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PhysioNet · PhysioBank · PhysioToolkit |
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PhysioNet offers free access via the web to large collections of
recorded physiologic signals and related open-source software. The
PhysioNet web site is a public service of
the PhysioNet Resource
funded by the National
Institutes of Health's NIBIB and NIGMS.
If this is your first visit, please try PhysioTour, a short self-guided tour that highlights the major features of PhysioNet. A brief introduction to PhysioNet, with attention to PhysioNet's significance to the NIH and its mission, is also available in HTML, ODP (OpenOffice Impress), PDF, and PPT formats. Support PhysioNet! [Read more] |
Visit the PhysioNet Bookstore for a selection of tutorial and reference books about this resource. [Link opens in another window.] |
The PhysioNet Resource, intended to stimulate current research and new investigations in the study of complex biomedical and physiologic signals, has three closely interdependent components:
PhysioBank is a large and growing archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community. PhysioBank currently includes databases of multi-parameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and patients with a variety of conditions with major public health implications, including sudden cardiac death, congestive heart failure, epilepsy, gait disorders, sleep apnea, and aging. These collections include data from a wide range of studies, as developed and contributed by members of the research community. To begin an exploration of PhysioBank, start here.
PhysioToolkit is a large and growing library of software for physiologic signal processing and analysis, detection of physiologically significant events using both classical techniques and novel methods based on statistical physics and nonlinear dynamics, interactive display and characterization of signals, creation of new databases, simulation of physiologic and other signals, quantitative evaluation and comparison of analysis methods, and analysis of nonequilibrium and nonstationary processes. A unifying theme of many of the research projects that contribute software to PhysioToolkit is the extraction of ``hidden'' information from biomedical signals, information that may have diagnostic or prognostic value in medicine, or explanatory or predictive power in basic research. All PhysioToolkit software is available in source form under the GNU General Public License (GPL). To learn more about the contents of PhysioToolkit, begin here.
PhysioNet is not only the name of the Resource, but also of its web site, physionet.org. The PhysioNet web site was established by the Resource as its mechanism for free and open dissemination and exchange of recorded biomedical signals and open-source software for analyzing them, by providing facilities for cooperative analysis of data and evaluation of proposed new algorithms. In addition to providing free electronic access to PhysioBank data and PhysioToolkit software, the PhysioNet web site offers service and training via on-line tutorials to assist users at entry and more advanced levels. In cooperation with the annual Computers in Cardiology conference, PhysioNet hosts a series of challenges, in which researchers and students address unsolved problems of clinical or basic scientific interest using data and software provided by PhysioNet.
All data included in PhysioBank, and all software included in PhysioToolkit, are carefully reviewed. We invite you to participate in the ongoing review process. By sharing common data sets, and software in source form, the research community benefits from access to materials that have been rigorously scrutinized by many investigators. We further invite researchers to contribute data and software for review and possible inclusion in PhysioBank and PhysioToolkit. Please review our guidelines for contributors before submitting material.
Links to a variety of other on-line resources likely to be of interest to PhysioNet visitors are listed here.
Beginning in the mid-1970s, members of the PhysioNet team who were then working on some of the first microcomputer-based instruments for cardiac arrhythmia monitoring foresaw the usefulness of establishing shared databases of well-characterized ECG recordings, as a basis for evaluation, iterative improvement, and objective comparison of algorithms for automated arrhythmia analysis. A five-year effort culminated in the publication of the MIT-BIH Arrhythmia Database in 1980, which soon became the standard reference collection of its type, used by over 500 academic, hospital, and industry researchers and developers worldwide during the 1980s and 1990s. Other databases of ECGs and eventually other physiologic signals followed. By 1999, the MIT group distributed CD-ROMs containing 11 such collections, and had participated in the development of several others.
PhysioNet was established in 1999 as the outreach component of the Research Resource for Complex Physiologic Signals, a cooperative project initiated by a diverse group of computer scientists, physicists, mathematicians, biomedical researchers, clinicians, and educators at Boston's Beth Israel Deaconess Medical Center/Harvard Medical School, Boston University, and McGill University, all working together with the MIT group. Many of us have worked together for 20 years or even longer on problems relating to characterizing and understanding the dynamics of human physiology, the implications of dynamical change in diagnosis and treatment of pathophysiology, novel and robust techniques for physiologic monitoring in ambulatory subjects and critical care patients, and applications of model-based reasoning to medical decision support in intensive care. The MIT group contributed its 11 databases, and the software it had developed for exploring and analyzing them, to establish PhysioBank and PhysioToolkit. Free availability of these resources via the Internet catalyzed an even greater explosion of interest in them, as researchers and students worldwide who had no previous access to such data or software began new programs of research, and specialists began comparing their methods. These initial contributions were quickly supplemented by additional collections of data and software from their collaborators, and soon after, from many researchers worldwide. PhysioBank and PhysioToolkit have grown to many times their original sizes, and most of the growth has been thanks to the hard work and generosity of an international community of researchers.
At the time PhysioNet was established, members of the PhysioNet team at MIT were preparing to host Computers in Cardiology 2000. We hoped to introduce PhysioNet to our international colleagues who would be attending CinC, by encouraging participation in an activity that made effective use of the facilities provided by PhysioNet to stimulate rapid progress on an unsolved problem of practical clinical significance. A timely contribution of data made it possible to create the first PhysioNet/CinC Challenge, which attracted the attention of more than a dozen teams to the subject of detecting sleep apnea from the ECG. Their efforts were broadly successful, they discussed their findings at CinC 2000, and an annual tradition was born.
Originally established under the auspices of the NIH's National Center for Research Resources, PhysioNet has been funded since September 2007 under a cooperative agreement with the NIH's National Institute of Biomedical Imaging and Bioengineering (NIBIB), and with the NIH's National Institute of General Medical Sciences (NIGMS).
Methods for assessment of signal quality and detection of events in weakly correlated multiparameter data; false alarm reduction in the ICU; methods for multivariate trend analysis and forecasting, with applications in intensive care; cardiovascular system modeling (including adaptation to microgravity and orthostatic intolerance); novel signal processing techniques for automated or semi-automated patient diagnosis; web-enabled signal processing, with applications in research and telemedicine; data mining algorithms for efficient searching in very long time series; networked instrumentation for acquisition and remote viewing of real-time physiologic data (Gari Clifford, Roger Mark, George Moody).
Algorithms that quantify the transient and local properties of nonstationary physiologic signals and the cross-interactions among multiparameter signals; application of these techniques to detect changes that may precede the onset of catastrophic physiologic events, including epileptic seizures and sudden cardiac death; techniques for quantifying the dynamics of physiologic control; mathematical/physiological modeling of these control mechanisms; identification of new measures related to nonlinear dynamics and fractal scaling that have diagnostic/prognostic use in life-threatening cardiopulmonary pathologies (Madalena Costa, Leon Glass, Ary Goldberger, Jeff Hausdorff, Joe Mietus, CK Peng).
A list of recent publications by investigators affiliated with the Resource is available here. Also see the PhysioNet Contributors Page.
As PhysioNet grows, we want to enable community participation in all aspects of its development. If you have data, software, or expertise to offer, your contributions are welcome and appreciated. We have been working on a new facility intended to simplify and accelerate the process of transforming your contributed research data or software into fully documented and validated components of PhysioNet. The next few paragraphs describe this facility, which is currently under construction and testing, and which will be inaugurated in the next few months.
PhysioNet Works is a virtual laboratory where you can work together with us and with colleagues anywhere in the world to create, evaluate, improve, document, and prepare new data and software "works" for publication on PhysioNet. PhysioNet Works provides reliable web-accessible backup, tools for viewing and annotating your data interactively, and an active community of researchers who can help you by annotating, analyzing, and reviewing your data, and perhaps by contributing additional relevant data.
Anyone wishing to begin a PhysioNet Works project can post a project home page and (for data projects) a data sample, which will not be publicly viewable until the project has been approved. Upon approval, your project's home page and data sample will be made public, but you may choose to restrict access to some or all other components of your project to your invited collaborators for up to one year after the end of your grant. While work is in progress on your project, you have access to the full range of tools needed to prepare it for publication on PhysioNet, and to integrate it with existing PhysioNet content as appropriate. Once it is complete, your project can be moved to PhysioNet in minutes.
The aim of PhysioNet Works is to allow contributors to take on as much of the work of developing contributions into resources for research and education as they wish to take on. The PhysioNet team is using the PhysioNet Works technology to develop our own contributions, and we can help you with yours. Ultimately, by distributing the development work across the community, we expect to be able to bring many more projects to PhysioNet, faster.
We recognize that the PhysioNet Works model, which requires a commitment to publish work within an agreed interval, does not fit all projects. Those who cannot make the necessary commitment to publish can nevertheless use the PhysioNet Works technology on their own hardware, since (like all PhysioNet software) it is free and open-source.
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Updated Friday, 07-Nov-2008 12:40:41 EST
