DATA

Everything about data including open source, healthcare data sets and more, in one location.

MIMIC-IV-ED  Emergency Department

MIMIC-ED is a large, freely available database of emergency department (ED) admissions at the Beth Israel Deaconess Medical Center between 2011 and 2016. 448,972 ED stays with vital signs, triage information, medication reconciliation, medication administration, and discharge diagnoses available.

Reference article:Johnson, A., Bulgarelli, L., Pollard, T., Celi, L. A., Mark, R., & Horng, S. (2021). MIMIC-IV-ED (version 1.0). PhysioNet. https://doi.org/10.13026/77z6-9w59.

VItalDb dataset   Anesthesiology/Surgery

A comprehensive dataset of 6,388 surgical patients composed of intraoperative biosignals and clinical information from the Department of Anesthesiology and Pain Medicine, Seoul National University College of Medicine, Seoul, Korea .

Chest X-ray dataset with eye tracking  Imaging

Chest X-ray dataset with eye tracking and report dictation. Built on MIMIC Chest X-ray dataset.1,083 CXR images.

Related publication:

Karargyris, A., Kashyap, S., Lourentzou, I. et al. Creation and validation of a chest X-ray dataset with eye-tracking and report dictation for AI development.Sci Data 8, 92 (2021).

NuCLS   Pathology

CheXpert  Imaging

CheXpert is a  public dataset for chest radiograph interpretation, consisting of 224,316 chest radiographs of 65,240 patients from Stanford Hospital.

Genomic Data Commons(GDC) datasets  Genetics/Cancer

The GDC Portal is a platform from National Cancer Institute(NCI) with cancer related genomic data for 80,000+ cases.

CARING Research radiologist annotated COVID-19 X-rays from BIMCV dataset  Imaging

Annotations by CARING's (Centre for Advanced research in Imaging, Neuroscience and Genomics) expert radiologists on COVID-19 positive X-rays.The corresponding X-rays were released by Medical Imaging Data Bank of the Valencia region (BIMCV). 

BIMCV-COVID19 Imaging Datasets Imaging

BIMCV-COVID19+ dataset is a large dataset with chest X-ray images  and computed tomography (CT) imaging of COVID-19 patients along with their radiographic findings, pathologies, polymerase chain reaction (PCR), immunoglobulin antibody tests and radiographic reports from Medical Imaging Databank in Valencian Region Medical Image Bank (BIMCV).These iterations of the database include 7377 CR, 9463 DX and 6687 CT studies.

RICORD: The RSNA International COVID-19 Open Annotated Radiology Database  Imaging

This database is the first multi-institutional, multi-national expert annotated COVID-19 imaging dataset.Annotated by three radiologists with majority vote adjudication by board certified radiologists,RICORD consists of 240 thoracic CT scans and 1,000 chest radiographs contributed from four international sites.

VinBigData Chest X-ray abnormalities detection Imaging

Provided on Kaggle by the Vingroup Big Data Institute (VinBigData) aims to promote fundamental research and investigate novel and highly-applicable technologies.A dataset consisting of 18,000 images that have been annotated by experienced radiologists.

EchoNet -Dynamic Cardiology

The EchoNet-Dynamic database includes 10,030 labeled echocardiogram videos and human expert annotations (measurements, tracings, and calculations) to provide a baseline to study cardiac motion and chamber sizes

PGxCorpus: a Manually Annotated Corpus for Pharmacogenomics  Pharmacology/Genetics

941 sentences from 911 PubMed abstracts, annotated with PGx entities of interest (mainly genes variations, gene, drugs and phenotypes), and relationships between those.

CENTAUR LABS    General

40+ speciality classified list of open source datasets for healthcare with direct links to the datasets and more information.

DATA WORLD - HEALTHCARE   General

More than a 100 healthcare related datasets from around the world, classified and annotated.

Determinants of COVID-19 mortality in the United States dataset (BrainX)  General

Dataset created for the purpose of continuing research into COVID-19. However with information from all 50 states and the District of Columbia, many US statistics can be compared.

Drug Induced Liver injury(DILI) Dataset Pharmacy

The DILIrank dataset is an updated version of the LTKB Benchmark dataset. DILIrank consists of 1,036 FDA-approved drugs that are divided into four classes according to their potential for causing drug-induced liver injury (DILI).

SUSTech -SYSU dataset Ophthalmology

Dataset for automatically segmenting and classifying corneal ulcers with 712 ocular staining images and the associated segmentation labels for flaky corneal ulcers.

Harvard Dataverse General

4000+ healthcare datasets made available from Harvard University.Searchable and diverse.

PanNUke Dataset  Pathology

Semi automatically generated nuclei instance segmentation and classification dataset with exhaustive nuclei labels across 19 different tissue types. The dataset consists of 481 visual fields, of which 312 are randomly sampled from more than 20K whole slide images at different magnifications, from multiple data sources.

ACR COVID-19 Imaging Dataset  Radiology/Imaging

A dataset with Images,mainly Chest X-rays from COVID-19 patients.

C3.ai COVID-19 Data Lake   General/Infectious disease

Multiple data sources for COVID-19 in a unified data model, ready for analysis at one place.

COVID-19 Open Research Dataset Challenge (CORD-19)  General/Infectious disease

In response to the COVID-19 pandemic, the White House and a coalition of leading research groups have prepared the COVID-19 Open Research Dataset (CORD-19). CORD-19 is a resource of over 29,000 scholarly articles, including over 13,000 with full text, about COVID-19, SARS-CoV-2, and related coronaviruses.

Novel Corona Virus 2019 Dataset  General/Infectious disease

From World Health Organization - On 31 December 2019, WHO was alerted to several cases of pneumonia in Wuhan City, Hubei Province of China.

This dataset has daily level information on the number of affected cases, deaths and recovery from 2019 novel coronavirus. Please note that this is a time series data and so the number of cases on any given day is the cumulative number.

The data is available since 22 Jan, 2020.

 The RSNA 2019 Brain CT Hemorrhage Dataset.  Imaging

Largest collection of Intracranial hemorrhage CT scans.874 035 images with expert annotations. Reference: Construction of a Machine Learning Dataset through Collaboration: The RSNA 2019 Brain CT Hemorrhage Challenge

PHYSIONET(MIMIC/eICU Collaborative) General/Critical Care

https://physionet.org/about/database/

MIMIC - IV Dataset (https://physionet.org/content/mimiciv/0.4/)

One of the best sources of datasets in healthcare.Primarily from ICU patients.

Includes:

• Clinical datasets such as MIMIC,eICU collaborative and Pediatic ICU datasets.
• Waveform datasets with ECG,EEG,arterial blood pressure waveform.
• ECG datasets with various pathophysiologic changes and drug interactions.
• Fetal datasets including sounds and ECG.
• Gait and Balance datasets include gait dynamics for patients with various neurodegenerative disorders.
• Neuro and Myoelectic datasets with EEG,EMG and evoked potential waveforms.
• Image datasets with Chest X-rays and MRI images.
• Computed Tomography Images for Intracranial Hemorrhage Detection and Segmentation
• Miscellaneous datasets with text, language,posture and other datasets.

ADNI Database  Neurology/Imaging

Alzheimer's disease patient's imaging(MRI), clinical, genomic, and biomarker data for the purposes of scientific investigation, teaching, or planning clinical research studies.

http://adni.loni.usc.edu/data-samples/access-data/

RIM-ONE  Ophthalomology

RIM-ONE is a database for optic disc and cup segmentation evaluation by Medical Image Analysis group.

downloads

AmsterdamUMCdb  Critical Care

Contains data related to 23,376 intensive care unit and high dependency unit admissions at Amsterdam University Medical Center of adult patients from 2003-2016.

https://github.com/AmsterdamUMC/AmsterdamUMCdb/wiki

FDA Adverse Event Reporting System (FAERS)  Pharmacy

The FDA Adverse Event Reporting System (FAERS) is a database that contains adverse event reports, medication error reports and product quality complaints resulting in adverse events that were submitted to FDA

Malaria Dataset Microbiology

A repository of segmented cells from the thin blood smear slide images from the Malaria Screener research activity.The dataset contains a total of 27,558 cell images with equal instances of parasitized and uninfected cells.

MESSIDOR: Methods to Evaluate Segmentation and Indexing Techniques in the field of Retinal Ophthalmology  Ophthalmology

1200 Retinal image dataset with annotation.

http://www.adcis.net/en/third-party/messidor/

RIGA Dataset :Retinal fundus images for glaucoma analysis  Ophthalmology

A de-identified dataset of retinal fundus images for glaucoma analysis (RIGA) derived from three sources with 750 original images and 4500 manual marked images

https://deepblue.lib.umich.edu/data/concern/data_sets/3b591905z

High-Resolution Fundus (HRF) Image Database  Ophthalmology

The public database contains 15 images of healthy patients, 15 images of patients with diabetic retinopathy and 15 images of glaucomatous patients.

https://www5.cs.fau.de/research/data/fundus-images/

DR HAGIS:Diabetic Retinopathy, Hypertension, Age-related macular degeneration and Glacuoma ImageS  Ophthalmology

39 images for development of vessel extraction algorithms suitable for retinal screening programmes.

https://personalpages.manchester.ac.uk/staff/niall.p.mcloughlin/

NLST Datasets: National Cancer Institute   Cancer

Datasets from National Cancer Institute of over 54000 patients. They include data on participant characteristics, screening exam results, diagnostic procedures, lung cancer, and mortality. Images from over 75,000 CT screening exams are available. Over 1,200 pathology images from a subset of NLST lung cancer patients (~500 of over 2,000 patients) may be viewed.

https://biometry.nci.nih.gov/cdas/datasets/nlst/

NSRR Datasets:National Sleep Research Resource   Pulmonary

Polysomnography dataset from NSRR for sleep studies.Large collection of deidentified physiologic signals perfect for ML development.

https://sleepdata.org/datasets

The HAM10000 dataset  Dermatology

A large collection of multi-source dermatoscopic images of common pigmented skin lesions containing 10000 images.

https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/DBW86T

Associated publication link below:

The HAM10000 dataset, a large collection of multi-source dermatoscopic images of common pigmented skin lesions

Philipp Tschandl, Cliff Rosendahl & Harald Kittler

UCI Machine Learning Repository  General

This open source repository has more than 400 datasets including healthcare(100+) and non-healthcare ones in searchable and categorized format.

http://archive.ics.uci.edu/ml/datasets.php

Centers for Medicare and Medicaid(CMS) datasets with ResDAC link.  General

CMS datasets provide US Medicare and Medicaid datasets.

https://data.cms.gov

ResDAC(The Research Data Assistance Center) provides free support to users of CMS datasets.

https://www.resdac.org/learn

Center for disease control(CDC) Datasets  General

Center for disease control's datasets.Useful for incidence,prevalance of various disorders and mortality data from across the US.

https://data.cdc.gov

Healthcare Cost and Utilization Project (HCUP) datasets  General

Agency for Healthcare Research and Quality's HCUP datasets used to identify, track, and analyze US national trends in health care utilization, access, charges, quality, and outcomes.

https://hcup-us.ahrq.gov/databases.jsp

NHS datasets   General

UK government's National Health services datasets.NHS choices datasets are useful for NLP and sentiment analysis both for GPs and hospitals.

https://data.gov.uk/dataset/73740ffe-cecb-4cba-afb9-51ea996187a1/nhs-england-nhs-choices-hospitals-patient-comments-and-ratings

OASIS Brain MRI dataset  Neuroimaging

Brain MRI datasets from Open Accesss series of Imaging Studies(OASIS).

http://www.oasis-brains.org/#data

OpenNEURO  Neuro

A free and open platform for sharing MRI, MEG, EEG, iEEG, and ECoG data with over 200 datasets.

https://openneuro.org

National Cancer Institute(NCI)-SEER datasets  Cancer

Cancer epidemiology data available through NCI's Surveillance,Epidemiology and End Result Program(SEER)

https://seer.cancer.gov/data-software/

BROAD Institute's Cancer program datasets  Cancer and Genomics

Cancer and genomics datasets.

http://portals.broadinstitute.org/cgi-bin/cancer/datasets.cgi

MURA  Imaging

A dataset of 14,000+ anonymized, radiologist labeled musculoskeletal X-rays from 12,000+ patients from Stanford ML group.

https://stanfordmlgroup.github.io/competitions/mura/

Read their article: https://arxiv.org/abs/1712.06957

fastMRI  Imaging

1500+ knee MRI anonymized dataset from NYU.

https://fastmri.med.nyu.edu