some common Linux distributions. These files can be unzipped with tools that support version 4.5 or later such as 7zip.

Comments and questions can be addressed to iCite@mail.nih.gov

A database of federally funded biomedical research projects conducted at universities, hospitals, and other research institutions that provides a central point of access to reports, data, and analyses of NIH research. The RePORTER has replaced the CRISP database. The database, maintained by the Office of Extramural Research at the National Institutes of Health, includes projects funded by the National Institutes of Health (NIH), Substance Abuse and Mental Health Services (SAMHSA), Health Resources and Services Administration (HRSA), Food and Drug Administration (FDA), Centers for Disease Control and Prevention (CDCP), Agency for Health Care Research and Quality (AHRQ), and Office of Assistant Secretary of Health (OASH).