Awesome Healthcare Datasets

A curated list of awesome healthcare datasets for machine learning, research, and exploration.

Contents

• Awesome Healthcare Datasets
  • Contents
  • Clinical Data
  • Imaging Data
  • Omics Data
  • Biomedical Knowledge Graphs
  • Public Health Data
  • Biomedical Literature
  • Miscellaneous
  • License

Clinical Data

1. MIMIC-III Clinical Database - Deidentified health data associated with ~40,000 critical care patients. Includes demographics, vital signs, laboratory tests, medications, and more.
2. eICU Collaborative Research Database - A multi-center database comprising deidentified health data associated with over 200,000 admissions to ICUs across the United States between 2014-2015.
3. MIMIC-IV - An update to MIMIC-III, containing deidentified data associated with patients admitted to a tertiary academic medical center in Boston, MA, USA from 2008-2019.
4. AmsterdamUMCdb - A database containing deidentified health data from the Amsterdam University Medical Center, including structured and unstructured data from patient records.
5. MIMIC-IV-ED - Emergency department data from the MIMIC-IV database.
6. MIMIC-IV-Note - Deidentified free-text clinical notes from the MIMIC-IV database.
7. MIMIC-III Waveform Database - Waveform data from the MIMIC-III database.
8. MIMIC-IV Waveform Database - Waveform data from the MIMIC-IV database.
9. eICU Collaborative Research Database - A multi-center database comprising deidentified health data associated with over 200,000 admissions to ICUs across the United States between 2014-2015.
10. MIMIC-II Clinical Database - An older version of the MIMIC database, containing data from 2001 to 2008.
11. MIMIC-IV-ECHO - Echocardiogram data from the MIMIC-IV database.
12. AMR-UTI - Antimicrobial Resistance in Urinary Tract Infections dataset.
13. Abdominal and Direct Fetal ECG Database - Multichannel fetal electrocardiogram recordings obtained from 5 different women in labor.

Imaging Data

1. TCIA (The Cancer Imaging Archive) - A large archive of medical images of cancer accessible for public download.
2. Chest X-Ray Dataset - A dataset consisting of 5,863 chest X-Ray images, annotated with the presence of pneumonia.
3. RSNA Intracranial Hemorrhage Detection - A dataset of head CT scans, annotated with intracranial hemorrhage labels.
4. MICCAI 2015 Challenge on Multimodal Brain Tumor Segmentation - Brain tumor segmentation dataset.
5. Non-Small Cell Lung Cancer CT Scan Dataset - CT scans of non-small cell lung cancer patients.
6. PROSTATEx - Prostate MRI scans with segmentations and annotations.
7. Labeled Optical Coherence Tomography - Retinal OCT images with layer segmentations and fluid labels.
8. MosMedData: Chest CT Scans with COVID-19 Related Findings - Chest CT scans of COVID-19 patients.
9. LUng Nodule Analysis (LUNA16) - Chest CT scans with annotated lung nodules.
10. NIH Chest X-ray Dataset of 14 Common Thorax Disease Categories - Chest X-ray images with disease labels.
11. DeepLesion - A large-scale dataset of CT images with annotated lesions.
12. Medical Segmentation Decathlon Datasets - Various medical imaging datasets for segmentation tasks.
13. cataracts-2018-train - Cataract images dataset.
14. dHCP 2nd data release -- sourcedata - Developmental Human Connectome Project dataset.
15. dHCP 2nd data release -- fMRI pipeline - Developmental Human Connectome Project dataset (fMRI pipeline).
16. PADCHEST_SJ - Chest X-ray images with multiple labels in Spanish.
17. CAMELYON17 breast cancer - Lymph node sections annotated with metastases.
18. A multimodal dental dataset facilitating machine learning research and clinic services - Dental X-rays, CBCT scans, and dental records.
19. MIMIC-IV-ECG - Diagnostic electrocardiogram data from the MIMIC-IV database.
20. MURA (musculoskeletal radiographs) - Bone X-rays labeled for abnormalities.
21. National COVID-19 Chest Image Database (NCCID) - Chest X-rays, CT scans, and MRIs of COVID-19 patients in the UK.
22. Cell Painting Gallery - A collection of cell images for drug discovery and basic research.
23. International Neuroimaging Data-Sharing Initiative (INDI) - Neuroimaging datasets from various sources.
24. Cancer Imaging Archive - A large archive of cancer imaging data.
25. Open Access Series of Imaging Studies (OASIS) - MRI data in young, middle-aged, and elderly adults.
26. Allen Cell Imaging Collections - 3D cell imaging data for basic research and computational tool development.
27. BossDB Open Neuroimagery Datasets - Various neuroimaging datasets.
28. Clinical Proteomic Tumor Analysis Consortium 3 (CPTAC-3) - Proteomic data from cancer samples.
29. IBL Neuropixels Reproducible Ephys Data on AWS - Electrophysiological recordings from the International Brain Laboratory.
30. NYU Langone & FAIR FastMRI Dataset - Knee MRIs for accelerated MRI reconstruction research.
31. The Human Connectome Project - A collection of neuroimaging and behavioral data.
32. RadGraph - Radiology reports annotated with entities and relations.
33. RadNLI - A natural language inference dataset for radiology reports.
34. RadQA - A question-answering dataset for radiology reports.

Omics Data

1. TCGA (The Cancer Genome Atlas) - A landmark cancer genomics program that molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types.
2. GTEx (Genotype-Tissue Expression) - A resource to study tissue-specific gene expression and regulation, with data from 54 non-diseased tissue sites across nearly 1000 individuals.
3. 1000 Genomes Project - A catalog of human genetic variation, including SNPs and structural variants, based on the genomes of 2,504 individuals from 26 populations.
4. Cancer Cell Line Encyclopedia (CCLE) - Detailed genetic and pharmacologic characterization of a large panel of human cancer cell lines.
5. Genome Aggregation Database - Aggregated and harmonized sequence data from large-scale sequencing projects.
6. Open Bioinformatics Reference Data for Galaxy - Bioinformatics reference data for the Galaxy platform.
7. CoMMpass from the Multiple Myeloma Research Foundation - Genomic and clinical data from multiple myeloma patients.
8. NIH NCBI Sequence Read Archive (SRA) on AWS - Next-generation sequencing data from various studies.
9. Basic Local Alignment Sequences Tool (BLAST) Databases - Sequence databases for use with the BLAST tool.
10. Encyclopedia of DNA Elements (ENCODE) - Data from the ENCODE project, which aims to identify all functional elements in the human genome.
11. Genome in a Bottle on AWS - Reference genomes and benchmarking data for genome sequencing and assembly.
12. OpenCell on AWS - 3D images and meshes of cells and organelles.
13. Refgenie reference genome assets - A standardized, versioned, and programmatically accessible collection of reference genome assets.

Biomedical Knowledge Graphs

1. UMLS (Unified Medical Language System) - A compendium of many controlled vocabularies in the biomedical sciences, providing a mapping structure among these vocabularies.
2. SNOMED CT - A comprehensive, multilingual clinical healthcare terminology for clinical documentation and reporting.
3. RxNorm - A normalized naming system for generic and branded drugs.
4. LOINC (Logical Observation Identifiers Names and Codes) - A database and universal standard for identifying medical laboratory observations.
5. MeSH (Medical Subject Headings) - A controlled vocabulary thesaurus used for indexing articles in PubMed.
6. DrugBank - A comprehensive, freely accessible, online database containing information on drugs and drug targets.
7. Orphanet Rare Disease Ontology - A vocabulary for rare diseases, capturing relationships between diseases, genes, and other relevant features.
8. GWAS Catalog - A catalog of published genome-wide association studies (GWAS) and their findings.
9. ICD-10 (International Classification of Diseases, 10th Revision) - A medical classification list by the World Health Organization (WHO).
10. ICD-9 (International Classification of Diseases, 9th Revision) - An older version of the ICD medical classification list.
11. CPT (Current Procedural Terminology) - A medical code set maintained by the American Medical Association (AMA).
12. Gene Ontology - A bioinformatics resource that provides information about gene product function using ontologies.
13. Disease Ontology - An ontology that provides a standardized description of human disease terms, phenotype characteristics, and related medical vocabulary.
14. RxMix - A database of prescription drugs and their ingredients.
15. RxTerms - A drug interface terminology based on RxNorm.
16. Dailymed - A database of marketed drugs and their labels.
17. Experimental Factor Ontology - An ontology for describing experimental variables in biomedical experiments.
18. UBERON anatomy - A cross-species anatomy ontology.
19. Open-targets - A platform for accessing and analyzing drug target data.
20. Genetic and Rare Diseases - Information on rare diseases and their associated genes.
21. International Classification of Diseases for Oncology - A domain-specific extension of the International Classification of Diseases for tumor diseases.
22. Kyoto Encyclopedia of Genes and Genomes - A resource for understanding high-level functions and utilities of the biological system.
23. Medical Dictionary for Regulatory Activities Terminology - A standardised medical terminology for regulatory communication.
24. Online Mendelian Inheritance in Man - A catalog of human genes and genetic disorders.
25. DisGeNET - A discovery platform containing publicly available collections of genes and variants associated with human diseases.
26. PharmGKB - A pharmacogenomics knowledge resource that encompasses clinical information including dosing guidelines and drug labels, potentially clinically actionable gene-drug associations, and genotype-phenotype relationships.

Public Health Data

1. Global Health Observatory (GHO) - World Health Organization's data repository for global health data, including data on various health topics and SDGs.
2. CDC WONDER - Wide-ranging Online Data for Epidemiologic Research from the Centers for Disease Control and Prevention (CDC).
3. Medicare.gov Data - Official U.S. government site for Medicare data, including data on hospitals, nursing homes, physicians, and more.
4. World Bank Health Data - A collection of World Bank datasets on various health indicators and related data.
5. Global Burden of Disease (GBD) - A comprehensive regional and global assessment of mortality and disability from major diseases, injuries, and risk factors.
6. UNICEF Data - Global data on the situation of children worldwide.
7. OECD Health Statistics - Comprehensive source of comparable statistics on health and health systems across OECD countries.
8. Humanitarian Data Exchange - An open platform for sharing data across crises and organisations.

Biomedical Literature

1. PubMed Central Open Access Subset - A subset of PubMed Central that contains full-text open access articles.
2. CORD-19 - A dataset of scholarly articles about COVID-19, SARS-CoV-2, and related coronaviruses.
3. LitCovid - A curated literature hub for tracking up-to-date scientific information about COVID-19.
4. PubMed - A database of more than 33 million citations for biomedical literature from MEDLINE, life science journals, and online books.
5. Europe PMC - An open science platform that enables access to a worldwide collection of life science publications and preprints from trusted sources.
6. Microsoft Academic Graph - A heterogeneous graph containing scientific publication records, citation relationships between those publications, as well as authors, institutions, journals, conferences, and fields of study.
7. Semantic Scholar Open Research Corpus - A large corpus of scientific papers with rich metadata, paper abstracts, resolved bibliographic references, and structured full text.

Miscellaneous

1. PhysioNet - A large and growing archive of physiological data, including datasets on ECG, EEG, and more.
2. HealthData.gov - Dedicated to making high value health data more accessible to entrepreneurs, researchers, and policy makers in the hopes of better health outcomes for all.
3. Human Mortality Database - Provides detailed mortality and population data to those interested in the history of human longevity.
4. Global Health Observatory (GHO) Data Repository - WHO's gateway to health-related statistics for more than 1000 indicators for its 194 Member States.
5. Medicare Provider Utilization and Payment Data - Data on services and procedures provided to Medicare beneficiaries.
6. OpenNeuro - A free and open platform for sharing MRI, MEG, EEG, iEEG, and ECoG data.
7. National Health and Nutrition Examination Survey (NHANES) - A program of studies designed to assess the health and nutritional status of adults and children in the United States.
8. All of Us Research Program - An effort to gather data from one million or more people living in the United States to accelerate research and improve health.
9. UK Biobank - A large-scale biomedical database and research resource containing in-depth genetic and health information from half a million UK participants.
10. Canadian Open Neuroscience Platform (CONP) - A platform for sharing neuroscience data and tools.

License

This list is released into the public domain. See the license file for more details.