From 92e366be1ce83687f09dac785c6465b1149803e8 Mon Sep 17 00:00:00 2001
From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com>
Date: Mon, 16 Sep 2024 21:00:39 +0200
Subject: [PATCH 1/5] update heart rate

---
 concepts/HeartRate.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/concepts/HeartRate.yml b/concepts/HeartRate.yml
index dc66431..60a7cf8 100644
--- 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'

From 8dc6743dd48e1ffdba3964fdccededd253eb169d Mon Sep 17 00:00:00 2001
From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com>
Date: Mon, 16 Sep 2024 21:38:30 +0200
Subject: [PATCH 2/5] update concepts

---
 concepts/BodyTemperature.yml                            | 8 ++++++++
 concepts/DiastolicBloodPressue_Arterial_Invasive.yml    | 8 ++++++++
 concepts/DiastolicBloodPressue_Arterial_noninvasive.yml | 8 ++++++++
 concepts/MeanBloodPressue_Arterial_Invasive.yml         | 8 ++++++++
 concepts/MeanBloodPressue_Arterial_Noninvasive.yml      | 8 ++++++++
 concepts/OxygenSaturation_Peripheral.yml                | 8 ++++++++
 concepts/SystolicBloodPressure_Arterial_Invasive.yml    | 8 ++++++++
 concepts/SystolicBloodPressure_Arterial_noninvasive.yml | 8 ++++++++
 8 files changed, 64 insertions(+)

diff --git a/concepts/BodyTemperature.yml b/concepts/BodyTemperature.yml
index df4d01a..053132e 100644
--- 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/DiastolicBloodPressue_Arterial_Invasive.yml b/concepts/DiastolicBloodPressue_Arterial_Invasive.yml
index a1c8f8a..75f63a7 100644
--- 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
index 41fad79..e89de0f 100644
--- 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/MeanBloodPressue_Arterial_Invasive.yml b/concepts/MeanBloodPressue_Arterial_Invasive.yml
index a0aa170..e5dfad6 100644
--- 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
index 9f8d9fe..73ba465 100644
--- 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/OxygenSaturation_Peripheral.yml b/concepts/OxygenSaturation_Peripheral.yml
index c3da6a0..e9361f6 100644
--- 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
index 714f507..33ed4c9 100644
--- 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
index 87bdcd9..7cd9339 100644
--- 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'

From 6da3fab7112fcbefc4d6897fc51c809701b0ab5f Mon Sep 17 00:00:00 2001
From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com>
Date: Thu, 19 Sep 2024 21:03:24 +0200
Subject: [PATCH 3/5] add concepts

---
 concepts/Age.yml        | 8 ++++++++
 concepts/BodyHeight.yml | 8 ++++++++
 concepts/Gender.yml     | 8 ++++++++
 3 files changed, 24 insertions(+)

diff --git a/concepts/Age.yml b/concepts/Age.yml
index 64414ef..42aa8c3 100644
--- 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
index 48bc93f..1ff260a 100644
--- 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/Gender.yml b/concepts/Gender.yml
index 4a5a0d4..e6f34fb 100644
--- a/concepts/Gender.yml
+++ b/concepts/Gender.yml
@@ -12,6 +12,14 @@ mapper:
     table: chartevents
   source: mimiciv
   unit: ''
+- klass: EICUPationObservationMapper
+  params:
+    fields:
+      value: gender
+    schema: eicu_crd
+    table: patient
+  source: eicu
+  unit: ''
 name: Gender
 unit: ''
 upper_limit: ''

From 34dfdc6fe8912bb86a7c9a37b473c768df9965de Mon Sep 17 00:00:00 2001
From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com>
Date: Mon, 23 Sep 2024 20:53:17 +0200
Subject: [PATCH 4/5] fix definitions

---
 concepts/Adrenaline_dosage.yml     | 2 +-
 concepts/Dobutamine_dosage.yml     | 2 +-
 concepts/Norepinephrine_dosage.yml | 2 +-
 concepts/Vancomycine_dosage.yml    | 2 +-
 concepts/Vasopressine_dosage.yml   | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/concepts/Adrenaline_dosage.yml b/concepts/Adrenaline_dosage.yml
index 7aa22e3..8838920 100644
--- 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/Dobutamine_dosage.yml b/concepts/Dobutamine_dosage.yml
index 687e768..5db0a1c 100644
--- 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/Norepinephrine_dosage.yml b/concepts/Norepinephrine_dosage.yml
index c73c2bf..59b0436 100644
--- 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/Vancomycine_dosage.yml b/concepts/Vancomycine_dosage.yml
index b9d9fce..4f57af2 100644
--- 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
index 21acf64..84381d1 100644
--- 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'

From 345c761bca1531b3ee72c92cb1ee10d65681fef7 Mon Sep 17 00:00:00 2001
From: Paul-B98 <115164840+Paul-B98@users.noreply.github.com>
Date: Fri, 4 Oct 2024 15:37:23 +0200
Subject: [PATCH 5/5] fix mimic concepts

---
 concepts/Creatinine_absolute_serum.yml |  6 +++---
 concepts/Gender.yml                    | 10 ++++++----
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/concepts/Creatinine_absolute_serum.yml b/concepts/Creatinine_absolute_serum.yml
index 3b1cd79..b017c79 100644
--- 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/Gender.yml b/concepts/Gender.yml
index e6f34fb..c292eac 100644
--- a/concepts/Gender.yml
+++ b/concepts/Gender.yml
@@ -6,10 +6,12 @@ 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