silky / clinicaldatasources

Open or Easy Access Clinical Data Sources for Biomedical Research

Clinical Data Sources

We are assembling a repository of clinical data sources (Electronic Health Record, Clinical trials, Imaging etc.) that are either public or have low friction application processes. If you have any comments, corrections, or know of any additional sources, please add it as a pull request.

Types of data:

• Patient Demographics: P
• Lab tests: L
• Textual Patient Notes: T
• Imaging: I
• Other: O

Name	Description	Data Types	Patient Count	Ease of Access	Publication/Citation Guidelines
MIMIC	MIMIC is an openly available dataset developed by the MIT Lab for Computational Physiology, comprising deidentified health data associated with ~40,000 critical care patients. It includes demographics, vital signs, laboratory tests, medications, and more.	P, L, T	~45,000	Simple Application	Link
Physionet 2012	Tthe focus of the PhysioNet/CinC Challenge 2012 is to develop methods for patient-specific prediction of in-hospital mortality. Participants will use information collected during the first two days of an ICU stay to predict which patients survive their hospitalizations, and which patients do not.	P, L	12,000 ICU stays	Public	Link
i2b2	In order to enhance the ability of natural language processing (NLP) tools to prise increasingly fine grained information from clinical records, i2b2 has previously provided sets of fully deidentified notes from the Research Patient Data Repository at Partners HealthCare for a series of NLP Challenges organized by Dr. Ozlem Uzuner. We are pleased to now make those notes available to the community for general research purposes. At this time we are releasing the notes (~1,500) from the first four i2b2 Challenges as i2b2 NLP Research Data Sets. A similar set of notes from the most recent i2b2 Challenge will be released on the one year anniversary of that Challenge.	T	~1,500	Simple Application (DUA)	Link (depends on data usage)
PRO-ACT ALS	PRO-ACT provides users with easy access to: 1) Over 10,700 fully de-identified clinical patient records, 2) Placebo and treatment-arm data from 23 Phase II/III clinical trials, 3) Demographic, lab, medical and family history, and other data elements, 4) More than 10 million longitudinally collected data points	P, L	10,700	Simple Application	Link
Cancer Imaging Archive	TCIA is a service which de-identifies and hosts a large archive of medical images of cancer accessible for public download. The data are organized as “Collections”, typically patients related by a common disease (e.g. lung cancer), image modality (MRI, CT, etc) or research focus. DICOM is the primary file format used by TCIA for image storage. Supporting data related to the images such as patient outcomes, treatment details, genomics, pathology, and expert analyses are also provided when available.	I, some studies have others	Most studies < 100	Many Public	Usage Publication
National Biomedical Imaging Archive	Welcome to the National Biomedical Imaging Archive (NBIA). NBIA is a searchable repository of in vivo images that provides the biomedical research community, industry, and academia with access to image archives to be used in the development and validation of analytical software tools that support: Lesion detection and classification, Accelerated diagnostic imaging decision, Quantitative imaging assessment of drug response	I	Most studies < 100	Many Public	NA
Open Access Series of Imaging Studies (OASIS)	The Open Access Series of Imaging Studies (OASIS) is a project aimed at making MRI data sets of the brain freely available to the scientific community. By compiling and freely distributing MRI data sets, we hope to facilitate future discoveries in basic and clinical neuroscience. OASIS is made available by the Washington University Alzheimer’s Disease Research Center, Dr. Randy Buckner at the Howard Hughes Medical Institute (HHMI) at Harvard University, the Neuroinformatics Research Group (NRG) at Washington University School of Medicine, and the Biomedical Informatics Research Network (BIRN).	I	416 (study 1), 150 (study 2)	Public	Study 1 Study 2

To the extent possible under law, Brett Beaulieu-Jones has waived all copyright and related or neighboring rights to Open or Easy Access Clinical Data Sources for Biomedical Research. This work is published from: United States.