Issue/14 add variables

concepts/Adrenaline_dosage.yml

@@ -0,0 +1,17 @@
+description: ''
+identifiers:
+  loinc: ''
+  snomed: ''
+lower_limit: ''
+mapper:
+- klass: MimicDosageMapper
+  params:
+    constraints:
+      itemid: '221289'
+    schema: mimiciv_icu
+    table: inputevents
+  source: mimiciv
+  unit: mg/time
+name: Adrenaline_dosage
+unit: ug/kg/min
+upper_limit: ''

concepts/Age.yml

@@ -0,0 +1,27 @@
+description: Patient's age
+identifiers:
+  loinc: '30525-0'
+  snomed: '397669002'
+lower_limit: '0'
+mapper:
+- klass: MimicObservationMapper
+  params:
+    fields:
+      value: age
+      timestamp: admittime
+    constraints: {}
+    schema: mimiciv_derived
+    table: age
+  source: mimiciv
+  unit: year
+- klass: EICUPationObservationMapper
+  params:
+    fields:
+      value: age
+    schema: eicu_crd
+    table: patient
+  source: eicu
+  unit: year
+name: Age
+unit: year
+upper_limit: '130'

concepts/AirwayPlateauPressure.yml

@@ -0,0 +1,17 @@
+description: Airway Plateau Pressure of a patient
+identifiers:
+  loinc: ''
+  snomed: ''
+lower_limit: '0'
+mapper:
+- klass: MimicObservationMapper
+  params:
+    constraints:
+      itemid: '224696'
+    schema: mimiciv_icu
+    table: chartevents
+  source: mimiciv
+  unit: mmHg
+name: AirwayPlateauPressure
+unit: mmHg
+upper_limit: '100'

concepts/BodyHeight.yml

@@ -0,0 +1,25 @@
+description: Height of a patient's body
+identifiers:
+  loinc: 8302-2
+  snomed: '1153637007'
+lower_limit: '0'
+mapper:
+- klass: MimicObservationMapper
+  params:
+    constraints:
+      itemid: '226730'
+    schema: mimiciv_icu
+    table: chartevents
+  source: mimiciv
+  unit: cm
+- klass: EICUPationObservationMapper
+  params:
+    fields:
+      value: admissionheight
+    schema: eicu_crd
+    table: patient
+  source: eicu
+  unit: cm
+name: BodyHeight
+unit: cm
+upper_limit: '300'

concepts/BodyTemperature.yml

@@ -0,0 +1,25 @@
+description: Temperature of a patient's body, irrespective of site
+identifiers:
+  loinc: ''
+  snomed: ''
+lower_limit: '20'
+mapper:
+- klass: MimicObservationMapper
+  params:
+    constraints:
+      itemid: '223762'
+    schema: mimiciv_icu
+    table: chartevents
+  source: mimiciv
+  unit: °C
+- klass: EICUObservationMapper
+  params:
+    fields:
+      value: temperature
+    schema: eicu_crd
+    table: vitalperiodic
+  source: eicu
+  unit: °C
+name: BodyTemperature
+unit: °C
+upper_limit: '45'

concepts/BodyWeight.yml

@@ -0,0 +1,25 @@
+description: Weight of a patien's body
+identifiers:
+  loinc: 29463-7
+  snomed: '27113001'
+lower_limit: '0'
+mapper:
+- klass: MimicObservationMapper
+  params:
+    constraints:
+      itemid: '224639'
+    schema: mimiciv_icu
+    table: chartevents
+  source: mimiciv
+  unit: kg
+- klass: EICUPationObservationMapper
+  params:
+    fields:
+      value: admissionWeight
+    schema: eicu_crd
+    table: patient
+  source: eicu
+  unit: cm
+name: BodyWeight
+unit: kg
+upper_limit: '500'

concepts/BreathingRate.yml

@@ -0,0 +1,25 @@
+description: Actual breathing rate of patient
+identifiers:
+  loinc: ''
+  snomed: ''
+lower_limit: '0'
+mapper:
+- klass: MimicObservationMapper
+  params:
+    constraints:
+      itemid: '224690'
+    schema: mimiciv_icu
+    table: chartevents
+  source: mimiciv
+  unit: 1/min
+- klass: EICUObservationMapper
+  params:
+    fields:
+      value: respiration
+    schema: eicu_crd
+    table: vitalperiodic
+  source: eicu
+  unit: 1/min
+name: BreathingRate
+unit: 1/min
+upper_limit: '100'

concepts/Creatinine_absolute_serum.yml

@@ -0,0 +1,17 @@
+description: ''
+identifiers:
+  loinc: ''
+  snomed: ''
+lower_limit: '0'
+mapper:
+- klass: MimicObservationMapper
+  params:
+    constraints:
+      itemid: '220615'
+    schema: mimiciv_icu
+    table: chartevents
+  source: mimiciv
+  unit: 'mg/dl'
+name: Creatinine_absolute_serum
+unit: mg/dl
+upper_limit: '1000000'

concepts/DiastolicBloodPressue_Arterial_Invasive.yml

@@ -0,0 +1,25 @@
+description: Diastolic arterial pressure of a patient
+identifiers:
+  loinc: 76213-8
+  snomed: '251073000'
+lower_limit: '0'
+mapper:
+- klass: MimicObservationMapper
+  params:
+    constraints:
+      itemid: '220051'
+    schema: mimiciv_icu
+    table: chartevents
+  source: mimiciv
+  unit: mmHg
+- klass: EICUObservationMapper
+  params:
+    fields:
+      value: systemicdiastolic
+    schema: eicu_crd
+    table: vitalperiodic
+  source: eicu
+  unit: mmHg
+name: DiastolicBloodPressue_Arterial_Invasive
+unit: mmHg
+upper_limit: '200'

concepts/DiastolicBloodPressue_Arterial_noninvasive.yml

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+description: Diastolic arterial pressure of a patient
+identifiers:
+  loinc: ''
+  snomed: '251074006'
+lower_limit: '0'
+mapper:
+- klass: MimicObservationMapper
+  params:
+    constraints:
+      itemid: '220180'
+    schema: mimiciv_icu
+    table: chartevents
+  source: mimiciv
+  unit: mmHg
+- klass: EICUObservationMapper
+  params:
+    fields:
+      value: noninvasivediasystolic
+    schema: eicu_crd
+    table: vitalaperiodic
+  source: eicu
+  unit: mmHg
+name: DiastolicBloodPressue_Arterial_noninvasive
+unit: mmHg
+upper_limit: '200'

concepts/Dobutamine_dosage.yml

@@ -0,0 +1,17 @@
+description: ''
+identifiers:
+  loinc: ''
+  snomed: ''
+lower_limit: ''
+mapper:
+- klass: MimicDosageMapper
+  params:
+    constraints:
+      itemid: '221653'
+    schema: mimiciv_icu
+    table: inputevents
+  source: mimiciv
+  unit: mg/time
+name: Dobutamine_dosage
+unit: ug/kg/min
+upper_limit: ''

concepts/FiO2.yml

@@ -0,0 +1,17 @@
+description: Inspired oxygen concentration of a patient
+identifiers:
+  loinc: ''
+  snomed: ''
+lower_limit: '0'
+mapper:
+- klass: MimicObservationMapper
+  params:
+    constraints:
+      itemid: '223835'
+    schema: mimiciv_icu
+    table: chartevents
+  source: mimiciv
+  unit: '%'
+name: FiO2
+unit: '%'
+upper_limit: '100'

concepts/Gender.yml

@@ -0,0 +1,27 @@
+description: Patient's gender
+identifiers:
+  loinc: ''
+  snomed: ''
+lower_limit: ''
+mapper:
+- klass: MimicObservationMapper
+  params:
+    fields:
+      value: gender
+      timestamp: anchor_year
+    constraints: {}
+    schema: mimiciv_hosp
+    table: patients
+  source: mimiciv
+  unit: ''
+- klass: EICUPationObservationMapper
+  params:
+    fields:
+      value: gender
+    schema: eicu_crd
+    table: patient
+  source: eicu
+  unit: ''
+name: Gender
+unit: ''
+upper_limit: ''

concepts/HeartRate.yml

@@ -1,18 +1,25 @@
+description: heart rate of a patient, source agnostic
+identifiers:
+  loinc: 8867-4
+  snomed: '364075005'
+lower_limit: '0'
+mapper:
+- klass: MimicObservationMapper
+  params:
+    constraints:
+      itemid: '220045'
+    schema: mimiciv_icu
+    table: chartevents
+  source: mimiciv
+  unit: bpm
+- klass: EICUObservationMapper
+  params:
+    fields:
+      value: heartrate
+    schema: eicu_crd
+    table: vitalperiodic
+  source: eicu
+  unit: bpm
 name: HeartRate
-description: Heart rate is the speed of the heartbeat measured by the number of contractions of the heart per minute (bpm).
 unit: bpm
-upper_limit: 300
-lower_limit: 0
-identifiers: 
-  snomed: "364075005"
-  loinc: "8867-4"
-#schema: FHIRObservation
-mapper:
-  - klass: MimicObservationMapper
-    source: mimic
-    unit: bpm
-    params:
-      schema: mimiciv_icu
-      table: chartevents
-      constraints:
-        itemid: "220045"
+upper_limit: '300'

concepts/MeanBloodPressue_Arterial_Invasive.yml

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+description: Mean arterial pressure of a patient
+identifiers:
+  loinc: ''
+  snomed: '251075007'
+lower_limit: '0'
+mapper:
+- klass: MimicObservationMapper
+  params:
+    constraints:
+      itemid: '220052'
+    schema: mimiciv_icu
+    table: chartevents
+  source: mimiciv
+  unit: mmHg
+- klass: EICUObservationMapper
+  params:
+    fields:
+      value: systemicmean
+    schema: eicu_crd
+    table: vitalperiodic
+  source: eicu
+  unit: mmHg
+name: MeanBloodPressue_Arterial_Invasive
+unit: mmHg
+upper_limit: '200'

concepts/MeanBloodPressue_Arterial_Noninvasive.yml

@@ -0,0 +1,25 @@
+description: Diastolic arterial pressure of a patient
+identifiers:
+  loinc: ''
+  snomed: '174255007'
+lower_limit: '0'
+mapper:
+- klass: MimicObservationMapper
+  params:
+    constraints:
+      itemid: '220181'
+    schema: mimiciv_icu
+    table: chartevents
+  source: mimiciv
+  unit: mmHg
+- klass: EICUObservationMapper
+  params:
+    fields:
+      value: noninvasivemean
+    schema: eicu_crd
+    table: vitalaperiodic
+  source: eicu
+  unit: mmHg
+name: MeanBloodPressue_Arterial_Noninvasive
+unit: mmHg
+upper_limit: '200'