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

 

 

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.

 

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

 

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/

 

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

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/

 

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

NLTK : Natural language toolkit   general

One stop to learn Natural Language processing and more.

Bird, Steven, Edward Loper and Ewan Klein (2009), Natural Language Processing with Python. O’Reilly Media Inc.

https://www.nltk.org

DAIR.AI   general

An excellent resource for trends and updates in AI, especially NLP by Elvis Saravia.

https://medium.com/dair-ai

Data science article collection  general

An excellent collection of articles on data science.

https://www.datasciencecentral.com/profiles/blogs/30-seminal-articles-every-data-scientist-should-read

eICU Collaborative Dataset  critical care

eICU collaborative dataset of more than 130,000 patients across 300 hospitals.Deidentified dataset available for collaborative research includes vitals,clinical notes,APACHE score,diagnosis,treatment information and more.

https://www.nature.com/articles/sdata2018178

Google Dataset Search  general

Google's powerful search engine to assist with dataset search.

https://toolbox.google.com/datasetsearch

NIH CXR14 dataset  imaging

Over 100,000 anonymized chest x-ray images and their corresponding data from more than 30,000 patients, including many with advanced lung disease.

https://nihcc.app.box.com/v/ChestXray-NIHCC

 

NIH Deep Lesion  imaging

NIH release of  a dataset containing 32,000 CT scan images with annotated lesions  belonging to 4400 unique patients.

https://www.nih.gov/news-events/news-releases/nih-clinical-center-releases-dataset-32000-ct-images

 

Blue Button 2.0  general

A CMS initiative to democratize research and development using beneficiary data.Greater than 70 million patient dataset available.Learn more through links below:

https://bluebutton.cms.gov

https://www.youtube.com/watch?v=v5b8T6EELp8

National Institute of Health  general

The link below is for NIH's strategic plan for data science in healthcare.A must read for anyone using data in healthcare for research and innovation.

https://datascience.nih.gov/sites/default/files/NIH_Strategic_Plan_for_Data_Science_Final_508.pdf

NIH Clinical Center  imaging

Largest open source Chest X-Ray data set available through NIH's clinical center.See the link in the article to access the data.Also available through GITHUB and KAGGLE.

https://www.nih.gov/news-events/news-releases/nih-clinical-center-provides-one-largest-publicly-available-chest-x-ray-datasets-scientific-community

 

GITHUB  general

Thanks to Andrew L. Beam and many other contributors on the GITHUB page.Visit via link below or through the BRAINX COMMUNITY on LinkedIn.

https://github.com/beamandrew/medical-data

https://www.linkedin.com/groups/13599549

KAGGLE  general

Kaggle is a good source for de-identified datasets in healthcare.Visit the page using link below and explore.

https://www.kaggle.com/datasets

 

DataMed  general

A biomedical data search engine which searches for datasets across registries.

https://datamed.org/index.php

 

Mendeley  general

A place to store, share or find data.A platform for biomedical  research.

https://www.mendeley.com/datasets

 

Nature  general

Detailed data repositories for biomedical research.

https://www.nature.com/sdata/policies/repositories