AndreaBozzo/ceres-open-data-index huggingface dataset:
Disaster Lit

This resource was retired on June 1, 2021 and is no longer updated. These data remain available to support research and development efforts.

Disaster Lit®: Database for Disaster Medicine and Public Health is a dataset of links to disaster medicine and public health documents available on the Internet at no cost. Documents include expert guidelines, research reports, conference proceedings, training classes, factsheets, websites, databases, and similar materials selected from over 700 organizations for a professional audience. Materials were selected from non-commercial publishing sources and supplement disaster-related resources from PubMed (biomedical journal literature) and MedlinePlus (health information for the public).

Tags: disaster-information
Organization: U.S. Department of Health & Human Services
GENE-TOX (Genetic Toxicology Data Bank)

GENE-TOX provided genetic toxicology (mutagenicity) test data from expert peer review of open scientific literature for more than 3,000 chemicals from the United States Environmental Protection Agency (EPA) covering the years 1991 - 1998.  GENE-TOX is no longer updated.

Tags: data-distribution
Organization: U.S. Department of Health & Human Services
Database of Short Genetic Variations (dbSNP)

Database of Short Genetic Variations (dbSNP) contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.

Tags: api, dataset, genetics, genomics, tools-utilities
Organization: U.S. Department of Health & Human Services
RxTerms

RxTerms is a drug interface terminology derived from RxNorm for prescription writing or medication history recording (e.g. in e-prescribing systems, PHRs). RxTerms is derived only from the non-proprietary content of RxNorm, which is developed and maintained by the U.S. National Library of Medicine. No fee or license is required to use the RxTerms data.  Technical documentation at https://wwwcf.nlm.nih.gov/umlslicense/rxtermApp/rxTermFileStructure.cfm

Tags: api, dataset, drug-terminology, drugs, health-data-standards, terminologies
Organization: U.S. Department of Health & Human Services
Pillbox (retired January 28, 2021)

This resource was retired on January 28, 2021 and is no longer updated.  These data remain available to support research and development efforts.  Pillbox's final image library is available at https://ftp.nlm.nih.gov/projects/pillbox/pillbox_production_images_full_202008.zip.  For more information on Pillbox's retirement visit https://www.nlm.nih.gov/pubs/techbull/ja20/ja20_pillbox_discontinue.html.

Pillbox contains metadata for oral solid dosage form medications, derived from FDA drug labeling, including physical characteristics, active and inactive ingredients, National Drug Codes, information about firms marketing those products, selected information from RxNorm, and links to images provided by the National Library of Medicine.

Tags: drug-label, medication
Organization: U.S. Department of Health & Human Services
Sequence Read Archive (SRA)

The Sequence Read Archive (SRA) stores sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome Analyzer®, Life Technologies AB SOLiD System®, Helicos Biosciences Heliscope®, Complete Genomics®, and Pacific Biosciences SMRT®.

Tags: genetics, genomics, tools-utilities
Organization: U.S. Department of Health & Human Services
ChemIDplus

ChemIDplus, the Chemical Identification Plus Database, is no longer updated. These are the final files from February 22, 2023. All ChemIDplus data have been incorporated into PubChem.

ChemIDplus was a dictionary of over 400,000 chemicals (names, synonyms, and structures). ChemIDplus includes links to NLM and other databases and resources, including links to federal, state and international agencies.  NLM makes a subset of ChemIDplus data available for download. The ChemIDplus Subset does not include the structure or the toxicity data available from the NLM web versions of the database. The ChemIDplus Subset is updated monthly.

Tags: chemicals, chemistry, dataset
Organization: U.S. Department of Health & Human Services
Medical Text Indexer (MTI)

A system for producing indexing recommendations to assist in the indexing process at NLM.  Currently provides indexing recommendations to more than 100 journals based on the NLM Medical Subject Headings (MeSH) vocabulary.

MTI is the main product of the Indexing Initiative project and has been providing indexing recommendations based on the Medical Subject Headings (MeSH®) vocabulary since 2002. In 2011, NLM expanded MTI's role by designating it as the first-line indexer (MTIFL) for a few journals; today the MTIFL workflow includes over 350 journals and continues to increase. The close collaboration of the NLM Index Section, Lister Hill National Center for Biomedical Communications, and Office of Computer & Communications Systems continues to expand and refine the ability of MTI to provide assistance to the indexers.

Tags: api, history-of-medicine, medical-informatics, terminologies, tools-utilities
Organization: U.S. Department of Health & Human Services
Directory of History of Medicine Collections

The collections described in this Directory database provide research and reference services to scholars interested in the history of the health sciences. Some of the subjects include: dentistry, veterinary medicine, nursing, biomedical sciences, military medicine, and pharmacy. While the Directory is by no means exhaustive, it serves to draw attention to the depth and variety of history of medicine collections available to researchers. In the future, we expect that more institutions will wish to be included.

Tags: history-of-medicine, library-services, reference
Organization: U.S. Department of Health & Human Services
NCBI Virus

NCBI Virus is an integrative, value-added resource designed to support retrieval, display and analysis of a curated collection of virus sequences and large sequence datasets. Its goal is to increase the usability of viral sequence data archived in GenBank and other NCBI repositories.

This resource includes resources previously included in HIV-1, Human Protein Interaction Database, Influenza Virus Resource, and Virus Variation.

Tags: genomics, protein, sars-cov-2, virus
Organization: U.S. Department of Health & Human Services
Partners in Information Access for the Public Health Workforce (PHPartners) (retired September 14, 2021)

Partners in Information Access for the Public Health Workforce (PHPartners) is a web portal and current awareness service of information for the public health workforce. Alerts the communities to meetings, webinars, new web-born reports (analyses, statistics), datasets, and general news. Currently contains over 4,000 items.

This resource was retired on September 14, 2021 and is no longer updated.

Tags: public-health
Organization: U.S. Department of Health & Human Services
Value Set Authority Center

The VSAC is a repository and authoring tool for public value sets created by external programs. Value sets are lists of codes and corresponding terms, from NLM-hosted standard clinical vocabularies (such as SNOMED CT®, RxNorm, LOINC® and others), that define clinical concepts to support effective and interoperable health information exchange. The VSAC does not create value set content. The VSAC also provides downloadable access to all official versions of value sets specified by the Centers for Medicare & Medicaid Services (CMS) electronic Clinical Quality Measures (eCQMs). For information on CMS eCQMs, visit the eCQI Resource Center. The VSAC is provided by the National Library of Medicine (NLM), in collaboration with the Office of the National Coordinator for Health Information Technology (ONC) and CMS.

Tags: api, clinical-quality-measures, cqm, dataset, health-data-standards, icd, rxnorm, snomed, terminologies
Organization: U.S. Department of Health & Human Services
OLDMEDLINE Data

The OLDMEDLINE subset in PubMed® represents journal article citations from two print indexes: Cumulated Index Medicus (CIM) and the Current List of Medical Literature (CLML). Created by the National Library of Medicine® (NLM®), there are approximately 2,011,000 article citations from international biomedical journals that cover the fields of medicine, preclinical sciences and allied health sciences from 1946 through 1965. OLDMEDLINE records, which are included in the MEDLINE® database, can be searched via PubMed.

The OLDMEDLINE subset in PubMed contains citations from the 1960 through 1965 Cumulated Index Medicus (CIM) print indexes and the 1946 through 1959 Current List of Medical Literature (CLML) print indexes. The OLDMEDLINE subset does not include citations from the Quarterly Cumulative Index Medicus (QCIM) print indexes. A hand search of the QCIM print indexes is necessary to ensure comprehensive review of medical periodical literature of the world from 1946 through 1956.

Tags: dataset, literature
Organization: U.S. Department of Health & Human Services
Whole Genome Shotgun Submissions

Whole Genome Shotgun (WGS) projects are genome assemblies of incomplete genomes or incomplete chromosomes of prokaryotes or eukaryotes that are generally being sequenced by a whole genome shotgun strategy. WGS projects may be annotated, but annotation is not required. NCBI has a Prokaryotic Genomes Annotation Pipeline that may be requested at the time the genome files are submitted to GenBank. This pipeline generates a submission-ready annotated file that is posted back to the submitter for review and which the submitter could edit prior to data release.

The public WGS projects are at the list of WGS projects. https://www.ncbi.nlm.nih.gov/Traces/wgs/

Tags: computational-biology, dataset, genomics
Organization: U.S. Department of Health & Human Services
MeSH Population Groups (Type 5 SCR)

Working with partners across NIH, led by NIMHD and the NLM OBSSR-Behavioral Ontology Working Group, MeSH on November 29, 2022 added Federally recognized American Indian and Alaskan Native (AI/AN) tribal names and ethnic/ethnolinguistic minority terms as newly created type 5 SCR designated as “Population Groups”. These minority names (1,700+ terms) were mapped and reviewed by subject matter experts and scientists within NIH and from outside including Network of the National Library of Medicine members.

Structure: All type 5 SCRs have common fields
1.	CC=5 Population Group 
2.	ST=T098 Population Groups
3.	HM= At least one HM is to an MH under Population Groups [M01.686]
4.	TH= NIMHD(2023)

Tags: mesh, population-groups
Organization: U.S. Department of Health & Human Services
MeSH 2023 - New Headings with Scope Notes

This dataset includes all newly added MeSH Main Headings for 2023. Headings play a central role in MeSH vocabulary as a unit of Indexing and retrieval. With the exception of Class 3 Descriptors, all descriptors are organized into a numbered tree structure or hierarchy that allows users to browse in a orderly fashion from broader to narrower topics.  Scope Notes provide a concise summary describing the meaning and scope of the MeSH Descriptor.

Tags: mesh, mesh-2023-update
Organization: U.S. Department of Health & Human Services
Soil health alterations with compost additions to natural and remediated heavy metal-contaminated mineland soils

Soil health data. This dataset is not publicly accessible because: Owned by primary author. It can be accessed through the following means: Contact primary author. Format: Data is excel spreadsheets. 

This dataset is associated with the following publication:
Umeobi, E., T. Ducey, M. Johnson, and J. Ippolito. Soil health alterations with compost additions to natural and remediated heavy metal-contaminated mineland soils.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH. Ecomed Verlagsgesellschaft AG, Landsberg,  GERMANY,  s11356-025-36602-1, (2025).

Tags: compost, remediation, soil-amendments, soil-health
Organization: U.S. Environmental Protection Agency
Integrating Transcriptomic and Targeted New Approach Methodologies into a Tiered Framework for Chemical Bioactivity Screening

Dataset for Jesse Rogers et al., 'Integrating Transcriptomic and Targeted New Approach Methodologies into a Tiered Framework for Chemical Bioactivity Screening' published in Environmental Health Perspectives, Vol 133, Issue 6, 067013, June 2025. DOI: https://doi.org/10.1289/EHP16024, PMC12165737

R scripts for reproducing all analyses are available on Github (https://github.com/USEPA/CompTox-HTTr-RCAS). All sequencing data are available via the Gene Expression Omnibus repository (accessionnumbers GSE274318 for U-2 OS and GSE284321 for HepaRG). High-throughput screening assay data are available from InvitroDB via download 29 or the USEPA CompTox Chemicals Dashboard(https://comptox.epa.gov/dashboard/). 

This dataset is associated with the following publication:
Rogers, J., J. Bundy, J. Harrill, R. Judson, K. Friedman, and L. Everett. Integrating Transcriptomic and Targeted New Approach Methodologies into a Tiered Framework for Chemical Bioactivity Screening.   ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA, 133(6): 067013, (2025).

Tags: chemical-prioritization, hazard-assessment, high-throughput-transcriptomics, new-approach-methodologies
Organization: U.S. Environmental Protection Agency
Assisted Reproductive Technology (ART) Surveillance

<p>In 1992, Congress enacted the Fertility Clinic Success Rate and Certification Act (FCSRCA). The act requires CDC to collect  data from clinics and submit an annual report to Congress on Assisted Reproductive Technology (ART) success rates. In 1996, CDC initiated the ART Surveillance System to collect cycle specific and clinic specific data from all medical clinics practicing ART in the United States and its territories.  The data collected include patient's diagnosis, type of ART,  clinical information pertaining to the ART procedure, and information on pregnancy outcomes.</p>

Tags: infertility, quality-measurement, reproductive-health
Organization: U.S. Department of Health & Human Services
CDC WONDER: Vaccine Adverse Event Reporting System (VAERS)

<p>The Vaccine Adverse Event Reporting System (VAERS) online database on CDC WONDER provides counts and percentages of adverse event case reports after vaccination, by symptom, vaccine product, manufacturer, onset interval, outcome category, year and month vaccinated, year and month reported, age, sex and state / territory. The Vaccine Adverse Event Reporting System is a cooperative program for vaccine safety of the Centers for Disease Control and Prevention (CDC) and the Food and Drug Administration (FDA). VAERS is a post-marketing safety surveillance program, collecting information about adverse events (possible side effects) that occur after the administration of US licensed vaccines.  Data are from the US Department of Health and Human Services (DHHS), Public Health Service (PHS), Food and Drug Administration (FDA)/ Centers for Disease Control (CDC), Vaccine Adverse Event Reporting System (VAERS).</p>

Tags: adverse-event, aefi, age, immunization, manufacturer, medra, month, onset, outcome, population-statistics, report-date, safety, sex, side-effect, state, symptom, territory, vaccination-date, vaccine, vaers, year
Organization: U.S. Department of Health & Human Services
Medical Expenditure Panel Survey (MEPS) Insurance Component Complete Table Series PDFs

The Medical Expenditure Panel Survey Insurance Component (MEPS-IC) is an annual survey of private employers and State and local governments. The MEPS-IC produces national and State level estimates of employer-sponsored insurance, including offered plans, costs, employee eligibility, and number of enrollees. PDF files are available for complete sets of table series on employer-based health insurance at the national, state, and metropolitan area levels. The MEPS-IC is sponsored by the Agency for Healthcare Research and Quality and is fielded by the U.S. Census Bureau.

Tags: agency-for-healthcare-research-and-quality-department-of-health-human-services, insurance, medical-expenditure, meps
Organization: U.S. Department of Health & Human Services
CDC WONDER: Online Tuberculosis Information System (OTIS)

<p>The Online Tuberculosis Information System (OTIS) on CDC WONDER contains information on verified tuberculosis (TB) cases reported to the Centers for Disease Control and Prevention (CDC) by state health departments, the District of Columbia and Puerto Rico since 1993. These data were extracted from the CDC national TB surveillance system. OTIS reports case counts, incidence rates, population counts, percentage of cases that completed therapy within 1 year of diagnosis, and percentage of cases tested for drug susceptibility. Data for 22 variables are included in the data set, including: age groups, race / ethnicity, sex, vital status, year reported, state, metropolitan area, several patient risk factors, directly observed therapy, disease verification criteria and multi-drug resistant TB. Each year these data are updated with an additional year of cases plus revisions to cases reported in previous years. OTIS is produced by the U.S. Department of Health and Human Services, Public Health Service, Centers for Disease Control and Prevention (CDC), National Center for HIV/AIDS, viral Hepatitis, STD and TB Prevention (NCHHSTP).</p>

Tags: age, alcohol-use, case, correctional-facility, drug-resistant, drug-susceptibility, epidemiology, ethnicity, foreign-born, hiv-status, homeless, incidence, injecting-drug-use, isoniazid, long-term-care-facility, metropolitan-area, msa, occupation, pulmonary, race, rifampin, sex, state, tb, therapy, tuberculosis, verification-criteria, vital-status, year
Organization: U.S. Department of Health & Human Services
Data_Analysis_Crop_Yield_N_Loss_FMS

the dataset includes: 1. EPIC_outputs are EPIC yearly output files from Rainfed/Irrigated corn grain simulations using 2006/2011 fertilizer management scenario for the simulation periods of 2002 to 2009 and 2010 to 2017 (e.g. CornGrainIrrig-2006FMS_yrs2002-09.csv: yearly output from 2002 to 2009 for Irrigated Corn grain using 2006 fertilizer management scenario; CornGrainRainfed-2011FMS_yrs2010-2017.csv: yearly output from 2010 to 2017 for Rainfed Corn grain using 2011 fertilizer management scenario); 2. \EPIC_outputsAggregated are saved average annual EPIC output aggregated over entire CONUS or GRIDCELL used for GIS maps including Figures 4, 5 and 9 (e.g.  CONUS_2006FMS_AvgOf2003-2009.csv: average annual EPIC output using 2006 fertilizer management scenario for period from 2003 to 2009 and aggregated over CONUS  
CONUS_GRIDCELL_2006FMS_AvgOf2003-2009.csv: average annual EPIC output using 2006 fertilizer management scenario for period from 2003 to 2009 and aggregated over  each CONUS GRIDCELL); 3.\SummaryData_FromEPIC_for_Tables_Figs are saved summarized data for all the tables and Figs in Excel sheets. 

This dataset is associated with the following publication:
Wang, X., Y. Yuan, V. Benson, and L. Ran. An Integrated Multi-Media Modeling System for Regional- to National-Scale Nitrogen and Crop Productivity Assessments.   Agriculture. MDPI, Basel,  SWITZERLAND, 15(10): 1017, (2025).

Tags: crop-yield, fertilizer-management-scenario, integrated-multi-media-modeling-system, nitrogen-loss, regional-to-national-assessment
Organization: U.S. Environmental Protection Agency
Aid to Families with Dependent Children Quality Control Review Panel Decisions

<p>Decisions issued by the Aid to Families with Dependent Children (AFDC) Quality Control Review Panel of the Departmental Appeals Board concerning the AFDC program (predecessor of Temporary Aid for Needy Families) established by title IV-A of the Social Security Act.</p>

Tags: acf, administrative, adopt, afdc, affirm, appeal, appellate, assessment, assistance, award, balance, beneficiary, benefit, billing, board, cancellation, charge, children, code, collect, compliance, control, cost, coverage, crd, dab, debar, debt, decision, denial, determination, disallowance, disapprove, discontinuation, eligibility, enforcement, enrollment, exclusion, expenditure, fiscal, food-stamp, funding, grant, health-care, hearing, income, invalid, judge, law, marketing, misconduct, modify, non-compliance, overpayment, participation, patient, payment, penalty, quality, recipient, reduction, repay, rescind, reverse, review, sanction, schip, ssa, ssn, tanf, termination, underpayment, violation, welfare, withhold
Organization: U.S. Department of Health & Human Services
Custodial Parents Living in Poverty

<p>Office of Child Support Enforecment (OCSE) Story Behind the Numbers - Child Support Fact Sheet #3.  This fact sheet focuses on data reported in a recent U.S. Census Bureau report, Custodial Mothers and Fathers and Their Child Support: 2011. The data reported are estimated based on a biennial survey of custodial parents, the Child Support Supplement to the Current Population Survey, March/April 2012, co-sponsored by the Office of Child Support Enforcement.  The proportion of custodial parents living below poverty line continues to increase in 2011. The report found that 4.2 million custodial parents lived in poverty in 2011, representing 29 percent of all custodial parents, about twice the poverty rate for the total population. These statistics reinforce the essential role that child support services can play in helping low-income families, especially during an economic downturn.</p>

Tags: administrative, arrears-management, case-management, child-support-fact-sheet, childrens-health, economic-stability, iv-d-program, job-services, other, poverty, promising-practices, state-local-child-support-agencies, story-behind-the-numbers, us-census-bureau
Organization: U.S. Department of Health & Human Services
Child Support Enforcement Handbook

<p>This handbook describes the basic steps to follow to establish paternity, to obtain a support order, and to collect the support due.</p>

Tags: administrative, arrears, assistance, cases-initiated-in-state, cases-open, child, child-support, child-support-enforcement, children, childrens-health, current-assistance, custodial-parent, employees, former-assistance, good-cause, health-insurance, interstate-cases, iv-d-offices, medicaid, medical-coverage, medical-support, never-assistance, noncustodial-parent, open-cases, open-interstate-cases, out-of-wedlock, parent, paternity, paternity-established, support, support-distributed, support-due, title-iv-a, title-iv-d, title-iv-e, tribal-iv-a
Organization: U.S. Department of Health & Human Services
NIH Research Portfolio Online Reporting Tools: Expenditures and Results (RePORTER)

<p>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 <a href="https://reporter.nih.gov">https://reporter.nih.gov</a>.  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.</p>

Tags: acf, ahrq, behavioral, biomedical, biomedical-research, cdc, contracts, disease, exporter, extramural, fda, grants, health, hrsa, institution, intramural, investigator, nih, patent, prevention, publication, report, reporter, research, va
Organization: U.S. Department of Health & Human Services