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

 

 

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

 

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

 

MIMIC-CXR  imaging

The largest publicly available dataset of de-identified Chest x-rays. 370,000+ chest x-rays with 14 labels in the first version.

Version 2.0 with radiologist text reports and additional data available through link below.

https://physionet.org/content/mimic-cxr/2.0.0/

 

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

 

MIMIC/Physionet  critical care

Excellent data set for text based and waveform based projects which has been used in research worldwide.

https://mimic.physionet.org

 

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