From bf5518628a59ad51902ce037437446c5b32b64d5 Mon Sep 17 00:00:00 2001 From: Abdulrahman Date: Mon, 7 Nov 2022 23:28:22 -0500 Subject: [PATCH 1/4] Add vital signs mapping for MIMIC-IV v2.0 SSSOM standard --- .../concept_map/chartevents_to_loinc.csv | 43 +++++++++++++++++++ .../concept_map/chartevents_to_omop.csv | 43 +++++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 mimic-iv/concepts/concept_map/chartevents_to_loinc.csv create mode 100644 mimic-iv/concepts/concept_map/chartevents_to_omop.csv diff --git a/mimic-iv/concepts/concept_map/chartevents_to_loinc.csv b/mimic-iv/concepts/concept_map/chartevents_to_loinc.csv new file mode 100644 index 000000000..65a902bf1 --- /dev/null +++ b/mimic-iv/concepts/concept_map/chartevents_to_loinc.csv @@ -0,0 +1,43 @@ +subject_id,subject_label,predicate_id,object_id,object_label,mapping_justification,author_id,reviewer_id,confidence,comment +mimic:220045,Heart Rate,skos:exactMatch,loinc:8867-4,Heart rate,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220210,Respiratory Rate,skos:exactMatch,loinc:9279-1,Respiratory rate,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220277,O2 saturation pulseoxymetry,skos:exactMatch,loinc:59408-5,Oxygen saturation in Arterial blood by Pulse oximetry,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220179,Non Invasive Blood Pressure systolic,skos:exactMatch,loinc:76534-7,Systolic blood pressure by Noninvasive,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220180,Non Invasive Blood Pressure diastolic,skos:exactMatch,loinc:76535-4,Diastolic blood pressure by Noninvasive,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220181,Non Invasive Blood Pressure mean,skos:exactMatch,loinc:76536-2,Mean blood pressure by Noninvasive,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220052,Arterial Blood Pressure mean,skos:exactMatch,loinc:8478-0,Mean blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220050,Arterial Blood Pressure systolic,skos:exactMatch,loinc:8480-6,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220051,Arterial Blood Pressure diastolic,skos:exactMatch,loinc:8462-4,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223761,Temperature Fahrenheit,skos:exactMatch,loinc:8310-5,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220060,Pulmonary Artery Pressure diastolic,skos:exactMatch,loinc:8385-7,Pulmonary artery Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220059,Pulmonary Artery Pressure systolic,skos:exactMatch,loinc:8440-0,Pulmonary artery Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220061,Pulmonary Artery Pressure mean,skos:exactMatch,loinc:8414-5,Pulmonary artery Mean blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223762,Temperature Celsius,skos:exactMatch,loinc:8310-5,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:225312,ART BP Mean,skos:exactMatch,loinc:8478-0,Mean blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:225309,ART BP Systolic,skos:exactMatch,loinc:8480-6,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:225310,ART BP Diastolic,skos:exactMatch,loinc:8462-4,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226329,Blood Temperature CCO (C),skos:exactMatch,loinc:60834-9,Blood temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226531,Admission Weight (lbs.),skos:exactMatch,loinc:29463-7,Body weight,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:228640,EtCO2,skos:exactMatch,loinc:19891-1,Carbon dioxide [Partial pressure] in Exhaled gas --at end expiration,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226512,Admission Weight (Kg),skos:exactMatch,loinc:29463-7,Body weight,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:227632,Arctic Sun/Alsius Temp #1 C,skos:closeMatch,loinc:8310-5,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,0.8, +mimic:227634,Arctic Sun/Alsius Temp #2 C,skos:closeMatch,loinc:8310-5,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,0.8, +mimic:226707,Height,skos:exactMatch,loinc:8302-2,Body height,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226730,Height (cm),skos:exactMatch,loinc:8302-2,Body height,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223763,Bladder Pressure,,,,,,,,No suitable LOINC code +mimic:224359,QTc,skos:exactMatch,loinc:8636-3,Q-T interval corrected,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224167,Manual Blood Pressure Systolic Left,skos:closeMatch,loinc:8480-6,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224643,Manual Blood Pressure Diastolic Left,skos:closeMatch,loinc:8462-4,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:227243,Manual Blood Pressure Systolic Right,skos:closeMatch,loinc:8480-6,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:227242,Manual Blood Pressure Diastolic Right,skos:closeMatch,loinc:8462-4,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224192,Pulsus Paradoxus,skos:exactMatch,loinc:8452-5,Systolic blood pressure.inspiration - expiration,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224646,Orthostatic BPs sitting,skos:exactMatch,loinc:8459-0,Systolic blood pressure--sitting,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226094,Orthostatic BPd sitting,skos:exactMatch,loinc:8453-3,Diastolic blood pressure--sitting,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224645,Orthostatic BPs lying,skos:exactMatch,loinc:8461-6,Systolic blood pressure--supine,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226092,Orthostatic BPd lying,skos:exactMatch,loinc:8455-8,Diastolic blood pressure--supine,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223765,Orthostatic HR sitting,skos:exactMatch,loinc:69000-8,Heart rate --sitting,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224166,Doppler BP,,,,,,,,No suitable LOINC code +mimic:223766,Orthostatic BPs standing,skos:exactMatch,loinc:8460-8,Systolic blood pressure--standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226096,Orthostatic BPd standing,skos:exactMatch,loinc:8454-1,Diastolic blood pressure--standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223764,Orthostatic HR lying,skos:exactMatch,loinc:68999-2,Heart rate --supine,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224647,Orthostatic HR standing,skos:exactMatch,loinc:69001-6,Heart rate --standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, \ No newline at end of file diff --git a/mimic-iv/concepts/concept_map/chartevents_to_omop.csv b/mimic-iv/concepts/concept_map/chartevents_to_omop.csv new file mode 100644 index 000000000..2eeecba12 --- /dev/null +++ b/mimic-iv/concepts/concept_map/chartevents_to_omop.csv @@ -0,0 +1,43 @@ +subject_id,subject_label,predicate_id,object_id,object_label,mapping_justification,author_id,reviewer_id,confidence,comment +mimic:220045,Heart Rate,skos:exactMatch,omop:3027018,Heart rate,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220210,Respiratory Rate,skos:exactMatch,omop:3024171,Respiratory rate,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220277,O2 saturation pulseoxymetry,skos:exactMatch,omop:40762499,Oxygen saturation in Arterial blood by Pulse oximetry,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220179,Non Invasive Blood Pressure systolic,skos:exactMatch,omop:21492239,Systolic blood pressure by Noninvasive,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220180,Non Invasive Blood Pressure diastolic,skos:exactMatch,omop:21492240,Diastolic blood pressure by Noninvasive,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220181,Non Invasive Blood Pressure mean,skos:exactMatch,omop:21492241,Mean blood pressure by Noninvasive,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220052,Arterial Blood Pressure mean,skos:exactMatch,omop:3027598,Mean blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220050,Arterial Blood Pressure systolic,skos:exactMatch,omop:3004249,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220051,Arterial Blood Pressure diastolic,skos:exactMatch,omop:3012888,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223761,Temperature Fahrenheit,skos:exactMatch,omop:3020891,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220060,Pulmonary Artery Pressure diastolic,skos:exactMatch,omop:3017188,Pulmonary artery Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220059,Pulmonary Artery Pressure systolic,skos:exactMatch,omop:3005606,Pulmonary artery Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220061,Pulmonary Artery Pressure mean,skos:exactMatch,omop:3028074,Pulmonary artery Mean blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223762,Temperature Celsius,skos:exactMatch,omop:3020891,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:225312,ART BP Mean,skos:exactMatch,omop:3027598,Mean blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:225309,ART BP Systolic,skos:exactMatch,omop:3004249,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:225310,ART BP Diastolic,skos:exactMatch,omop:3012888,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226329,Blood Temperature CCO (C),skos:exactMatch,omop:21490586,Blood temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226531,Admission Weight (lbs.),skos:exactMatch,omop:3025315,Body weight,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:228640,EtCO2,skos:exactMatch,omop:3035357,Carbon dioxide [Partial pressure] in Exhaled gas --at end expiration,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226512,Admission Weight (Kg),skos:exactMatch,omop:3025315,Body weight,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:227632,Arctic Sun/Alsius Temp #1 C,skos:closeMatch,omop:3020891,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,0.8, +mimic:227634,Arctic Sun/Alsius Temp #2 C,skos:closeMatch,omop:3020891,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,0.8, +mimic:226707,Height,skos:exactMatch,omop:3036277,Body height,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226730,Height (cm),skos:exactMatch,omop:3036277,Body height,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223763,Bladder Pressure,,,,,,,,No suitable LOINC code +mimic:224359,QTc,skos:exactMatch,omop:3026258,Q-T interval corrected,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224167,Manual Blood Pressure Systolic Left,skos:closeMatch,omop:3004249,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224643,Manual Blood Pressure Diastolic Left,skos:closeMatch,omop:3012888,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:227243,Manual Blood Pressure Systolic Right,skos:closeMatch,omop:3004249,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:227242,Manual Blood Pressure Diastolic Right,skos:closeMatch,omop:3012888,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224192,Pulsus Paradoxus,skos:exactMatch,omop:3034464,Systolic blood pressure.inspiration - expiration,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224646,Orthostatic BPs sitting,skos:exactMatch,omop:3018586,Systolic blood pressure--sitting,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226094,Orthostatic BPd sitting,skos:exactMatch,omop:3034703,Diastolic blood pressure--sitting,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224645,Orthostatic BPs lying,skos:exactMatch,omop:3009395,Systolic blood pressure--supine,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226092,Orthostatic BPd lying,skos:exactMatch,omop:3013940,Diastolic blood pressure--supine,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223765,Orthostatic HR sitting,skos:exactMatch,omop:40771525,Heart rate --sitting,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224166,Doppler BP,,,,,,,,No suitable LOINC code +mimic:223766,Orthostatic BPs standing,skos:exactMatch,omop:3035856,Systolic blood pressure--standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226096,Orthostatic BPd standing,skos:exactMatch,omop:3019962,Diastolic blood pressure--standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223764,Orthostatic HR lying,skos:exactMatch,omop:40771524,Heart rate --supine,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224647,Orthostatic HR standing,skos:exactMatch,omop:40771526,Heart rate --standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, \ No newline at end of file From 1fe91c3e651d8cc71b75c925c6808936f77ae3bc Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Sat, 4 Nov 2023 03:24:17 -0400 Subject: [PATCH 2/4] adds updated mimic data version and nw mappings following sssom data structure. --- .../concepts/concept_map/chartevents_to_loinc.csv | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/mimic-iv/concepts/concept_map/chartevents_to_loinc.csv b/mimic-iv/concepts/concept_map/chartevents_to_loinc.csv index 65a902bf1..f71841f6d 100644 --- a/mimic-iv/concepts/concept_map/chartevents_to_loinc.csv +++ b/mimic-iv/concepts/concept_map/chartevents_to_loinc.csv @@ -40,4 +40,17 @@ mimic:224166,Doppler BP,,,,,,,,No suitable LOINC code mimic:223766,Orthostatic BPs standing,skos:exactMatch,loinc:8460-8,Systolic blood pressure--standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, mimic:226096,Orthostatic BPd standing,skos:exactMatch,loinc:8454-1,Diastolic blood pressure--standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, mimic:223764,Orthostatic HR lying,skos:exactMatch,loinc:68999-2,Heart rate --supine,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:224647,Orthostatic HR standing,skos:exactMatch,loinc:69001-6,Heart rate --standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, \ No newline at end of file +mimic:224647,Orthostatic HR standing,skos:exactMatch,loinc:69001-6,Heart rate --standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320045,skos:exactMatch,loinc:8867-4,semapv:ManualMappingCuration,PULSE,Heart rate,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320277,skos:exactMatch,loinc:59408-5,semapv:ManualMappingCuration,PULSE OXIMETRY,Oxygen saturation in Arterial blood by Pulse oximetry,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320210,skos:exactMatch,loinc:9279-1,semapv:ManualMappingCuration,RESPIRATIONS,Respiratory rate,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320180,skos:exactMatch,loinc:76535-4,semapv:ManualMappingCuration,BP DIASTOLIC,Diastolic blood pressure by Noninvasive,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320179,skos:exactMatch,loinc:76534-7,semapv:ManualMappingCuration,BP SYSTOLIC,Systolic blood pressure by Noninvasive,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:323761,skos:exactMatch,loinc:8310-5,semapv:ManualMappingCuration,TEMPERATURE,Body temperature,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320051,skos:exactMatch,loinc:8462-4,semapv:ManualMappingCuration,R ARTERIAL LINE BLOOD PRESSURE,Diastolic blood pressure,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320050,skos:exactMatch,loinc:8480-6,semapv:ManualMappingCuration,R ARTERIAL LINE BLOOD PRESSURE,Systolic blood pressure,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:326531,skos:exactMatch,loinc:29463-7,semapv:ManualMappingCuration,WEIGHT/SCALE,Body weight,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:300001,skos:exactMatch,loinc:39156-5,semapv:ManualMappingCuration,R BMI,Body mass index (BMI) [Ratio],orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320051,skos:exactMatch,loinc:8462-4,semapv:ManualMappingCuration,R ARTERIAL LINE BLOOD PRESSURE 2,Diastolic blood pressure,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320050,skos:exactMatch,loinc:8480-6,semapv:ManualMappingCuration,R ARTERIAL LINE BLOOD PRESSURE 2,Systolic blood pressure,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:326707,skos:exactMatch,loinc:8302-2,semapv:ManualMappingCuration,HEIGHT,Body height,orcid:0000-0001-8822-1885,orcid:0000-0002-9348-9285,1, \ No newline at end of file From 3415da02145c47f85ce13d68b2caadf691dcb489 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Sat, 4 Nov 2023 03:53:05 -0400 Subject: [PATCH 3/4] adds inhouse2omop in addition to inhouse2loinc. --- .../concepts/concept_map/chartevents_to_omop.csv | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/mimic-iv/concepts/concept_map/chartevents_to_omop.csv b/mimic-iv/concepts/concept_map/chartevents_to_omop.csv index 2eeecba12..7bb707086 100644 --- a/mimic-iv/concepts/concept_map/chartevents_to_omop.csv +++ b/mimic-iv/concepts/concept_map/chartevents_to_omop.csv @@ -40,4 +40,17 @@ mimic:224166,Doppler BP,,,,,,,,No suitable LOINC code mimic:223766,Orthostatic BPs standing,skos:exactMatch,omop:3035856,Systolic blood pressure--standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, mimic:226096,Orthostatic BPd standing,skos:exactMatch,omop:3019962,Diastolic blood pressure--standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, mimic:223764,Orthostatic HR lying,skos:exactMatch,omop:40771524,Heart rate --supine,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:224647,Orthostatic HR standing,skos:exactMatch,omop:40771526,Heart rate --standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, \ No newline at end of file +mimic:224647,Orthostatic HR standing,skos:exactMatch,omop:40771526,Heart rate --standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320045,skos:exactMatch,omop:3027018,semapv:ManualMappingCuration,PULSE,Heart rate,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320277,skos:exactMatch,omop:40762499,semapv:ManualMappingCuration,PULSE OXIMETRY,Oxygen saturation in Arterial blood by Pulse oximetry,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320210,skos:exactMatch,omop:3024171,semapv:ManualMappingCuration,RESPIRATIONS,Respiratory rate,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320180,skos:exactMatch,omop:21492240,semapv:ManualMappingCuration,BP DIASTOLIC,Diastolic blood pressure by Noninvasive,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320179,skos:exactMatch,omop:21492239,semapv:ManualMappingCuration,BP SYSTOLIC,Systolic blood pressure by Noninvasive,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:323761,skos:exactMatch,omop:3020891,semapv:ManualMappingCuration,TEMPERATURE,Body temperature,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320051,skos:exactMatch,omop:3012888,semapv:ManualMappingCuration,R ARTERIAL LINE BLOOD PRESSURE,Diastolic blood pressure,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320050,skos:exactMatch,omop:3004249,semapv:ManualMappingCuration,R ARTERIAL LINE BLOOD PRESSURE,Systolic blood pressure,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:326531,skos:exactMatch,omop:3025315,semapv:ManualMappingCuration,WEIGHT/SCALE,Body weight,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:300001,skos:exactMatch,omop:3038553,semapv:ManualMappingCuration,R BMI,Body mass index (BMI) [Ratio],orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320051,skos:exactMatch,omop:3012888,semapv:ManualMappingCuration,R ARTERIAL LINE BLOOD PRESSURE 2,Diastolic blood pressure,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:320050,skos:exactMatch,omop:3004249,semapv:ManualMappingCuration,R ARTERIAL LINE BLOOD PRESSURE 2,Systolic blood pressure,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +northwestern:326707,skos:exactMatch,omop:3036277,semapv:ManualMappingCuration,HEIGHT,Body height,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, \ No newline at end of file From dbd118f4a44f311d956867de8b64cf1715746abc Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Tue, 7 Nov 2023 11:29:52 -0500 Subject: [PATCH 4/4] updates mapping justification and retains csv file format. --- .../concept_map/chartevents_to_loinc.csv | 80 +++++++++---------- .../concept_map/chartevents_to_omop.csv | 80 +++++++++---------- 2 files changed, 80 insertions(+), 80 deletions(-) diff --git a/mimic-iv/concepts/concept_map/chartevents_to_loinc.csv b/mimic-iv/concepts/concept_map/chartevents_to_loinc.csv index f71841f6d..73cb1d5f3 100644 --- a/mimic-iv/concepts/concept_map/chartevents_to_loinc.csv +++ b/mimic-iv/concepts/concept_map/chartevents_to_loinc.csv @@ -1,46 +1,46 @@ subject_id,subject_label,predicate_id,object_id,object_label,mapping_justification,author_id,reviewer_id,confidence,comment -mimic:220045,Heart Rate,skos:exactMatch,loinc:8867-4,Heart rate,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220210,Respiratory Rate,skos:exactMatch,loinc:9279-1,Respiratory rate,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220277,O2 saturation pulseoxymetry,skos:exactMatch,loinc:59408-5,Oxygen saturation in Arterial blood by Pulse oximetry,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220179,Non Invasive Blood Pressure systolic,skos:exactMatch,loinc:76534-7,Systolic blood pressure by Noninvasive,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220180,Non Invasive Blood Pressure diastolic,skos:exactMatch,loinc:76535-4,Diastolic blood pressure by Noninvasive,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220181,Non Invasive Blood Pressure mean,skos:exactMatch,loinc:76536-2,Mean blood pressure by Noninvasive,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220052,Arterial Blood Pressure mean,skos:exactMatch,loinc:8478-0,Mean blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220050,Arterial Blood Pressure systolic,skos:exactMatch,loinc:8480-6,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220051,Arterial Blood Pressure diastolic,skos:exactMatch,loinc:8462-4,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:223761,Temperature Fahrenheit,skos:exactMatch,loinc:8310-5,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220060,Pulmonary Artery Pressure diastolic,skos:exactMatch,loinc:8385-7,Pulmonary artery Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220059,Pulmonary Artery Pressure systolic,skos:exactMatch,loinc:8440-0,Pulmonary artery Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220061,Pulmonary Artery Pressure mean,skos:exactMatch,loinc:8414-5,Pulmonary artery Mean blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:223762,Temperature Celsius,skos:exactMatch,loinc:8310-5,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:225312,ART BP Mean,skos:exactMatch,loinc:8478-0,Mean blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:225309,ART BP Systolic,skos:exactMatch,loinc:8480-6,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:225310,ART BP Diastolic,skos:exactMatch,loinc:8462-4,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:226329,Blood Temperature CCO (C),skos:exactMatch,loinc:60834-9,Blood temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:226531,Admission Weight (lbs.),skos:exactMatch,loinc:29463-7,Body weight,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:228640,EtCO2,skos:exactMatch,loinc:19891-1,Carbon dioxide [Partial pressure] in Exhaled gas --at end expiration,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:226512,Admission Weight (Kg),skos:exactMatch,loinc:29463-7,Body weight,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:227632,Arctic Sun/Alsius Temp #1 C,skos:closeMatch,loinc:8310-5,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,0.8, -mimic:227634,Arctic Sun/Alsius Temp #2 C,skos:closeMatch,loinc:8310-5,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,0.8, -mimic:226707,Height,skos:exactMatch,loinc:8302-2,Body height,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:226730,Height (cm),skos:exactMatch,loinc:8302-2,Body height,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220045,Heart Rate,skos:exactMatch,loinc:8867-4,Heart rate,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220210,Respiratory Rate,skos:exactMatch,loinc:9279-1,Respiratory rate,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220277,O2 saturation pulseoxymetry,skos:exactMatch,loinc:59408-5,Oxygen saturation in Arterial blood by Pulse oximetry,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220179,Non Invasive Blood Pressure systolic,skos:exactMatch,loinc:76534-7,Systolic blood pressure by Noninvasive,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220180,Non Invasive Blood Pressure diastolic,skos:exactMatch,loinc:76535-4,Diastolic blood pressure by Noninvasive,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220181,Non Invasive Blood Pressure mean,skos:exactMatch,loinc:76536-2,Mean blood pressure by Noninvasive,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220052,Arterial Blood Pressure mean,skos:exactMatch,loinc:8478-0,Mean blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220050,Arterial Blood Pressure systolic,skos:exactMatch,loinc:8480-6,Systolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220051,Arterial Blood Pressure diastolic,skos:exactMatch,loinc:8462-4,Diastolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223761,Temperature Fahrenheit,skos:exactMatch,loinc:8310-5,Body temperature,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220060,Pulmonary Artery Pressure diastolic,skos:exactMatch,loinc:8385-7,Pulmonary artery Diastolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220059,Pulmonary Artery Pressure systolic,skos:exactMatch,loinc:8440-0,Pulmonary artery Systolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220061,Pulmonary Artery Pressure mean,skos:exactMatch,loinc:8414-5,Pulmonary artery Mean blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223762,Temperature Celsius,skos:exactMatch,loinc:8310-5,Body temperature,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:225312,ART BP Mean,skos:exactMatch,loinc:8478-0,Mean blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:225309,ART BP Systolic,skos:exactMatch,loinc:8480-6,Systolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:225310,ART BP Diastolic,skos:exactMatch,loinc:8462-4,Diastolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226329,Blood Temperature CCO (C),skos:exactMatch,loinc:60834-9,Blood temperature,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226531,Admission Weight (lbs.),skos:exactMatch,loinc:29463-7,Body weight,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:228640,EtCO2,skos:exactMatch,loinc:19891-1,Carbon dioxide [Partial pressure] in Exhaled gas --at end expiration,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226512,Admission Weight (Kg),skos:exactMatch,loinc:29463-7,Body weight,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:227632,Arctic Sun/Alsius Temp #1 C,skos:closeMatch,loinc:8310-5,Body temperature,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,0.8, +mimic:227634,Arctic Sun/Alsius Temp #2 C,skos:closeMatch,loinc:8310-5,Body temperature,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,0.8, +mimic:226707,Height,skos:exactMatch,loinc:8302-2,Body height,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226730,Height (cm),skos:exactMatch,loinc:8302-2,Body height,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, mimic:223763,Bladder Pressure,,,,,,,,No suitable LOINC code -mimic:224359,QTc,skos:exactMatch,loinc:8636-3,Q-T interval corrected,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:224167,Manual Blood Pressure Systolic Left,skos:closeMatch,loinc:8480-6,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:224643,Manual Blood Pressure Diastolic Left,skos:closeMatch,loinc:8462-4,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:227243,Manual Blood Pressure Systolic Right,skos:closeMatch,loinc:8480-6,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:227242,Manual Blood Pressure Diastolic Right,skos:closeMatch,loinc:8462-4,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:224192,Pulsus Paradoxus,skos:exactMatch,loinc:8452-5,Systolic blood pressure.inspiration - expiration,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:224646,Orthostatic BPs sitting,skos:exactMatch,loinc:8459-0,Systolic blood pressure--sitting,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:226094,Orthostatic BPd sitting,skos:exactMatch,loinc:8453-3,Diastolic blood pressure--sitting,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:224645,Orthostatic BPs lying,skos:exactMatch,loinc:8461-6,Systolic blood pressure--supine,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:226092,Orthostatic BPd lying,skos:exactMatch,loinc:8455-8,Diastolic blood pressure--supine,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:223765,Orthostatic HR sitting,skos:exactMatch,loinc:69000-8,Heart rate --sitting,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224359,QTc,skos:exactMatch,loinc:8636-3,Q-T interval corrected,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224167,Manual Blood Pressure Systolic Left,skos:closeMatch,loinc:8480-6,Systolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224643,Manual Blood Pressure Diastolic Left,skos:closeMatch,loinc:8462-4,Diastolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:227243,Manual Blood Pressure Systolic Right,skos:closeMatch,loinc:8480-6,Systolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:227242,Manual Blood Pressure Diastolic Right,skos:closeMatch,loinc:8462-4,Diastolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224192,Pulsus Paradoxus,skos:exactMatch,loinc:8452-5,Systolic blood pressure.inspiration - expiration,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224646,Orthostatic BPs sitting,skos:exactMatch,loinc:8459-0,Systolic blood pressure--sitting,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226094,Orthostatic BPd sitting,skos:exactMatch,loinc:8453-3,Diastolic blood pressure--sitting,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224645,Orthostatic BPs lying,skos:exactMatch,loinc:8461-6,Systolic blood pressure--supine,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226092,Orthostatic BPd lying,skos:exactMatch,loinc:8455-8,Diastolic blood pressure--supine,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223765,Orthostatic HR sitting,skos:exactMatch,loinc:69000-8,Heart rate --sitting,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, mimic:224166,Doppler BP,,,,,,,,No suitable LOINC code -mimic:223766,Orthostatic BPs standing,skos:exactMatch,loinc:8460-8,Systolic blood pressure--standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:226096,Orthostatic BPd standing,skos:exactMatch,loinc:8454-1,Diastolic blood pressure--standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:223764,Orthostatic HR lying,skos:exactMatch,loinc:68999-2,Heart rate --supine,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:224647,Orthostatic HR standing,skos:exactMatch,loinc:69001-6,Heart rate --standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223766,Orthostatic BPs standing,skos:exactMatch,loinc:8460-8,Systolic blood pressure--standing,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226096,Orthostatic BPd standing,skos:exactMatch,loinc:8454-1,Diastolic blood pressure--standing,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223764,Orthostatic HR lying,skos:exactMatch,loinc:68999-2,Heart rate --supine,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224647,Orthostatic HR standing,skos:exactMatch,loinc:69001-6,Heart rate --standing,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, northwestern:320045,skos:exactMatch,loinc:8867-4,semapv:ManualMappingCuration,PULSE,Heart rate,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, northwestern:320277,skos:exactMatch,loinc:59408-5,semapv:ManualMappingCuration,PULSE OXIMETRY,Oxygen saturation in Arterial blood by Pulse oximetry,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, northwestern:320210,skos:exactMatch,loinc:9279-1,semapv:ManualMappingCuration,RESPIRATIONS,Respiratory rate,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, diff --git a/mimic-iv/concepts/concept_map/chartevents_to_omop.csv b/mimic-iv/concepts/concept_map/chartevents_to_omop.csv index 7bb707086..b6937b8a7 100644 --- a/mimic-iv/concepts/concept_map/chartevents_to_omop.csv +++ b/mimic-iv/concepts/concept_map/chartevents_to_omop.csv @@ -1,46 +1,46 @@ subject_id,subject_label,predicate_id,object_id,object_label,mapping_justification,author_id,reviewer_id,confidence,comment -mimic:220045,Heart Rate,skos:exactMatch,omop:3027018,Heart rate,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220210,Respiratory Rate,skos:exactMatch,omop:3024171,Respiratory rate,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220277,O2 saturation pulseoxymetry,skos:exactMatch,omop:40762499,Oxygen saturation in Arterial blood by Pulse oximetry,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220179,Non Invasive Blood Pressure systolic,skos:exactMatch,omop:21492239,Systolic blood pressure by Noninvasive,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220180,Non Invasive Blood Pressure diastolic,skos:exactMatch,omop:21492240,Diastolic blood pressure by Noninvasive,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220181,Non Invasive Blood Pressure mean,skos:exactMatch,omop:21492241,Mean blood pressure by Noninvasive,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220052,Arterial Blood Pressure mean,skos:exactMatch,omop:3027598,Mean blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220050,Arterial Blood Pressure systolic,skos:exactMatch,omop:3004249,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220051,Arterial Blood Pressure diastolic,skos:exactMatch,omop:3012888,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:223761,Temperature Fahrenheit,skos:exactMatch,omop:3020891,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220060,Pulmonary Artery Pressure diastolic,skos:exactMatch,omop:3017188,Pulmonary artery Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220059,Pulmonary Artery Pressure systolic,skos:exactMatch,omop:3005606,Pulmonary artery Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:220061,Pulmonary Artery Pressure mean,skos:exactMatch,omop:3028074,Pulmonary artery Mean blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:223762,Temperature Celsius,skos:exactMatch,omop:3020891,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:225312,ART BP Mean,skos:exactMatch,omop:3027598,Mean blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:225309,ART BP Systolic,skos:exactMatch,omop:3004249,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:225310,ART BP Diastolic,skos:exactMatch,omop:3012888,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:226329,Blood Temperature CCO (C),skos:exactMatch,omop:21490586,Blood temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:226531,Admission Weight (lbs.),skos:exactMatch,omop:3025315,Body weight,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:228640,EtCO2,skos:exactMatch,omop:3035357,Carbon dioxide [Partial pressure] in Exhaled gas --at end expiration,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:226512,Admission Weight (Kg),skos:exactMatch,omop:3025315,Body weight,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:227632,Arctic Sun/Alsius Temp #1 C,skos:closeMatch,omop:3020891,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,0.8, -mimic:227634,Arctic Sun/Alsius Temp #2 C,skos:closeMatch,omop:3020891,Body temperature,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,0.8, -mimic:226707,Height,skos:exactMatch,omop:3036277,Body height,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:226730,Height (cm),skos:exactMatch,omop:3036277,Body height,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220045,Heart Rate,skos:exactMatch,omop:3027018,Heart rate,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220210,Respiratory Rate,skos:exactMatch,omop:3024171,Respiratory rate,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220277,O2 saturation pulseoxymetry,skos:exactMatch,omop:40762499,Oxygen saturation in Arterial blood by Pulse oximetry,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220179,Non Invasive Blood Pressure systolic,skos:exactMatch,omop:21492239,Systolic blood pressure by Noninvasive,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220180,Non Invasive Blood Pressure diastolic,skos:exactMatch,omop:21492240,Diastolic blood pressure by Noninvasive,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220181,Non Invasive Blood Pressure mean,skos:exactMatch,omop:21492241,Mean blood pressure by Noninvasive,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220052,Arterial Blood Pressure mean,skos:exactMatch,omop:3027598,Mean blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220050,Arterial Blood Pressure systolic,skos:exactMatch,omop:3004249,Systolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220051,Arterial Blood Pressure diastolic,skos:exactMatch,omop:3012888,Diastolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223761,Temperature Fahrenheit,skos:exactMatch,omop:3020891,Body temperature,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220060,Pulmonary Artery Pressure diastolic,skos:exactMatch,omop:3017188,Pulmonary artery Diastolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220059,Pulmonary Artery Pressure systolic,skos:exactMatch,omop:3005606,Pulmonary artery Systolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:220061,Pulmonary Artery Pressure mean,skos:exactMatch,omop:3028074,Pulmonary artery Mean blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223762,Temperature Celsius,skos:exactMatch,omop:3020891,Body temperature,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:225312,ART BP Mean,skos:exactMatch,omop:3027598,Mean blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:225309,ART BP Systolic,skos:exactMatch,omop:3004249,Systolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:225310,ART BP Diastolic,skos:exactMatch,omop:3012888,Diastolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226329,Blood Temperature CCO (C),skos:exactMatch,omop:21490586,Blood temperature,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226531,Admission Weight (lbs.),skos:exactMatch,omop:3025315,Body weight,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:228640,EtCO2,skos:exactMatch,omop:3035357,Carbon dioxide [Partial pressure] in Exhaled gas --at end expiration,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226512,Admission Weight (Kg),skos:exactMatch,omop:3025315,Body weight,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:227632,Arctic Sun/Alsius Temp #1 C,skos:closeMatch,omop:3020891,Body temperature,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,0.8, +mimic:227634,Arctic Sun/Alsius Temp #2 C,skos:closeMatch,omop:3020891,Body temperature,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,0.8, +mimic:226707,Height,skos:exactMatch,omop:3036277,Body height,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226730,Height (cm),skos:exactMatch,omop:3036277,Body height,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, mimic:223763,Bladder Pressure,,,,,,,,No suitable LOINC code -mimic:224359,QTc,skos:exactMatch,omop:3026258,Q-T interval corrected,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:224167,Manual Blood Pressure Systolic Left,skos:closeMatch,omop:3004249,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:224643,Manual Blood Pressure Diastolic Left,skos:closeMatch,omop:3012888,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:227243,Manual Blood Pressure Systolic Right,skos:closeMatch,omop:3004249,Systolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:227242,Manual Blood Pressure Diastolic Right,skos:closeMatch,omop:3012888,Diastolic blood pressure,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:224192,Pulsus Paradoxus,skos:exactMatch,omop:3034464,Systolic blood pressure.inspiration - expiration,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:224646,Orthostatic BPs sitting,skos:exactMatch,omop:3018586,Systolic blood pressure--sitting,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:226094,Orthostatic BPd sitting,skos:exactMatch,omop:3034703,Diastolic blood pressure--sitting,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:224645,Orthostatic BPs lying,skos:exactMatch,omop:3009395,Systolic blood pressure--supine,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:226092,Orthostatic BPd lying,skos:exactMatch,omop:3013940,Diastolic blood pressure--supine,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:223765,Orthostatic HR sitting,skos:exactMatch,omop:40771525,Heart rate --sitting,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224359,QTc,skos:exactMatch,omop:3026258,Q-T interval corrected,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224167,Manual Blood Pressure Systolic Left,skos:closeMatch,omop:3004249,Systolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224643,Manual Blood Pressure Diastolic Left,skos:closeMatch,omop:3012888,Diastolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:227243,Manual Blood Pressure Systolic Right,skos:closeMatch,omop:3004249,Systolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:227242,Manual Blood Pressure Diastolic Right,skos:closeMatch,omop:3012888,Diastolic blood pressure,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224192,Pulsus Paradoxus,skos:exactMatch,omop:3034464,Systolic blood pressure.inspiration - expiration,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224646,Orthostatic BPs sitting,skos:exactMatch,omop:3018586,Systolic blood pressure--sitting,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226094,Orthostatic BPd sitting,skos:exactMatch,omop:3034703,Diastolic blood pressure--sitting,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224645,Orthostatic BPs lying,skos:exactMatch,omop:3009395,Systolic blood pressure--supine,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226092,Orthostatic BPd lying,skos:exactMatch,omop:3013940,Diastolic blood pressure--supine,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223765,Orthostatic HR sitting,skos:exactMatch,omop:40771525,Heart rate --sitting,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, mimic:224166,Doppler BP,,,,,,,,No suitable LOINC code -mimic:223766,Orthostatic BPs standing,skos:exactMatch,omop:3035856,Systolic blood pressure--standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:226096,Orthostatic BPd standing,skos:exactMatch,omop:3019962,Diastolic blood pressure--standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:223764,Orthostatic HR lying,skos:exactMatch,omop:40771524,Heart rate --supine,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, -mimic:224647,Orthostatic HR standing,skos:exactMatch,omop:40771526,Heart rate --standing,HumanCurated,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223766,Orthostatic BPs standing,skos:exactMatch,omop:3035856,Systolic blood pressure--standing,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:226096,Orthostatic BPd standing,skos:exactMatch,omop:3019962,Diastolic blood pressure--standing,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:223764,Orthostatic HR lying,skos:exactMatch,omop:40771524,Heart rate --supine,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, +mimic:224647,Orthostatic HR standing,skos:exactMatch,omop:40771526,Heart rate --standing,semapv:ManualMappingCuration,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, northwestern:320045,skos:exactMatch,omop:3027018,semapv:ManualMappingCuration,PULSE,Heart rate,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, northwestern:320277,skos:exactMatch,omop:40762499,semapv:ManualMappingCuration,PULSE OXIMETRY,Oxygen saturation in Arterial blood by Pulse oximetry,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1, northwestern:320210,skos:exactMatch,omop:3024171,semapv:ManualMappingCuration,RESPIRATIONS,Respiratory rate,orcid:0000-0001-8822-1884,orcid:0000-0002-9348-9284,1,