endoreg-db 0.8.4.4__py3-none-any.whl → 0.8.8.0__py3-none-any.whl

endoreg_db/data/_examples/finding/data.yaml

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+- model: endoreg_db.finding
+  fields:
+    name: "placeholder"
+    name_de: "Platzhalter"
+    name_en: "Placeholder"
+    description: "This is a placeholder finding."
+
+- model: endoreg_db.finding
+  fields:
+    name: "post-intervention-wound"
+    name_de: "Postinterventionelle Wunde"
+    finding_interventions: ["colon_lesion_clip"]
+    examinations: [
+      "colonoscopy"
+      ]
+
+    finding_types: ["macroscopic"]
+
+- model: endoreg_db.finding
+  fields:
+    name: "tumor"
+    name_de: "Tumor"
+    name_en: "Tumor"
+    finding_interventions: []
+    examinations:
+      [
+        "colonoscopy",
+        "endosonography_upper_gi",
+        "endosonography_lower_gi",
+        "ercp",
+        "small_bowel_endoscopy",
+        "capsule_endoscopy",
+      ]
+
+    finding_types: ["macroscopic"]
+
+- model: endoreg_db.finding
+  fields:
+    name: "inflammation"
+    name_de: "Entzündung"
+    name_en: "Inflammation"
+    finding_interventions: []
+    examinations:
+      [
+        "colonoscopy",
+        "endosonography_upper_gi",
+        "endosonography_lower_gi",
+        "ercp",
+        "small_bowel_endoscopy",
+        "capsule_endoscopy",
+      ]
+    finding_types: ["macroscopic"]
+
+- model: endoreg_db.finding
+  fields:
+    name: "erosion"
+    name_de: "Erosion"
+    name_en: "Erosion"
+    finding_interventions: []
+    examinations:
+      [
+        "colonoscopy",
+        "endosonography_upper_gi",
+        "endosonography_lower_gi",
+        "ercp",
+        "small_bowel_endoscopy",
+        "capsule_endoscopy",
+      ]
+
+    finding_types: ["macroscopic"]
+
+- model: endoreg_db.finding
+  fields:
+    name: "ulcer"
+    name_de: "Ulcus"
+    name_en: "Ulcer"
+    finding_interventions: []
+    examinations:
+      [
+        "colonoscopy",
+        "endosonography_upper_gi",
+        "endosonography_lower_gi",
+        "ercp",
+        "small_bowel_endoscopy",
+        "capsule_endoscopy",
+      ]
+    finding_types: ["macroscopic"]
+
+- model: endoreg_db.finding
+  fields:
+    name: "scar"
+    name_de: "Narbe"
+    name_en: "Scar"
+    finding_interventions: []
+    examinations:
+      [
+        "colonoscopy",
+        "endosonography_upper_gi",
+        "endosonography_lower_gi",
+        "ercp",
+        "small_bowel_endoscopy",
+        "capsule_endoscopy",
+      ]
+
+    finding_types: ["macroscopic"]

endoreg_db/data/_examples/finding/examination_setting.yaml

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+- model: endoreg_db.finding
+  fields:
+    name: "examination_setting"
+    examinations: [
+      "gastroscopy",
+      "endosonography_upper_gi",
+      "endosonography_lower_gi",
+      "ercp",
+      "small_bowel_endoscopy",
+      "capsule_endoscopy",
+      "percutaneous_transhepatic_biliary_drainage",
+      "colonoscopy",
+      "colonoscopy_austria_screening",
+    ]
+
+    finding_types: ["summary"]

endoreg_db/data/_examples/finding/medication_related.yaml

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+- model: endoreg_db.finding
+  fields:
+    name: "sedation"
+    description: "Sedation during an examination"
+    examinations:
+      [
+        "gastroscopy",
+        "endosonography_upper_gi",
+        "endosonography_lower_gi",
+        "ercp",
+        "small_bowel_endoscopy",
+        "capsule_endoscopy",
+        "percutaneous_transhepatic_biliary_drainage",
+        "colonoscopy",
+        "colonoscopy_austria_screening",
+      ]
+
+    finding_types: ["medication_related"]

endoreg_db/data/_examples/finding/outcome.yaml

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+- model: endoreg_db.finding
+  fields:
+    name: "colonoscopy_austria_screening_outcome"
+    description: "Outcome of colonoscopy Austria screening."
+    examinations:
+      [
+        "colonoscopy_austria_screening",
+      ]
+    finding_types: 
+      [
+        "summary"
+      ]

endoreg_db/data/_examples/finding_classification/colonoscopy_bowel_preparation.yaml

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+- 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",
+        "bowel_prep_boston_1",
+        "bowel_prep_boston_2",
+        "bowel_prep_boston_3",
+      ]
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "bowel_prep_boston_simplified"
+    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",
+        "bowel_prep_boston_1",
+        "bowel_prep_boston_2",
+        "bowel_prep_boston_3",
+      ]
+
+#Aronchick
+- model: endoreg_db.finding_classification
+  fields:
+    name: "bowel_prep_aronchick"
+    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",
+        "bowel_prep_aronchick_1",
+        "bowel_prep_aronchick_2",
+        "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"]
+    choices:
+      [
+        "bowel_prep_perfect",
+        "bowel_prep_good",
+        "bowel_prep_fair",
+        "bowel_prep_poor",
+        "bowel_prep_poor_in_rc_only",
+      ]

endoreg_db/data/_examples/finding_classification/colonoscopy_jnet.yaml

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+
+- 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",
+    ]    
+    examinations: [
+      "colonoscopy"
+    ]
+    findings: [
+      "colon_polyp",
+    ]
+    choices: [
+      "colon_lesion_jnet_1",
+      "colon_lesion_jnet_2a",
+      "colon_lesion_jnet_2b",
+      "colon_lesion_jnet_3",
+    ]

endoreg_db/data/_examples/finding_classification/colonoscopy_kudo.yaml

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+
+- 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"
+    examinations: [
+      "colonoscopy"
+    ]
+    findings: [
+      "colon_polyp",
+    ]
+    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",
+    ]

endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_circularity.yaml

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+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colon_lesion_circularity_default"
+    name_de: "Kolonläsion - Zirkularität"
+    name_en: "Colon lesion - circularity"
+    classification_types: [
+      "colon_lesion_circularity",
+      "morphology"
+    ]    
+    examinations: [
+      "colonoscopy"
+    ]
+    findings: [
+      "colon_polyp",
+    ]
+    choices: [
+      "colon_lesion_circularity_false",
+      "colon_lesion_circularity_true"
+    ]

endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_planarity.yaml

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+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colon_lesion_planarity_default"
+    classification_types: [
+      "colon_lesion_planarity",
+      "morphology"
+    ]
+    name_de: "Planaritätsklassifikation Kolonläsion"
+    name_en: "Colon Lesion Planarity Classification"
+    examinations: [
+      "colonoscopy"
+    ]
+    findings: [
+      "colon_polyp",
+    ]
+    choices: [
+      "colon_lesion_planarity_flat", 
+      "colon_lesion_planarity_flat_elevated",
+      "colon_lesion_planarity_sessile",
+      "colon_lesion_planarity_pedunculated",
+      "colon_lesion_planarity_excavated",
+      "colon_lesion_planarity_unknown"
+    ]

endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_size.yaml

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+- model: endoreg_db.finding_classification
+  fields:
+    name: "colon_lesion_size_categorical"
+    classification_types: [
+      "colon_lesion_size",
+      "morphology"
+    ]
+    name_de: "Größenklassifikation Kolonläsion (kategorisch)"
+    name_en: "Colon Lesion Size Classification (categorical)"
+    examinations: [
+      "colonoscopy"
+    ]
+    findings: [
+      "colon_polyp",
+      "tumor",
+      "erosion",
+      "ulcer",
+      "scar"
+    ]
+    choices: [
+      "colon_lesion_size_categorical_diminutive",
+      "colon_lesion_size_categorical_small",
+      "colon_lesion_size_categorical_medium",
+      "colon_lesion_size_categorical_large"
+    ]
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colon_lesion_size_mm"
+    classification_types: [
+      "colon_lesion_size",
+      "morphology"
+    ]
+    name_de: "Größenklassifikation Kolonläsion (numerisch)"
+    name_en: "Colon Lesion Size Classification (numerical)"
+    examinations: [
+      "colonoscopy"
+    ]
+    findings: [
+      "colon_polyp",
+      "tumor",
+      "erosion",
+      "ulcer",
+      "scar"
+    ]
+    choices: [
+      "colon_lesion_size_oval_mm"
+    ]
+
+- model: endoreg_db.finding_classification
+  fields:
+    name: "colon_lesion_size_austria_categorical"
+    classification_types: [
+      "colon_lesion_size",
+      "morphology"
+    ]
+    examinations: [
+      "colonoscopy_austria_screening"
+    ]
+    findings: [
+      "colon_polyp",
+    ]
+    choices: [
+      "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"
+    ]

endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_surface.yaml

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+- model: endoreg_db.finding_classification
+  fields:
+    name: "colon_lesion_surface_intact_default"
+    classification_types: [
+      "colon_lesion_surface_intact",
+      "morphology"
+    ]
+    name_de: "Oberflächenklassifikation Kolonläsion"
+    name_en: "Colon Lesion Surface Classification"
+    examinations: [
+      "colonoscopy"
+    ]
+    findings: [
+      "colon_polyp",
+    ]
+    choices: [
+      "colon_lesion_surface_intact",
+      "colon_lesion_surface_eroded",
+      "colon_lesion_surface_ulcerated"
+    ]

endoreg_db/data/_examples/finding_classification/colonoscopy_location.yaml

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+- 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/_examples/finding_classification/colonoscopy_lst.yaml

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+- 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/_examples/finding_classification/colonoscopy_nice.yaml

@@ -0,0 +1,20 @@
+- 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/_examples/finding_classification/colonoscopy_paris.yaml

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+
+- 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/_examples/finding_classification/colonoscopy_sano.yaml

@@ -0,0 +1,22 @@
+
+- 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/_examples/finding_classification/colonoscopy_summary.yaml

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+
+- 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/_examples/finding_classification/complication_generic.yaml

@@ -0,0 +1,25 @@
+
+- 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",
+    ]