Database Open Access

MIMIC-III Waveform Database Matched Subset

Benjamin Moody George Moody Mauricio Villarroel Gari D. 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. D., & 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

Discovery

DOI (version 1.0):
https://doi.org/10.13026/c2294b

DOI (latest version):
https://doi.org/10.13026/v217-zr73

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>/p07
Name Size Modified
Parent Directory
p070016
p070026
p070048
p070077
p070080
p070097
p070099
p070100
p070104
p070115
p070119
p070123
p070131
p070142
p070148
p070150
p070178
p070180
p070184
p070188
p070210
p070212
p070223
p070226
p070251
p070252
p070254
p070261
p070267
p070273
p070313
p070319
p070329
p070330
p070339
p070355
p070359
p070363
p070368
p070380
p070386
p070393
p070396
p070415
p070420
p070425
p070427
p070447
p070451
p070463
p070469
p070485
p070491
p070494
p070496
p070499
p070500
p070505
p070508
p070514
p070516
p070520
p070534
p070543
p070547
p070563
p070570
p070572
p070576
p070592
p070605
p070609
p070617
p070628
p070651
p070667
p070694
p070698
p070705
p070714
p070715
p070717
p070723
p070740
p070745
p070755
p070763
p070764
p070784
p070786
p070794
p070795
p070807
p070822
p070838
p070842
p070845
p070854
p070864
p070871
p070884
p070886
p070906
p070922
p070929
p070933
p070950
p070957
p070971
p070974
p070989
p071006
p071011
p071013
p071025
p071059
p071070
p071072
p071079
p071089
p071091
p071108
p071117
p071119
p071142
p071164
p071169
p071184
p071190
p071191
p071193
p071194
p071206
p071213
p071219
p071230
p071243
p071244
p071260
p071262
p071277
p071283
p071287
p071296
p071298
p071304
p071307
p071311
p071328
p071336
p071347
p071353
p071365
p071375
p071405
p071413
p071414
p071420
p071458
p071461
p071473
p071477
p071479
p071491
p071496
p071500
p071501
p071513
p071514
p071527
p071531
p071532
p071533
p071534
p071545
p071582
p071583
p071586
p071596
p071616
p071638
p071645
p071652
p071660
p071683
p071702
p071707
p071709
p071717
p071722
p071735
p071739
p071764
p071774
p071793
p071808
p071848
p071857
p071862
p071869
p071871
p071872
p071880
p071924
p071929
p071940
p071942
p071951
p071952
p071962
p071986
p071988
p072000
p072017
p072031
p072032
p072040
p072043
p072048
p072073
p072083
p072091
p072095
p072097
p072107
p072113
p072143
p072146
p072151
p072160
p072170
p072172
p072189
p072196
p072197
p072203
p072209
p072231
p072233
p072236
p072248
p072269
p072270
p072273
p072280
p072282
p072287
p072300
p072308
p072314
p072317
p072323
p072327
p072328
p072350
p072353
p072358
p072377
p072402
p072407
p072408
p072416
p072424
p072426
p072439
p072455
p072459
p072467
p072482
p072522
p072530
p072541
p072545
p072554
p072555
p072562
p072571
p072584
p072592
p072623
p072627
p072634
p072639
p072644
p072647
p072666
p072667
p072671
p072678
p072723
p072739
p072753
p072763
p072766
p072778
p072779
p072790
p072797
p072819
p072823
p072836
p072847
p072849
p072883
p072885
p072891
p072908
p072914
p072924
p072930
p072931
p072941
p072978
p072992
p072998
p072999
p073011
p073015
p073020
p073048
p073055
p073059
p073063
p073068
p073076
p073087
p073090
p073110
p073118
p073124
p073126
p073129
p073131
p073134
p073135
p073143
p073156
p073175
p073190
p073200
p073224
p073231
p073241
p073242
p073243
p073249
p073265
p073280
p073299
p073302
p073320
p073322
p073371
p073376
p073384
p073397
p073398
p073409
p073429
p073443
p073454
p073457
p073460
p073465
p073471
p073473
p073477
p073479
p073499
p073504
p073521
p073530
p073537
p073540
p073546
p073557
p073582
p073595
p073608
p073611
p073614
p073615
p073645
p073648
p073661
p073673
p073682
p073683
p073684
p073686
p073693
p073702
p073713
p073722
p073749
p073755
p073756
p073760
p073767
p073770
p073798
p073807
p073811
p073816
p073833
p073843
p073867
p073868
p073874
p073884
p073893
p073896
p073902
p073946
p073953
p073955
p073971
p073979
p074001
p074032
p074039
p074046
p074160
p074188
p074211
p074215
p074220
p074223
p074229
p074230
p074232
p074252
p074258
p074260
p074284
p074289
p074319
p074332
p074346
p074354
p074364
p074379
p074386
p074397
p074404
p074408
p074410
p074418
p074419
p074421
p074426
p074438
p074441
p074443
p074445
p074454
p074463
p074482
p074486
p074493
p074496
p074503
p074514
p074533
p074535
p074546
p074578
p074584
p074610
p074618
p074626
p074630
p074639
p074640
p074677
p074683
p074687
p074693
p074696
p074701
p074702
p074709
p074711
p074727
p074733
p074755
p074763
p074765
p074771
p074779
p074795
p074798
p074805
p074816
p074820
p074835
p074851
p074852
p074856
p074860
p074866
p074880
p074888
p074889
p074894
p074899
p074913
p074924
p074937
p074955
p074964
p074967
p074976
p074982
p075001
p075013
p075014
p075023
p075027
p075029
p075034
p075046
p075051
p075061
p075071
p075073
p075083
p075086
p075100
p075107
p075114
p075138
p075142
p075155
p075160
p075170
p075200
p075206
p075223
p075241
p075244
p075249
p075261
p075300
p075305
p075320
p075326
p075333
p075347
p075350
p075354
p075355
p075360
p075369
p075371
p075403
p075425
p075428
p075476
p075488
p075492
p075500
p075509
p075510
p075514
p075525
p075536
p075557
p075561
p075575
p075576
p075581
p075582
p075607
p075618
p075626
p075627
p075631
p075638
p075644
p075655
p075658
p075666
p075668
p075670
p075696
p075733
p075741
p075759
p075764
p075771
p075772
p075775
p075779
p075793
p075795
p075796
p075800
p075826
p075830
p075838
p075851
p075856
p075865
p075870
p075883
p075886
p075894
p075899
p075906
p075919
p075928
p075929
p075930
p075941
p075946
p075960
p075966
p075972
p075986
p075998
p076001
p076007
p076008
p076012
p076028
p076034
p076051
p076058
p076066
p076074
p076084
p076090
p076096
p076109
p076116
p076120
p076134
p076143
p076151
p076154
p076165
p076173
p076178
p076186
p076191
p076193
p076196
p076237
p076249
p076251
p076253
p076257
p076261
p076265
p076282
p076318
p076319
p076327
p076332
p076333
p076361
p076372
p076390
p076392
p076397
p076410
p076418
p076430
p076435
p076450
p076457
p076459
p076476
p076477
p076480
p076494
p076514
p076520
p076536
p076544
p076547
p076557
p076558
p076561
p076562
p076568
p076578
p076580
p076589
p076594
p076602
p076637
p076639
p076646
p076659
p076667
p076670
p076675
p076676
p076698
p076709
p076711
p076717
p076726
p076761
p076771
p076780
p076797
p076800
p076801
p076802
p076803
p076811
p076812
p076820
p076841
p076844
p076857
p076875
p076876
p076880
p076886
p076896
p076899
p076915
p076925
p076930
p076945
p076955
p076957
p076968
p076974
p076988
p076990
p077000
p077010
p077011
p077014
p077037
p077053
p077070
p077094
p077115
p077129
p077131
p077135
p077177
p077188
p077203
p077205
p077206
p077213
p077220
p077221
p077223
p077227
p077242
p077245
p077259
p077276
p077280
p077301
p077310
p077312
p077325
p077330
p077341
p077360
p077380
p077383
p077413
p077452
p077478
p077484
p077487
p077488
p077500
p077520
p077524
p077526
p077532
p077537
p077543
p077553
p077561
p077578
p077595
p077617
p077618
p077623
p077660
p077664
p077665
p077673
p077676
p077686
p077689
p077691
p077697
p077702
p077718
p077729
p077730
p077733
p077771
p077772
p077787
p077794
p077804
p077805
p077807
p077815
p077826
p077834
p077836
p077842
p077847
p077850
p077873
p077875
p077882
p077927
p077947
p077949
p077951
p077957
p077960
p077975
p077988
p077992
p078005
p078007
p078009
p078010
p078023
p078050
p078076
p078100
p078101
p078117
p078143
p078145
p078152
p078155
p078158
p078168
p078171
p078182
p078195
p078213
p078214
p078216
p078221
p078226
p078234
p078238
p078251
p078292
p078293
p078306
p078308
p078318
p078325
p078336
p078342
p078346
p078356
p078357
p078366
p078368
p078375
p078410
p078411
p078416
p078419
p078424
p078431
p078441
p078459
p078463
p078473
p078474
p078476
p078481
p078487
p078504
p078505
p078506
p078515
p078517
p078530
p078536
p078556
p078557
p078559
p078565
p078597
p078615
p078641
p078666
p078672
p078678
p078685
p078686
p078691
p078693
p078716
p078729
p078779
p078782
p078822
p078839
p078840
p078855
p078876
p078879
p078891
p078892
p078910
p078911
p078934
p078939
p078948
p078956
p078959
p078966
p078979
p078988
p079006
p079016
p079032
p079038
p079050
p079051
p079060
p079075
p079081
p079084
p079089
p079090
p079096
p079126
p079137
p079154
p079163
p079168
p079183
p079184
p079188
p079210
p079224
p079228
p079249
p079283
p079285
p079288
p079294
p079297
p079306
p079308
p079310
p079330
p079352
p079355
p079358
p079365
p079372
p079392
p079396
p079413
p079414
p079422
p079423
p079425
p079426
p079427
p079437
p079450
p079452
p079480
p079523
p079532
p079538
p079539
p079551
p079556
p079574
p079575
p079576
p079584
p079589
p079602
p079617
p079619
p079626
p079645
p079649
p079655
p079664
p079671
p079673
p079678
p079694
p079709
p079735
p079746
p079754
p079762
p079768
p079792
p079795
p079808
p079814
p079838
p079846
p079851
p079875
p079876
p079880
p079894
p079900
p079922
p079923
p079929
p079931
p079962
p079976
p079998