Merge pull request #16 from aidh-ms/issue/69-rework-eicu

Rework EICU
aidh-ms · Oct 7, 2024 · 9d024eb · 9d024eb
2 parents a180646 + 345c761
commit 9d024eb
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Showing 18 changed files with 110 additions and 12 deletions.
diff --git a/concepts/Adrenaline_dosage.yml b/concepts/Adrenaline_dosage.yml
@@ -4,7 +4,7 @@ identifiers:
   snomed: ''
 lower_limit: ''
 mapper:
-- klass: MimicObservationMapper
+- klass: MimicDosageMapper
   params:
     constraints:
       itemid: '221289'

diff --git a/concepts/Age.yml b/concepts/Age.yml
@@ -14,6 +14,14 @@ mapper:
     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'
diff --git a/concepts/BodyHeight.yml b/concepts/BodyHeight.yml
@@ -12,6 +12,14 @@ mapper:
     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'
diff --git a/concepts/BodyTemperature.yml b/concepts/BodyTemperature.yml
@@ -12,6 +12,14 @@ mapper:
     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'
diff --git a/concepts/Creatinine_absolute_serum.yml b/concepts/Creatinine_absolute_serum.yml
@@ -8,10 +8,10 @@ mapper:
   params:
     constraints:
       itemid: '220615'
-    schema: mimic_hosp
-    table: labevents
+    schema: mimiciv_icu
+    table: chartevents
   source: mimiciv
-  unit: ''
+  unit: 'mg/dl'
 name: Creatinine_absolute_serum
 unit: mg/dl
 upper_limit: '1000000'
diff --git a/concepts/DiastolicBloodPressue_Arterial_Invasive.yml b/concepts/DiastolicBloodPressue_Arterial_Invasive.yml
@@ -12,6 +12,14 @@ mapper:
     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'
diff --git a/concepts/DiastolicBloodPressue_Arterial_noninvasive.yml b/concepts/DiastolicBloodPressue_Arterial_noninvasive.yml
@@ -12,6 +12,14 @@ mapper:
     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'
diff --git a/concepts/Dobutamine_dosage.yml b/concepts/Dobutamine_dosage.yml
@@ -4,7 +4,7 @@ identifiers:
   snomed: ''
 lower_limit: ''
 mapper:
-- klass: MimicObservationMapper
+- klass: MimicDosageMapper
   params:
     constraints:
       itemid: '221653'

diff --git a/concepts/Gender.yml b/concepts/Gender.yml
@@ -6,12 +6,22 @@ lower_limit: ''
 mapper:
 - klass: MimicObservationMapper
   params:
-    constraints:
-      itemid: '226228'
-    schema: mimiciv_icu
-    table: chartevents
+    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: ''
diff --git a/concepts/HeartRate.yml b/concepts/HeartRate.yml
@@ -12,6 +12,14 @@ mapper:
     table: chartevents
   source: mimiciv
   unit: bpm
+- klass: EICUObservationMapper
+  params:
+    fields:
+      value: heartrate
+    schema: eicu_crd
+    table: vitalperiodic
+  source: eicu
+  unit: bpm
 name: HeartRate
 unit: bpm
 upper_limit: '300'
diff --git a/concepts/MeanBloodPressue_Arterial_Invasive.yml b/concepts/MeanBloodPressue_Arterial_Invasive.yml
@@ -12,6 +12,14 @@ mapper:
     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'
diff --git a/concepts/MeanBloodPressue_Arterial_Noninvasive.yml b/concepts/MeanBloodPressue_Arterial_Noninvasive.yml
@@ -12,6 +12,14 @@ mapper:
     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'
diff --git a/concepts/Norepinephrine_dosage.yml b/concepts/Norepinephrine_dosage.yml
@@ -4,7 +4,7 @@ identifiers:
   snomed: ''
 lower_limit: ''
 mapper:
-- klass: MimicObservationMapper
+- klass: MimicDosageMapper
   params:
     constraints:
       itemid: '221906'

diff --git a/concepts/OxygenSaturation_Peripheral.yml b/concepts/OxygenSaturation_Peripheral.yml
@@ -12,6 +12,14 @@ mapper:
     table: chartevents
   source: mimiciv
   unit: '%'
+- klass: EICUObservationMapper
+  params:
+    fields:
+      value: sao2
+    schema: eicu_crd
+    table: vitalperiodic
+  source: eicu
+  unit: '%'
 name: OxygenSaturation_Peripheral
 unit: '%'
 upper_limit: '100'
diff --git a/concepts/SystolicBloodPressure_Arterial_Invasive.yml b/concepts/SystolicBloodPressure_Arterial_Invasive.yml
@@ -12,6 +12,14 @@ mapper:
     table: chartevents
   source: mimiciv
   unit: mmHg
+- klass: EICUObservationMapper
+  params:
+    fields:
+      value: systemicsystolic
+    schema: eicu_crd
+    table: vitalperiodic
+  source: eicu
+  unit: mmHg
 name: SystolicBloodPressure_Arterial_Invasive
 unit: mmHg
 upper_limit: '300'
diff --git a/concepts/SystolicBloodPressure_Arterial_noninvasive.yml b/concepts/SystolicBloodPressure_Arterial_noninvasive.yml
@@ -12,6 +12,14 @@ mapper:
     table: chartevents
   source: mimiciv
   unit: mmHg
+- klass: EICUObservationMapper
+  params:
+    fields:
+      value: noninvasivesystolic
+    schema: eicu_crd
+    table: vitalaperiodic
+  source: eicu
+  unit: mmHg
 name: SystolicBloodPressure_Arterial_noninvasive
 unit: mmHg
 upper_limit: '200'
diff --git a/concepts/Vancomycine_dosage.yml b/concepts/Vancomycine_dosage.yml
@@ -4,7 +4,7 @@ identifiers:
   snomed: ''
 lower_limit: ''
 mapper:
-- klass: MimicObservationMapper
+- klass: MimicDosageMapper
   params:
     constraints:
       itemid: '225798'

diff --git a/concepts/Vasopressine_dosage.yml b/concepts/Vasopressine_dosage.yml
@@ -4,7 +4,7 @@ identifiers:
   snomed: ''
 lower_limit: ''
 mapper:
-- klass: MimicObservationMapper
+- klass: MimicDosageMapper
   params:
     constraints:
       itemid: '222315'