The MIMIC-III Waveform Database Matched Subset

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.

You may also download subsections of the matched subset if 2.4 TB is too much to download at once. For example:

mkdir -p /usr/database/mimic3wdb/matched/p00
rsync -CaLvz physionet.org::mimic3wdb-matched/p00 /usr/database/mimic3wdb/matched/p00

 Name                            Last modified      Size  Description
 Parent Directory                                     -   
 DOI                             2017-08-07 18:16   20   
 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
 p00/                            2017-07-01 08:00    -   
 p01/                            2017-07-01 08:00    -   
 p02/                            2017-07-01 08:00    -   
 p03/                            2017-07-01 08:00    -   
 p04/                            2017-07-01 08:00    -   
 p05/                            2017-07-01 08:00    -   
 p06/                            2017-07-01 08:00    -   
 p07/                            2017-07-01 08:00    -   
 p08/                            2017-07-01 08:00    -   
 p09/                            2017-07-01 08:00    -