endoreg-db 0.8.8.0__py3-none-any.whl → 0.8.9.2__py3-none-any.whl

endoreg_db/data/_examples/finding_classification_choice/bowel_preparation.yaml

@@ -1,78 +0,0 @@
-# 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

@@ -1,32 +0,0 @@
-- 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

@@ -1,15 +0,0 @@
-- 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

@@ -1,23 +0,0 @@
-- 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

@@ -1,15 +0,0 @@
-- 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

@@ -1,17 +0,0 @@
-- 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_planarity_default.yaml

@@ -1,49 +0,0 @@
-- 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

@@ -1,14 +0,0 @@
-- 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

@@ -1,36 +0,0 @@
-- 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
-

endoreg_db/data/_examples/finding_classification_choice/colonoscopy_size.yaml

@@ -1,82 +0,0 @@
-- 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

@@ -1,15 +0,0 @@
-- 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

@@ -1,15 +0,0 @@
-- 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

@@ -1,15 +0,0 @@
-- 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

@@ -1,24 +0,0 @@
-# "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

@@ -1,20 +0,0 @@
-- 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

@@ -1,19 +0,0 @@
-- 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

@@ -1,11 +0,0 @@
-- 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

@@ -1,48 +0,0 @@
-#####
-# 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

@@ -1,43 +0,0 @@
-# --- 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_"