endoreg-db 0.8.6.1__py3-none-any.whl → 0.8.8.9__py3-none-any.whl

endoreg_db/data/finding_classification/colonoscopy_location.yaml

@@ -1,80 +0,0 @@
-- model: endoreg_db.finding_classification
-  fields:
-    name: "colonoscopy_location_default"
-    name_de: "Koloskopie Standard"
-    name_en: "Colonoscopy Default"
-    classification_types: [
-      "location",
-    ]
-    examinations: [
-      "colonoscopy"
-    ]
-    finding_types: [
-      "macroscopic"
-    ]
-    findings: [
-      "colon_polyp",
-      "tumor",
-      "erosion",
-      "ulcer",
-      "scar"
-    ]
-    choices: [
-      "terminal_ileum",
-      "cecum",
-      "ascending_colon",
-      "right_flexure",
-      "transverse_colon",
-      "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",
-    ]
-    examinations: [
-      "colonoscopy"
-    ]
-    finding_types: [
-      "macroscopic"
-    ]
-    findings: [
-      "colon_polyp",
-      # "tumor",
-      # "erosion",
-      # "ulcer",
-      # "scar"
-    ]
-    choices: [
-      "left_colon",
-      "right_colon",
-      "rectum"
-    ]
-
-- model: endoreg_db.finding_classification
-  fields:
-    name: "colonoscopy_austria_screening_location"
-    name_de: "Koloskopie Österreich Screening Lokalisation"
-    name_en: "Colonoscopy Austria Screening Location"
-    classification_types: [
-      "location",
-    ]
-    examinations: [
-      "colonoscopy_austria_screening"
-    ]
-    findings: [
-      "colon_polyp",
-    ]
-    choices: [
-      "left_colon",
-      "right_colon",
-      "sigmoid_colon",
-      "rectum",
-    ]

endoreg_db/data/finding_classification/colonoscopy_lst.yaml

@@ -1,21 +0,0 @@
-- model: endoreg_db.finding_classification
-  fields:
-    name: "colon_lesion_lst"
-    classification_types: [
-      "colon_lesion_shape",
-      "morphology"
-    ]
-    name_de: "Oberflächenklassifikation Kolonläsion"
-    name_en: "Colon Lesion Surface Classification"
-    examinations: [
-      "colonoscopy"
-    ]
-    findings: [
-      "colon_polyp",
-    ]
-    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"
-    ]

endoreg_db/data/finding_classification/colonoscopy_nice.yaml

@@ -1,20 +0,0 @@
-- 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"
-    examinations: [
-      "colonoscopy"
-    ]
-    findings: [
-      "colon_polyp",
-    ]
-    choices: [
-      "colon_lesion_NICE_type_1",
-      "colon_lesion_NICE_type_2",
-      "colon_lesion_NICE_type_3"
-    ]

endoreg_db/data/finding_classification/colonoscopy_paris.yaml

@@ -1,26 +0,0 @@
-
-- model: endoreg_db.finding_classification
-  fields:
-    name: "colon_lesion_paris"
-    classification_types: [
-      "colon_lesion_shape",
-      "morphology"
-    ]
-    name_de: "Formklassifikation Kolonläsion"
-    name_en: "Colon Lesion Shape Classification"
-    examinations: [
-      "colonoscopy"
-    ]
-    findings: [
-      "colon_polyp",
-    ]
-    choices: [
-      "colon_paris_Is", # maps to colon_lesion_planarity_sessile
-      "colon_paris_Ip", # colon_lesion_planarity_pedunculated
-      "colon_paris_IIa", 
-      "colon_paris_IIb",
-      "colon_paris_IIc",
-      "colon_paris_III",
-      "colon_paris_IIa_IIc",
-      "colon_paris_IIb_IIc"
-    ]

endoreg_db/data/finding_classification/colonoscopy_sano.yaml

@@ -1,22 +0,0 @@
-
-- model: endoreg_db.finding_classification
-  fields:
-    name: "colon_lesion_kudo"
-    classification_types: [
-      "colon_lesion_capillary_pattern",
-      "morphology"
-    ]
-    name_de: "Oberflächenklassifikation Kolonläsion"
-    name_en: "Colon Lesion Surface Classification"
-    examinations: [
-      "colonoscopy"
-    ]
-    findings: [
-      "colon_polyp",
-    ]
-    choices: [
-      "colon_lesion_sano_1",
-      "colon_lesion_sano_2",
-      "colon_lesion_sano_3a",
-      "colon_lesion_sano_3b",
-    ]

endoreg_db/data/finding_classification/colonoscopy_summary.yaml

@@ -1,53 +0,0 @@
-
-- model: endoreg_db.finding_classification
-  fields:
-    name: "colonoscopy_not_complete_reason"
-    classification_types: []
-    examinations: [
-      "colonoscopy",
-      "colonoscopy_austria_screening",
-    ]
-    findings: [
-      "colonoscopy_complete",
-    ]
-    choices: [
-      "colonoscopy_incomplete_insufficient_preparation",
-      "colonoscopy_incomplete_complication",
-      "colonoscopy_incomplete_pain",
-      "colonoscopy_incomplete_stenosis",
-      "colonoscopy_incomplete_other",
-    ]
-
-- model: endoreg_db.finding_classification
-  fields:
-    name: "colonoscopy_austria_screening_findings_summary_worst"
-    classification_types: []
-    examinations: [
-      "colonoscopy_austria_screening",
-    ]
-    findings: [
-      "colonoscopy_austria_screening_findings_summary",
-    ]
-    choices: [
-      "colonoscopy_worst_finding_colon_cancer",
-      "colonoscopy_worst_finding_other",
-      "colonoscopy_worst_finding_polyp",
-      "colonoscopy_worst_finding_rectum_cancer",
-    ]
-
-- model: endoreg_db.finding_classification
-  fields:
-    name: "colonoscopy_screening_outcome_overall"
-    classification_types: []
-    examinations: [
-      "colonoscopy_austria_screening",
-    ]
-    findings: [
-      "colonoscopy_austria_screening_outcome",
-    ]
-    choices: [
-      "outcome_restitutio_ad_integrum",
-      "outcome_death",
-      "outcome_unknown",
-      "outcome_lasting_disability",
-    ]

endoreg_db/data/finding_classification/complication_generic.yaml

@@ -1,25 +0,0 @@
-
-- model: endoreg_db.finding_classification
-  fields:
-    name: "complication_generic_type"
-    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: [
-      "complication",
-    ]
-    choices: [
-      "complication_generic_type_cardiorespiratory",
-      "complication_generic_type_bleeding",
-      "complication_generic_type_perforation",
-      "complication_generic_type_other",
-    ]

endoreg_db/data/finding_classification/examination_setting_generic.yaml

@@ -1,40 +0,0 @@
-
-- 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/finding_classification/histology_colo.yaml

@@ -1,51 +0,0 @@
-- 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/finding_classification/intervention_required.yaml

@@ -1,26 +0,0 @@
-
-- 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/finding_classification/medication_related.yaml

@@ -1,23 +0,0 @@
-
-- 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/finding_classification/visualized.yaml

@@ -1,33 +0,0 @@
-
-- 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/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/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/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/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/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/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/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/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
-