endoreg-db 0.5.3__py3-none-any.whl → 0.6.1__py3-none-any.whl

endoreg_db/data/finding_location_classification_choice/colonoscopy.yaml

@@ -0,0 +1,240 @@
+- model: endoreg_db.finding_location_classification_choice
+  fields:
+    name: "terminal_ileum"
+    name_de: "terminales Ileum"
+    name_en: "Terminal Ileum"
+    organs: ["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_location_classification_choice
+  fields:
+    name: "cecum"
+    name_de: "Caecum"
+    name_en: "Cecum"
+    organs: ["colon"]
+    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_location_classification_choice
+  fields:
+    name: "ascending_colon"
+    name_de: "Colon ascendens"
+    name_en: "Ascending Colon"
+    organs: ["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_location_classification_choice
+  fields:
+    name: "right_flexure"
+    name_de: "Rechte Flexur"
+    name_en: "Right Flexure"
+    organs: ["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: 80
+        max: 180
+        mean: null
+        std: null
+        distribution: "uniform"
+        description: "Insertion depth of the colonoscope in cm (rectified)"
+        required: false
+
+- model: endoreg_db.finding_location_classification_choice
+  fields:
+    name: "transverse_colon"
+    name_de: "Colon transversum"
+    name_en: "Transverse Colon"
+    organs: ["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_location_classification_choice
+  fields:
+    name: "descending_colon"
+    name_de: "Colon descendens"
+    name_en: "Descending Colon"
+    organs: ["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_location_classification_choice
+  fields:
+    name: "sigmoid_colon"
+    name_de: "Colon sigmoideum"
+    name_en: "Sigmoid Colon"
+    organs: ["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_location_classification_choice
+  fields:
+    name: "rectum"
+    name_de: "Rektum"
+    name_en: "Rectum"
+    organs: ["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_location_classification_choice
+  fields:
+    name: "anal_canal"
+    name_de: "Analkanal"
+    name_en: "Anal Canal"
+    organs: ["rectum"]
+    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_location_classification_choice
+  fields:
+    name: "left_colon"
+    name_de: "linkes Kolon"
+    name_en: "Left Colon"
+    organs: ["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_location_classification_choice
+  fields:
+    name: "right_colon"
+    name_de: "rechtes Kolon"
+    name_en: "Right Colon"
+    organs: ["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/finding_morphology_classification/colonoscopy.yaml

@@ -0,0 +1,48 @@
+- model: endoreg_db.finding_morphology_classification
+  fields:
+    name: "colon_lesion_size_categorical"
+    classification_type: "colon_lesion_size"
+    name_de: "Größenklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Size Classification (categorical)"
+    
+- model: endoreg_db.finding_morphology_classification
+  fields:
+    name: "colon_lesion_size_mm"
+    classification_type: "colon_lesion_size"
+    name_de: "Größenklassifikation Kolonläsion (numerisch)"
+    name_en: "Colon Lesion Size Classification (numerical)"
+
+- model: endoreg_db.finding_morphology_classification
+  fields:
+    name: "colon_lesion_surface_intact_default"
+    classification_type: "colon_lesion_surface_intact"
+    name_de: "Oberflächenklassifikation Kolonläsion"
+    name_en: "Colon Lesion Surface Classification"
+
+- model: endoreg_db.finding_morphology_classification
+  fields:
+    name: "colon_lesion_planarity_default"
+    classification_type: "colon_lesion_planarity"
+    name_de: "Planaritätsklassifikation Kolonläsion"
+    name_en: "Colon Lesion Planarity Classification"
+
+- model: endoreg_db.finding_morphology_classification
+  fields:
+    name: "colon_lesion_circularity_default"
+    name_de: "Kolonläsion - Zirkularität"
+    name_en: "Colon lesion - circularity"
+    classification_type: "colon_lesion_circularity"    
+
+- model: endoreg_db.finding_morphology_classification
+  fields:
+    name: "colon_lesion_nice"
+    classification_type: "colon_lesion_advanced_imaging"
+    name_de: "Kolonläsion - NICE"
+    name_en: "Colon lesion - NICE"
+
+- model: endoreg_db.finding_morphology_classification
+  fields:
+    name: "colon_lesion_paris"
+    classification_type: "colon_lesion_shape"
+    name_de: "Formklassifikation Kolonläsion"
+    name_en: "Colon Lesion Shape Classification"

endoreg_db/data/finding_morphology_classification_choice/colon_lesion_circularity_default.yaml

@@ -0,0 +1,34 @@
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_circularity_false"
+    name_de: "Kolonläsion - Zirkularität"
+    name_en: "Colon lesion - circularity"
+    classification: "colon_lesion_circularity_default"
+    description: "Category for non-circular lesions"
+
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_circularity_true"
+    name_de: "Kolonläsion - Zirkularität"
+    name_en: "Colon lesion - circularity"
+    classification: "colon_lesion_circularity_default"
+    description: "Category for circular lesions"
+    numerical_descriptors:
+      length:
+        unit: "milimeter"
+        min: 0
+        max: 100
+        default: null
+        distribution: "uniform"
+        description: "Length of the lesion in mm"
+        required: true
+      circumference:
+        unit: "percent"
+        min: 33
+        max: 100
+        mean: 50
+        std: 10
+        default: null
+        distribution: "normal"
+        description: "Circumference of the lesion in %"
+        required: true

endoreg_db/data/finding_morphology_classification_choice/colon_lesion_nice.yaml

@@ -0,0 +1,20 @@
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_NICE_type_1"
+    name_de: "Kolonläsion - NICE Typ 1"
+    name_en: "Colon lesion - NICE type 1"
+    classification: "colon_lesion_nice"
+
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_NICE_type_2"
+    name_de: "Kolonläsion - NICE Typ 2"
+    name_en: "Colon lesion - NICE type 2"
+    classification: "colon_lesion_nice"
+
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_NICE_type_3"
+    name_de: "Kolonläsion - NICE Typ 3"
+    name_en: "Colon lesion - NICE type 3"
+    classification: "colon_lesion_nice"

endoreg_db/data/finding_morphology_classification_choice/colon_lesion_paris.yaml

@@ -0,0 +1,65 @@
+- model: endoreg_db.finiding_morphology_classification_choice
+  fields:
+    name: "colon_paris_Is"
+    name_de: "Kolonläsion Formklassifikation (Paris Is)"
+    name_en: "Colon Lesion Shape Classification (Paris Is)"
+    classification: "colon_lesion_paris"
+    description: "Shape classification for colon lesions (Paris Is)"
+
+- model: endoreg_db.finiding_morphology_classification_choice
+  fields:
+    name: "colon_paris_Ip"
+    name_de: "Kolonläsion Formklassifikation (Paris Ip)"
+    name_en: "Colon Lesion Shape Classification (Paris Ip)"
+    classification: "colon_lesion_paris"
+    description: "Shape classification for colon lesions (Paris Ip)"
+
+- model: endoreg_db.finiding_morphology_classification_choice
+  fields:
+    name: "colon_paris_IIa"
+    name_de: "Kolonläsion Formklassifikation (Paris IIa)"
+    name_en: "Colon Lesion Shape Classification (Paris IIa)"
+    classification: "colon_lesion_paris"
+    description: "Shape classification for colon lesions (Paris IIa)"
+
+- model: endoreg_db.finiding_morphology_classification_choice
+  fields:
+    name: "colon_paris_IIb"
+    name_de: "Kolonläsion Formklassifikation (Paris IIb)"
+    name_en: "Colon Lesion Shape Classification (Paris IIb)"
+    classification: "colon_lesion_paris"
+    description: "Shape classification for colon lesions (Paris IIb)"
+
+- model: endoreg_db.finiding_morphology_classification_choice
+  fields:
+    name: "colon_paris_IIc"
+    name_de: "Kolonläsion Formklassifikation (Paris IIc)"
+    name_en: "Colon Lesion Shape Classification (Paris IIc)"
+    classification: "colon_lesion_paris"
+    description: "Shape classification for colon lesions (Paris IIc)"
+
+- model: endoreg_db.finiding_morphology_classification_choice
+  fields:
+    name: "colon_paris_III"
+    name_de: "Kolonläsion Formklassifikation (Paris III)"
+    name_en: "Colon Lesion Shape Classification (Paris III)"
+    classification: "colon_lesion_paris"
+    description: "Shape classification for colon lesions (Paris III)"
+
+# IIa+IIc
+- model: endoreg_db.finiding_morphology_classification_choice
+  fields:
+    name: "colon_paris_IIa_IIc"
+    name_de: "Kolonläsion Formklassifikation (Paris IIa+IIc)"
+    name_en: "Colon Lesion Shape Classification (Paris IIa+IIc)"
+    classification: "colon_lesion_paris"
+    description: "Shape classification for colon lesions (Paris IIa+IIc)"
+
+# IIb+IIc
+- model: endoreg_db.finiding_morphology_classification_choice
+  fields:
+    name: "colon_paris_IIb_IIc"
+    name_de: "Kolonläsion Formklassifikation (Paris IIb+IIc)"
+    name_en: "Colon Lesion Shape Classification (Paris IIb+IIc)"
+    classification: "colon_lesion_paris"
+    description: "Shape classification for colon lesions (Paris IIb+IIc)"

endoreg_db/data/finding_morphology_classification_choice/colon_lesion_planarity_default.yaml

@@ -0,0 +1,56 @@
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_planarity_flat"
+    name_de: "Kolonläsion - Planarität flach"
+    name_en: "Colon lesion - planarity flat"
+    classification: "colon_lesion_planarity_default"
+    description: "Category for flat lesions"
+
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_planarity_flat_elevated"  
+    name_de: "Kolonläsion - Planarität flach-erhaben"
+    name_en: "Colon lesion - planarity flat-elevated"
+    classification: "colon_lesion_planarity_default"
+    description: "Category for flat-elevated lesions (surface +/- 2 mm)"
+
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_planarity_sessile"
+    name_de: "Kolonläsion - Planarität sessil"
+    name_en: "Colon lesion - planarity sessile"
+    classification: "colon_lesion_planarity_default"
+    description: "Category for sessile lesions (surface > 2 mm)"
+
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_planarity_pedunculated"
+    name_de: "Kolonläsion - Planarität gestielt"
+    name_en: "Colon lesion - planarity pedunculated"
+    classification: "colon_lesion_planarity_default"
+    description: "Category for pedunculated lesions (surface on a stalk)"
+
+# excavated
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_planarity_excavated"
+    name_de: "Kolonläsion - Planarität exkaviert"
+    name_en: "Colon lesion - planarity excavated"
+    classification: "colon_lesion_planarity_default"
+    description: "Category for excavated lesions (surface below surrounding mucosa)"
+    subcategories:
+      description:
+        choices: ["unspecified", "focal", "diffuse", "total"]
+        probability: [0.5, 0.2, 0.2, 0.1]
+        default: "unspecified"
+        required: true
+
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_planarity_unknown"
+    name_de: "Kolonläsion - Planarität unbekannt"
+    name_en: "Colon lesion - planarity unknown"
+    classification: "colon_lesion_planarity_default"
+
+
+    

endoreg_db/data/finding_morphology_classification_choice/colon_lesion_surface_intact_default.yaml

@@ -0,0 +1,39 @@
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_surface_intact"
+    name_de: "Kolonläsion - Oberfläche intakt"
+    name_en: "Colon lesion - surface intact"
+    classification: "colon_lesion_surface_intact_default"
+    description: "Category for intact lesion surfaces"
+
+# eroded
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_surface_eroded"
+    name_de: "Kolonläsion - Oberfläche erodiert"
+    name_en: "Colon lesion - surface eroded"
+    classification: "colon_lesion_surface_intact_default"
+    description: "Category for eroded lesion surfaces"
+    subcategories:
+      description:
+        choices: ["unspecified", "focal", "diffuse"]
+        default: "unspecified"
+        probability: [0.5, 0.2, 0.3]
+        required: true
+
+
+# ulcerated
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_surface_ulcerated"
+    name_de: "Kolonläsion - Oberfläche ulzeriert"
+    name_en: "Colon lesion - surface ulcerated"
+    classification: "colon_lesion_surface_intact_default"
+    description: "Category for ulcerated lesion surfaces"
+    subcategories:
+      description:
+        choices: ["unspecified", "focal", "diffuse"]
+        default: "unspecified"
+        probability: [0.5, 0.2, 0.3]
+        required: true
+

endoreg_db/data/finding_morphology_classification_choice/colonoscopy_size.yaml

@@ -0,0 +1,57 @@
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_size_categorical_diminutive"
+    name_de: "Größenklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Size Classification (categorical)"
+    classification: "colon_lesion_size_categorical"
+    description: "Diminutive (< 6 mm)"
+
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_size_categorical_small"
+    name_de: "Größenklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Size Classification (categorical)"
+    classification: "colon_lesion_size_categorical"
+    description: "Small (6 - 9 mm)"
+
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_size_categorical_medium"
+    name_de: "Größenklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Size Classification (categorical)"
+    classification: "colon_lesion_size_categorical"
+    description: "Medium (10 - 19 mm)"
+
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_size_categorical_large"
+    name_de: "Größenklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Size Classification (categorical)"
+    classification: "colon_lesion_size_categorical"
+    description: "Large (> 19 mm)"
+
+##########
+
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_size_oval_mm"
+    name_de: "Formklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Shape Classification (categorical)"
+    classification: "colon_lesion_size_mm"
+    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

endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml

@@ -0,0 +1,79 @@
+- model: endoreg_db.finding_morphology_classification_type
+  fields:
+    name: "colon_lesion_size"
+    name_de: "Größenklassifikation Kolonläsion"
+    name_en: "Colon Lesion Size Classification"
+
+    required_by_findings: [
+      "colon_polyp"
+    ]
+    optional_for_findings: [
+      "tumor"
+    ]
+
+- model: endoreg_db.finding_morphology_classification_type
+  fields:
+    name: "colon_lesion_shape"
+    name_de: "Formklassifikation Kolonläsion"
+    name_en: "Colon Lesion Shape Classification"
+
+    required_by_findings: [
+      "colon_polyp"
+    ]
+    optional_for_findings: [
+      "tumor"
+    ]
+
+- model: endoreg_db.finding_morphology_classification_type
+  fields:
+    name: "colon_lesion_surface_intact"
+    name_de: "Oberflächenklassifikation Kolonläsion"
+    name_en: "Colon Lesion Surface Classification"
+
+    required_by_findings: [
+      "colon_polyp"
+    ]
+    optional_for_findings: [
+      "tumor"
+    ]
+
+- model: endoreg_db.finding_morphology_classification_type
+  fields:
+    name: "colon_lesion_planarity"
+    name_de: "Planaritätsklassifikation Kolonläsion"
+    name_en: "Colon Lesion Planarity Classification"
+
+    required_by_findings: [
+      "colon_polyp"
+    ]
+    optional_for_findings: [
+
+    ]
+
+# Circularity
+- model: endoreg_db.finding_morphology_classification_type
+  fields:
+    name: "colon_lesion_circularity"
+    name_de: "Kolonläsion - Zirkularität"
+    name_en: "Colon lesion - circularity"
+
+    required_by_findings: [
+      "colon_polyp"
+    ]
+    optional_for_findings: [
+      "tumor"
+    ]
+
+# colon_lesion_advanced_imaging
+- model: endoreg_db.finding_morphology_classification_type
+  fields:
+    name: "colon_lesion_advanced_imaging"
+    name_de: "Kolonläsion - Advanced Imaging"
+    name_en: "Colon lesion - Advanced Imaging"
+
+    required_by_findings: [
+      "colon_polyp"
+    ]
+    optional_for_findings: [
+      "tumor"
+    ]

endoreg_db/data/finding_type/data.yaml

@@ -0,0 +1,30 @@
+- model: endoreg_db.finding_type
+  fields:
+    name: "macroscopic"
+    name_de: "Makroskopisch"
+    name_en: "Macroscopic"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "iatrogenic"
+    name_de: "Iatrogen"
+    name_en: "Iatrogenic"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "postinterventional_immediate"
+    name_de: "Postinterventionell unmittelbar"
+    name_en: "Postinterventional Immediate"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "postinterventional_delayed"
+    name_de: "Postinterventionell verzögert"
+    name_en: "Postinterventional Delayed"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "bleeding"
+    name_de: "Blutung"
+    name_en: "Bleeding"
+