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>/p00
Name Size Modified
Parent Directory
p000020
p000030
p000033
p000052
p000079
p000085
p000107
p000109
p000123
p000124
p000125
p000135
p000138
p000145
p000154
p000160
p000177
p000184
p000188
p000194
p000208
p000214
p000217
p000222
p000262
p000263
p000271
p000279
p000283
p000292
p000298
p000301
p000302
p000308
p000317
p000318
p000328
p000333
p000357
p000369
p000377
p000379
p000402
p000406
p000408
p000409
p000416
p000422
p000427
p000439
p000462
p000470
p000491
p000495
p000507
p000515
p000518
p000521
p000523
p000543
p000549
p000550
p000565
p000571
p000586
p000593
p000600
p000605
p000608
p000618
p000625
p000631
p000634
p000638
p000639
p000650
p000652
p000666
p000668
p000670
p000672
p000682
p000689
p000695
p000700
p000703
p000708
p000710
p000719
p000735
p000736
p000743
p000747
p000749
p000770
p000772
p000773
p000776
p000784
p000787
p000793
p000798
p000801
p000808
p000818
p000822
p000834
p000843
p000849
p000852
p000865
p000870
p000871
p000875
p000878
p000886
p000891
p000894
p000895
p000901
p000906
p000907
p000925
p000946
p000948
p000952
p000963
p000974
p000981
p000992
p001002
p001004
p001006
p001012
p001021
p001028
p001029
p001030
p001033
p001038
p001042
p001044
p001046
p001049
p001072
p001075
p001083
p001092
p001097
p001104
p001121
p001123
p001135
p001143
p001144
p001158
p001160
p001170
p001174
p001182
p001190
p001192
p001200
p001207
p001217
p001222
p001224
p001226
p001241
p001244
p001257
p001279
p001280
p001313
p001331
p001337
p001338
p001347
p001354
p001357
p001378
p001396
p001398
p001408
p001409
p001414
p001418
p001430
p001438
p001449
p001453
p001457
p001459
p001474
p001476
p001485
p001501
p001502
p001521
p001524
p001526
p001528
p001531
p001546
p001551
p001557
p001563
p001569
p001578
p001586
p001604
p001606
p001613
p001650
p001673
p001679
p001693
p001709
p001744
p001747
p001754
p001758
p001761
p001763
p001778
p001785
p001791
p001795
p001802
p001818
p001824
p001840
p001854
p001855
p001861
p001885
p001888
p001892
p001898
p001900
p001908
p001924
p001931
p001932
p001935
p001941
p001944
p001949
p001950
p001973
p001978
p001979
p001986
p001991
p001995
p002014
p002029
p002034
p002045
p002049
p002052
p002063
p002066
p002067
p002075
p002090
p002092
p002100
p002104
p002148
p002154
p002157
p002172
p002185
p002187
p002200
p002211
p002213
p002224
p002228
p002229
p002237
p002240
p002246
p002251
p002261
p002264
p002265
p002274
p002280
p002301
p002305
p002317
p002326
p002332
p002340
p002343
p002361
p002362
p002369
p002374
p002389
p002395
p002397
p002403
p002442
p002458
p002466
p002467
p002477
p002479
p002480
p002488
p002492
p002498
p002502
p002513
p002514
p002530
p002536
p002549
p002561
p002577
p002578
p002586
p002589
p002610
p002611
p002619
p002636
p002639
p002653
p002659
p002664
p002672
p002686
p002700
p002703
p002722
p002725
p002742
p002744
p002747
p002754
p002755
p002773
p002784
p002787
p002791
p002798
p002827
p002830
p002834
p002846
p002858
p002906
p002917
p002919
p002921
p002946
p002968
p002974
p002981
p002990
p002996
p003021
p003024
p003026
p003039
p003052
p003057
p003066
p003084
p003097
p003099
p003129
p003133
p003138
p003158
p003165
p003171
p003174
p003176
p003192
p003214
p003218
p003221
p003242
p003245
p003250
p003261
p003266
p003267
p003272
p003278
p003279
p003286
p003287
p003290
p003301
p003302
p003321
p003330
p003340
p003345
p003351
p003358
p003360
p003365
p003372
p003386
p003404
p003424
p003441
p003462
p003473
p003474
p003490
p003491
p003495
p003498
p003506
p003512
p003513
p003515
p003516
p003521
p003530
p003533
p003543
p003552
p003554
p003555
p003566
p003570
p003571
p003586
p003593
p003606
p003612
p003617
p003619
p003622
p003623
p003633
p003635
p003640
p003642
p003652
p003654
p003673
p003674
p003675
p003680
p003695
p003744
p003745
p003746
p003748
p003759
p003764
p003768
p003780
p003792
p003794
p003798
p003821
p003830
p003853
p003860
p003863
p003866
p003883
p003884
p003886
p003889
p003914
p003917
p003920
p003929
p003932
p003935
p003939
p003949
p003952
p003957
p003977
p003986
p003987
p003992
p003995
p004018
p004041
p004053
p004059
p004064
p004068
p004076
p004077
p004109
p004113
p004115
p004136
p004142
p004175
p004180
p004188
p004194
p004248
p004249
p004252
p004254
p004261
p004266
p004270
p004286
p004290
p004292
p004308
p004313
p004317
p004324
p004329
p004331
p004338
p004346
p004347
p004348
p004350
p004351
p004356
p004369
p004393
p004401
p004404
p004405
p004406
p004409
p004413
p004420
p004431
p004436
p004439
p004448
p004451
p004457
p004462
p004465
p004474
p004477
p004481
p004490
p004520
p004533
p004538
p004565
p004566
p004568
p004587
p004588
p004593
p004599
p004618
p004630
p004632
p004633
p004641
p004655
p004656
p004664
p004679
p004685
p004688
p004713
p004738
p004742
p004770
p004771
p004778
p004784
p004786
p004787
p004788
p004800
p004802
p004804
p004805
p004807
p004808
p004829
p004833
p004837
p004847
p004852
p004853
p004859
p004860
p004862
p004865
p004870
p004893
p004894
p004900
p004903
p004904
p004906
p004909
p004915
p004923
p004935
p004944
p004951
p004955
p004958
p004966
p004968
p004974
p004987
p005023
p005030
p005037
p005056
p005058
p005062
p005071
p005078
p005080
p005107
p005114
p005124
p005126
p005163
p005171
p005175
p005193
p005195
p005196
p005199
p005201
p005205
p005223
p005237
p005239
p005254
p005259
p005272
p005274
p005277
p005282
p005289
p005292
p005307
p005321
p005336
p005343
p005345
p005348
p005349
p005354
p005362
p005369
p005382
p005400
p005407
p005417
p005442
p005451
p005453
p005459
p005476
p005478
p005485
p005493
p005494
p005496
p005506
p005521
p005525
p005548
p005549
p005569
p005574
p005591
p005604
p005606
p005607
p005609
p005612
p005618
p005619
p005620
p005637
p005642
p005645
p005646
p005672
p005675
p005683
p005685
p005686
p005696
p005701
p005709
p005710
p005712
p005714
p005719
p005722
p005727
p005738
p005742
p005748
p005766
p005772
p005784
p005786
p005791
p005808
p005818
p005821
p005830
p005832
p005841
p005847
p005850
p005871
p005875
p005879
p005885
p005896
p005901
p005908
p005909
p005911
p005913
p005933
p005937
p005957
p005960
p005995
p006000
p006010
p006017
p006028
p006039
p006042
p006052
p006053
p006063
p006064
p006069
p006070
p006075
p006078
p006085
p006089
p006090
p006116
p006131
p006132
p006145
p006158
p006174
p006178
p006179
p006180
p006194
p006195
p006202
p006204
p006206
p006214
p006229
p006233
p006254
p006256
p006262
p006279
p006288
p006294
p006299
p006309
p006314
p006317
p006321
p006323
p006335
p006338
p006358
p006359
p006365
p006374
p006378
p006381
p006382
p006398
p006407
p006411
p006428
p006437
p006440
p006449
p006455
p006464
p006470
p006475
p006478
p006485
p006497
p006519
p006522
p006533
p006534
p006535
p006539
p006553
p006555
p006557
p006561
p006566
p006581
p006583
p006598
p006601
p006602
p006604
p006605
p006607
p006621
p006636
p006637
p006649
p006652
p006659
p006667
p006669
p006673
p006687
p006688
p006691
p006692
p006702
p006708
p006718
p006728
p006729
p006749
p006800
p006804
p006809
p006839
p006841
p006850
p006868
p006875
p006876
p006889
p006892
p006901
p006914
p006917
p006933
p006939
p006940
p006944
p006945
p006953
p006958
p006967
p006981
p006983
p006988
p007009
p007023
p007048
p007051
p007084
p007095
p007102
p007105
p007107
p007115
p007125
p007136
p007138
p007149
p007153
p007160
p007172
p007175
p007183
p007184
p007192
p007212
p007213
p007217
p007224
p007225
p007232
p007234
p007241
p007251
p007253
p007262
p007263
p007265
p007289
p007299
p007303
p007320
p007328
p007339
p007347
p007360
p007365
p007371
p007381
p007389
p007397
p007400
p007410
p007415
p007422
p007427
p007432
p007438
p007442
p007445
p007448
p007452
p007468
p007470
p007472
p007477
p007478
p007479
p007482
p007487
p007490
p007492
p007497
p007512
p007517
p007519
p007521
p007522
p007528
p007529
p007532
p007533
p007542
p007567
p007585
p007612
p007614
p007618
p007629
p007632
p007644
p007650
p007651
p007654
p007655
p007666
p007681
p007683
p007685
p007688
p007695
p007704
p007705
p007720
p007728
p007755
p007758
p007760
p007782
p007784
p007786
p007798
p007799
p007809
p007819
p007825
p007842
p007849
p007860
p007866
p007874
p007881
p007886
p007894
p007897
p007908
p007910
p007944
p007960
p007965
p007966
p007968
p007969
p007977
p007979
p007981
p007985
p007996
p008009
p008013
p008040
p008057
p008061
p008062
p008068
p008070
p008072
p008084
p008087
p008099
p008105
p008109
p008115
p008120
p008121
p008122
p008126
p008138
p008141
p008142
p008154
p008167
p008170
p008186
p008198
p008207
p008221
p008228
p008231
p008249
p008258
p008259
p008267
p008269
p008272
p008273
p008274
p008275
p008281
p008298
p008318
p008336
p008347
p008363
p008368
p008393
p008396
p008406
p008415
p008422
p008426
p008432
p008445
p008450
p008451
p008452
p008461
p008466
p008467
p008471
p008489
p008493
p008509
p008516
p008524
p008532
p008533
p008546
p008548
p008557
p008566
p008568
p008569
p008573
p008608
p008654
p008670
p008674
p008698
p008718
p008723
p008726
p008734
p008735
p008748
p008749
p008779
p008780
p008795
p008799
p008814
p008822
p008832
p008848
p008870
p008871
p008879
p008890
p008896
p008897
p008905
p008906
p008915
p008917
p008929
p008932
p008936
p008945
p008947
p008949
p008964
p008970
p008984
p008985
p008989
p008990
p008996
p009001
p009005
p009016
p009021
p009031
p009036
p009043
p009048
p009058
p009062
p009070
p009105
p009112
p009124
p009128
p009130
p009139
p009148
p009170
p009176
p009178
p009225
p009226
p009233
p009238
p009249
p009251
p009253
p009258
p009268
p009269
p009271
p009274
p009278
p009286
p009289
p009295
p009297
p009300
p009308
p009311
p009324
p009330
p009332
p009335
p009338
p009341
p009354
p009356
p009358
p009361
p009363
p009364
p009366
p009372
p009389
p009393
p009397
p009398
p009425
p009430
p009434
p009460
p009473
p009486
p009494
p009498
p009518
p009523
p009526
p009537
p009555
p009569
p009575
p009607
p009615
p009630
p009637
p009642
p009648
p009664
p009667
p009672
p009675
p009676
p009678
p009685
p009686
p009687
p009705
p009708
p009714
p009732
p009753
p009783
p009798
p009844
p009847
p009870
p009871
p009882
p009889
p009891
p009920
p009923
p009949
p009950
p009951
p009958
p009962
p009965
p009967
p009968
p009971
p009973
p009987
p009991
p009993
p009998