Health databases & datasets: Global

HDB-0010

WHO Global Health Observatory

World Health Organization The WHO's repository of health indicators for its member states: mortality, disease burden, health systems, environmental health and more, with an open OData API. The starting point for cross-country health comparisons. Open dataset Open access HDB-0011

ClinicalTrials.gov

US National Library of Medicine A registry of clinical studies, spanning interventional trials and observational studies in 200+ countries, with protocols, eligibility criteria and posted results. Fully open with a modern REST API. Trial registry Open access HDB-0012

PubMed / MEDLINE

US National Library of Medicine The primary index of biomedical literature: 37M+ citations with abstracts, MeSH indexing and links to full text. Free to search, with E-utilities APIs and annual baseline downloads for text mining. Literature database Open access HDB-0014

IQVIA Real-World Data

IQVIA Holdings Inc. IQVIA Real-World Data is a commercial real-world data offering from IQVIA Holdings, providing longitudinal prescription, claims and EHR-derived data across dozens of countries alongside analytics and consulting services. It supports pharmaceutical commercial analytics and real-world evidence through enterprise contracts. Commercial provider Paid HDB-0024

H1

H1 Inc. H1 is a global healthcare data and intelligence platform that aggregates information on millions of healthcare professionals, clinical trials, patient recruitment data, and prescriber insights across 6 continents. The platform serves pharmaceutical, payer, provider, and digital health organizations for sales, marketing, clinical development, and compliance workflows through subscription and licensing agreements. Commercial provider By application HDB-0025

ZoomInfo Healthcare Solutions

ZoomInfo ZoomInfo is a B2B data and intelligence platform that maintains verified contact information and profiles for healthcare professionals, organizations, and decision-makers across the healthcare and life sciences sectors. The platform is used by pharmaceutical companies, medical device manufacturers, and healthcare service providers for lead generation, sales prospecting, and marketing through paid subscription. Commercial provider Paid HDB-0026

Veeva OpenData

Veeva Systems Veeva OpenData is a cloud-based reference data solution that contains verified information on healthcare professionals, healthcare organizations, and their affiliations across 100+ countries. The platform serves life sciences companies for commercial operations, CRM integration, and compliance workflows through direct provisioning, API integration, or data file delivery. Commercial provider Paid HDB-0031

IQVIA OneKey

IQVIA IQVIA OneKey is a global healthcare professional and healthcare organization reference database containing information on healthcare professionals and organizations worldwide. The platform serves the life sciences industry for commercial operations, sales, marketing, compliance, and analytics through commercial licensing agreements with data provisioned via direct access, API, or data files. Commercial provider Paid HDB-0032

Embase

Elsevier Biomedical abstract and indexing database containing 44+ million records from 8,100+ journals, conference abstracts, and clinical trials dating from 1947 to present. Designed for systematic reviews, drug safety monitoring, and evidence-based research; accessed through paid institutional subscriptions or individual access options. Literature database Paid HDB-0033

Cochrane Library

Cochrane Curated collection of systematic reviews and meta-analyses synthesizing healthcare research, with all reviews available free after 12 months of publication. Supports evidence-based decision making through institutional subscriptions or free national provision access in 14+ countries. Literature database Free registration HDB-0034

CINAHL

EBSCO Nursing and allied health literature index containing 1.25+ million records from 3,700+ journals, books, pamphlets, and dissertations. Provides CINAHL Subject Headings indexing with multiple product tiers offering varying levels of full-text access; accessed through institutional subscriptions or trials. Literature database Paid HDB-0035

Scopus

Elsevier Multidisciplinary abstract and citation database indexing 100+ million records from journals, books, conference proceedings, and preprints across all research disciplines. Features AI-powered analytics and discovery tools; accessed through institutional subscriptions with free preview mode available to individuals. Literature database Paid HDB-0036

Web of Science

Clarivate Citation-indexed research discovery platform covering 34,000+ journals with 278+ million records and 3.3+ billion citation links across 254 subject categories from 1864-present. Includes specialty databases for patents, dissertations, and preprints; accessed through institutional subscriptions only. Literature database Paid HDB-0037

APA PsycInfo

American Psychological Association Behavioral and social sciences database indexing 6+ million peer-reviewed records from 2,400+ journals, books, and dissertations in 30 languages from 50 countries. Updated twice weekly with coverage spanning 600 years; accessed through institutional licenses or individual subscriptions with free 30-day trials available. Literature database Paid HDB-0038

Europe PMC

EMBL-EBI Open biomedical literature repository developed by EMBL-EBI containing 48+ million articles, preprints, books, and theses from global sources. Freely accessible to anyone worldwide with REST APIs and bulk download capabilities; supported by 35 international research funders as an ELIXIR core data resource. Literature database Open access HDB-0039

Trip Database

Trip (independent organization) Evidence-filtered medical search engine providing rapid access to clinical guidelines, systematic reviews, and primary research organized by research quality level. Offers free basic search and paid Trip Pro tier ($55/year individual or institutional licensing) with enhanced filtering and features. Literature database Free registration HDB-0043

gnomAD (Genome Aggregation Database)

Broad Institute, Collaborators The Genome Aggregation Database is a resource of aggregated exome and whole-genome sequencing data containing over 241 million genetic variants from over 141,000 diverse individuals, curated by the Broad Institute and collaborators. Summary data are freely available without restrictions through the gnomAD browser, cloud storage, and programmatic interfaces. Open dataset Open access HDB-0044

IGSR / 1000 Genomes Project

European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute The International Genome Sample Resource maintains human genetic variation data from the 1000 Genomes Project, including updated reference assemblies and new datasets, operated by EMBL-EBI. All data are openly accessible through the IGSR portal with searchable filtering tools for accessing samples by population and sequencing method. Open dataset Open access HDB-0054

ISIC Archive

International Skin Imaging Collaboration The ISIC Archive is a large open-source repository containing approximately 549,571 dermatological images of skin lesions including melanomas, nevi, and other skin conditions, with clinical and histological metadata. The archive supports algorithm development for melanoma detection and dermatological diagnosis through curated datasets and annual machine learning challenges. Open dataset Open access HDB-0055

OpenNeuro

Stanford Center for Reproducible Neuroscience OpenNeuro is a free, open-access repository for sharing human and non-human brain imaging data in standardized Brain Imaging Data Structure (BIDS) format, hosting over 600 datasets across multiple modalities including fMRI, structural MRI, EEG, MEG, and PET. Each dataset receives a persistent DOI and is released under Creative Commons CC0 license for maximum data reuse. Open dataset Open access HDB-0064

OECD Health Statistics

Organisation for Economic Co-operation and Development (OECD) OECD Health Statistics is a comprehensive database of health and health systems data maintained by the OECD, covering 35+ member countries. It provides comparable statistics on health expenditure, resources, services utilization, and key health indicators for policy analysis and research. Open dataset Open access HDB-0066

IHME Global Health Data Exchange (GHDx)

Institute for Health Metrics and Evaluation (IHME) The Global Health Data Exchange (GHDx) is IHME's catalog of health and demographic data, including estimates from the Global Burden of Disease study assessing mortality and disability from diseases and injuries globally. Access requires free registration and is available for non-commercial use under IHME's free-of-charge agreement. Open dataset Free registration HDB-0067

Human Mortality Database

UC Berkeley & Max Planck Institute for Demographic Research The Human Mortality Database (HMD) is a joint project providing detailed harmonized mortality and population data for 41 developed countries and regions. Data is openly available under open data principles and can be downloaded as files or accessed through country-specific interfaces and Excel tables. Open dataset Open access HDB-0068

The DHS Program

USAID / Avenir Health The DHS Program is a USAID-funded effort that conducts Demographic and Health Surveys across 90+ countries to collect data on population, health, and nutrition. Survey data is available free for academic research through the STATcompiler tool and downloadable datasets with free registration. Open dataset Free registration HDB-0069

Our World in Data - Health

University of Oxford (Oxford Martin Programme on Global Development) Our World in Data maintains a collection of global health datasets including life expectancy, disease burden, healthcare spending, and disease prevalence, drawn from WHO, World Bank, IHME, and UN agencies. Data is presented through interactive visualizations available under Creative Commons licensing. Open dataset Open access HDB-0072

SNOMED CT

SNOMED International SNOMED CT is a systematized nomenclature of medicine clinical terminology system maintained by SNOMED International, a non-profit organization. It provides standardized international multilingual clinical terminology used globally to code clinical findings, procedures, diagnoses, and medical concepts in healthcare systems. Terminology Credentialed HDB-0073

LOINC

Regenstrief Institute LOINC is an international standard for identifying health observations, measurements, and laboratory tests maintained by the Regenstrief Institute at Indiana University. It enables healthcare systems to identify, exchange, and aggregate clinical data using unique standardized codes for laboratory and clinical observations. Terminology Open access HDB-0075

WHO ICD-11

World Health Organization The International Classification of Diseases 11th Revision (ICD-11) is the global standard for diagnostic health information maintained by the World Health Organization. It provides a standardized system for classifying diseases, disorders, injuries, and health conditions used worldwide for healthcare management and clinical documentation. Terminology Open access HDB-0077

DrugBank

University of Alberta DrugBank is a comprehensive online database containing detailed information on drugs, drug targets, and drug interactions created and maintained by the University of Alberta and The Metabolomics Innovation Centre in Canada. It provides structured biomedical knowledge on approved and experimental drugs used by researchers for drug discovery and pharmacology research. Terminology Free registration HDB-0078

WHO ATC/DDD Index

WHO Collaborating Centre for Drug Statistics Methodology The Anatomical Therapeutic Chemical (ATC) Classification System and Defined Daily Dose (DDD) system is maintained by the WHO Collaborating Centre for Drug Statistics Methodology hosted by the Norwegian Institute of Public Health. It provides an international standard system for classifying drugs and measuring medication usage in drug utilization research and monitoring. Terminology Free registration HDB-0079

OHDSI Athena

Observational Health Data Sciences and Informatics Athena is a web application for distributing and browsing standardized vocabularies for the Observational Medical Outcomes Partnership (OMOP) Common Data Model maintained by OHDSI. It integrates over 136 vocabularies including SNOMED CT, LOINC, and RxNorm to facilitate data harmonization across observational health research networks. Terminology Open access HDB-0080

INDEPTH Network Health and Demographic Surveillance Systems (HDSS)

International Network for the Demographic Evaluation of Populations and Their Health (INDEPTH) INDEPTH operates 47 health and demographic surveillance system (HDSS) field sites across 19 countries in Africa, Asia, and Oceania, capturing longitudinal data on vital events and population health for over 3.8 million individuals. The network provides access to fully documented datasets through its data repository (data.indepth-network.org), enabling research on mortality, fertility, migration, and disease patterns in low- and middle-income countries. Open dataset Credentialed HDB-0141

PAHO/EIH Open Data

Pan American Health Organization (PAHO/WHO) PAHO/EIH Open Data (formerly PLISA) is a regional health information platform providing over 140 health indicators covering countries and territories across the Americas since 1995. The platform includes disease incidence and mortality data, vaccination coverage, outbreak information, non-communicable disease indicators, mental health data, and environmental health determinants disaggregated by age, sex, and urban-rural distribution. Open dataset Open access HDB-0147

WHO ICTRP (International Clinical Trials Registry Platform)

World Health Organization ICTRP is a WHO-operated search portal that aggregates clinical trial registration data from 18 primary registries across multiple countries and regions, including trials in all phases and across all therapeutic areas. The platform provides a unified search interface for finding trial information while linking to the original records maintained by contributing registries. Trial registry Open access HDB-0154

OHDSI

OHDSI Collaborative OHDSI is an international open-science collaborative that standardizes and coordinates observational health databases through the OMOP Common Data Model for large-scale analytics and real-world evidence generation. The network operates through a decentralized community of researchers and data partners who can conduct collaborative studies using harmonized health data while maintaining local data governance. Research database Free registration HDB-0160

TriNetX

TriNetX (private company) TriNetX operates a global federated real-world data network connecting healthcare sites across multiple countries. The platform serves pharmaceutical companies, healthcare providers, academic institutions, and researchers through a commercial subscription model for clinical trial design support, patient cohort identification, and real-world evidence research. Commercial provider Paid HDB-0169

WHO Data Platform

World Health Organization The WHO Data Platform (data.who.int) is a centralized interactive digital portal providing access to trusted global health data and statistics across thousands of health indicators. The platform offers browsable data by country and indicator, downloadable datasets, interactive visualizations tracking Triple Billion targets and health emergencies, and country-level health profiles. Open dataset Open access HDB-0170

WHO Global Health Expenditure Database (National Health Accounts)

World Health Organization The WHO Global Health Expenditure Database provides comparable health spending data for 195 countries and territories since 2000, including breakdowns by funding sources, financing arrangements, health functions, and disease-specific expenditures. The database is updated annually and tracks capital investments and country-level health expenditure profiles. Open dataset Open access HDB-0171

World Bank Health, Nutrition and Population Statistics

World Bank The World Bank provides comprehensive health, nutrition, and population statistics through its DataBank platform, offering over 50 health-related indicators including mortality rates, life expectancy, disease prevalence, immunization rates, and nutritional status measures. Data covers 195 countries with downloadable formats in CSV, XML, and Excel. Open dataset Open access HDB-0172

UNAIDS AIDSinfo

UNAIDS UNAIDS AIDSinfo provides comprehensive HIV/AIDS epidemiological estimates, country-reported data on national AIDS responses, service coverage metrics, and financial resource tracking with over 85 indicators on HIV funding. The platform includes data on key populations, HIV-related policies and legal frameworks, and health inequalities in HIV progress. Open dataset Open access HDB-0173

Global Fund Data Explorer

The Global Fund to Fight AIDS, Tuberculosis and Malaria The Global Fund Data Explorer provides public access to performance metrics and results data related to AIDS, tuberculosis, and malaria programs funded through the Global Fund. The platform enables stakeholders and the public to track grant performance, funding allocation, and programmatic outcomes. Open dataset Open access HDB-0174

Gapminder Health Datasets

Gapminder Foundation Gapminder provides free interactive data visualization tools and datasets on global health, demographics, and development indicators sourced from the UN and other reliable international sources. The platform offers animated datasets and visualization tools to examine health trends and misconceptions about global health progress. Open dataset Open access HDB-0175

Grand Challenge

Diagnostic Image Analysis Group (DIAG), Radboud University Medical Center A platform hosting 419+ open medical imaging challenges and datasets across diverse imaging modalities and anatomical sites. Participants can submit algorithms, access benchmark datasets, and benchmark their models against peer submissions in real time. Research database Free registration HDB-0176

MedMNIST

Jiancheng Yang et al. A collection of 18 standardized medical imaging datasets (12 2D and 6 3D) spanning multiple modalities including pathology, retinal imaging, breast ultrasound, and chest radiography. Datasets are pre-processed and curated for machine learning benchmarking with consistent train-validation-test splits. Open dataset Open access HDB-0204

INDEPTH Data Repository (iSHARE)

International Network for the Demographic Evaluation of Populations and Their Health (INDEPTH) The INDEPTH iSHARE repository archives high-quality longitudinal datasets from 30+ Health and Demographic Surveillance System sites across sub-Saharan Africa and Asia, providing population-based health and demographic data in a standardized format. The repository enables cross-site comparative research and access to microdata that would otherwise remain dispersed across individual HDSS institutions. Research database Free registration HDB-0210

African Index Medicus (AIM)

World Health Organization Africa Regional Office An international database indexing African health literature, including peer-reviewed journal articles, theses, and technical reports from 320+ African health journals, with over 20,000 bibliographic references and 14,383 full-text documents. The database provides access to locally-published biomedical information in English, French, and Portuguese, complementing other WHO systems and giving visibility to African health research. Literature database Open access HDB-0228

Malaria Atlas Project (MAP)

Telethon Kids Institute (Perth, Australia) and Ifakara Health Institute (Dar es Salaam, Tanzania) MAP combines global malaria data with geospatial analytics and machine learning to generate high-resolution risk maps, burden estimates, and intervention coverage assessments for malaria control. The platform provides annual calculations of cases and deaths, tracks antimalarial drug and diagnostic coverage, and offers tools for commodity planning and impact evaluation across endemic regions. Open dataset Open access HDB-0229

PEPFAR Monitoring, Evaluation, and Reporting (MER) Database

amfAR (The Foundation for AIDS Research), in partnership with U.S. PEPFAR program The PEPFAR MER Database is a tool for exploring HIV/AIDS program performance and epidemiological data from the U.S. President's Emergency Plan for AIDS Relief across 36 country programs. It provides access to programmatic indicators on prevention, treatment, care, and support services, enabling civil society organizations and researchers to monitor and analyze PEPFAR's impact in high-burden African countries. Open dataset Open access HDB-0273

HBSC: Health Behaviour in School-aged Children Study

WHO collaborative study, coordinated by University of Bergen International Coordinating Centre WHO cross-national longitudinal study monitoring health, well-being, and behavior of adolescents aged 11, 13, and 15 years in their social context, conducted every four years across 51 countries and regions in Europe, Central Asia, and North America. The interactive data browser provides access to nine topic areas including mental health, substance use, physical activity, and social relationships. Research database Open access HDB-0306

Vivli

Vivli (independent nonprofit) Vivli is a global platform hosting de-identified individual participant data from completed clinical trials contributed by pharmaceutical sponsors, research organizations and CROs. Researchers apply for access to datasets through a controlled-access repository and secure research environment, with priority given to nonprofit and public health research. IPD repository By application HDB-0308

Project Data Sphere

Project Data Sphere (independent nonprofit) Project Data Sphere is an open-access repository of de-identified patient-level data from late-phase oncology clinical trials, maintained by pharmaceutical sponsors, research institutions, and the PDS research program. Researchers can access datasets and analytical tools free after registration with no research proposal required. IPD repository Free registration HDB-0309

ClinicalStudyDataRequest.com

ClinicalStudyDataRequest.com Consortium ClinicalStudyDataRequest.com is a consortium platform where pharmaceutical sponsors and research organizations list individual participant datasets from completed trials available for researcher access. External investigators submit data-access requests for de-identified datasets; approved requests are facilitated through the platform. IPD repository By application HDB-0310

Infectious Diseases Data Observatory

University of Oxford, Centre for Global Health Research IDDO curates and harmonizes individual participant data from studies of malaria, COVID-19, visceral leishmaniasis, schistosomiasis, and other infectious diseases, including the World-Wide Antimalarial Resistance Network (WWARN) and ISARIC data on COVID-19. De-identified IPD standardized to CDISC is freely available to nonprofit researchers; data inquiries are managed through the platform. IPD repository By application HDB-0318

CPAD (Critical Path for Alzheimer's Disease) / CODR-AD

Critical Path Institute (C-Path) A repository of Alzheimer's disease and mild cognitive impairment clinical trial data from globally executed randomized controlled trials. Researchers and developers apply for access to de-identified, fully standardized patient-level records across 28 studies containing 6,955 individual participant records. IPD repository By application HDB-0331

Flatiron Health — Real-World Data

Flatiron Health (Roche) Flatiron Health, a subsidiary of Roche, licenses de-identified oncology electronic health record data curated into longitudinal patient records with structured treatment and outcome fields. Life sciences companies use it to generate real-world evidence for drug development and regulatory submissions, with access by commercial agreement. Commercial provider Paid HDB-0333

Tempus — Real-World Data

Tempus Tempus licenses de-identified multimodal oncology data linking clinical records with DNA and RNA sequencing results, imaging and whole-slide images into longitudinal patient records. Life sciences companies license the data into their own environment or analyse it in Tempus Lens, the company's hosted analysis platform. Commercial provider Paid HDB-0339

Segmed

Segmed Segmed licenses de-identified medical imaging data across modalities including CT, MRI, X-ray, ultrasound, PET/CT, mammography and echocardiography, linked to clinical records and pathology results. Life sciences, medical device and AI companies use it for algorithm development and research under commercial agreement. Commercial provider Paid HDB-0348

Evaluate — Evaluate Pharma

Evaluate (Norstella) Evaluate Pharma is a subscription platform providing consensus analyst forecasts for marketed and pipeline drugs alongside company and therapy area financial data. Pharmaceutical companies, investment banks and consultancies use it for portfolio assessment and commercial benchmarking. Commercial provider Paid HDB-0349

Clarivate — Cortellis

Clarivate Cortellis is Clarivate's subscription drug development intelligence platform, indexing pipeline drugs, company profiles, patents and clinical and regulatory outcomes. Pharmaceutical and biotech companies use it for portfolio strategy, business development and competitive analysis. Commercial provider Paid HDB-0350

Springer Nature — AdisInsight

Springer Nature AdisInsight is Springer Nature's drug development database tracking compounds from discovery through post-marketing surveillance, compiled from journals, trial registries, company announcements and regulatory filings. It is licensed by subscription and used for competitive monitoring and drug safety intelligence. Commercial provider Paid HDB-0351

GlobalData — Pharma Intelligence Center

GlobalData The Pharma Intelligence Center is GlobalData's subscription platform covering drug pipelines, clinical trials, patents, regulatory milestones, sales data and therapy area analysis. Subscribers access it as dashboards and downloadable datasets for competitive and market analysis. Commercial provider Paid HDB-0352

PharmaCircle

PharmaCircle PharmaCircle is a subscription database of drugs, biologics and combination products, curated alongside formulation, drug delivery, manufacturing and regulatory information. It is used for competitive intelligence, formulation research and business development across the life sciences industry. Commercial provider Paid HDB-0353

DrugPatentWatch

DrugPatentWatch DrugPatentWatch tracks biopharmaceutical patents, exclusivities, litigation and generic entry opportunities, compiled from USPTO, FDA and international patent register sources. Generic manufacturers, biotech companies and payers subscribe for portfolio and competitive analysis. Commercial provider Paid HDB-0354

Beacon Intelligence

Beacon Intelligence (Hanson Wade) Beacon is a subscription clinical trial and drug development database organised into modality- and disease-specific modules covering drugs, trials and companies. It is used to track targeted therapies including cell and gene therapy, antibody-drug conjugates and targeted protein degradation from preclinical stages through commercialisation. Commercial provider Paid HDB-0355

Norstella — Biomedtracker

Norstella Biomedtracker, part of Norstella, tracks late-stage drug pipeline progress and regulatory milestones and publishes likelihood-of-approval analysis. It is licensed by subscription and used for pipeline forecasting and competitive intelligence. Commercial provider Paid HDB-0366

Medidata — Synthetic Control Arm®

Medidata Solutions (Dassault Systèmes) Medidata licenses de-identified patient-level data from historical clinical trials, standardised to common covariates and endpoints, for use in constructing external control arms. Sponsors use it in registrational and early-phase development and in regulatory submissions; Medidata is part of Dassault Systèmes. Commercial provider Paid HDB-0367

Certara — CODEX

Certara CODEx is Certara's curated database of clinical trial results organised into indication-specific collections across oncology, immunology, cardiovascular, metabolic, CNS, pain, respiratory and ophthalmology. It is licensed for comparative efficacy analysis, network meta-analysis and safety benchmarking. Commercial provider Paid HDB-0368

Phesi — Trial Accelerator

Phesi Trial Accelerator is Phesi's clinical development database of completed trials, research projects and de-identified patient records, indexed by indication and geography. Sponsors and CROs license it as a self-service platform for feasibility analysis, site selection and trial performance prediction. Commercial provider Paid HDB-0369

Clarivate — Cortellis Clinical Trials Intelligence

Clarivate Cortellis Clinical Trials Intelligence is Clarivate's indexed database of global clinical trials with linked biomarker, trial site and sponsor records across a broad range of diseases. It is licensed for protocol benchmarking, site feasibility assessment and competitive intelligence. Commercial provider Paid HDB-0372

Diaceutics — DXRX

Diaceutics PLC DXRX is Diaceutics's platform aggregating de-identified diagnostic testing data, clinical records and genomic results contributed by laboratories across multiple countries. Pharmaceutical companies and diagnostic developers license it for precision medicine development and to characterise testing patterns in target populations. Commercial provider Paid HDB-0480

MeSH (Medical Subject Headings)

National Library of Medicine (NLM/NIH) MeSH is the NLM's controlled vocabulary thesaurus organized in a hierarchical structure and used for indexing articles in PubMed and the NLM catalog. It contains thousands of descriptors (main headings) and qualifiers (subheadings) for systematically indexing biomedical literature, and is maintained through continuous updates to incorporate new terms from the scientific literature. Terminology Open access HDB-0481

HL7 FHIR Terminologies

Health Level Seven (HL7) International HL7 FHIR (Fast Healthcare Interoperability Resources) Terminologies define the standard codes, value sets, and code systems for healthcare data exchange and integration. The specification covers how to represent coded values in FHIR resources, binding strengths for value sets, and integration with major terminologies like SNOMED CT, LOINC, ICD, and RxNorm for standardizing both structured and unstructured health data. Terminology Open access HDB-0485

Human Phenotype Ontology

The Jackson Laboratory A standardized vocabulary of phenotypic abnormalities and clinical findings in human disease. Maintained by the Monarch Initiative and widely used for clinical annotation, genetic diagnosis, and rare disease research. Terminology Open access HDB-0486

Gene Ontology

The Gene Ontology Consortium The world's source of structured information on gene functions across molecular, cellular, and organismal levels, with standardized terms for describing gene products. Freely available for browsing, searching, downloading, and API access with support from the National Human Genome Research Institute. Terminology Open access HDB-0487

HGNC (Hugo Gene Nomenclature Committee)

HUGO Gene Nomenclature Committee The authoritative resource for approved human gene nomenclature and symbols, maintained as the international standard for official gene names. All data files and archives are freely available in a publicly accessible repository. Terminology Open access HDB-0488

ChEBI (Chemical Entities of Biological Interest)

EMBL-EBI (European Bioinformatics Institute) An open-access database and ontology of chemical entities used in biological research, ions, and complexes. Each entry includes chemical nomenclature following IUPAC standards, literature citations, and cross-references to other databases. Terminology Open access HDB-0489

Disease Ontology

Institute for Genome Sciences, University of Maryland A, semantically-structured ontology organizing disease knowledge through etiology-based classification and providing searchable disease terminology. Recognized as a Global Core Biodata Resource with monthly releases of OBO, OWL, and JSON ontology files available freely through GitHub. Terminology Open access HDB-0490

Mondo Disease Ontology

Monarch Initiative A unified disease terminology system that harmonizes disease definitions across the world by merging multiple disease resources into one coherent ontology. Contains disease concepts with precise mappings between different medical databases and is released under CC-BY 4.0. Terminology Open access HDB-0491

NCI Thesaurus

National Cancer Institute A cancer research terminology system developed by the National Cancer Institute as part of the Enterprise Vocabulary Services. Provides standardized terminology for oncology research, clinical trials, and cancer informatics applications. Terminology Open access HDB-0492

UCUM (Unified Code for Units of Measure)

Regenstrief Institute and UCUM Organization A code system enabling unambiguous electronic communication of measurements and their associated units across international science, engineering, and business. Adopted by major organizations including IEEE, DICOM, LOINC, and HL7, and incorporated into ISO 11240:2012 standard. Terminology Open access HDB-0494

TNM Classification of Malignant Tumours

Union for International Cancer Control (UICC) A globally recognized standard for classifying the extent of cancer spread using T (primary tumor), N (lymph node involvement), and M (metastatic spread) components. Maintained by UICC for years with the 9th edition (2025) published through Wiley, with free educational materials available. Terminology Paid HDB-0502

LSHTM Data Compass

London School of Hygiene & Tropical Medicine A curated digital repository of research datasets, code, and tools produced by LSHTM and collaborators, public health, and infectious disease. Datasets include qualitative and quantitative individual-level data with varying access levels; restricted datasets require registration and approval. Research database Free registration HDB-0533

OMIM (Online Mendelian Inheritance in Man)

Johns Hopkins University OMIM (Online Mendelian Inheritance in Man) is a catalogue of human genes and genetic phenotypes, focused on Mendelian disorders and the relationships between genes and disease. It is authored and edited at the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, is updated daily, and is free to browse with registration required for bulk downloads. Terminology Free registration HDB-0534

Orphanet (Rare Disease Database)

INSERM (Institut National de la Santé et de la Recherche Médicale), France Orphanet is a reference portal on rare diseases and orphan drugs, maintaining an inventory and classification of rare diseases together with the ORPHAcode nomenclature, directories of expert centres, diagnostic tests and patient organisations. It was established by INSERM in France in 1997 and is now run by a consortium of partner countries; the website is free to use and bulk datasets are published through Orphadata. Terminology Open access HDB-0562

Noodle

Helena Bioinformatics Noodle is a biomedical literature discovery service over a corpus assembled from PubMed, Europe PMC and OpenAlex, in which publications are linked to gene, variant and phenotype mentions drawn from the Human Phenotype Ontology, Ensembl, ClinVar and gnomAD. Search is open without registration and accepts free text as well as PMID, DOI, PMCID, gene, variant and phenotype identifiers, with results grouped into articles, genes, variants and phenotypes. Literature database Open access HDB-0593

PubTator3

NCBI / US National Library of Medicine PubTator3 is an annotated version of the biomedical literature produced by NCBI's computational biology group, in which PubMed abstracts and PMC full-text articles are tagged with gene, disease, chemical, variant and species mentions and with the relations between them. It can be searched by entity or relation on the web without registration, and the annotations are also available through an API and bulk FTP download. Literature database Open access HDB-0606

Arcadia

Arcadia Arcadia is a healthcare data platform that aggregates and normalises clinical, claims and administrative data from a client's own sources and connected networks. It is licensed to health systems, payers and provider networks for population health and financial analytics rather than sold as a dataset. Commercial provider Credentialed HDB-0607

DISGENET

MedBioinformatics Solutions SL DISGENET is a curated database of gene-disease and variant-disease associations assembled from expert-curated repositories and text-mined literature, operated by MedBioinformatics Solutions. It is used for target identification, biomarker discovery and variant interpretation, and is licensed for access through a REST API, an R package and a Cytoscape plug-in. Commercial provider Paid HDB-0629

Global Index Medicus (GIM)

World Health Organization The Global Index Medicus is a bibliographic index of scientific and technical health literature maintained by the World Health Organization, comprising regional indexes covering the African, Eastern Mediterranean, South-East Asian, Latin American and Caribbean, and Western Pacific regions. It is used to search and retrieve bibliographic records on health sciences by title, author, subject, or DeCS/MeSH descriptors, and is accessible freely through the WHO website. Literature database Open access