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

endoreg_db/data/_examples/finding_classification/examination_setting_generic.yaml

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+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "examination_setting_generic_location"
+    classification_types: []
+    examinations: [
+      "gastroscopy",
+      "endosonography_upper_gi",
+      "endosonography_lower_gi",
+      "ercp",
+      "small_bowel_endoscopy",
+      "capsule_endoscopy",
+      "percutaneous_transhepatic_biliary_drainage",
+      "colonoscopy",
+    ]
+    findings: [
+      "examination_setting",
+    ]
+    choices: [
+      "examination_setting_generic_location_inpatient",
+      "examination_setting_generic_location_outpatient",
+    ]
+
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colonoscopy_austria_screening_final_examination_setting"
+    classification_types: []
+    examinations: [
+      "colonoscopy_austria_screening",
+    ]
+    findings: [
+      "examination_setting",
+    ]
+    choices: [
+      "examination_setting_generic_location_inpatient",
+      "examination_setting_generic_location_outpatient",
+      "examination_setting_operative",
+      "examination_setting_conservative"
+    ]

endoreg_db/data/_examples/finding_classification/histology_colo.yaml

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+- model: endoreg_db.finding_classification
+  fields:
+    name: "colonoscopy_polyp_histology"
+    classification_types: []
+    examinations: [
+      "colonoscopy",
+      "colonoscopy_austria_screening",
+    ]
+    findings: [
+      "colon_polyp",
+    ]
+    choices: [
+      "histology_polyp_hyperplastic",
+      "histology_polyp_adenoma_tubular",
+      "histology_polyp_adenoma_tubulovillous",
+      "histology_polyp_adenoma_villous",
+      "histology_polyp_sessile_serrated_lesion"
+    ]
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colonoscopy_polyp_histology_dysplasia"
+    classification_types: []
+    examinations: [
+      "colonoscopy",
+      "colonoscopy_austria_screening",
+    ]
+    findings: [
+      "colon_polyp",
+    ]
+    choices: [
+      "histology_dysplasia_none",
+      "histology_dysplasia_low_grade",
+      "histology_dysplasia_high_grade",
+    ]
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colonoscopy_histology_dignity"
+    classification_types: []
+    examinations: [
+      "colonoscopy",
+      "colonoscopy_austria_screening",
+    ]
+    findings: [
+      "colon_polyp",
+    ]
+    choices: [
+      "histology_dignity_benign",
+      "histology_dignity_malign",
+    ]

endoreg_db/data/_examples/finding_classification/intervention_required.yaml

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+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "intervention_required"
+    classification_types: []
+    examinations: [
+      "gastroscopy",
+      "endosonography_upper_gi",
+      "endosonography_lower_gi",
+      "ercp",
+      "small_bowel_endoscopy",
+      "capsule_endoscopy",
+      "percutaneous_transhepatic_biliary_drainage",
+      "colonoscopy",
+      "colonoscopy_austria_screening",
+    ]
+    findings: [
+      "colon_polyp",
+      "post-intervention-wound",
+      "ulcer",
+
+    ]
+    choices: [
+      "yes",
+      "no",
+    ]

endoreg_db/data/_examples/finding_classification/medication_related.yaml

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+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "sedation_performed"
+    classification_types: []
+    examinations: [
+      "gastroscopy",
+      "endosonography_upper_gi",
+      "endosonography_lower_gi",
+      "ercp",
+      "small_bowel_endoscopy",
+      "capsule_endoscopy",
+      "percutaneous_transhepatic_biliary_drainage",
+      "colonoscopy",
+      "colonoscopy_austria_screening",
+    ]
+    findings: [
+      "sedation",
+    ]
+    choices: [
+      "yes",
+      "no",
+    ]

endoreg_db/data/_examples/finding_classification/visualized.yaml

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+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "visualized"
+    classification_types: []
+    examinations: [
+      "gastroscopy",
+      "endosonography_upper_gi",
+      "endosonography_lower_gi",
+      "ercp",
+      "small_bowel_endoscopy",
+      "capsule_endoscopy",
+      "percutaneous_transhepatic_biliary_drainage",
+      "colonoscopy",
+      "colonoscopy_austria_screening",
+    ]
+    findings: [
+      "cecum",
+      "terminal_ileum",
+      "ileocecal_valve",
+      "ascending_colon",
+      "right_flexure",
+      "transverse_colon",
+      "left_flexure",
+      "descending_colon",
+      "sigmoid_colon",
+      "rectum",
+      "rectum_anus",
+    ]
+    choices: [
+      "yes",
+      "no",
+    ]

endoreg_db/data/_examples/finding_classification_choice/bowel_preparation.yaml

@@ -0,0 +1,78 @@
+# Boston
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "bowel_prep_boston_0"
+    name_de: "0"
+    name_en: "bowel_prep_boston_0"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "bowel_prep_boston_1"
+    name_de: "1"
+    name_en: "bowel_prep_boston_1"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "bowel_prep_boston_2"
+    name_de: "2"
+    name_en: "bowel_prep_boston_2"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "bowel_prep_boston_3"
+    name_de: "3"
+    name_en: "bowel_prep_boston_3"
+
+# Aronchick
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "bowel_prep_aronchick_0"
+    name_de: "Inadäquat"
+    name_en: "Inadequate"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "bowel_prep_aronchick_1"
+    name_en: "Fair"
+    name_de: "Ausreichend"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    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/colon_lesion_circularity_default.yaml

@@ -0,0 +1,32 @@
+- model: endoreg_db.finding_morphology_classification_choice
+  fields:
+    name: "colon_lesion_circularity_false"
+    name_de: "Kolonläsion - Zirkularität"
+    name_en: "Colon lesion - circularity"
+    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"
+    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/_examples/finding_classification_choice/colon_lesion_jnet.yaml

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+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_jnet_1"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_jnet_2a"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_jnet_2b"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_jnet_3"

endoreg_db/data/_examples/finding_classification_choice/colon_lesion_kudo.yaml

@@ -0,0 +1,23 @@
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_kudo_1"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_kudo_2"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_kudo_3s"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_kudo_3l"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_kudo_4"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_kudo_5i"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_kudo_5n"

endoreg_db/data/_examples/finding_classification_choice/colon_lesion_lst.yaml

@@ -0,0 +1,15 @@
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_lst_granular_homogeneous"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_lst_granular_nodular_mixed"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_lst_non_granular_flat_elevated"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_lst_non_granular_pseudodepressed"

endoreg_db/data/_examples/finding_classification_choice/colon_lesion_nice.yaml

@@ -0,0 +1,17 @@
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_NICE_type_1"
+    name_de: "Kolonläsion - NICE Typ 1"
+    name_en: "Colon lesion - NICE type 1"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_NICE_type_2"
+    name_de: "Kolonläsion - NICE Typ 2"
+    name_en: "Colon lesion - NICE type 2"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_NICE_type_3"
+    name_de: "Kolonläsion - NICE Typ 3"
+    name_en: "Colon lesion - NICE type 3"

endoreg_db/data/_examples/finding_classification_choice/colon_lesion_paris.yaml

@@ -0,0 +1,57 @@
+- 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)"
+    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)"
+    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)"
+    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)"
+    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)"
+    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)"
+    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)"
+    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)"
+    description: "Shape classification for colon lesions (Paris IIb+IIc)"

endoreg_db/data/_examples/finding_classification_choice/colon_lesion_planarity_default.yaml

@@ -0,0 +1,49 @@
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_planarity_flat"
+    name_de: "Kolonläsion - Planarität flach"
+    name_en: "Colon lesion - planarity flat"
+    description: "Category for flat lesions"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_planarity_flat_elevated"  
+    name_de: "Kolonläsion - Planarität flach-erhaben"
+    name_en: "Colon lesion - planarity flat-elevated"
+    description: "Category for flat-elevated lesions (surface +/- 2 mm)"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_planarity_sessile"
+    name_de: "Kolonläsion - Planarität sessil"
+    name_en: "Colon lesion - planarity sessile"
+    description: "Category for sessile lesions (surface > 2 mm)"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_planarity_pedunculated"
+    name_de: "Kolonläsion - Planarität gestielt"
+    name_en: "Colon lesion - planarity pedunculated"
+    description: "Category for pedunculated lesions (surface on a stalk)"
+
+# excavated
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_planarity_excavated"
+    name_de: "Kolonläsion - Planarität exkaviert"
+    name_en: "Colon lesion - 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: "colon_lesion_planarity_unknown"
+    name_de: "Kolonläsion - Planarität unbekannt"
+    name_en: "Colon lesion - planarity unknown"
+
+

endoreg_db/data/_examples/finding_classification_choice/colon_lesion_sano.yaml

@@ -0,0 +1,14 @@
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_sano_1"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_sano_2"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_sano_3a"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_sano_3b"

endoreg_db/data/_examples/finding_classification_choice/colon_lesion_surface_intact_default.yaml

@@ -0,0 +1,36 @@
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_surface_intact"
+    name_de: "Kolonläsion - Oberfläche intakt"
+    name_en: "Colon lesion - surface intact"
+    description: "Category for intact lesion surfaces"
+
+# eroded
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_surface_eroded"
+    name_de: "Kolonläsion - Oberfläche erodiert"
+    name_en: "Colon lesion - 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: "colon_lesion_surface_ulcerated"
+    name_de: "Kolonläsion - Oberfläche ulzeriert"
+    name_en: "Colon lesion - 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
+