from PhysioNet, the research resource for complex physiologic signals


Contributing to PhysioNet

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!

  1. If you have not already done so, create a PhysioNetWorks account for yourself. See PhysioNetWorks for details on this step and those that follow.
  2. 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.
  3. 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.
  4. 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 below.

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 classes:

The PhysioBank archive index and the PhysioToolkit 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.

Guidelines

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.

Data Contributions

We follow these guidelines in soliciting and accepting contributions of data:

Preparing a contribution of data:

Software Contributions

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.

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 journal.

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.

Preferred formats

All publicly accessible files on PhysioNet must be written in open formats. This allows them to be checked for PHI 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):

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:

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 as well.

Other formats: 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).