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Adds initial mimic-northwestern derived concept mappings #1660

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Adds initial mimic-northwestern derived concept mappings #1660

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7b3ea8b
adds mimic-northwestern derived concept mappings
danamouk Oct 18, 2023
95914e6
minor edit and rename.
danamouk Oct 19, 2023
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -25,6 +25,7 @@ The repository contains one top-level folder containing community developed code
- [mimic-iv-cxr](/mimic-iv-cxr) - code for loading and analyzing both dicom (mimic-iv-cxr/dcm) and text (mimic-iv-cxr/txt) data. In order to clearly indicate that MIMIC-CXR can be linked with MIMIC-IV, we have named this folder mimic-iv-cxr, and any references to MIMIC-CXR / MIMIC-IV-CXR are interchangeable.
- [mimic-iv-ed](/mimic-iv-ed) - build scripts for MIMIC-IV-ED.
- mimic-iv-waveforms - TBD
- mimic-northwestern(/mimic-northwestern) - derived mapping concepts for MIMIC-Northwestern, a large harmonized multi-center COVID-rich ICU database. The database comprises derived concepts from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) spanning 2020 to 2022.

Each subfolder has a README with further detail regarding its content.

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39 changes: 39 additions & 0 deletions mimic-northwestern/mimic/mimic_vital_signs.csv
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itemid,label,abbreviation,category,unitname,loinc,loinc_label,omop_id,author_id,reviewer_id
220045,Heart Rate,HR,Routine Vital Signs,bpm,8867-4,Heart rate,3027018,0000-0001-8822-1884,0000-0002-9348-9284
220210,Respiratory Rate,RR,Respiratory,insp/min,9279-1,Respiratory rate,3024171,0000-0001-8822-1884,0000-0002-9348-9284
220277,O2 saturation pulseoxymetry,SpO2,Respiratory,%,59408-5,Oxygen saturation in Arterial blood by Pulse oximetry,40762499,0000-0001-8822-1884,0000-0002-9348-9284
220179,Non Invasive Blood Pressure systolic,NBPs,Routine Vital Signs,mmHg,76534-7,Systolic blood pressure by Noninvasive,21492239,0000-0001-8822-1884,0000-0002-9348-9284
220180,Non Invasive Blood Pressure diastolic,NBPd,Routine Vital Signs,mmHg,76535-4,Diastolic blood pressure by Noninvasive,21492240,0000-0001-8822-1884,0000-0002-9348-9284
220181,Non Invasive Blood Pressure mean,NBPm,Routine Vital Signs,mmHg,76536-2,Mean blood pressure by Noninvasive,21492241,0000-0001-8822-1884,0000-0002-9348-9284
220052,Arterial Blood Pressure mean,ABPm,Routine Vital Signs,mmHg,8478-0,Mean blood pressure,3027598,0000-0001-8822-1884,0000-0002-9348-9284
220050,Arterial Blood Pressure systolic,ABPs,Routine Vital Signs,mmHg,8480-6,Systolic blood pressure,3004249,0000-0001-8822-1884,0000-0002-9348-9284
220051,Arterial Blood Pressure diastolic,ABPd,Routine Vital Signs,mmHg,8462-4,Diastolic blood pressure,3012888,0000-0001-8822-1884,0000-0002-9348-9284
223761,Temperature Fahrenheit,Temperature F,Routine Vital Signs,°F,8310-5,Body temperature,3020891,0000-0001-8822-1884,0000-0002-9348-9284
225312,ART BP Mean,ART BP Mean,Routine Vital Signs,mmHg,8478-0,Mean blood pressure,3027598,0000-0001-8822-1884,0000-0002-9348-9284
225309,ART BP Systolic,ART BP Systolic,Routine Vital Signs,mmHg,8480-6,Systolic blood pressure,3004249,0000-0001-8822-1884,0000-0002-9348-9284
225310,ART BP Diastolic,ART BP Diastolic,Routine Vital Signs,mmHg,8462-4,Diastolic blood pressure,3012888,0000-0001-8822-1884,0000-0002-9348-9284
223762,Temperature Celsius,Temperature C,Routine Vital Signs,°C,8310-5,Body temperature,3020891,0000-0001-8822-1884,0000-0002-9348-9284
228640,EtCO2,EtCO2,Routine Vital Signs,None,19891-1,Carbon dioxide [Partial pressure] in Exhaled gas --at end expiration,3035357,0000-0001-8822-1884,0000-0002-9348-9284
226329,Blood Temperature CCO (C),Blood Temp CCO (C),Routine Vital Signs,°C,60834-9,Blood temperature,21490586,0000-0001-8822-1884,0000-0002-9348-9284
226531,Admission Weight (lbs.),Admission Weight (lbs.),General,None,29463-7,Body weight,3025315,0000-0001-8822-1884,0000-0002-9348-9284
226512,Admission Weight (Kg),Admission Weight (Kg),General,kg,29463-7,Body weight,3025315,0000-0001-8822-1884,0000-0002-9348-9284
226730,Height (cm),Height (cm),General,cm,8302-2,Body height,3036277,0000-0001-8822-1884,0000-0002-9348-9284
226707,Height,Height,General,Inch,8302-2,Body height,3036277,0000-0001-8822-1884,0000-0002-9348-9284
224359,QTc,QTc,Routine Vital Signs,sec,8636-3,Q-T interval corrected,3026258,0000-0001-8822-1884,0000-0002-9348-9284
226094,Orthostatic BPd sitting,Orthostatic BPd sitting,Routine Vital Signs,mmHg,8453-3,Diastolic blood pressure--sitting,3034703,0000-0001-8822-1884,0000-0002-9348-9284
224646,Orthostatic BPs sitting,Orthostatic BPs sitting,Routine Vital Signs,mmHg,8459-0,Systolic blood pressure--sitting,3018586,0000-0001-8822-1884,0000-0002-9348-9284
226096,Orthostatic BPd standing,Orthostatic BPd standing,Routine Vital Signs,mmHg,8454-1,Diastolic blood pressure--standing,3019962,0000-0001-8822-1884,0000-0002-9348-9284
223766,Orthostatic BPs standing,Orthostatic BPs standing,Routine Vital Signs,mmHg,8460-8,Systolic blood pressure--standing,3035856,0000-0001-8822-1884,0000-0002-9348-9284
224645,Orthostatic BPs lying,Orthostatic BPs lying,Routine Vital Signs,mmHg,8461-6,Systolic blood pressure--supine,3009395,0000-0001-8822-1884,0000-0002-9348-9284
226092,Orthostatic BPd lying,Orthostatic BPd lying,Routine Vital Signs,mmHg,8455-8,Diastolic blood pressure--supine,3013940,0000-0001-8822-1884,0000-0002-9348-9284
223765,Orthostatic HR sitting,Orthostatic HR sitting,Routine Vital Signs,bpm,69000-8,Heart rate --sitting,40771525,0000-0001-8822-1884,0000-0002-9348-9284
223764,Orthostatic HR lying,Orthostatic HR lying,Routine Vital Signs,bpm,68999-2,Heart rate --supine,40771524,0000-0001-8822-1884,0000-0002-9348-9284
224647,Orthostatic HR standing,Orthostatic HR standing,Routine Vital Signs,bpm,69001-6,Heart rate --standing,40771526,0000-0001-8822-1884,0000-0002-9348-9284
224643,Manual Blood Pressure Diastolic Left,Manual BPd L,Routine Vital Signs,mmHg,8462-4,Diastolic blood pressure,3012888,0000-0001-8822-1884,0000-0002-9348-9284
224167,Manual Blood Pressure Systolic Left,Manual BPs L,Routine Vital Signs,mmHg,8480-6,Systolic blood pressure,3004249,0000-0001-8822-1884,0000-0002-9348-9284
227243,Manual Blood Pressure Systolic Right,Manual BPs R,Routine Vital Signs,mmHg,8480-6,Systolic blood pressure,3004249,0000-0001-8822-1884,0000-0002-9348-9284
227242,Manual Blood Pressure Diastolic Right,Manual BPd R,Routine Vital Signs,mmHg,8462-4,Diastolic blood pressure,3012888,0000-0001-8822-1884,0000-0002-9348-9284
224192,Pulsus Paradoxus,Pulsus Paradoxus,Routine Vital Signs,None,8452-5,Systolic blood pressure.inspiration - expiration,3034464,0000-0001-8822-1884,0000-0002-9348-9284
220059,Pulmonary Artery Pressure systolic,PAPs,Hemodynamics,mmHg,8440-0,Pulmonary artery Systolic blood pressure,3005606,0000-0001-8822-1884,0000-0002-9348-9284
220060,Pulmonary Artery Pressure diastolic,PAPd,Hemodynamics,mmHg,8385-7,Pulmonary artery Diastolic blood pressure,3017188,0000-0001-8822-1884,0000-0002-9348-9284
220061,Pulmonary Artery Pressure mean,PAPm,Hemodynamics,mmHg,8414-5,Pulmonary artery Mean blood pressure,3028074,0000-0001-8822-1884,0000-0002-9348-9284
14 changes: 14 additions & 0 deletions mimic-northwestern/northwestern/nw_vital_signs.csv
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itemid,label,abbreviation,category,unitname,loinc,loinc_label,omop_id,author_id,reviewer_id
320045,PULSE,HR,Routine Vital Signs,bpm,8867-4,Heart rate,3027018,0000-0001-5561-6396,0000-0001-8822-1884
320277,PULSE OXIMETRY,SpO2,Respiratory,%,59408-5,Oxygen saturation in Arterial blood by Pulse oximetry,40762499,0000-0001-5561-6396,0000-0001-8822-1884
320210,RESPIRATIONS,RR,Respiratory,insp/min,9279-1,Respiratory rate,3024171,0000-0001-5561-6396,0000-0001-8822-1884
320180,BP DIASTOLIC,NBPd,Routine Vital Signs,mmHg,76535-4,Diastolic blood pressure by Noninvasive,21492240,0000-0001-5561-6396,0000-0001-8822-1884
320179,BP SYSTOLIC,NBPs,Routine Vital Signs,mmHg,76534-7,Systolic blood pressure by Noninvasive,21492239,0000-0001-5561-6396,0000-0001-8822-1884
323761,TEMPERATURE,Temperature F,Routine Vital Signs,F,8310-5,Body temperature,3020891,0000-0001-5561-6396,0000-0001-8822-1884
320051,R ARTERIAL LINE BLOOD PRESSURE,ABPd,Routine Vital Signs,mmHg,8462-4,Diastolic blood pressure,3012888,0000-0001-5561-6396,0000-0001-8822-1884
320050,R ARTERIAL LINE BLOOD PRESSURE,ABPs,Routine Vital Signs,mmHg,8480-6,Systolic blood pressure,3004249,0000-0001-5561-6396,0000-0001-8822-1884
326531,WEIGHT/SCALE,Admission Weight,General,Ounce,29463-7,Body weight,3025315,0000-0001-5561-6396,0000-0001-8822-1884
300001,R BMI,BMI,General,Kg/m^2,39156-5,Body mass index (BMI) [Ratio],3038553,0000-0001-5561-6396,0000-0001-8822-1884
320051,R ARTERIAL LINE BLOOD PRESSURE 2,ABPd,Routine Vital Signs,mmHg,8462-4,Diastolic blood pressure,3012888,0000-0001-5561-6396,0000-0001-8822-1884
320050,R ARTERIAL LINE BLOOD PRESSURE 2,ABPs,Routine Vital Signs,mmHg,8480-6,Systolic blood pressure,3004249,0000-0001-5561-6396,0000-0001-8822-1884
326707,HEIGHT,Height,General,Inch,8302-2,Body height,3036277,0000-0001-5561-6396,0000-0001-8822-1884
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