endoreg-db 0.3.4__py3-none-any.whl → 0.3.6__py3-none-any.whl

endoreg_db/data/examination/examinations/data.yaml

@@ -1,17 +1,66 @@
-- model: report.Examination
-  fields:
-    name: "colonoscopy"
-    name_de: "Koloskopie"
-    name_en: "Colonoscopy"
-    examination_types: [
-      "endoscopy"
-    ]
-
-- model: report.Examination
-  fields:
-    name: "gastroscopy"
-    name_de: "Gastroskopie"
-    name_en: "Gastroscopy"
-    examination_types: [
-      "endoscopy"
+- model: report.Examination
+  fields:
+    name: "colonoscopy"
+    name_de: "Koloskopie"
+    name_en: "Colonoscopy"
+    examination_types: [
+      "endoscopy"
+    ]
+
+- model: report.Examination
+  fields:
+    name: "gastroscopy"
+    name_de: "Gastroskopie"
+    name_en: "Gastroscopy"
+    examination_types: [
+      "endoscopy"
+    ]
+
+# endosonography_upper_gi
+- model: report.Examination
+  fields:
+    name: "endosonography_upper_gi"
+    name_de: "Endosonographie oberer GI-Trakt"
+    name_en: "Endosonography Upper GI Tract"
+    examination_types: [
+      "endoscopy"
+    ]
+
+- model: report.Examination
+  fields:
+    name: "endosonography_lower_gi"
+    name_de: "Endosonographie unterer GI-Trakt"
+    name_en: "Endosonography Lower GI Tract"
+    examination_types: [
+      "endoscopy"
+    ]
+
+# ERCP
+- model: report.Examination
+  fields:
+    name: "ercp"
+    name_de: "ERCP"
+    name_en: "ERCP"
+    examination_types: [
+      "endoscopy"
+    ]
+
+# small bowel endoscopy
+- model: report.Examination
+  fields:
+    name: "small_bowel_endoscopy"
+    name_de: "Dünndarmendoskopie"
+    name_en: "Small Bowel Endoscopy"
+    examination_types: [
+      "endoscopy"
+    ]
+
+# capsule endoscopy
+- model: report.Examination
+  fields:
+    name: "capsule_endoscopy"
+    name_de: "Kapselendoskopie"
+    name_en: "Capsule Endoscopy"
+    examination_types: [
+      "endoscopy"
     ]

endoreg_db/data/examination/time/data.yaml

@@ -1,48 +1,48 @@
-- model: report.ExaminationTime
-  fields:
-    name: "colonoscopy-total-time"
-    name_de: "Koloskopie Zeiten"
-    name_en: "Colonoscopy Times"
-    time_types: [
-      "colonoscopy-time"
-    ]
-  
-# withdrawal-time
-- model: report.ExaminationTime
-  fields:
-    name: "withdrawal-time"
-    name_de: "Withdrawal Time"
-    name_en: "Withdrawal Time"
-    time_types: [
-      "colonoscopy-time"
-    ]
-
-# cecum-time
-- model: report.ExaminationTime
-  fields:
-    name: "cecum-time"
-    name_de: "Zökum Zeit"
-    name_en: "Cecum Time"
-    time_types: [
-      "colonoscopy-time"
-    ]
-
-# intubation-time
-- model: report.ExaminationTime
-  fields:
-    name: "intubation-time"
-    name_de: "Intubationszeit"
-    name_en: "Intubation Time"
-    time_types: [
-      "colonoscopy-time"
-    ]
-
-# colonoscopy-intervention-time
-- model: report.ExaminationTimeType
-  fields:
-    name: "colonoscopy-intervention-time"
-    name_de: "Interventionszeit"
-    name_en: "Intervention Time"
-    time_types: [
-      "colonoscopy-time"
+- model: report.ExaminationTime
+  fields:
+    name: "colonoscopy-total-time"
+    name_de: "Koloskopie Zeiten"
+    name_en: "Colonoscopy Times"
+    time_types: [
+      "colonoscopy-time"
+    ]
+  
+# withdrawal-time
+- model: report.ExaminationTime
+  fields:
+    name: "withdrawal-time"
+    name_de: "Withdrawal Time"
+    name_en: "Withdrawal Time"
+    time_types: [
+      "colonoscopy-time"
+    ]
+
+# cecum-time
+- model: report.ExaminationTime
+  fields:
+    name: "cecum-time"
+    name_de: "Zökum Zeit"
+    name_en: "Cecum Time"
+    time_types: [
+      "colonoscopy-time"
+    ]
+
+# intubation-time
+- model: report.ExaminationTime
+  fields:
+    name: "intubation-time"
+    name_de: "Intubationszeit"
+    name_en: "Intubation Time"
+    time_types: [
+      "colonoscopy-time"
+    ]
+
+# colonoscopy-intervention-time
+- model: report.ExaminationTimeType
+  fields:
+    name: "colonoscopy-intervention-time"
+    name_de: "Interventionszeit"
+    name_en: "Intervention Time"
+    time_types: [
+      "colonoscopy-time"
     ]

endoreg_db/data/examination/time-type/data.yaml

@@ -1,8 +1,8 @@
-- model:
-  fields:
-    name: "colonoscopy-time"
-    name_de: "Koloskopie-Zeit"
-    name_en: "Colonoscopy Time"
-    examinations: [
-      "colonoscopy"
+- model:
+  fields:
+    name: "colonoscopy-time"
+    name_de: "Koloskopie-Zeit"
+    name_en: "Colonoscopy Time"
+    examinations: [
+      "colonoscopy"
     ]

endoreg_db/data/examination/type/data.yaml

@@ -1,5 +1,5 @@
-- model: report.ExaminationType
-  fields:
-    name: "endoscopy"
-    name_de: "Endoskopie"
-    name_en: "Endoscopy"
+- model: report.ExaminationType
+  fields:
+    name: "endoscopy"
+    name_de: "Endoskopie"
+    name_en: "Endoscopy"

endoreg_db/data/gender/data.yaml

@@ -0,0 +1,18 @@
+- model: endoreg_db.gender
+  fields:
+    name: "male"
+    name_de: "männlich"
+    name_en: "male"
+    abbreviation: "m"
+- model: endoreg_db.gender
+  fields:
+    name: "female"
+    name_de: "weiblich"
+    name_en: "female"
+    abbreviation: "f"
+- model: endoreg_db.gender
+  fields:
+    name: "other"
+    name_de: "andere"
+    name_en: "other"
+    abbreviation: "x"

endoreg_db/data/information_source/data.yaml

@@ -1,30 +1,30 @@
-- model: endoreg_db.InformationSource
-  fields:
-    name: treating_physician
-- model: endoreg_db.InformationSource
-  fields:
-    name: treating_physician_anamnestic
-- model: endoreg_db.InformationSource
-  fields:
-    name: physicians_note_anamnestic
-- model: endoreg_db.InformationSource
-  fields:
-    name: patient_anamnestic
-- model: endoreg_db.InformationSource
-  fields:
-    name: physical_measurement
-- model: endoreg_db.InformationSource
-  fields:
-    name: family_anamnestic
-- model: endoreg_db.InformationSource
-  fields:
-    name: physical_examination
-- model: endoreg_db.InformationSource
-  fields:
-    name: unknown
-- model: endoreg_db.InformationSource
-  fields:
-    name: prediction
-- model: endoreg_db.InformationSource
-  fields:
-    name: annotation
+- model: endoreg_db.InformationSource
+  fields:
+    name: treating_physician
+- model: endoreg_db.InformationSource
+  fields:
+    name: treating_physician_anamnestic
+- model: endoreg_db.InformationSource
+  fields:
+    name: physicians_note_anamnestic
+- model: endoreg_db.InformationSource
+  fields:
+    name: patient_anamnestic
+- model: endoreg_db.InformationSource
+  fields:
+    name: physical_measurement
+- model: endoreg_db.InformationSource
+  fields:
+    name: family_anamnestic
+- model: endoreg_db.InformationSource
+  fields:
+    name: physical_examination
+- model: endoreg_db.InformationSource
+  fields:
+    name: unknown
+- model: endoreg_db.InformationSource
+  fields:
+    name: prediction
+- model: endoreg_db.InformationSource
+  fields:
+    name: annotation

endoreg_db/data/information_source/medication.yaml

@@ -0,0 +1,6 @@
+- model: endoreg_db.InformationSource
+  fields:
+    name: "fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"
+    name_de: "Fachinformation Apixaban (Eliquis) 2.5mg, Bristol Meyer Squibbs"
+    name_en: "Apixaban (Eliquis) 2.5mg, Bristol Meyer Squibbs"
+    date: "2024-04-28"

endoreg_db/data/lab_value/cardiac_enzymes.yaml

@@ -0,0 +1,31 @@
+# Creatine kinase: Female: 30–135 U/L; male: 55–170 U/L 
+# Creatine kinase MB (CKMB): ˂5% of total 
+# Troponin: ≤0.04 ng/mL
+
+- model: endoreg_db.lab_value
+  fields:
+    name: "creatine_kinase"
+    name_de: "Kreatinkinase"
+    name_en: "Creatine Kinase"
+    abbreviation: "CK"
+    default_unit: "units per liter"
+    normal_range_gender_dependent: true
+    default_normal_range: {
+      "female": {
+        "min": 30,
+        "max": 135
+      },
+      "male": {
+        "min": 55,
+        "max": 170
+      }
+    }
+
+- model: endoreg_db.lab_value
+  fields:
+    name: "creatine_kinase_mb_fraction"
+    name_de: "Kreatinkinase MB"
+    name_en: "Creatine Kinase MB"
+    abbreviation: "CKMB%"
+    default_unit: "percent"
+    default_normal_range: {"max": 5}

endoreg_db/data/lab_value/coagulation.yaml

@@ -0,0 +1,49 @@
+# Prothrombin time: 11–13 seconds 
+- model: endoreg_db.lab_value
+  fields:
+    name: "prothrombin_time"
+    name_de: "Prothrombinzeit"
+    name_en: "Prothrombin time"
+    abbreviation: "PTT"
+    default_unit: "seconds"
+    default_normal_range: {"min": 11, "max": 13}
+
+# International normalized ratio (INR): 0.9-1.2
+- model: endoreg_db.lab_value
+  fields:
+    name: "international_normalized_ratio"
+    name_de: "International Normalisierte Ratio"
+    name_en: "International normalized ratio"
+    abbreviation: "INR"
+    default_unit: "ratio"
+    default_normal_range: {"min": 0.9, "max": 1.2}
+
+# Activated partial thromboplastin time (aPTT): 25–35 seconds 
+- model: endoreg_db.lab_value
+  fields:
+    name: "activated_partial_thromboplastin_time"
+    name_de: "Aktivierte partielle Thromboplastinzeit"
+    name_en: "Activated partial thromboplastin time"
+    abbreviation: "aPTT"
+    default_unit: "seconds"
+    default_normal_range: {"min": 25, "max": 35}
+
+# Fibrinogen: 150-350 mg/dL (1.5-3.5 g/L)
+- model: endoreg_db.lab_value
+  fields:
+    name: "fibrinogen"
+    name_de: "Fibrinogen"
+    name_en: "Fibrinogen"
+    abbreviation: "Fib"
+    default_unit: "miligram per deciliter"
+    default_normal_range: {"min": 150, "max": 350}
+
+# Bleeding time:  <8 minutes
+- model: endoreg_db.lab_value
+  fields:
+    name: "bleeding_time"
+    name_de: "Blutungszeit"
+    name_en: "Bleeding time"
+    abbreviation: "BT"
+    default_unit: "minutes"
+    default_normal_range: {"max": 8}

endoreg_db/data/lab_value/electrolytes.yaml

@@ -0,0 +1,190 @@
+# Electrolytes
+# https://emedicine.medscape.com/article/2172316-overview?form=fpf 2024/04/27
+- model: endoreg_db.lab_value
+  fields:
+    name: "ammonia"
+    name_de: "Ammoniak"
+    name_en: "Ammonia"
+    default_unit: "microgram per deciliter"
+    default_normal_range: {"min": 40, "max": 70}
+
+- model: endoreg_db.lab_value
+  fields:
+    name: "ceruloplasmin"
+    name_de: "Ceruloplasmin"
+    name_en: "Ceruloplasmin"
+    default_unit: "miligram per deciliter"
+    default_normal_range: {"min": 25, "max": 43}
+
+- model: endoreg_db.lab_value  
+  fields:
+    name: "chloride"
+    name_de: "Chlorid"
+    name_en: "Chloride"
+    default_unit: "milimole per liter"
+    default_normal_range: {"min": 95, "max": 105}
+
+- model: endoreg_db.lab_value  
+  fields:
+    name: "copper"
+    name_de: "Kupfer"
+    name_en: "Copper"
+    default_unit: "microgram per deciliter"
+    default_normal_range: {"min": 100, "max": 200}
+
+- model: endoreg_db.lab_value  
+  fields:
+    name: "creatinine"
+    name_de: "Kreatinin"
+    name_en: "Creatinine"
+    default_unit: "miligram per deciliter"
+    default_normal_range: {"min": 0.8, "max": 1.3}
+
+- model: endoreg_db.lab_value
+  fields:
+    name: "blood_urea_nitrogen"
+    name_de: "Harnstoff"
+    name_en: "Blood Urea Nitrogen"
+    default_unit: "miligram per deciliter"
+    default_normal_range: {"min": 8, "max": 20}
+
+- model: endoreg_db.lab_value
+  fields:
+    name: "ferritin"
+    name_de: "Ferritin"
+    name_en: "Ferritin"
+    default_unit: "nanogram per mililiter"
+    default_normal_range: {"min": 24, "max": 336}
+
+# Glucose:70–99 mg/dL 
+- model: endoreg_db.lab_value
+  fields:
+    name: "glucose"
+    name_de: "Glukose"
+    name_en: "Glucose"
+    default_unit: "miligram per deciliter"
+    default_normal_range: {"min": 70, "max": 99}
+# Inorganic phosphorous: 3-4.5 mg/dL
+- model: endoreg_db.lab_value
+  fields:
+    name: "inorganic_phosphorous"
+    name_de: "Anorganisches Phosphor"
+    name_en: "Inorganic Phosphorous"
+    default_unit: "miligram per deciliter"
+    default_normal_range: {"min": 3, "max": 4.5}
+
+# Ionized calcium: 1.12–1.23 mmol/L 
+- model: endoreg_db.lab_value
+  fields:
+    name: "ionized_calcium"
+    name_de: "Ionisiertes Calcium"
+    name_en: "Ionized Calcium"
+    default_unit: "milimole per liter"
+    default_normal_range: {"min": 1.12, "max": 1.23}
+
+# Magnesium: 1.6–2.6 mg/dL 
+- model: endoreg_db.lab_value
+  fields:
+    name: "magnesium"
+    name_de: "Magnesium"
+    name_en: "Magnesium"
+    default_unit: "miligram per deciliter"
+    default_normal_range: {"min": 1.6, "max": 2.6}
+
+# Phosphate: 2.5 to 4.5 mg/dL (0.81 to 1.45 mmol/L) 
+- model: endoreg_db.lab_value
+  fields:
+    name: "phosphate"
+    name_de: "Phosphat"
+    name_en: "Phosphate"
+    default_unit: "miligram per deciliter"
+    default_normal_range: {"min": 2.5, "max": 4.5}
+
+# Potassium: 3.5–5.0 mEq/L 
+- model: endoreg_db.lab_value
+  fields:
+    name: "potassium"
+    name_de: "Kalium"
+    name_en: "Potassium"
+    default_unit: "miliequivalent per liter"
+    default_normal_range: {"min": 3.5, "max": 5.0}
+
+# Pyruvate: .08-0.16 mmol/L
+- model: endoreg_db.lab_value
+  fields:
+    name: "pyruvate"
+    name_de: "Pyruvat"
+    name_en: "Pyruvate"
+    default_unit: "milimole per liter"
+    default_normal_range: {"min": 0.08, "max": 0.16}
+
+# Sodium: 136–145 mEq/L 
+- model: endoreg_db.lab_value
+  fields:
+    name: "sodium"
+    name_de: "Natrium"
+    name_en: "Sodium"
+    default_unit: "miliequivalent per liter"
+    default_normal_range: {"min": 136, "max": 145}
+
+# Total calcium: 2-2.6 mmol/L (9-10.5 mg/dL) 
+- model: endoreg_db.lab_value
+  fields:
+    name: "total_calcium"
+    name_de: "Gesamtcalcium"
+    name_en: "Total Calcium"
+    default_unit: "milimole per liter"
+    default_normal_range: {"min": 2, "max": 2.6}
+
+# Total iron-binding capacity: 250–310 μg/dL 
+- model: endoreg_db.lab_value
+  fields:
+    name: "total_iron_binding_capacity"
+    name_de: "Gesamteisenbindungskapazität"
+    name_en: "Total Iron-binding Capacity"
+    default_unit: "microgram per deciliter"
+    default_normal_range: {"min": 250, "max": 310}
+
+# Total serum iron: 50–150 μg/dL 
+- model: endoreg_db.lab_value
+  fields:
+    name: "total_serum_iron"
+    name_de: "Gesamteisenspiegel"
+    name_en: "Total Serum Iron"
+    default_unit: "microgram per deciliter"
+    default_normal_range: {"min": 50, "max": 150}
+
+
+# Transferrin: 200–400 mg/dL 
+- model: endoreg_db.lab_value
+  fields:
+    name: "transferrin"
+    name_de: "Transferrin"
+    name_en: "Transferrin"
+    default_unit: "miligram per deciliter"
+    default_normal_range: {"min": 200, "max": 400}
+
+# Urea: 1.2-3 mmol/L
+- model: endoreg_db.lab_value
+  fields:
+    name: "urea"
+    name_de: "Harnstoff"
+    name_en: "Urea"
+    default_unit: "milimole per liter"
+    default_normal_range: {"min": 1.2, "max": 3 }
+# Uric acid: 0.18-0.48 mmol/L 
+- model: endoreg_db.lab_value
+  fields:
+    name: "uric_acid"
+    name_de: "Harnsäure"
+    name_en: "Uric Acid"
+    default_unit: "milimole per liter"
+    default_normal_range: {"min": 0.18, "max": 0.48}
+# Zinc: 75–140 μg/dL 
+- model: endoreg_db.lab_value
+  fields:
+    name: "zinc"
+    name_de: "Zink"
+    name_en: "Zinc"
+    default_unit: "microgram per deciliter"
+    default_normal_range: {"min": 75, "max": 140}

endoreg_db/data/lab_value/gastrointestinal_function.yaml

@@ -0,0 +1,121 @@
+
+
+- model: endoreg_db.lab_value
+  fields:
+    name: "albumin"
+    name_de: "Albumin"
+    name_en: "Albumin"
+    default_unit: "gram per deciliter"
+    default_normal_range: {"min": 3.5, "max": 5.5}
+
+- model: endoreg_db.lab_value
+  fields:
+    name: "alkaline_phosphatase"
+    name_de: "Alkalische Phosphatase"
+    name_en: "Alkaline Phosphatase"
+    default_unit: "units per liter"
+    default_normal_range: {"min": 30, "max": 120}
+
+# ALT and GPT are the same enzyme
+- model: endoreg_db.lab_value 
+  fields:
+    name: "alanine_aminotransferase"
+    name_de: "Alanin-Aminotransferase"
+    name_en: "Alanine Aminotransferase"
+    abbreviation: "ALT"
+    default_unit: "units per liter"
+    default_normal_range: {"min": 10, "max": 40}
+
+- model: endoreg_db.lab_value
+  fields:
+    name: "glutamic_pyruvic_transaminase"
+    name_de: "Glutamat-Pyruvat-Transaminase"
+    name_en: "Glutamic-Pyruvic Transaminase"
+    abbreviation: "GPT"
+    default_unit: "units per liter"
+    default_normal_range: {"min": 10, "max": 40}
+
+- model: endoreg_db.lab_value 
+  fields:
+    name: "amylase"
+    name_de: "Amylase"
+    name_en: "Amylase"
+    default_unit: "units per liter"
+    default_normal_range: {"min": 25, "max": 125}
+
+# Aspartate aminotransferase (AST): 10–40 U/L 
+- model: endoreg_db.lab_value
+  fields:
+    name: "aspartate_aminotransferase"
+    name_de: "Aspartat-Aminotransferase"
+    name_en: "Aspartate Aminotransferase"
+    abbreviation: "AST"
+    default_unit: "units per liter"
+    default_normal_range: {"min": 10, "max": 40}
+
+# AST and GOT are the same
+- model: endoreg_db.lab_value
+  fields:
+    name: "glutamic_oxaloacetic_transaminase"
+    name_de: "Glutamat-Oxalacetat-Transaminase"
+    name_en: "Glutamic-Oxaloacetic Transaminase"
+    abbreviation: "GOT"
+    default_unit: "units per liter"
+    default_normal_range: {"min": 10, "max": 40}
+
+
+# Direct bilirubin: 0.1–0.3 mg/dL 
+- model: endoreg_db.lab_value
+  fields:
+    name: "direct_bilirubin"
+    name_de: "Direktes Bilirubin"
+    name_en: "Direct Bilirubin"
+    default_unit: "miligram per deciliter"
+    default_normal_range: {"min": 0.1, "max": 0.3}
+
+# Gamma glutamyl transferase: Female: 8–40 U/L; male: 9–50 U/L
+- model: endoreg_db.lab_value
+  fields:
+    name: "gamma_glutamyl_transferase"
+    name_de: "Gamma-Glutamyl-Transferase"
+    name_en: "Gamma-Glutamyl Transferase"
+    abbreviation: "GGT"
+    default_unit: "units per liter"
+    normal_range_gender_dependent: true
+    default_normal_range: {
+      "female": {
+        "min": 8,
+        "max": 40
+      },
+      "male": {
+        "min": 9,
+        "max": 50
+      }
+    }
+
+# Lipase: 10–140 U/L 
+- model: endoreg_db.lab_value
+  fields:
+    name: "lipase"
+    name_de: "Lipase"
+    name_en: "Lipase"
+    default_unit: "units per liter"
+    default_normal_range: {"min": 10, "max": 140}
+
+# Total bilirubin: 0.3–1.0 mg/dL 
+- model: endoreg_db.lab_value
+  fields:
+    name: "total_bilirubin"
+    name_de: "Gesamtbilirubin"
+    name_en: "Total Bilirubin"
+    default_unit: "miligram per deciliter"
+    default_normal_range: {"min": 0.3, "max": 1.0}
+
+# Total protein: 5.5–9.0 g/dL 
+- model: endoreg_db.lab_value
+  fields:
+    name: "total_protein"
+    name_de: "Gesamtprotein"
+    name_en: "Total Protein"
+    default_unit: "gram per deciliter"
+    default_normal_range: {"min": 5.5, "max": 9.0}