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WFDB / PhysioNet Formats

George B. Moody Harvard-MIT Division of Health Sciences and Technology Cambridge, Massachusetts. WFDB / PhysioNet Formats. What are WFDB and PhysioNet?. WFDB = WaveForm DataBase subroutine (function) library collection of formats directly readable and writable by the WFDB library

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WFDB / PhysioNet Formats

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  1. George B. Moody Harvard-MIT Division of Health Sciences and Technology Cambridge, Massachusetts WFDB / PhysioNet Formats

  2. What are WFDB and PhysioNet? • WFDB = WaveForm DataBase • subroutine (function) library • collection of formats directly readable and writable by the WFDB library • PhysioNet: NIH/NCRR funded research resource • large collections of signals, time series, and related software freely available at http://physionet.org/

  3. What is a Waveform Database? • A collection of records (recordings of signals and annotations), each consisting of: • one (text) header file • any number of (binary) signal files • any number of (binary) annotation files • Not a relational database!

  4. WFDB Storage Formats • Header files: short text files that name and describe signal files belonging to a record • Signal files: binary files containing one or more digitized signals; most fixed-length binary formats are supported • Annotation files: binary files containing labels, each pointing to a specific sample, with attributes describing a feature of the signal at that time

  5. Patient Information • PhysioBank databases are constructed from deidentified data (a requirement for free access) • Clinical databases incorporating WFDB files may include PHI in external files (recommended) or in header files with user-defined PHI fields (not recommended)

  6. Raw Data Storage • Signals may have different sampling frequencies • Signals may have different numbers of bits per sample • Signals in the same record may be stored in different formats (e.g., to optimize for each signal) • Measures taken at non-uniform intervals may be stored as annotations

  7. Event Definition and Storage • New event types may be added without programming • Existing event types may be modified by adding new information (but why?) • Events may be fixed to a channel if appropriate • Events may overlap • Events can link to other events (and to external files by URI)

  8. Measurements of Channels • All “channels” (signals, time series, periodic and non-periodic measurements) are readable as numbers or viewable graphically • WFDB specifies a range of acceptable storage formats, does not dictate presentation

  9. Tabulations of Information • Many WFDB applications extract information from WFDB-compatible files and present it in tabular form • Tables are presentations of raw data; WFDB formats don't specify how data should be presented

  10. WAVE: a WFDB Viewer

  11. Further Information • PhysioNet: http://physionet.org/ • Examples of WFDB records: http://physionet.org/physiobank • Web-based viewer: http://physionet.org/cgi-bin/chart • WFDB library: http://physionet.org/physiotools/wfdb.shtml • and more: george@mit.edu

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