The MIMIC-III Waveform Database Matched Subset

This is version 1.0 of the MIMIC-III Waveform Database Matched Subset (August 2017; 22,317 waveform records and 22,247 numerics records matched with 10,282 MIMIC-III Clinical Database records.)

The MIMIC-III database is described in

Johnson AEW, Pollard TJ, Shen L, Lehman L, Feng M, Ghassemi M, Moody B, Szolovits P, Celi LA, and Mark RG. MIMIC-III, a freely accessible critical care database. Scientific Data (2016). DOI:10.1038/sdata.2016.35.

Please cite this publication when referencing this material, and also include the standard citation for PhysioNet:

Goldberger AL, Amaral LAN, Glass L, Hausdorff JM, Ivanov PCh, Mark RG, Mietus JE, Moody GB, Peng C-K, Stanley HE. PhysioBank, PhysioToolkit, and PhysioNet: Components of a New Research Resource for Complex Physiologic Signals. Circulation 101(23):e215-e220 [Circulation Electronic Pages; http://circ.ahajournals.org/cgi/content/full/101/23/e215]; 2000 (June 13).

The MIMIC-III Waveform Database Matched Subset (mimic3wdb/matched) contains all MIMIC-III Waveform Database records that have been associated with MIMIC-III Clinical Database records. The record matching process is ongoing, and more records may be added to the matched subset in the future.

All data associated with a particular patient have been placed into a single subdirectory, named according to the patient's MIMIC-III Subject_ID. These subdirectories are further divided into ten intermediate-level directories (p00 to p09).

The name of each mimic3wdb/matched waveform record is of the form

pXX/pXXNNNN/pXXNNNN-YYYY-MM-DD-hh-mm

where XXNNNN is the matching MIMIC-III Clinical Database Subject_ID, and YYYY, MM, DD, hh, and mm are the surrogate year, month (01-12), and day (01-31), and the real hour (00-23) and minute (00-59), derived from the starting date and time of day of the mimic3wdb/matched record. The surrogate dates match those of the corresponding MIMIC-III Clinical Database records.

In most cases, the waveform record is paired with a numerics record (see the description of numerics records on the MIMIC-III Waveform Database home page). The numerics record names are of the form

pXX/pXXNNNN/pXXNNNN-YYYY-MM-DD-hh-mmn

i.e., identical to the name of the associated waveform record except for the appended n.

Frequently there are multiple waveform and numerics record pairs associated with a given clinical record; all of them will appear in the same subdirectory in such a case, and their names will indicate their chronologic sequence. For example, MIMIC-III Clinical Database record p000079 has been matched with two waveform and numerics record pairs, named

p000079-2175-09-26-01-25    p000079-2175-09-26-01-25n
p000079-2175-09-26-12-28    p000079-2175-09-26-12-28n

Each mimic3wdb/matched record is also an undated mimic3wdb record (i.e., it also belongs to the full MIMIC-III Waveform Database). Only the surrogate-dated mimic3wdb/matched header (.hea) files are unique to the MIMIC-III Waveform Database Matched Subset; the others, with names of the form 3*.hea and 3*.dat, are copies of the like-named files in the full database. (Actually, they are symbolic links to the original files, a distinction that matters only when copying them using rsync, which can be used to download them quickly if the undated records have been downloaded previously.)

See the MIMIC-III Waveform Database home page for additional information about these records.

See the releaseinfo page for information about the releases of the MIMIC-III waveform database and its matched subset.

Downloading the Matched Subset

Most users will not need to download the entire MIMIC-III Waveform Database Matched Subset. For those who think they do, please see Can I download an entire PhysioBank database in one step? in the PhysioNet FAQ.

If you have already downloaded parts 0 through 9 of the MIMIC-III Waveform Database, version 3, and your OS supports symbolic links, use this command (as in the FAQ) to download the Matched Subset:

rsync -Cavz physionet.org::mimic3wdb-matched /usr/database/mimic3wdb/matched

The command above will require only a few minutes in most cases, since nearly all of the files in the Matched Subset are shared with files in parts 0 through 9 that have been downloaded already.

If, however, you wish to download the Matched Subset without having previously downloaded the entire MIMIC-III Waveform Database, or if your OS does not support symbolic links, use these commands instead:

mkdir -p /usr/database/mimic3wdb/matched
rsync -CaLvz physionet.org::mimic3wdb-matched /usr/database/mimic3wdb/matched

This command will download about 2.4 TB, and will require at least a few hours; if you do not have a high-speed network connection it may require a day or more.

Icon  Name                            Last modified      Size  Description
[PARENTDIR] Parent Directory - [DIR] p00/ 2017-07-01 08:00 - [DIR] p01/ 2017-07-01 08:00 - [DIR] p02/ 2017-07-01 08:00 - [DIR] p03/ 2017-07-01 08:00 - [DIR] p04/ 2017-07-01 08:00 - [DIR] p05/ 2017-07-01 08:00 - [DIR] p06/ 2017-07-01 08:00 - [DIR] p07/ 2017-07-01 08:00 - [DIR] p08/ 2017-07-01 08:00 - [DIR] p09/ 2017-07-01 08:00 - [   ] RECORDS 2017-08-04 18:01 131K list of record names [   ] RECORDS-numerics 2017-08-04 18:08 826K list of record names [   ] RECORDS-waveforms 2017-08-04 18:08 806K list of record names [   ] DOI 2017-08-07 18:16 20

Questions and Comments

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Updated Friday, 28 October 2016 at 16:58 EDT

PhysioNet is supported by the National Institute of General Medical Sciences (NIGMS) and the National Institute of Biomedical Imaging and Bioengineering (NIBIB) under NIH grant number 2R01GM104987-09.