Database Open Access

MIMIC-IV-ECG: Diagnostic Electrocardiogram Matched Subset

Brian Gow Tom Pollard Larry A Nathanson Alistair Johnson Benjamin Moody Chrystinne Fernandes Nathaniel Greenbaum Jonathan W Waks Parastou Eslami Tanner Carbonati Ashish Chaudhari Elizabeth Herbst Dana Moukheiber Seth Berkowitz Roger Mark Steven Horng

Published: Sept. 15, 2023. Version: 1.0


When using this resource, please cite: (show more options)
Gow, B., Pollard, T., Nathanson, L. A., Johnson, A., Moody, B., Fernandes, C., Greenbaum, N., Waks, J. W., Eslami, P., Carbonati, T., Chaudhari, A., Herbst, E., Moukheiber, D., Berkowitz, S., Mark, R., & Horng, S. (2023). MIMIC-IV-ECG: Diagnostic Electrocardiogram Matched Subset (version 1.0). PhysioNet. https://doi.org/10.13026/4nqg-sb35.

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-IV-ECG module contains approximately 800,000 diagnostic electrocardiograms across nearly 160,000 unique patients. These diagnostic ECGs use 12 leads and are 10 seconds in length. They are sampled at 500 Hz. This subset contains all of the ECGs for patients who appear in the MIMIC-IV Clinical Database. When a cardiologist report is available for a given ECG, we provide the needed information to link the waveform to the report. The patients in MIMIC-IV-ECG have been matched against the MIMIC-IV Clinical Database, making it possible to link to information across the MIMIC-IV modules.


Background

An Electrocardiogram or ECG / EKG measures the electrical activity associated with the heart [1]. Diagnostic ECGs are a standard part of a patients care [2]. The standard ECG leads are denoted as lead I, II, III, aVF, aVR, aVL, V1, V2, V3, V4, V5, V6. They are routinely obtained when admitted to the Emergency Department or to a hospital floor. ECGs will typically be repeated for patients who exhibit cardiac symptoms such as chest pain or abnormal rhythms. Daily ECGs may be obtained following acute cardiovascular events such as myocardial infarction. Patients in the Intensive Care Unit (ICU) are continuously monitored to detect rhythm abnormalities, but full ECGs are needed to evaluate evidence of cardiac ischemia or infarction. However, diagnostic ECGs typically only comprise a small part of understanding the overall condition of a subject at the hospital. To fully understand how to best treat a given patient, a broader set of data is collected which may include: patient demographics, diagnosis, medications, lab tests, and additional information. This broader set of clinical information is shared as part of the MIMIC-IV Clinical Database [3]. The MIMIC-IV-ECG Matched Subset contains the vast majority of diagnostic ECGs collected between 2008 - 2019 for subjects in MIMIC-IV.


Methods

As part of routine care, diagnostic ECGs are collected across Beth Israel Deaconess Medical Center (BIDMC). Three types of information associated with an ECG are presented here. The electrocardiogram waveforms themselves, the machine measurements (ex: average RR interval as calculated by the machine), and the cardiologist reports. Identifiers connected to the ECGs allow this information to be connected back to the patients overall electronic health record. All of the information is de-identified to satisfy the US Health Insurance Portability and Accountability Act of 1996 (HIPAA) Safe Harbor requirements.

Electronic Health Record

Patients from the MIMIC-IV Clinical Database who had ECGs collected between 2008 - 2019 are included as part of MIMIC-IV-ECG. The diagnostic ECGs are collected on machines from various manufacturers including Burdick/Spacelabs, Philips, and General Electric. When the ECG is collected, the machine is populated with the patient's demographics and their medical record number (MRN).

As part of de-identification the raw identifiers are shifted. The patient's MRN was used to match a given 12-lead ECG record to the corresponding subject ID in the MIMIC-IV Clinical Database. As another part of the de-identification, the date-time information was shifted to obscure the actual date and time. Relative date-time information for a given subject is preserved though. The shifted date-times were matched against date-times in the subject's MIMIC-IV Clinical Database records. A unique study_id was generated for each record.

Electrocardiogram Waveforms

If a patient appears in the MIMIC-IV Clinical Database, all of their available ECG waveforms were pulled. This includes ECGs from the BIDMC emergency department, hospital (including the ICU), and outpatient care centers. We converted the ECGs from the manufacturers format to the open WFDB format 16 [4] with each WFDB record comprised of a header (.hea) file and a signal (.dat) file. The files were then transferred from BIDMC to MIT for additional processing.

We scrubbed the WFDB header files for PHI such that only the signal information, subject ID, and shifted date-time are provided. Timestamps for events in the MIMIC-IV Clinical Database, such as drug administration, are aligned with the timestamps in MIMIC-IV-ECG. However, some of the diagnostic ECGs provided here were collected outside of ED or ICU visits at the hospital. Since the MIMIC-IV Clinical Database is comprised solely of ED and ICU data, the ECG timestamp can occur before or after a visit from the clinical database.

Machine Measurements

The ECG machine generates summary reports and summary measures (ex: RR interval, QRS onset and end, etc.) for each diagnostic ECG. We collectively refer to these as machine measurements. The machine output is parsed and any PHI is removed. In particular, the MRN is shifted to subject_id, the de-identified study_id is assigned in a manner consistent with the ECG waveform files, and the raw Cart ID is randomly shifted to create a de-identified cart_id. There was no PHI in the report lines. 

The global machine measures are provided in this release. These global measures are calculated across all 12 leads. Machine measurements for individual leads may be released in a future version of this project. 

Cardiologist Reports

Most ECG waveforms get read by a cardiologist and an associated report is generated from the reading. We provide information for linking a waveform with its associated report where available. 

The de-identified free-text notes from these ECG reports will be made available as part of the MIMIC-IV-Note module [5] at a later time. These ECG reports are de-identified using a rule-based approach [6, 7, 8], similar to that used for other MIMIC reports.


Data Description

Electrocardiogram Waveforms

Approximately 800,000 ten-second-long 12 lead diagnostic ECGs across nearly 160,000 unique subjects are provided in the MIMIC-IV-ECG module. Around 5% of the available diagnostic ECGs were withheld from this release so they can be used as a hidden test set in workshops and challenges. The ECGs are sampled at 500 Hz. The patients in this module have been matched with the MIMIC-IV Clinical Database. Many of the provided diagnostic ECGs overlap with a MIMIC-IV hospital or emergency department stay but a number of them do not overlap. Approximately 55% of the ECGs overlap with a hospital admission and 25% overlap with an emergency department visit.

The ECGs are grouped into subdirectories based on subject_id. Each DICOM record path follows the pattern: files/pNNNN/pXXXXXXXX/sZZZZZZZZ/ZZZZZZZZ, where:

  • NNNN is the first four characters of the subject_id,
  • XXXXXXXX is the subject_id,
  • ZZZZZZZZ is the study_id

An example of the file structure is as follows:

files
├── p1000
|   └── p10001725
|       └── s41420867
|           ├── 41420867.dat
|           └── 41420867.hea
└── p1002
    └── p10023771
        ├── s42745010
        │   ├── 42745010.dat
        │   └── 42745010.hea
        ├── s46989724
        │   ├── 46989724.dat
        │   └── 46989724.hea
        └── s42460255
            ├── 42460255.dat
            └── 42460255.hea

Above we find two subjects p10001725 (under the p1000 group level directory) and p10023771 (under the p1002 group level directory). For subject p10001725 we find one study: s41420867. For p10023771 we find three studies: s42745010, s46989724, s42460255. The study identifiers are completely random, and their order has no implications for the chronological order of the actual studies. Each study has a like named .hea and .dat file, comprising the WFDB record. 

The record_list.csv file contains the file name and path for each WFDB record. It also provides the corresponding subject ID and study ID. The subject ID can be used to link a subject from MIMIC-IV-ECG to the other modules in the MIMIC-IV Clinical Database. 

Machine Measurements

Machine measurements for each ECG waveform are provided in the machine_measurements.csv file. A data dictionary provides a description for each of the columns in machine_measurements_data_dictionary.csv. The machine measurements table provides the machine generated reports in columns report_0..report_17. The report lines are provided as generated by the machine. In some cases there will be a column with no text in between columns with text (ex: report_0: <text_a>, report_1: empty, report_2: <text_b>). In addition to the summary measurements (rr_interval, qrs_onset, qrs_end, etc.) columns for the machine's bandwidth and filter settings (filtering) are provided. A cart_id is provided which can be used to track which machine was used for a given ECG. Finally, the subject_id, study_id, and ecg_time are provided, consistent with the ECG waveform files themselves. 

Cardiologist Reports 

A little more than 600,000 cardiologist reports are available for the ~800,000 diagnostic ECGs. Not all diagnostic ECGs get read by a cardiologist. This is the primary reason that there are fewer reports than waveforms.

The waveform_note_links.csv table provides a note_id for the associated ECG waveform. This note_id can be used to link between a waveform and the free-text note in the MIMIC-IV-Note module. Each note_id is composed of the subject ID, the abbreviation for the domain (EK) that the report comes from, and a sequential integer. The sequential integer is also listed in its own column, note_seq, and can be used to decipher the order in which ECGs were collected for a given subject across all of their visits. This table also contains the subject ID, study ID, and waveform path.

BigQuery

The information from the record_list.csv, machine_measurements.csv, and waveform_note_links.csv tables are available on BigQuery [9].


Usage Notes

This module provides MIMIC-IV users an additional, potentially important piece of information for their research using MIMIC. 

There are some limitations with this dataset. The date and time for each ECG were recorded by the machine's internal clock, which in most cases was not synchronized with any external time source. As a result, the ECG time stamps could be significantly out of sync with the corresponding time stamps in the MIMIC-IV Clinical Database, MIMIC-IV Waveform Database, or other modules in MIMIC-IV. An additional limitation, as noted above, is that some of the ECGs provided here were collected outside of the ED and ICU. This means that the timestamps for those ECGs won't overlap with data from the MIMIC-IV Clinical Database.

The signals can be viewed in Lightwave by clicking the Visualize waveforms links in the Files section below. Additionally, the signals can be read by using the WFDB toolboxes provided on PhysioNet: WFDB (in C) [10], WFDB-Matlab [11], and WFDB-Python [12]. Here is a basic script for reading a downloaded record from this project and plotting it by using the WFDB-Python toolbox:


import wfdb 
rec_path = '/files/p1000/p10001725/s41420867/41420867' 
rd_record = wfdb.rdrecord(rec_path) 
wfdb.plot_wfdb(record=rd_record, figsize=(24,18), title='Study 41420867 example', ecg_grids='all')

where rec_path is the path to the name of the .hea and .dat files for the record you'd like to plot.

Here we provide an example of how subject p10023771 from MIMIC-IV-ECG can be linked to their admission information in the MIMIC-IV Clinical Database.  Executing this from BigQuery:

SELECT * FROM `physionet-data.mimiciv_hosp.admissions` WHERE subject_id=10023771

we see that the patient only has one admission to the hospital with an admittime = 2113-08-25T07:15:00 and a dischtime = 2113-08-30T14:15:00. We also need to check to see if they were seen in the emergency department and not admitted to the hospital:

SELECT * FROM `physionet-data.mimiciv_ed.edstays` WHERE subject_id = 10023771

We observe that they did not have a stay in the emergency department.

Next, we get the timestamps from the diagnostic ECGs by checking the base_date and base_time variables. These are the variables used in the WFDB format for storing date and time. They correspond with the timestamps for the diagnostic ECGs that are provided in the summary tables. We then save the result to a csv file:


from pathlib import Path
import pandas as pd

import wfdb

# get the path to all the study .hea files for p10023771
paths = list(Path("p10023771/.").rglob("*.hea"))

# get date and time for each study
date_times = {'study':[],'date':[],'time':[]} # use a dictionary to store the date and time for each study
for file in paths:
    study = file.stem
    metadata = wfdb.rdheader(f'{file.parent}/{file.stem}')
    date_times['study'].append(study)
    date_times['date'].append(metadata.base_date)
    date_times['time'].append(metadata.base_time)

df_date_times = pd.DataFrame(data=date_times)
df_date_times.to_csv('p10023771_date_times.csv', index=False)

We observe the following for the 3 diagnostic ECGs for p10023771

study datetime
42745010 2110-07-23T08:43
46989724 2113-08-19T07:18
42460255 2113-08-25T13:58

where the date is given before the T as YYYY-MM-DD and the time is given after the T as HH:MM. Comparing this to the subjects admission in the MIMIC-IV Clinical Database:

admittime dischtime
2113-08-25T07:15 2113-08-30T14:15

we observe that s42745010 and s46989724 occurred prior to their only hospital admission while s42460255 occurred during their hospital admission. 

We can also check the available cardiologist reports for this subject by running this command in BigQuery:


SELECT * FROM `lcp-consortium.mimic_ecg.reports` WHERE subject_id = 10023771

We find that there are cardiologist reports available for s46989724 and s42460255 but not s42745010. Please note that only members who are part of our consortium can access the cardiologist reports / notes from lcp-consortium on BigQuery.


Release Notes

MIMIC-IV-ECG v1.0

This release removes the sensitive information (i.e. free-text note) from the cardiologist reports. We now simply provide information for linking between the waveforms in this module and their associated free-text note in MIMIC-IV-Note module. Since that sensitive information has been removed, the project access has been changed to open instead of requiring credentialling. 


Ethics

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.


Acknowledgements

SH, RM, BG, DM, and TP are funded by the Massachusetts Life Sciences Center, Nov. 30, 2020. NG is supported by National Institutes of Health National Library of Medicine Biomedical Informatics and Data Science Research Training Program under grant number T15LM007092-30. BG, TP, AJ, BM, CF, DM, and RM are supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) under NIH grant number R01EB030362.


Conflicts of Interest

The author(s) have no conflicts of interest to declare.


References

  1. Geselowitz DB. On the theory of the electrocardiogram. Proceedings of the IEEE. 1989 Jun;77(6):857-76.
  2. Harris PR. The Normal electrocardiogram: resting 12-Lead and electrocardiogram monitoring in the hospital. Critical Care Nursing Clinics. 2016 Sep 1;28(3):281-96.
  3. Johnson, A., Bulgarelli, L., Pollard, T., Horng, S., Celi, L. A., & Mark, R. (2021). MIMIC-IV (version 1.0). PhysioNet. https://doi.org/10.13026/s6n6-xd98.
  4. Documentation for the Waveform Database (WFDB) file format. https://wfdb.io/ [Accessed 21 June 2022]
  5. Johnson, A., Pollard, T., Horng, S., Celi, L. A., & Mark, R. (2023). MIMIC-IV-Note: Deidentified free-text clinical notes (version 2.2). PhysioNet. https://doi.org/10.13026/1n74-ne17.
  6. Margaret Douglass, Computer-assisted de-identification of free-text nursing notes. Master's Thesis, 2005. MIT.
  7. Neamatullah, I., Douglass, M.M., Lehman, L.H., Reisner, A., Villarroel, M., Long, W.J., Szolovits, P., Moody, G.B., Mark, R.G., Clifford, G.D. (2007). De-Identification Software Package (version 1.1). PhysioNet. doi:10.13026/C20M3F
  8. Neamatullah I, Douglass MM, Lehman LH, Reisner A, Villarroel M, Long WJ, Szolovits P, Moody GB, Mark RG, Clifford GD. Automated de-identification of free-text medical records. BMC medical informatics and decision making. 2008 Dec;8(1):1-7. doi:10.1186/1472-6947-8-32
  9. Documentation about using the Medical Information Mart for Intensive Care (MIMIC) Database with Google BigQuery. https://mimic.mit.edu/docs/gettingstarted/cloud/ [Accessed 21 June 2022]
  10. Documentation for the Waveform Database (WFDB) toolbox in C. https://physionet.org/content/wfdb/10.7.0/ [Accessed 21 June 2022]
  11. Documentation for the Waveform Database (WFDB) toolbox for Matlab. https://physionet.org/content/wfdb-matlab/0.10.0/ [Accessed 21 June 2022]
  12. Documentation for the Waveform Database (WFDB) toolbox for Python. https://physionet.org/content/wfdb-python/3.4.1/ [Accessed 21 June 2022]

Parent Projects
MIMIC-IV-ECG: Diagnostic Electrocardiogram 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
Corresponding Author
You must be logged in to view the contact information.
Versions
  • 0.1 - Dec. 23, 2022
  • 0.2 - Feb. 8, 2023
  • 0.3 - July 21, 2023
  • 1.0 - Sept. 15, 2023

Files

Total uncompressed size: 90.4 GB.

Access the files

Visualize waveforms

Folder Navigation: <base>/files/p1329/p13297743
Name Size Modified
Parent Directory
s40014445
s40040651
s40087019
s40179267
s40205602
s40237483
s40466932
s40570833
s40612491
s40618143
s40751566
s40942673
s41062097
s41085913
s41104118
s41115349
s41116059
s41139687
s41161551
s41185621
s41191166
s41200160
s41214322
s41260295
s41273488
s41315068
s41345757
s41393194
s41433035
s41516908
s41668476
s41737091
s41822463
s41837026
s41846454
s41987297
s42042540
s42083603
s42110500
s42123450
s42198509
s42214485
s42221913
s42224472
s42308969
s42327048
s42375112
s42496506
s42509680
s42521577
s42561080
s42592799
s42618567
s42651819
s42666084
s42745222
s42788883
s42811312
s42916270
s42950165
s42990501
s43151491
s43197891
s43297935
s43303994
s43310939
s43409698
s43434182
s43560987
s43730206
s43785250
s43826061
s43841976
s43844792
s43848395
s43906513
s43916552
s44137205
s44239974
s44243367
s44245883
s44279158
s44281306
s44316115
s44425129
s44456190
s44458495
s44467020
s44527770
s44645237
s44807514
s44888250
s44889554
s44892675
s44922671
s44922782
s44932015
s44939962
s44947877
s44959113
s44966011
s44981364
s45102822
s45108624
s45165267
s45311696
s45326769
s45375880
s45406744
s45408472
s45516953
s45573104
s45640274
s45722912
s45792146
s45811632
s45943575
s45957119
s46047302
s46048900
s46111427
s46157931
s46245053
s46264270
s46318816
s46331467
s46553842
s46604436
s46633330
s46767153
s46833204
s46880584
s46880883
s47008080
s47091567
s47159588
s47301683
s47350302
s47375167
s47416190
s47460693
s47521696
s47697124
s47785718
s47853067
s47858496
s47886340
s47912874
s47993834
s48007750
s48042129
s48053727
s48094199
s48111095
s48158155
s48165737
s48229198
s48255148
s48261460
s48335294
s48337928
s48377267
s48655115
s48728810
s48806285
s49079738
s49095190
s49123908
s49135014
s49161437
s49181910
s49226354
s49271183
s49289071
s49366424
s49397950
s49585320
s49632282
s49641116
s49684259
s49702177
s49838921
s49934918