PhysioNet is growing, thanks to the generosity of our contributors around the world.
Your contributions are welcome.
PhysioNet is a forum for the exchange of data and software among
researchers. We welcome contributions of data to
PhysioBank, and of software to PhysioToolkit.
If you have publications that are based on
your contributed data or software (or on existing PhysioBank or
PhysioToolkit materials), we encourage you to contribute copies (or
citations) to the PhysioNet Publications pages. If you have developed
tutorials, class notes or problem sets, or other materials that can
help others to understand or use PhysioNet better, please share them
with the community.
We created PhysioNetWorks as a
collaborative virtual laboratory for development of data and software that will
be contributed to PhysioNet (whether immediately or at some time in the
future). All contributions go first to PhysioNetWorks for review before they
appear in PhysioBank, PhysioToolkit, or the PhysioNet Library.
Submitting your contribution
Please read this entire page before submitting your contribution!
- If you have not already done so, create a PhysioNetWorks account for
yourself. See PhysioNetWorks
for details on this step and those that follow.
- Create a PhysioNetWorks project for your contribution and
upload your files to it. (If you have many files, or if they require more
than one gigabyte, just a sample of your files is sufficient.) During
this period, the project is visible only to you. When ready, mark your
project as ready to activate.
- We will review your contribution (usually within a day or
two, but not on weekends or US holidays). If your project is suitable
for eventual free dissemination on PhysioNet, it will be activated as
a restricted-access project that you may share with selected colleagues
if you wish. If your project requires additional work before it can
be activated, you will receive an email describing what is needed.
- PhysioNetWorks provides an environment in which you and your
collaborators can continue to add to and further develop your contribution.
When you are ready, mark your project as ready to publish.
At this time, the contents of your project should conform to the guidelines
We strongly urge contributors to use PhysioNetWorks to upload their files,
but we will accept contributions on standard media (CDs, DVDs, flash memory,
USB drives) if necessary. Please contact us if you cannot upload your contribution.
All contributions are reviewed
Rigorous review of the data and software available from PhysioNet is
essential so that researchers can confidently make use of these materials.
For this reason, we attempt to make explicit the extent to which all data
and software have been reviewed, by assigning each item to one of three
- Class 1 databases and software are fully supported.
Class 1 databases have been carefully scrutinized and have been thoroughly
annotated. Class 1 software has been extensively and rigorously tested. We
will correct and document any remaining errors, and encourage users to bring
these to our attention.
- Class 2 databases and software are archival copies of
materials that support published research, contributed by authors or journals.
We will maintain copies of the original data and software together with
corrections submitted by the authors. We encourage users to report errors
directly to the authors; if you do not receive a response from the authors
after a reasonable time, please let us know.
- Class 3 databases include collections of data that
may have been less thoroughly studied than those in class 1, but that may
be of interest to the research community. These databases include works in
progress, to which users are invited to contribute. In some cases, these
databases may be archived on their creators' web sites. Class 3 software
includes code that may need further testing or development; again, you
are invited to dig in and help their creators transform these works in progress
into robust and useful tools for research.
archive index and
software index indicate which fully supported databases and
software belong to class 1. We make class 2 and class 3 data and
software available via PhysioNet as a service to the research
community. Contributed data and software are placed in classes 2 and
3 on acceptance, and may be admitted to class 1 after review and a
public comment period.
PhysioNetWorks hosts works in progress that have not
yet been admitted to one of the classes above. In order to establish
and to maintain the highest standard of quality in the data and
software available from PhysioNet, we use the guidelines below to
determine when a work in progress is complete. When both its author
and PhysioNet agree, a completed work can be transferred to a suitable
publicly accessible area of PhysioNet.
We follow these guidelines in soliciting and accepting contributions of data:
Selection of subjects: Although data from longitudinal,
population-based studies are ideal, we accept data from other types of
studies provided that the method of selection has been carefully documented.
At least a minimum of demographic information (age, gender, medications,
diagnoses) should be available for each subject; additional demographic
information (e.g., race, ethnicity) is desirable. Anonymity of all
subjects must be assured. For data from experimental in
vivo or in vitro studies, we favor studies where meaningful
time series have been collected and detailed descriptions of the experimental
conditions are provided.
Recording and data preparation: Almost all PhysioBank data
were originally recorded digitally. We may accept analog recordings
if no comparable data are available to us in digital form.
Technical details of the recordings (signal types, transducer types
and locations, recording bandwidth, instrumentation used) must be
supplied. Please consult us for recommendations before digitizing
Verifiability: Databases of derived time series (such as
heart rate or RR interval time series) are of limited interest and
value, unless the original signals from which the time series were
derived are included so that independent verification is possible.
Moreover, information contained in the original signals is often
useful for purposes other than those served by the derived time
series. Although we will sometimes accept databases containing only
derived time series (see, for example, the Gait Maturation
Database), we strongly encourage contributions that include the
Annotation: Depending on the nature of the data, annotations at
varying levels of detail may be required. In most cases, an initial set of
annotations should be provided or funded by the contributor. We will provide
training and facilities to visiting contributors in order to accomplish this
Preparing a contribution of data:
- Health information that would permit identification of
individual human subjects cannot be shared freely under US
law, which governs what PhysioNet can do. PhysioNet provides
software that can
assist in removing
from your data so that they can be included in PhysioBank. If you
have questions about this requirement, please
us for help.
- Upload a plain text file containing a brief description of your data set
(no more than one page). Call this file "README". This should
Much, if not all, of this information will also be in the abstract that
you prepare at the time you create your PhysioNetWorks project. The
README can be a copy of the abstract in this case.
- The name by which you would like the data set known
- The name(s) of the creator(s) of the data set
- A paragraph or two describing the data set: What are its
contents? How were recordings made? How were subjects
selected? How were annotations (if any) created and
verified? If you defined your own annotation types,
what are they? (If your annotation scheme is too complex
to describe in a sentence or two, please supply a separate
file describing the annotations, and include a reference
to that file in your "README".)
- References to any published works (include URLs if available
on-line) that describe or make use of the data set, in the
form in which these works should be cited in any future
- Contact information: your name and e-mail address, and,
if possible, the name and e-mail address of an alternate
contact who can answer or refer technical questions about
the data set
- Supply a plain text file containing a list of the records by record
name, with one record name per line. Record names may contain
digits, underscores, and lower-case letters only. Call this file
- For any signals of types not listed in wfdbcal,
please supply additional one-line entries to be added to that
calibration file, in a plain text file named "CALIBRATION".
Details of the format are at the top of wfdbcal,
and also in wfdbcal(5).
- For each recording in your data set, supply one of the following:
- Optional: please include or give a reference to any accompanying
clinical information for a record in a file named
(where RECORD is replaced by the name of the record).
Alternatively, this information can be summarized for all records in
one file called info.txt.
We seek contributions of software to PhysioToolkit, with
emphasis on applications that are of potential value to users of
PhysioBank. Our guidelines for contributors of software, which we continue
to develop in consultation with our Advisory Board, are similar
in scope and intent to our guidelines for contributors of data.
We accept contributions of software only if sources are included and made
available under a license compliant with the Open
Source Definition. We have adopted this policy to protect all users of
PhysioToolkit, including ourselves. By adhering to this policy, we ensure that
users can verify that the software is performing its intended functions and no
others, and that the software can be modified to suit the varying requirements
of its users.
No access control:
We will not undertake to maintain access control over contributed software.
Such contributions, if accepted, will be made freely available to the
Conformity to stated use:
The software must be demonstrated to perform the task intended for it. If
its performance is dependent on its input data (as, for example, a QRS
detector), such dependencies must be characterized with reference to relevant
data from PhysioBank.
Conformity to interface standards: We encourage the use of common
interfaces. PhysioToolkit software tends to follow the ``toolbox'' approach as
pioneered in the UNIX environment. Relatively small applications that perform
well-defined tasks can be designed, implemented, and rigorously tested at
reasonable cost. With careful attention to interfaces, they can be designed to
inter-operate predictably and usefully with other tools. By contrast, the
``Swiss Army chainsaw'' approach, exemplified by the massive, monolithic
applications common in the commercial software industry, is ill-suited to rapid
development of software for leading-edge research.
Software accepted for inclusion in PhysioToolkit should be portable across
supported operating environments. Currently, these environments include
GNU/Linux, MacOS/X (Darwin) 10.2 and later, MS-Windows 9x and later (using
the freely available Cygwin
package), and Unix (including FreeBSD and Solaris).
We favor software that conforms to open systems standards (POSIX and,
for interactive software, X11). Most existing PhysioToolkit software is
written in the C programming language, for performance and portability.
Non-portable software may be accepted provisionally if comparable portable
software is unavailable.
Sources for all PhysioToolkit software must be deposited in the PhysioToolkit
software source archive. The sources for each package must include a working
makefile (a formal description of the dependencies of the source
files on each other and on any external sources, used by the make
utility to manage the compilation process). Each source file must include
comments at the beginning of the file to identify (at least) the name of
the file, the author, and the date of last revision.
User documentation: Each application (or independently usable
component, such as a subroutine library) must be documented by a
UNIX-format man (manual) page (see the WFDB Applications Guide for examples).
This requirement is to ensure that the contents of the PhysioToolkit
library can be searched using a wide variety of standard search
engines; man pages are mechanically reformatted as
hypertext for use on PhysioNet (see, for example, the
WFDB Applications Guide). At a minimum,
the man page for each application must include:
Where appropriate, additional material (examples, descriptions of algorithms
used, etc.) may be included in the man page. A very useful resource
for writing man pages is the
Linux Man Page
the name of the application and a one-line description of its intended use
a synopsis of its use and of any run-time options
any relevant cross-references to other software in PhysioToolkit or elsewhere
references to any other relevant documentation (e.g., tutorial materials)
the names and e-mail addresses of the original author(s), and of the current
PhysioNet Library contributions
We seek publications that are accompanied by contributions of original data
or software that may be of interest to other users of PhysioNet, as well as
papers that make use of existing PhysioBank data or PhysioToolkit software,
and relevant tutorials and other reference materials.
Please do not submit materials that cannot be reproduced freely. PhysioNet
does not assert a copyright on your contribution, but if you have transferred
your copyright privileges to a journal in which your work has appeared, you
must obtain permission to publish it on-line from the publisher of the
Accessibility: We aim to make all text on PhysioNet readable using
text-to-speech or text-to-Braille translators. Since PhysioNet is supported by
US federal funding, this is not only a goal but also
a legal requirement.
All PhysioNet users benefit from text that can be indexed and searched. Please
let us know if you find text pages that are not accessible so that we can
correct them, and if you are contributing files to be posted, especially
multi-column text or PDF files, please check that they are accessible. An easy
test for PDF files is to try to read them using the text-to-speech converter
included as a standard feature in Adobe Acrobat software.
All publicly accessible files on PhysioNet must be written in open formats.
This allows them to be checked for
and other inappropriate content. Use of open formats also ensures that files
remain usable even if the software used to create them becomes unavailable,
allows their contents to be indexed and searched, and provides access to
the widest audience.
For text, we prefer the following formats (in decreasing order of preference):
- LaTeX sources suitable for reformatting using
- Plain text
- PDF, if readable by text-to-speech converters (see this
If you are preparing material in HTML format for posting on PhysioNet, please
consider starting with our template. (This is not
required, but it will help you to lay out your pages in the style used here, and
it will reduce the amount of editing we will need to do with it.)
For illustrations within text, as well as other types of images, we prefer:
- vector formats for drawings, charts, graphs, and other types of line art;
EPS, PS, PDF, and SVG are examples of
open vector formats
- PNG or JPEG for photos and other continuous-tone images
Avoid using screen captures unless you are trying to illustrate the appearance
of a user interface; most plots in particular look better and load more quickly
if rendered using a suitable vector format.
For binary data files, we prefer any of the many formats that are compatible
with the WFDB library. More than 50
existing PhysioBank data collections use these formats; they are flexible,
efficient, and allow use of standard software tools such as those provided by
the PhysioBank ATM for visualization and analysis.
For text-encoded data files, we prefer TSV or CSV. XML is acceptable, especially for
data with complex structure, but be sure that a freely redistributable schema is
included or referenced in your contribution.
For software, sources are required.
PhysioNet sometimes provides file archives in zip, gzip, or bzip2 format for
downloading convenience, but the contents of such archives are not indexed
by the major search engines, so we almost always provide unpacked directories
Files in other formats will need to be converted to one of the formats above
before public release. You can help us, and ensure that the conversion is
correct, by performing the conversion yourself and comparing the results with
your original file(s).
Contributions are irrevocable
Just as readers of a printed journal expect to be able to read articles at any
time after they have been published, users of PhysioNet must be able to depend
on future availability of materials published here. For this reason, we must
refuse requests to withdraw contributed materials or to restrict their
distribution once they have been posted here (although updates are always
welcome and encouraged).