endoreg-db 0.8.8.0__py3-none-any.whl → 0.8.8.9__py3-none-any.whl

endoreg_db/data/finding_classification/00_generic.yaml

@@ -0,0 +1,44 @@
+- model: endoreg_db.finding_classification
+  fields:
+    name: "visualized"
+    classification_types:
+      - inferrable
+    choices:
+      - "yes"
+      - "no"
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "examination_setting_generic_location"
+    classification_types: []
+    choices:
+      - examination_setting_generic_location_inpatient
+      - examination_setting_generic_location_outpatient
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "sedation_performed"
+    classification_types: []
+    choices:
+      - "yes"
+      - "no"
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "examination_setting_generic_sedation"
+    classification_types: []
+    choices:
+      - "sedation_propofol"
+      - "sedation_midazolam"
+      - "sedation_propofol_midazolam"
+      - "sedation_other"
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "complication_generic_type"
+    classification_types: []
+    choices:
+      - complication_generic_type_cardiorespiratory
+      - complication_generic_type_bleeding
+      - complication_generic_type_perforation
+      - complication_generic_type_other

endoreg_db/data/finding_classification/00_generic_histology.yaml

@@ -0,0 +1,28 @@
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "histology_dysplasia_default"
+    classification_types:
+      - histology
+    choices:
+      - histology_dysplasia_none
+      - histology_dysplasia_low_grade
+      - histology_dysplasia_high_grade
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "histology_dignity_default"
+    classification_types:
+      - histology
+    choices:
+      - histology_dignity_benign
+      - histology_dignity_malign
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "histology_in_sano_default"
+    classification_types:
+      - histology
+    choices:
+      - "yes"
+      - "no"
+      - "na"

endoreg_db/data/finding_classification/00_generic_lesion.yaml

@@ -0,0 +1,52 @@
+- model: endoreg_db.finding_classification
+  fields:
+    name: "lesion_size_mm"
+    classification_types: ["size"]
+    name_de: "Größe (mm)"
+    name_en: "Size (mm)"
+    choices: ["lesion_size_oval_mm"]
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "lesion_length_mm"
+    classification_types: ["size"]
+    name_de: "Länge (mm)"
+    name_en: "Length (mm)"
+    choices:
+      - lesion_length_mm #TODO
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "lesion_planarity_default"
+    classification_types: ["planarity", "morphology"]
+    name_de: "Planaritätsklassifikation Kolonläsion"
+    name_en: "Colon Lesion Planarity Classification"
+    choices:
+      - lesion_planarity_flat
+      - lesion_planarity_flat_elevated
+      - lesion_planarity_sessile
+      - lesion_planarity_pedunculated
+      - lesion_planarity_excavated
+      - lesion_planarity_unknown
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "lesion_surface_intact_default"
+    classification_types:
+      - morphology
+    name_de: "Oberflächenklassifikation Kolonläsion"
+    name_en: "Colon Lesion Surface Classification"
+    choices:
+      - lesion_surface_intact
+      - lesion_surface_eroded
+      - lesion_surface_ulcerated
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "lesion_circularity_default"
+    name_de: "Zirkularität"
+    name_en: "Circularity"
+    classification_types: ["morphology"]
+    choices:
+      - lesion_circularity_false
+      - lesion_circularity_true

endoreg_db/data/finding_classification/{colonoscopy_bowel_preparation.yaml → 02_colonoscopy_baseline.yaml}

@@ -1,12 +1,37 @@
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colonoscopy_location_default"
+    name_de: "Koloskopie Standard"
+    name_en: "Colonoscopy Default"
+    classification_types: ["location"]
+    choices:
+      [
+        "terminal_ileum",
+        "cecum",
+        "ascending_colon",
+        "right_flexure",
+        "transverse_colon",
+        "left_flexure",
+        "descending_colon",
+        "sigmoid_colon",
+        "rectum",
+        "anal_canal",
+      ]
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colonoscopy_location_coarse"
+    name_de: "Koloskopie Grob"
+    name_en: "Colonoscopy Coarse"
+    classification_types: ["location"]
+    choices: ["left_colon", "right_colon", "rectum"]
+
 - model: endoreg_db.finding_classification
   fields:
     name: "bowel_prep_boston"
     classification_types: ["bowel_prep"]
     name_de: "Boston Bowel Preparation Scale"
     name_en: "Boston Bowel Preparation Scale"
-    examinations: ["colonoscopy"]
-    findings:
-      ["bowel_preparation_lc", "bowel_preparation_tc", "bowel_preparation_rc"]
     choices:
       [
         "bowel_prep_boston_0",
@@ -21,8 +46,6 @@
     classification_types: ["bowel_prep"]
     name_de: "Boston Bowel Preparation Scale"
     name_en: "Boston Bowel Preparation Scale"
-    examinations: ["colonoscopy"]
-    findings: ["bowel_preparation_simplified"]
     choices:
       [
         "bowel_prep_boston_0",
@@ -38,9 +61,6 @@
     classification_types: ["bowel_prep"]
     name_de: "Aronchick Bowel Preparation Scale"
     name_en: "Aronchick Bowel Preparation Scale"
-    examinations: ["colonoscopy"]
-    findings:
-      ["bowel_preparation_lc", "bowel_preparation_tc", "bowel_preparation_rc"]
     choices:
       [
         "bowel_prep_aronchick_0",
@@ -49,20 +69,15 @@
         "bowel_prep_aronchick_3",
       ]
 
-# Screening Austria
 - model: endoreg_db.finding_classification
   fields:
-    name: "bowel_prep_screening_austria"
-    classification_types: ["bowel_prep"]
-    name_de: "Darmvorbereitung Screening Österreich"
-    name_en: "Bowel Preparation Screening Austria"
-    examinations: ["colonoscopy_austria_screening"]
-    findings: ["bowel_prep_screening_austria"]
+    name: "colonoscopy_not_complete_reason"
+    classification_types: []
     choices:
       [
-        "bowel_prep_perfect",
-        "bowel_prep_good",
-        "bowel_prep_fair",
-        "bowel_prep_poor",
-        "bowel_prep_poor_in_rc_only",
+        "colonoscopy_incomplete_insufficient_preparation",
+        "colonoscopy_incomplete_complication",
+        "colonoscopy_incomplete_pain",
+        "colonoscopy_incomplete_stenosis",
+        "colonoscopy_incomplete_other",
       ]

endoreg_db/data/finding_classification/02_colonoscopy_histology.yaml

@@ -0,0 +1,13 @@
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colonoscopy_polyp_histology"
+    classification_types:
+      - histology
+    choices: [
+        "histology_polyp_hyperplastic",
+        "histology_polyp_adenoma_tubular",
+        "histology_polyp_adenoma_tubulovillous",
+        "histology_polyp_adenoma_villous",
+        "histology_polyp_sessile_serrated_lesion",
+        # unknown?
+      ]

endoreg_db/data/finding_classification/02_colonoscopy_other.yaml

@@ -0,0 +1,12 @@
+- model: endoreg_db.finding_classification
+  fields:
+    name: "hemorrhoids_grade"
+    classification_types: []
+    choices:
+      [
+        "hemorrhoids_grade_0_no_hemorrhoids",
+        "hemorrhoids_grade_1",
+        "hemorrhoids_grade_2",
+        "hemorrhoids_grade_3",
+        "hemorrhoids_grade_4",
+      ]

endoreg_db/data/finding_classification/02_colonoscopy_polyp.yaml

@@ -0,0 +1,101 @@
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colon_lesion_paris"
+    classification_types: ["shape", "morphology"]
+    name_de: "Formklassifikation Kolonläsion"
+    name_en: "Colon Lesion Shape Classification"
+    choices: [
+        "colon_lesion_paris_Is", # maps to colon_lesion_planarity_sessile
+        "colon_lesion_paris_Ip", # colon_lesion_planarity_pedunculated
+        "colon_lesion_paris_IIa",
+        "colon_lesion_paris_IIb",
+        "colon_lesion_paris_IIc",
+        "colon_lesion_paris_III",
+        "colon_lesion_paris_IIa_IIc",
+        "colon_lesion_paris_IIb_IIc",
+      ]
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colon_lesion_sano"
+    classification_types: ["capillary_pattern", "morphology"]
+    name_de: "Oberflächenklassifikation Kolonläsion"
+    name_en: "Colon Lesion Surface Classification"
+    choices:
+      [
+        "colon_lesion_sano_1",
+        "colon_lesion_sano_2",
+        "colon_lesion_sano_3a",
+        "colon_lesion_sano_3b",
+      ]
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colon_lesion_size_categorical"
+    classification_types: ["size", "morphology"]
+    name_de: "Größenklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Size Classification (categorical)"
+    choices: [
+        "colon_lesion_size_categorical_diminutive", # 0 - 5 mm
+        "colon_lesion_size_categorical_small", # 6 - 9 mm
+        "colon_lesion_size_categorical_medium", # 10 - 20 mm
+        "colon_lesion_size_categorical_large", # 21+ mm
+      ]
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colon_lesion_lst"
+    classification_types: ["shape", "morphology"]
+    name_de: "Oberflächenklassifikation Kolonläsion"
+    name_en: "Colon Lesion Surface Classification"
+    choices:
+      [
+        "colon_lesion_lst_granular_homogeneous",
+        "colon_lesion_lst_granular_nodular_mixed",
+        "colon_lesion_lst_non_granular_flat_elevated",
+        "colon_lesion_lst_non_granular_pseudodepressed",
+      ]
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colon_lesion_kudo"
+    classification_types: ["colon_lesion_advanced_imaging", "morphology"]
+    name_de: "Oberflächenklassifikation Kolonläsion"
+    name_en: "Colon Lesion Surface Classification"
+    choices:
+      [
+        "colon_lesion_kudo_1",
+        "colon_lesion_kudo_2",
+        "colon_lesion_kudo_3s",
+        "colon_lesion_kudo_3l",
+        "colon_lesion_kudo_4",
+        "colon_lesion_kudo_5i",
+        "colon_lesion_kudo_5n",
+      ]
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colon_lesion_jnet"
+    name_de: "Kolonläsion - JNET"
+    name_en: "Colon lesion - JNET"
+    classification_types: ["morphology", "colon_lesion_advanced_imaging"]
+    choices:
+      [
+        "colon_lesion_jnet_1",
+        "colon_lesion_jnet_2a",
+        "colon_lesion_jnet_2b",
+        "colon_lesion_jnet_3",
+      ]
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colon_lesion_nice"
+    classification_types: ["colon_lesion_advanced_imaging", "morphology"]
+    name_de: "Kolonläsion - NICE"
+    name_en: "Colon lesion - NICE"
+    choices:
+      [
+        "colon_lesion_NICE_type_1",
+        "colon_lesion_NICE_type_2",
+        "colon_lesion_NICE_type_3",
+      ]

endoreg_db/data/finding_classification_choice/{yes_no_na.yaml → 00_generic.yaml}

@@ -8,4 +8,8 @@
 
 - model: endoreg_db.finding_classification_choice
   fields:
-    name: "na"
+    name: "na"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "unknown"

endoreg_db/data/finding_classification_choice/{examination_setting_generic_types.yaml → 00_generic_baseline.yaml}

@@ -8,8 +8,16 @@
 
 - model: endoreg_db.finding_classification_choice
   fields:
-    name: "examination_setting_operative"
+    name: "sedation_propofol"
 
 - model: endoreg_db.finding_classification_choice
   fields:
-    name: "examination_setting_conservative"
+    name: "sedation_midazolam"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "sedation_propofol_midazolam"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "sedation_other"

endoreg_db/data/finding_classification_choice/{complication_generic_types.yaml → 00_generic_complication.yaml}

@@ -12,4 +12,4 @@
 
 - model: endoreg_db.finding_classification_choice
   fields:
-    name: "complication_generic_type_other"
+    name: "complication_generic_type_other"

endoreg_db/data/finding_classification_choice/{histology.yaml → 00_generic_histology.yaml}

@@ -1,6 +1,3 @@
-# "histology_dysplasia_none",
-# "histology_dysplasia_low_grade",
-# "histology_dysplasia_high_grade",
 - model: endoreg_db.finding_classification_choice
   fields:
     name: "histology_dysplasia_none"
@@ -21,4 +18,4 @@
 - model: endoreg_db.finding_classification_choice
   fields:
     name: "histology_dignity_malign"
-    description: "Histology: Malign"
+    description: "Histology: Malign"

endoreg_db/data/finding_classification_choice/00_generic_lesion.yaml

@@ -0,0 +1,158 @@
+# Planarity of lesions
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "lesion_planarity_flat"
+    name_de: "Planarität flach"
+    name_en: "planarity flat"
+    description: "Category for flat lesions"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "lesion_planarity_flat_elevated"
+    name_de: "Planarität flach-erhaben"
+    name_en: "planarity flat-elevated"
+    description: "Category for flat-elevated lesions (surface +/- 2 mm)"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "lesion_planarity_sessile"
+    name_de: "Planarität sessil"
+    name_en: "planarity sessile"
+    description: "Category for sessile lesions (surface > 2 mm)"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "lesion_planarity_pedunculated"
+    name_de: "Planarität gestielt"
+    name_en: "planarity pedunculated"
+    description: "Category for pedunculated lesions (surface on a stalk)"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "lesion_planarity_excavated"
+    name_de: "Planarität exkaviert"
+    name_en: "planarity excavated"
+    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_classification_choice
+  fields:
+    name: "lesion_planarity_unknown"
+    name_de: "Planarität unbekannt"
+    name_en: "planarity unknown"
+
+# Circularity of lesions
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "lesion_circularity_false"
+    name_de: "Zirkularität"
+    name_en: "Circularity"
+    description: "Category for non-circular lesions"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "lesion_circularity_true"
+    name_de: "Zirkularität"
+    name_en: "Circularity"
+    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
+
+# Size of oval lesions
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "lesion_size_oval_mm"
+    name_de: "Größe Ovaler Läsionen (mm)"
+    name_en: "Size of Oval Lesions (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
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "lesion_length_mm"
+    name_de: "Länge Läsion (mm)"
+    name_en: "Length of lesions (mm)"
+    description: "Length of lesions"
+    numerical_descriptors:
+      value:
+        unit: "mm"
+        min: 0
+        max: 100
+        distribution: "normal"
+        mean: 5
+        std: 3
+        description: "Largest diameter of the lesion in mm"
+        required: true
+
+# Surface of lesions
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "lesion_surface_intact"
+    name_de: "Oberfläche intakt"
+    name_en: "surface intact"
+    description: "Category for intact lesion surfaces"
+
+# eroded
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "lesion_surface_eroded"
+    name_de: "Oberfläche erodiert"
+    name_en: "surface eroded"
+    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_classification_choice
+  fields:
+    name: "lesion_surface_ulcerated"
+    name_de: "Oberfläche ulzeriert"
+    name_en: "surface ulcerated"
+    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_classification_choice/{bowel_preparation.yaml → 02_colonoscopy_bowel_preparation.yaml}

@@ -41,38 +41,9 @@
     name: "bowel_prep_aronchick_2"
     name_en: "Good"
     name_de: "Gut"
-    
+
 - model: endoreg_db.finding_classification_choice
   fields:
     name: "bowel_prep_aronchick_3"
     name_en: "Excellent"
     name_de: "Exzellent"
-
-# Screening Austria
-# Choices are "bowel_prep_perfect", "bowel_prep_good", 
-# "bowel_prep_fair", "bowel_prep_poor", "bowel_prep_poor_in_rc_only"
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "bowel_prep_perfect"
-    name_de: "Perfekt"
-    name_en: "Perfect"
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "bowel_prep_good"
-    name_de: "Gut"
-    name_en: "Good"
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "bowel_prep_fair"
-    name_de: "Befriedigend"
-    name_en: "Fair"
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "bowel_prep_poor"
-    name_de: "Schlecht"
-    name_en: "Poor"
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "bowel_prep_poor_in_rc_only"
-    name_de: "Schlecht (nur rechtes Kolon)"
-    name_en: "Poor (Right Colon Only)"  

endoreg_db/data/{_examples/finding_classification_choice/colonoscopy_not_complete_reason.yaml → finding_classification_choice/02_colonoscopy_generic.yaml}

@@ -16,4 +16,4 @@
 
 - model: endoreg_db.finding_classification_choice
   fields:
-    name: "colonoscopy_incomplete_other"
+    name: "colonoscopy_incomplete_other"

endoreg_db/data/finding_classification_choice/{histology_polyp.yaml → 02_colonoscopy_histology.yaml}

@@ -17,4 +17,4 @@
 - model: endoreg_db.finding_classification_choice
   fields:
     name: "histology_polyp_sessile_serrated_lesion"
-    description: "Histology: Sessile serrated lesion"
+    description: "Histology: Sessile serrated lesion"

endoreg_db/data/{_examples/finding_classification_choice/colonoscopy_location.yaml → finding_classification_choice/02_colonoscopy_location.yaml}

@@ -4,10 +4,7 @@
     name_de: "terminales Ileum"
     name_en: "Terminal Ileum"
     subcategories:
-      description: {
-        choices: ["unspecified"],
-        required: false
-      }
+      description: { choices: ["unspecified"], required: false }
     numerical_descriptors:
       cm_rectified:
         unit: "centimeter"
@@ -80,6 +77,28 @@
         description: "Insertion depth of the colonoscope in cm (rectified)"
         required: false
 
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "left_flexure"
+    name_de: "Linke Flexur"
+    name_en: "Left 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"

endoreg_db/data/finding_classification_choice/02_colonoscopy_other.yaml

@@ -0,0 +1,34 @@
+# Hemorrhoids classification
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "hemorrhoids_grade_0_no_hemorrhoids"
+    name_de: "Keine Hämorrhoiden"
+    name_en: "No hemorrhoids"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "hemorrhoids_grade_1"
+    name_de: "Grad 1"
+    name_en: "Grade 1"
+    description: "Mucosal hemorrhoids that do not prolapse"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "hemorrhoids_grade_2"
+    name_de: "Grad 2"
+    name_en: "Grade 2"
+    description: "Hemorrhoids that prolapse during straining but reduce spontaneously"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "hemorrhoids_grade_3"
+    name_de: "Grad 3"
+    name_en: "Grade 3"
+    description: "Hemorrhoids that prolapse during straining and require manual reduction"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "hemorrhoids_grade_4"
+    name_de: "Grad 4"
+    name_en: "Grade 4"
+    description: "Irreducible prolapsed hemorrhoids"