endoreg-db 0.8.6.1__py3-none-any.whl → 0.8.8.0__py3-none-any.whl

endoreg_db/data/_examples/finding_classification_choice/colonoscopy_location.yaml

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+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "terminal_ileum"
+    name_de: "terminales Ileum"
+    name_en: "Terminal Ileum"
+    subcategories:
+      description: {
+        choices: ["unspecified"],
+        required: false
+      }
+    numerical_descriptors:
+      cm_rectified:
+        unit: "centimeter"
+        min: 0
+        max: 180
+        description: "Insertion depth of the colonoscope in cm (rectified)"
+        required: false
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "cecum"
+    name_de: "Caecum"
+    name_en: "Cecum"
+    subcategories:
+      description:
+        choices: ["unspecified", "ileocecal-valve", "peri-appendicular"]
+        default: "unspecified"
+        probability: [0.5, 0.3, 0.2]
+        required: true
+    numerical_descriptors:
+      cm_rectified:
+        unit: "centimeter"
+        min: 60
+        max: 140
+        distribution: "uniform"
+        std: null
+        mean: null
+        description: "Insertion depth of the colonoscope in cm (rectified)"
+        required: false
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "ascending_colon"
+    name_de: "Colon ascendens"
+    name_en: "Ascending Colon"
+    subcategories:
+      description:
+        choices: ["unspecified", "proximal", "distal"]
+        probability: [0.5, 0.3, 0.2]
+        default: "unspecified"
+        required: true
+    numerical_descriptors:
+      cm_rectified:
+        unit: "centimeter"
+        min: 40
+        max: 100
+        distribution: "uniform"
+        description: "Insertion depth of the colonoscope in cm (rectified)"
+        required: false
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "right_flexure"
+    name_de: "Rechte Flexur"
+    name_en: "Right Flexure"
+    subcategories:
+      description:
+        choices: ["unspecified", "proximal", "distal"]
+        probability: [0.5, 0.3, 0.2]
+        default: "unspecified"
+        required: true
+    numerical_descriptors:
+      cm_rectified:
+        unit: "centimeter"
+        min: 80
+        max: 180
+        mean: null
+        std: null
+        distribution: "uniform"
+        description: "Insertion depth of the colonoscope in cm (rectified)"
+        required: false
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "transverse_colon"
+    name_de: "Colon transversum"
+    name_en: "Transverse Colon"
+    subcategories:
+      description:
+        choices: ["unspecified", "proximal", "distal"]
+        probability: [0.5, 0.3, 0.2]
+        default: "unspecified"
+        required: true
+    numerical_descriptors:
+      cm_rectified:
+        unit: "centimeter"
+        min: 40
+        max: 80
+        mean: null
+        std: null
+        distribution: "uniform"
+        description: "Insertion depth of the colonoscope in cm (rectified)"
+        required: false
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "descending_colon"
+    name_de: "Colon descendens"
+    name_en: "Descending Colon"
+    subcategories:
+      description:
+        choices: ["unspecified", "proximal", "distal"]
+        probability: [0.5, 0.3, 0.2]
+        default: "unspecified"
+        required: true
+    numerical_descriptors:
+      cm_rectified:
+        unit: "centimeter"
+        min: 35
+        max: 70
+        mean: null
+        std: null
+        distribution: "uniform"
+        description: "Insertion depth of the colonoscope in cm (rectified)"
+        required: false
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "sigmoid_colon"
+    name_de: "Colon sigmoideum"
+    name_en: "Sigmoid Colon"
+    subcategories:
+      description:
+        choices: ["unspecified", "proximal", "distal"]
+        probability: [0.5, 0.3, 0.2]
+        default: "unspecified"
+        required: true
+    numerical_descriptors:
+      cm_rectified:
+        unit: "centimeter"
+        min: 20
+        max: 50
+        description: "Insertion depth of the colonoscope in cm (rectified)"
+        required: true
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "rectum"
+    name_de: "Rektum"
+    name_en: "Rectum"
+    subcategories:
+      description:
+        choices: ["1/3", "2/3", "3/3"]
+        probability: [0.3, 0.3, 0.4]
+        default: "3/3"
+        required: true
+    numerical_descriptors:
+      cm_rectified:
+        unit: "centimeter"
+        min: 5
+        max: 20
+        description: "Insertion depth of the colonoscope in cm (rectified)"
+        required: true
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "anal_canal"
+    name_de: "Analkanal"
+    name_en: "Anal Canal"
+    subcategories:
+      description:
+        choices: ["unspecified", "proximal", "distal"]
+        probability: [0.5, 0.3, 0.2]
+        default: "unspecified"
+        required: false
+    numerical_descriptors:
+      cm_rectified:
+        unit: "centimeter"
+        min: 0
+        max: 3
+        mean: null
+        std: null
+        distribution: "uniform"
+        description: "Insertion depth of the colonoscope in cm (rectified)"
+        required: true
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "left_colon"
+    name_de: "linkes Kolon"
+    name_en: "Left Colon"
+    subcategories:
+      description:
+        choices: ["unspecified", "proximal", "distal"]
+        probability: [0.3, 0.3, 0.3]
+        default: "proximal"
+        required: true
+    numerical_descriptors:
+      cm_rectified:
+        unit: "centimeter"
+        min: 0
+        max: 180
+        mean: null
+        std: null
+        distribution: "uniform"
+        description: "Insertion depth of the colonoscope in cm (rectified)"
+        required: false
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "right_colon"
+    name_de: "rechtes Kolon"
+    name_en: "Right Colon"
+    subcategories:
+      description:
+        choices: ["unspecified", "proximal", "distal"]
+        probability: [0.3, 0.3, 0.3]
+        default: "proximal"
+        required: true
+    numerical_descriptors:
+      cm_rectified:
+        unit: "centimeter"
+        min: 0
+        max: 180
+        mean: null
+        std: null
+        distribution: "uniform"
+        description: "Insertion depth of the colonoscope in cm (rectified)"
+        required: false

endoreg_db/data/_examples/finding_classification_choice/colonoscopy_not_complete_reason.yaml

@@ -0,0 +1,19 @@
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colonoscopy_incomplete_insufficient_preparation"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colonoscopy_incomplete_complication"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colonoscopy_incomplete_pain"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colonoscopy_incomplete_stenosis"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colonoscopy_incomplete_other"

endoreg_db/data/_examples/finding_classification_choice/colonoscopy_size.yaml

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+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_size_categorical_diminutive"
+    name_de: "Größenklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Size Classification (categorical)"
+    description: "Diminutive (< 6 mm)"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_size_categorical_small"
+    name_de: "Größenklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Size Classification (categorical)"
+    description: "Small (6 - 9 mm)"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_size_categorical_medium"
+    name_de: "Größenklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Size Classification (categorical)"
+    description: "Medium (10 - 19 mm)"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_size_categorical_large"
+    name_de: "Größenklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Size Classification (categorical)"
+    description: "Large (> 19 mm)"
+
+##########
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_size_oval_mm"
+    name_de: "Formklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Shape Classification (categorical)"
+    description: "oval lesions"
+    numerical_descriptors:
+      largest_diameter_mm:
+        unit: "mm"
+        min: 0
+        max: 35
+        distribution: "normal"
+        mean: 5
+        std: 3
+        description: "Largest diameter of the lesion in mm"
+        required: true
+      perpendicular_diameter_mm:
+        unit: "mm"
+        min: 0
+        max: 35
+        description: "Perpendicular diameter of the lesion in mm"
+        required: false
+
+# Austria Screening Quality Assurance
+# "colon_lesion_size_austria_categorical_0_5",
+# "colon_lesion_size_austria_categorical_6_9",
+# "colon_lesion_size_austria_categorical_10_20",
+# "colon_lesion_size_austria_categorical_21_x"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_size_austria_categorical_0_5"
+    name_de: "Größenklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Size Classification (categorical)"
+    description: "0 - 5 mm"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_size_austria_categorical_6_9"
+    name_de: "Größenklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Size Classification (categorical)"
+    description: "6 - 9 mm"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_size_austria_categorical_10_20"
+    name_de: "Größenklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Size Classification (categorical)"
+    description: "10 - 20 mm"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_size_austria_categorical_21_x"
+    name_de: "Größenklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Size Classification (categorical)"
+    description: "> 20 mm"

endoreg_db/data/_examples/finding_classification_choice/colonoscopy_summary_worst_finding.yaml

@@ -0,0 +1,15 @@
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colonoscopy_worst_finding_polyp"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colonoscopy_worst_finding_rectum_cancer"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colonoscopy_worst_finding_colon_cancer"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colonoscopy_worst_finding_other"

endoreg_db/data/_examples/finding_classification_choice/complication_generic_types.yaml

@@ -0,0 +1,15 @@
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "complication_generic_type_cardiorespiratory"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "complication_generic_type_bleeding"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "complication_generic_type_perforation"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "complication_generic_type_other"

endoreg_db/data/_examples/finding_classification_choice/examination_setting_generic_types.yaml

@@ -0,0 +1,15 @@
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "examination_setting_generic_location_inpatient"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "examination_setting_generic_location_outpatient"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "examination_setting_operative"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "examination_setting_conservative"

endoreg_db/data/_examples/finding_classification_choice/histology.yaml

@@ -0,0 +1,24 @@
+# "histology_dysplasia_none",
+# "histology_dysplasia_low_grade",
+# "histology_dysplasia_high_grade",
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "histology_dysplasia_none"
+    description: "Histology: No dysplasia"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "histology_dysplasia_low_grade"
+    description: "Histology: Low-grade dysplasia"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "histology_dysplasia_high_grade"
+    description: "Histology: High-grade dysplasia"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "histology_dignity_benign"
+    description: "Histology: Benign"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "histology_dignity_malign"
+    description: "Histology: Malign"

endoreg_db/data/_examples/finding_classification_choice/histology_polyp.yaml

@@ -0,0 +1,20 @@
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "histology_polyp_hyperplastic"
+    description: "Histology: Hyperplastic polyp"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "histology_polyp_adenoma_tubular"
+    description: "Histology: Tubular adenoma"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "histology_polyp_adenoma_tubulovillous"
+    description: "Histology: Tubulovillous adenoma"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "histology_polyp_adenoma_villous"
+    description: "Histology: Villous adenoma"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "histology_polyp_sessile_serrated_lesion"
+    description: "Histology: Sessile serrated lesion"

endoreg_db/data/_examples/finding_classification_choice/outcome.yaml

@@ -0,0 +1,19 @@
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "outcome_restitutio_ad_integrum"
+    description: "Outcome: Restitutio ad integrum"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "outcome_death"
+    description: "Outcome: Death"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "outcome_unknown"
+    description: "Outcome: Unknown"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "outcome_lasting_disability"
+    description: "Outcome: Lasting disability"

endoreg_db/data/_examples/finding_classification_choice/yes_no_na.yaml

@@ -0,0 +1,11 @@
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "yes"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "no"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "na"

endoreg_db/data/_examples/finding_classification_type/colonoscopy_basic.yaml

@@ -0,0 +1,48 @@
+#####
+# Base types for distinguishing morphology and location
+# Related Fields
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "location"
+    name_de: "Lokalisation"
+    name_en: "Location"
+  
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "morphology"
+    name_de: "Morphologie"
+    name_en: "Morphology"
+
+#####
+
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "bowel_prep"
+
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colon_lesion_size"
+
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colon_lesion_surface_intact"
+
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colon_lesion_planarity"
+
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colon_lesion_circularity"
+
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colon_lesion_advanced_imaging"
+
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colon_lesion_shape"
+
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colon_lesion_capillary_pattern"

endoreg_db/data/_examples/finding_intervention/endoscopy.yaml

@@ -0,0 +1,43 @@
+# --- Begin kept interventions ---
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: percutaneous_transhepatic_cholangiography
+    description: "TODO: Add description"
+    intervention_types: []
+    required_lab_values: []
+    contraindications: []
+- model: endoreg_db.finding_intervention
+  fields:
+    name: sonography_guided_liver_punction
+    description: "TODO: Add description"
+    intervention_types: []
+    required_lab_values: []
+    contraindications: []
+- model: endoreg_db.finding_intervention
+  fields:
+    name: xray_guided_liver_punction
+    description: "TODO: Add description"
+    intervention_types: []
+    required_lab_values: []
+    contraindications: []
+- model: endoreg_db.finding_intervention
+  fields:
+    name: percutaneous_transhepatic_biliary_drainage
+    description: "TODO: Add description"
+    intervention_types: []
+    required_lab_values: []
+    contraindications: []
+- model: endoreg_db.finding_intervention
+  fields:
+    name: biliary_stent
+    description: "TODO: Add description"
+    intervention_types: []
+    required_lab_values: []
+    contraindications: []
+# --- End kept interventions ---
+
+# --- Removed interventions moved to other files ---
+# Removed: all items with names starting with "egd_"
+# Removed: all items with names starting with "erc", "ercp", "erp"
+# Removed: all items with names starting with "endosonography_upper_gi_"