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

endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml

@@ -1,229 +0,0 @@
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "terminal_ileum"
-    name_de: "terminales Ileum"
-    name_en: "Terminal Ileum"
-    subcategories:
-      description: {
-        choices: ["unspecified"],
-        required: false
-      }
-    numerical_descriptors:
-      cm_rectified:
-        unit: "centimeter"
-        min: 0
-        max: 180
-        description: "Insertion depth of the colonoscope in cm (rectified)"
-        required: false
-
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "cecum"
-    name_de: "Caecum"
-    name_en: "Cecum"
-    subcategories:
-      description:
-        choices: ["unspecified", "ileocecal-valve", "peri-appendicular"]
-        default: "unspecified"
-        probability: [0.5, 0.3, 0.2]
-        required: true
-    numerical_descriptors:
-      cm_rectified:
-        unit: "centimeter"
-        min: 60
-        max: 140
-        distribution: "uniform"
-        std: null
-        mean: null
-        description: "Insertion depth of the colonoscope in cm (rectified)"
-        required: false
-
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "ascending_colon"
-    name_de: "Colon ascendens"
-    name_en: "Ascending Colon"
-    subcategories:
-      description:
-        choices: ["unspecified", "proximal", "distal"]
-        probability: [0.5, 0.3, 0.2]
-        default: "unspecified"
-        required: true
-    numerical_descriptors:
-      cm_rectified:
-        unit: "centimeter"
-        min: 40
-        max: 100
-        distribution: "uniform"
-        description: "Insertion depth of the colonoscope in cm (rectified)"
-        required: false
-
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "right_flexure"
-    name_de: "Rechte Flexur"
-    name_en: "Right 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"
-    name_de: "Colon transversum"
-    name_en: "Transverse Colon"
-    subcategories:
-      description:
-        choices: ["unspecified", "proximal", "distal"]
-        probability: [0.5, 0.3, 0.2]
-        default: "unspecified"
-        required: true
-    numerical_descriptors:
-      cm_rectified:
-        unit: "centimeter"
-        min: 40
-        max: 80
-        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: "descending_colon"
-    name_de: "Colon descendens"
-    name_en: "Descending Colon"
-    subcategories:
-      description:
-        choices: ["unspecified", "proximal", "distal"]
-        probability: [0.5, 0.3, 0.2]
-        default: "unspecified"
-        required: true
-    numerical_descriptors:
-      cm_rectified:
-        unit: "centimeter"
-        min: 35
-        max: 70
-        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: "sigmoid_colon"
-    name_de: "Colon sigmoideum"
-    name_en: "Sigmoid Colon"
-    subcategories:
-      description:
-        choices: ["unspecified", "proximal", "distal"]
-        probability: [0.5, 0.3, 0.2]
-        default: "unspecified"
-        required: true
-    numerical_descriptors:
-      cm_rectified:
-        unit: "centimeter"
-        min: 20
-        max: 50
-        description: "Insertion depth of the colonoscope in cm (rectified)"
-        required: true
-
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "rectum"
-    name_de: "Rektum"
-    name_en: "Rectum"
-    subcategories:
-      description:
-        choices: ["1/3", "2/3", "3/3"]
-        probability: [0.3, 0.3, 0.4]
-        default: "3/3"
-        required: true
-    numerical_descriptors:
-      cm_rectified:
-        unit: "centimeter"
-        min: 5
-        max: 20
-        description: "Insertion depth of the colonoscope in cm (rectified)"
-        required: true
-
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "anal_canal"
-    name_de: "Analkanal"
-    name_en: "Anal Canal"
-    subcategories:
-      description:
-        choices: ["unspecified", "proximal", "distal"]
-        probability: [0.5, 0.3, 0.2]
-        default: "unspecified"
-        required: false
-    numerical_descriptors:
-      cm_rectified:
-        unit: "centimeter"
-        min: 0
-        max: 3
-        mean: null
-        std: null
-        distribution: "uniform"
-        description: "Insertion depth of the colonoscope in cm (rectified)"
-        required: true
-
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "left_colon"
-    name_de: "linkes Kolon"
-    name_en: "Left Colon"
-    subcategories:
-      description:
-        choices: ["unspecified", "proximal", "distal"]
-        probability: [0.3, 0.3, 0.3]
-        default: "proximal"
-        required: true
-    numerical_descriptors:
-      cm_rectified:
-        unit: "centimeter"
-        min: 0
-        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: "right_colon"
-    name_de: "rechtes Kolon"
-    name_en: "Right Colon"
-    subcategories:
-      description:
-        choices: ["unspecified", "proximal", "distal"]
-        probability: [0.3, 0.3, 0.3]
-        default: "proximal"
-        required: true
-    numerical_descriptors:
-      cm_rectified:
-        unit: "centimeter"
-        min: 0
-        max: 180
-        mean: null
-        std: null
-        distribution: "uniform"
-        description: "Insertion depth of the colonoscope in cm (rectified)"
-        required: false

endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml

@@ -1,19 +0,0 @@
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "colonoscopy_incomplete_insufficient_preparation"
-
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "colonoscopy_incomplete_complication"
-
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "colonoscopy_incomplete_pain"
-
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "colonoscopy_incomplete_stenosis"
-
-- model: endoreg_db.finding_classification_choice
-  fields:
-    name: "colonoscopy_incomplete_other"

endoreg_db/data/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/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/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/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_"

endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml

@@ -1,168 +0,0 @@
-- model: endoreg_db.finding_intervention
-  fields:
-    name: colon_lesion_polypectomy_cold_snare
-    description:
-      Cold snare polypectomy is a technique used to remove small polyps
-      from the colon. It is performed using a snare wire loop that is passed through
-      the colonoscope and used to remove the polyp by cutting it off at the base.
-      The procedure is usually done without the need for sedation and is considered
-      to be a safe and effective way to remove small polyps from the colon.
-    intervention_types:
-      - therapeutic
-      - invasive
-    required_lab_values:
-      - hemoglobin
-      - platelets
-      - international_normalized_ratio
-    contraindications:
-      - anticoagulation-therapeutic
-      - thrombocytopenia-severe
-- model: endoreg_db.finding_intervention
-  fields:
-    name: colon_lesion_polypectomy_hot_snare
-    description:
-      Hot snare polypectomy is a technique used to remove small polyps
-      from the colon. It is performed using a snare wire loop that is passed through
-      the colonoscope and used to remove the polyp by cutting it off at the base.
-      The procedure is usually done without the need for sedation and is considered
-      to be a safe and effective way to remove small polyps from the colon.
-    intervention_types:
-      - therapeutic
-      - invasive
-    required_lab_values:
-      - hemoglobin
-      - platelets
-      - international_normalized_ratio
-    contraindications:
-      - anticoagulation-therapeutic
-      - thrombocytopenia-severe
-- model: endoreg_db.finding_intervention
-  fields:
-    name: colon_lesion_injection_liftup
-    description:
-      Lift-up injection is a technique used to lift up a lesion in the
-      colon. It is performed by injecting a solution under the lesion to create a
-      cushion of fluid that lifts the lesion away from the colon wall. This allows
-      the lesion to be removed more easily and reduces the risk of complications during
-      the procedure.
-    intervention_types:
-      - diagnostic
-      - invasive
-    required_lab_values:
-      - hemoglobin
-      - platelets
-      - international_normalized_ratio
-    contraindications: []
-- model: endoreg_db.finding_intervention
-  fields:
-    name: colon_lesion_injection_vasoactive
-    description:
-      Vasoactive injection is a technique used to reduce bleeding from
-      a lesion in the colon. It is performed by injecting a solution into the lesion
-      that causes the blood vessels to constrict, reducing the flow of blood to the
-      area. This can help to stop bleeding and make it easier to remove the lesion
-      during the procedure.
-    intervention_types:
-      - therapeutic
-      - invasive
-    required_lab_values: []
-    contraindications: []
-- model: endoreg_db.finding_intervention
-  fields:
-    name: colon_lesion_biopsy
-    description:
-      Biopsy is a technique used to take a small sample of tissue from
-      a lesion in the colon. It is performed by inserting a small instrument through
-      the colonoscope and removing a small piece of tissue from the lesion. The tissue
-      sample is then sent to a laboratory for analysis to determine if the lesion
-      is cancerous or benign.
-    intervention_types:
-      - diagnostic
-      - invasive
-    required_lab_values: []
-    contraindications:
-      - anticoagulation-therapeutic
-      - thrombocytopenia-severe
-- model: endoreg_db.finding_intervention
-  fields:
-    name: colon_lesion_emr
-    description:
-      Endoscopic mucosal resection (EMR) is a technique used to remove
-      large polyps or early-stage cancers from the colon. It is performed by injecting
-      a solution under the lesion to create a cushion of fluid that lifts the lesion
-      away from the colon wall. A snare wire loop is then used to remove the lesion
-      by cutting it off at the base. The procedure is usually done under sedation
-      and is considered to be a safe and effective way to remove large polyps or early-stage
-      cancers from the colon.
-    intervention_types:
-      - therapeutic
-      - invasive
-    required_lab_values:
-      - hemoglobin
-      - platelets
-      - international_normalized_ratio
-    contraindications:
-      - anticoagulation-therapeutic
-      - thrombocytopenia-severe
-- model: endoreg_db.finding_intervention
-  fields:
-    name: colon_lesion_esd
-    description:
-      Endoscopic submucosal dissection (ESD) is a technique used to remove
-      large polyps or early-stage cancers from the colon. It is performed by injecting
-      a solution under the lesion to create a cushion of fluid that lifts the lesion
-      away from the colon wall. A snare wire loop is then used to remove the lesion
-      by cutting it off at the base. The procedure is usually done under sedation
-      and is considered to be a safe and effective way to remove large polyps or early-stage
-      cancers from the colon.
-    intervention_types:
-      - therapeutic
-      - invasive
-    required_lab_values:
-      - hemoglobin
-      - platelets
-      - international_normalized_ratio
-    contraindications:
-      - anticoagulation-therapeutic
-      - thrombocytopenia-severe
-- model: endoreg_db.finding_intervention
-  fields:
-    name: colon_lesion_clip
-    description:
-      Clip closure is a technique used to close a defect in the colon wall
-      after a polyp has been removed. It is performed by placing a small metal clip
-      over the defect to seal it and prevent bleeding or perforation. The clip is
-      left in place until the defect has healed, usually within a few days.
-    intervention_types:
-      - therapeutic
-      - invasive
-      - foreign_body
-    required_lab_values: []
-    contraindications: []
-- model: endoreg_db.finding_intervention
-  fields:
-    name: colon_lesion_over_the_scope_clip
-    description:
-      Over-the-scope clip (OTSC) is a clipping system used to close defects
-      in the GI tract.
-    intervention_types:
-      - therapeutic
-      - invasive
-    required_lab_values: []
-    contraindications: []
-- model: endoreg_db.finding_intervention
-  fields:
-    name: colon_lesion_eftr
-    description:
-      Endoscopic full-thickness resection (EFTR) is a technique used to
-      remove lesions in the colon.
-    intervention_types:
-      - therapeutic
-      - invasive
-    required_lab_values:
-      - hemoglobin
-      - platelets
-      - international_normalized_ratio
-    contraindications:
-      - anticoagulation-therapeutic
-      - thrombocytopenia-severe