Database Open Access

MIMIC-III Waveform Database Matched Subset

Benjamin Moody George Moody Mauricio Villarroel Gari Clifford Ikaro Silva

Published: April 7, 2020. Version: 1.0


When using this resource, please cite: (show more options)
Moody, B., Moody, G., Villarroel, M., Clifford, G., & Silva, I. (2020). MIMIC-III Waveform Database Matched Subset (version 1.0). PhysioNet. https://doi.org/10.13026/c2294b.

Additionally, please cite the original publication:

Johnson, A. E. W., Pollard, T. J., Shen, L., Lehman, L. H., Feng, M., Ghassemi, M., Moody, B., Szolovits, P., Celi, L. A., & Mark, R. G. (2016). MIMIC-III, a freely accessible critical care database. Scientific Data, 3, 160035.

Please include the standard citation for PhysioNet: (show more options)
Goldberger, A., Amaral, L., Glass, L., Hausdorff, J., Ivanov, P. C., Mark, R., ... & Stanley, H. E. (2000). PhysioBank, PhysioToolkit, and PhysioNet: Components of a new research resource for complex physiologic signals. Circulation [Online]. 101 (23), pp. e215–e220.

Abstract

The MIMIC-III Waveform Database Matched Subset contains 22,317 waveform records, and 22,247 numerics records, for 10,282 distinct ICU patients. These recordings typically include digitized signals such as ECG, ABP, respiration, and PPG, as well as periodic measurements such as heart rate, oxygen saturation, and systolic, mean, and diastolic blood pressure.

This database is a subset of the MIMIC-III Waveform Database, representing those records for which the patient has been identified, and their corresponding clinical records are available in the MIMIC-III Clinical Database.


Background

The MIMIC-III Waveform Database contains thousands of recordings of multiple physiologic signals (“waveforms”) and time series of vital signs (“numerics”) collected from bedside patient monitors in adult and neonatal intensive care units (ICUs).

An ICU bedside monitor collects a great deal of data, from which it is possible to infer something about a patient’s physiological state. However, in order to understand how these waveforms are influenced by disease state and treatment, and the extent to which phenomena observed in the waveform can serve as indicators of disease, it is necessary to look at the broader context: patient demographics, diagnoses, medications, lab tests, and other information that is recorded by caregivers in the electronic medical record.

Collecting this broad clinical context is the task of the MIMIC-III Clinical Database, which was created in parallel with the Waveform Database and contains information about many of the same patients. The Matched Subset consists of all of the waveform and numerics recordings for which the corresponding clinical record is also available.


Methods

The bedside monitors used for collecting this database were not directly linked to the hospital medical record system. The monitor could be configured to display the patient’s name and medical record number, for ease of identifying patients at the central station, but this was not automatically updated when a patient was admitted or transferred to the ICU. This information was only available when the ICU staff entered it manually into the monitoring system, and since entering this information was not critical to patient care, it was frequently omitted or incomplete. Furthermore, limitations of the data archiving software made it possible to identify the care unit from which a recording originated, but not the precise room or bed number.

As a result, only a subset of the waveform recordings actually contained enough information to reliably identify the patient, and of those, not all overlapped with the time period represented by the MIMIC-III Clinical Database [1]. Using all of the available information, through a process of mostly automated matching with some manual corrections, a total of 22,317 waveform records (34%) and 22,247 numerics records (35%) were found that could be linked to a corresponding patient in the Clinical Database.

For each of those records, a new WFDB header file was created, incorporating the subject ID as well as the surrogate date and time of the recording. Note that the raw signal files (such as 3314767_0004.dat and 3314767n.dat) and segment header files (such as 3314767_0004.hea) are identical to those in the original numbered records.

The project was approved by the Institutional Review Boards of Beth Israel Deaconess Medical Center (Boston, MA) and the Massachusetts Institute of Technology (Cambridge, MA). Requirement for individual patient consent was waived because the project did not impact clinical care and all protected health information was deidentified.


Data Description

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 (matched/p00 to matched/p09).

The name of each matched waveform record is of the form matched/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 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, which has the same name as the associated waveform record, with an n added to the end.

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 and p000079-2175-09-26-01-25n
  • p000079-2175-09-26-12-28 and 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 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.


Usage Notes

The following example illustrates the organization of the database:

  • Intermediate directory p04 contains all records with names that begin with p04 (patients with a subject_id between 40000 and 49999.)
  • All files associated with patient 44083 are contained within the directory p04/p044083. This directory contains two waveform records (p044083-2112-05-04-19-50 and p044083-2112-05-23-12-22) and two corresponding numerics records (p044083-2112-05-04-19-50n and p044083-2112-05-23-12-22n), recorded from two separate ICU stays.
  • The master waveform header file for the first stay (p044083-2112-05-04-19-50.hea) indicates that the record is 20342033 sample intervals (about 45 hours) in length, and begins at 19:50 on May 4, 2112. This date, as with all dates in MIMIC-III, has been anonymized by shifting it by a random number of days into the future. See header(5) in the WFDB Applications Guide for more information about the format of this file.
  • This waveform record consists of 41 segments (3314767_0001 through to 3314767_0041), as indicated by the master header file. The layout header file (3314767_layout.hea) indicates that four ECG signals (II, AVR, V, and MCL) were recorded, along with a respiration signal, photoplethysmogram, and arterial blood pressure. Not all of these signals are available simultaneously.
  • The header file for segment number 4 (3314767_0004.hea) shows us that during this segment, five signals are available: three ECG leads (II, V, and AVR), a respiration signal (RESP), and a PPG signal (PLETH).
  • The numerics header file (p044083-2112-05-04-19-50n.hea) shows us that a variety of measurements were recorded, including heart rate, invasive and non-invasive blood pressure, respiratory rate, ST segment elevation, oxygen saturation, and cardiac rhythm statistics. Just as with waveforms, not all of these measurements are available at all times.

Referring to the MIMIC-III Clinical Database Demo, we can see from the PATIENTS table that this patient was male, and his anonymized date of birth was November 15, 2057 (making him 54 years old at the time of this ICU stay):

subject_id gender dob dod
44083 M 2057-11-15 00:00:00 2114-02-20 00:00:00

The ICUSTAYS table shows us that he was admitted once to the SICU and twice to the CCU:

subject_id hadm_id icustay_id first_careunit intime outtime
44083 125157 265615 SICU 2112-05-04 19:03:39 2112-05-06 17:21:01
44083 131048 282640 CCU 2112-05-23 12:32:06 2112-05-25 14:59:50
44083 198330 286428 CCU 2112-05-29 02:01:33 2112-06-01 16:50:40

The first of these admissions corresponds to the waveform record above, as indicated by the date (2112-05-04). Note that the starting and ending date and time of the waveform record will not always match the precise admission or discharge time.

The hadm_id (125157) and icustay_id (265615) are linked to other tables in MIMIC-III that provide further information about this particular ICU stay, such as vital signs, laboratory tests, medications, and diagnoses.


Release Notes

This database is a subset of version 1.0 of the MIMIC-III Waveform Database. It also represents a superset of the records in the previously-released MIMIC-II Waveform Database Matched Subset. However, it uses a different directory structure (see Data Description above), as well as different subject IDs and surrogate dates. This version corresponds to version 1.4 of the MIMIC-III Clinical Database.


Acknowledgements

We wish to thank Philips Healthcare, as well as the Beth Israel Deaconess Medical Center, for their invaluable support in making this project possible.

Many people have contributed to this project over the past 18 years, and it would be impossible to list them all. In particular, we would like to acknowledge Michael Craig, Tin Kyaw, and Mohammed Saeed, for their efforts in collecting and organizing the original MIMIC-II Waveform Database, upon which this database is based.


Conflicts of Interest

The authors have no conflicts of interests to declare.


References

  1. Johnson, A. E. W., Pollard, T. J., Shen, L., Lehman, L. H., Feng, M., Ghassemi, M., Moody, B., Szolovits, P., Celi, L. A., & Mark, R. G. (2016). MIMIC-III, a freely accessible critical care database. Scientific Data, 3, 160035. https://dx.doi.org/10.1038/sdata.2016.35

Parent Projects
MIMIC-III Waveform Database Matched Subset was derived from: Please cite them when using this project.
Share
Access

Access Policy:
Anyone can access the files, as long as they conform to the terms of the specified license.

License (for files):
Open Data Commons Open Database License v1.0

Corresponding Author
You must be logged in to view the contact information.

Files

Total uncompressed size: 2.4 TB.

Access the files

Visualize waveforms

Folder Navigation: <base>/p09
Name Size Modified
Parent Directory
p090012
p090020
p090021
p090026
p090032
p090033
p090036
p090057
p090061
p090067
p090075
p090115
p090121
p090122
p090142
p090143
p090151
p090158
p090165
p090173
p090195
p090198
p090208
p090211
p090228
p090238
p090256
p090269
p090273
p090289
p090296
p090302
p090304
p090310
p090317
p090350
p090353
p090354
p090362
p090373
p090389
p090392
p090396
p090398
p090403
p090406
p090410
p090418
p090427
p090436
p090447
p090449
p090460
p090466
p090474
p090478
p090479
p090483
p090484
p090493
p090495
p090522
p090533
p090539
p090541
p090544
p090546
p090549
p090560
p090566
p090605
p090607
p090628
p090629
p090648
p090649
p090658
p090663
p090676
p090677
p090680
p090690
p090696
p090697
p090700
p090729
p090768
p090789
p090795
p090800
p090801
p090805
p090814
p090834
p090843
p090846
p090848
p090878
p090881
p090886
p090889
p090891
p090902
p090903
p090910
p090917
p090929
p090942
p090944
p090954
p090959
p090962
p090972
p090990
p090992
p091001
p091002
p091004
p091018
p091024
p091031
p091038
p091047
p091097
p091102
p091103
p091123
p091136
p091143
p091149
p091151
p091158
p091167
p091169
p091181
p091199
p091200
p091210
p091221
p091234
p091239
p091242
p091245
p091258
p091261
p091263
p091284
p091295
p091299
p091309
p091332
p091350
p091365
p091368
p091383
p091384
p091426
p091428
p091437
p091459
p091462
p091463
p091469
p091470
p091484
p091511
p091531
p091549
p091550
p091558
p091561
p091579
p091580
p091581
p091583
p091591
p091599
p091603
p091614
p091616
p091625
p091633
p091635
p091669
p091672
p091680
p091682
p091685
p091694
p091703
p091705
p091712
p091726
p091765
p091768
p091769
p091790
p091798
p091802
p091814
p091824
p091827
p091831
p091838
p091840
p091841
p091853
p091855
p091858
p091872
p091881
p091887
p091904
p091907
p091915
p091925
p091926
p091939
p091946
p091950
p091960
p091975
p091978
p091989
p092001
p092036
p092052
p092055
p092057
p092063
p092066
p092095
p092098
p092105
p092107
p092117
p092135
p092136
p092137
p092158
p092166
p092175
p092195
p092201
p092203
p092212
p092235
p092239
p092244
p092247
p092252
p092273
p092277
p092278
p092283
p092287
p092289
p092292
p092312
p092317
p092323
p092324
p092326
p092331
p092336
p092340
p092346
p092373
p092381
p092387
p092397
p092405
p092410
p092415
p092420
p092425
p092426
p092455
p092464
p092475
p092487
p092518
p092525
p092543
p092578
p092579
p092585
p092613
p092616
p092629
p092631
p092648
p092649
p092650
p092651
p092668
p092685
p092686
p092698
p092700
p092703
p092757
p092764
p092767
p092777
p092787
p092796
p092801
p092816
p092820
p092839
p092843
p092846
p092855
p092864
p092866
p092873
p092886
p092895
p092903
p092907
p092916
p092950
p092961
p092969
p092974
p092982
p092994
p092995
p092999
p093011
p093016
p093025
p093026
p093031
p093033
p093039
p093054
p093055
p093056
p093062
p093077
p093078
p093088
p093098
p093117
p093123
p093142
p093155
p093159
p093206
p093208
p093209
p093229
p093272
p093279
p093299
p093301
p093324
p093336
p093360
p093378
p093379
p093387
p093388
p093390
p093392
p093408
p093411
p093422
p093431
p093432
p093435
p093458
p093459
p093462
p093467
p093472
p093479
p093486
p093500
p093501
p093504
p093505
p093506
p093517
p093518
p093525
p093528
p093535
p093541
p093550
p093557
p093560
p093562
p093564
p093566
p093567
p093578
p093581
p093587
p093596
p093602
p093610
p093616
p093623
p093633
p093634
p093636
p093637
p093638
p093640
p093648
p093653
p093662
p093663
p093667
p093671
p093679
p093704
p093705
p093717
p093718
p093721
p093722
p093742
p093745
p093755
p093774
p093780
p093784
p093788
p093804
p093814
p093829
p093833
p093836
p093840
p093847
p093850
p093853
p093870
p093874
p093898
p093900
p093905
p093923
p093950
p093966
p093975
p093982
p093991
p094007
p094009
p094016
p094021
p094023
p094024
p094029
p094046
p094064
p094072
p094079
p094084
p094085
p094091
p094103
p094105
p094113
p094117
p094147
p094150
p094162
p094164
p094184
p094195
p094216
p094220
p094234
p094241
p094252
p094255
p094256
p094290
p094297
p094300
p094301
p094312
p094316
p094329
p094351
p094361
p094378
p094385
p094401
p094407
p094415
p094422
p094447
p094448
p094483
p094484
p094491
p094503
p094525
p094529
p094538
p094539
p094541
p094550
p094575
p094581
p094597
p094603
p094611
p094618
p094636
p094642
p094645
p094669
p094673
p094689
p094696
p094719
p094726
p094753
p094756
p094757
p094765
p094768
p094785
p094794
p094811
p094820
p094821
p094828
p094837
p094838
p094840
p094847
p094853
p094869
p094886
p094896
p094897
p094924
p094937
p094959
p094961
p094977
p094982
p094987
p094991
p094993
p094997
p095011
p095022
p095030
p095038
p095039
p095071
p095076
p095088
p095090
p095107
p095115
p095118
p095122
p095129
p095136
p095155
p095157
p095182
p095200
p095201
p095220
p095225
p095235
p095237
p095238
p095239
p095240
p095247
p095251
p095280
p095282
p095288
p095294
p095312
p095313
p095316
p095335
p095343
p095344
p095354
p095372
p095373
p095377
p095380
p095384
p095396
p095404
p095408
p095413
p095420
p095423
p095424
p095426
p095427
p095435
p095460
p095474
p095504
p095512
p095516
p095517
p095530
p095536
p095542
p095561
p095582
p095603
p095609
p095614
p095631
p095632
p095638
p095641
p095646
p095658
p095673
p095674
p095676
p095688
p095708
p095735
p095750
p095754
p095765
p095770
p095771
p095776
p095782
p095806
p095816
p095819
p095821
p095830
p095839
p095849
p095854
p095864
p095868
p095878
p095892
p095893
p095909
p095919
p095931
p095948
p095951
p095957
p095958
p095977
p095997
p096006
p096008
p096015
p096016
p096029
p096049
p096057
p096060
p096066
p096100
p096111
p096120
p096137
p096145
p096147
p096148
p096149
p096171
p096177
p096218
p096225
p096226
p096234
p096240
p096247
p096249
p096250
p096254
p096259
p096260
p096261
p096264
p096284
p096305
p096321
p096324
p096333
p096336
p096338
p096344
p096350
p096361
p096365
p096373
p096394
p096402
p096404
p096430
p096442
p096445
p096479
p096482
p096515
p096520
p096527
p096530
p096537
p096564
p096567
p096574
p096577
p096581
p096582
p096592
p096594
p096631
p096637
p096639
p096643
p096674
p096686
p096697
p096703
p096728
p096729
p096731
p096732
p096734
p096741
p096746
p096747
p096750
p096759
p096760
p096767
p096772
p096785
p096791
p096803
p096814
p096817
p096821
p096825
p096833
p096842
p096843
p096865
p096879
p096901
p096908
p096920
p096922
p096924
p096928
p096930
p096937
p096945
p096950
p096965
p096971
p096975
p096977
p096984
p097008
p097013
p097018
p097019
p097028
p097032
p097038
p097046
p097048
p097060
p097061
p097070
p097089
p097091
p097151
p097156
p097158
p097164
p097178
p097232
p097237
p097239
p097243
p097264
p097267
p097273
p097276
p097291
p097301
p097307
p097308
p097310
p097314
p097321
p097322
p097333
p097339
p097380
p097382
p097395
p097417
p097422
p097441
p097448
p097467
p097476
p097488
p097505
p097525
p097529
p097543
p097545
p097547
p097565
p097567
p097577
p097581
p097589
p097591
p097592
p097594
p097599
p097605
p097659
p097660
p097664
p097666
p097689
p097706
p097733
p097738
p097762
p097772
p097773
p097778
p097782
p097786
p097791
p097799
p097801
p097803
p097813
p097818
p097828
p097830
p097834
p097850
p097876
p097877
p097885
p097893
p097902
p097907
p097916
p097917
p097920
p097924
p097932
p097959
p097974
p097976
p097984
p098003
p098006
p098015
p098016
p098039
p098046
p098070
p098118
p098130
p098159
p098169
p098174
p098177
p098182
p098185
p098187
p098204
p098206
p098220
p098226
p098227
p098242
p098249
p098253
p098254
p098256
p098263
p098266
p098276
p098280
p098295
p098336
p098344
p098347
p098382
p098385
p098390
p098400
p098402
p098403
p098434
p098448
p098452
p098481
p098484
p098488
p098494
p098514
p098517
p098525
p098555
p098557
p098562
p098564
p098565
p098577
p098582
p098589
p098593
p098601
p098615
p098620
p098630
p098636
p098640
p098643
p098644
p098647
p098649
p098665
p098669
p098674
p098686
p098698
p098701
p098709
p098717
p098720
p098733
p098759
p098761
p098769
p098794
p098813
p098829
p098878
p098887
p098930
p098932
p098944
p098948
p098957
p098959
p098961
p098973
p098991
p098994
p099004
p099008
p099011
p099017
p099038
p099052
p099064
p099067
p099085
p099088
p099096
p099102
p099110
p099111
p099115
p099118
p099120
p099162
p099166
p099183
p099186
p099216
p099229
p099255
p099256
p099268
p099274
p099283
p099286
p099291
p099358
p099361
p099364
p099366
p099380
p099383
p099389
p099408
p099412
p099417
p099430
p099439
p099448
p099464
p099467
p099499
p099503
p099510
p099527
p099544
p099545
p099556
p099560
p099562
p099564
p099589
p099599
p099611
p099616
p099621
p099645
p099650
p099657
p099659
p099666
p099669
p099674
p099707
p099708
p099714
p099715
p099740
p099747
p099752
p099756
p099759
p099762
p099768
p099776
p099777
p099781
p099783
p099785
p099796
p099797
p099802
p099809
p099830
p099832
p099836
p099863
p099865
p099873
p099880
p099883
p099894
p099897
p099913
p099922
p099946
p099955
p099982
p099983
p099992
p099999