endoreg-db 0.6.0__py3-none-any.whl → 0.6.2__py3-none-any.whl

endoreg_db/data/event/neurology.yaml

@@ -0,0 +1,14 @@
+
+- model: endoreg_db.event
+  fields:
+    name: "stroke"
+    name_de: "Schlaganfall"
+    name_en: "Stroke"
+
+- model: endoreg_db.event
+  fields:
+    name: "transient_ischemic_attack"
+    name_de: "Transitorische ischämische Attacke"
+    name_en: "Transient Ischemic Attack"
+    
+    

endoreg_db/data/event/surgery.yaml

@@ -0,0 +1,13 @@
+- model: endoreg_db.event
+  fields:
+    name: "hip_replacement_surgery" #TODO : could match disease / indication / ...?
+    name_de: "Hüft-TEP Operation"
+    name_en: "Hip replacement surgery"
+    description: "Hip replacement surgery"
+
+- model: endoreg_db.event
+  fields:
+    name: "knee_replacement_surgery"
+    name_de: "Knie-TEP Operation"
+    name_en: "Knee replacement surgery"
+    description: "Knee replacement surgery"

endoreg_db/data/event/thrombembolism.yaml

@@ -0,0 +1,20 @@
+- model: endoreg_db.event
+  fields:
+    name: "deep_vein_thrombosis"
+    name_de: "Tiefe Beinvenenthrombose"
+    name_en: "Deep Vein Thrombosis"
+    description: "Deep Vein Thrombosis"
+
+- model: endoreg_db.event
+  fields:
+    name: "pulmonary_embolism"
+    name_de: "Lungenembolie"
+    name_en: "Pulmonary Embolism"
+    description: "Pulmonary Embolism"
+
+- model: endoreg_db.event
+  fields:
+    name: "recurrent_thrombembolism"
+    name_de: "Rezidivierende Thrombembolien"
+    name_en: "Recurrent Thrombembolism"
+    description: "Recurrent Thrombembolism"

endoreg_db/data/examination/examinations/data.yaml

@@ -0,0 +1,66 @@
+- model: report.Examination
+  fields:
+    name: "colonoscopy"
+    name_de: "Koloskopie"
+    name_en: "Colonoscopy"
+    examination_types: [
+      "endoscopy"
+    ]
+
+- model: report.Examination
+  fields:
+    name: "gastroscopy"
+    name_de: "Gastroskopie"
+    name_en: "Gastroscopy"
+    examination_types: [
+      "endoscopy"
+    ]
+
+# endosonography_upper_gi
+- model: report.Examination
+  fields:
+    name: "endosonography_upper_gi"
+    name_de: "Endosonographie oberer GI-Trakt"
+    name_en: "Endosonography Upper GI Tract"
+    examination_types: [
+      "endoscopy"
+    ]
+
+- model: report.Examination
+  fields:
+    name: "endosonography_lower_gi"
+    name_de: "Endosonographie unterer GI-Trakt"
+    name_en: "Endosonography Lower GI Tract"
+    examination_types: [
+      "endoscopy"
+    ]
+
+# ERCP
+- model: report.Examination
+  fields:
+    name: "ercp"
+    name_de: "ERCP"
+    name_en: "ERCP"
+    examination_types: [
+      "endoscopy"
+    ]
+
+# small bowel endoscopy
+- model: report.Examination
+  fields:
+    name: "small_bowel_endoscopy"
+    name_de: "Dünndarmendoskopie"
+    name_en: "Small Bowel Endoscopy"
+    examination_types: [
+      "endoscopy"
+    ]
+
+# capsule endoscopy
+- model: report.Examination
+  fields:
+    name: "capsule_endoscopy"
+    name_de: "Kapselendoskopie"
+    name_en: "Capsule Endoscopy"
+    examination_types: [
+      "endoscopy"
+    ]

endoreg_db/data/examination/time/data.yaml

@@ -0,0 +1,48 @@
+- model: report.ExaminationTime
+  fields:
+    name: "colonoscopy-total-time"
+    name_de: "Koloskopie Zeiten"
+    name_en: "Colonoscopy Times"
+    time_types: [
+      "colonoscopy-time"
+    ]
+  
+# withdrawal-time
+- model: report.ExaminationTime
+  fields:
+    name: "withdrawal-time"
+    name_de: "Withdrawal Time"
+    name_en: "Withdrawal Time"
+    time_types: [
+      "colonoscopy-time"
+    ]
+
+# cecum-time
+- model: report.ExaminationTime
+  fields:
+    name: "cecum-time"
+    name_de: "Zökum Zeit"
+    name_en: "Cecum Time"
+    time_types: [
+      "colonoscopy-time"
+    ]
+
+# intubation-time
+- model: report.ExaminationTime
+  fields:
+    name: "intubation-time"
+    name_de: "Intubationszeit"
+    name_en: "Intubation Time"
+    time_types: [
+      "colonoscopy-time"
+    ]
+
+# colonoscopy-intervention-time
+- model: report.ExaminationTimeType
+  fields:
+    name: "colonoscopy-intervention-time"
+    name_de: "Interventionszeit"
+    name_en: "Intervention Time"
+    time_types: [
+      "colonoscopy-time"
+    ]

endoreg_db/data/examination/time-type/data.yaml

@@ -0,0 +1,8 @@
+- model:
+  fields:
+    name: "colonoscopy-time"
+    name_de: "Koloskopie-Zeit"
+    name_en: "Colonoscopy Time"
+    examinations: [
+      "colonoscopy"
+    ]

endoreg_db/data/examination/type/data.yaml

@@ -0,0 +1,5 @@
+- model: report.ExaminationType
+  fields:
+    name: "endoscopy"
+    name_de: "Endoskopie"
+    name_en: "Endoscopy"

endoreg_db/data/examination_indication/endoscopy.yaml

@@ -0,0 +1,8 @@
+- model: endoreg_db.examination_indication
+  fields:
+    name: "colonoscopy"
+    name_de: "Koloskopie"
+    name_en: "Colonoscopy"
+    classification: "endoscopy_colonoscopy"
+    examination: "colonoscopy"
+

endoreg_db/data/examination_indication_classification/endoscopy.yaml

@@ -0,0 +1,8 @@
+- model: endoreg_db.examination_indication_classification
+  fields:
+    name: "endoscopy_colonoscopy"
+    name_de: "Koloskopie"
+    name_en: "Colonoscopy"
+
+    
+  

endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml

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+- model: endoreg_db.examination_indication_classification_choice
+  fields:
+    name: "colonoscopy_bleeding"
+    classification: "endoscopy_colonoscopy"
+    name_de: "Koloskopie: Blutung"
+    name_en: "Colonoscopy: Bleeding"
+    subcategories:
+      acuteness:
+        choices: ["N0", "N1", "N2", "N3", "N4", "N5"]
+        default: "N4"
+        probability: [0.005, 0.005, 0.01, 0.13, 0.35, 0.5]
+        required: false
+        description: "Acuteness of the examination (N0: immediate, N1: < 1h, N2: < 6h, N3: < 12h, N4: < 24h, N5: >= 24h)"
+
+- model: endoreg_db.examination_indication_classification_choice
+  fields:
+    name: "colonoscopy_surveillance"
+    classification: "endoscopy_colonoscopy"
+    name_de: "Koloskopie: Überwachung"
+    name_en: "Colonoscopy: Surveillance"
+    subcategories:
+      reason:
+        choices: [
+          "unknown",
+          "polypectomy_surveillance",
+          "known_polyposis_syndrome",
+          "known_inflammatory_bowel_disease",
+          "suspected_inflammatory_bowel_disease",
+          "positive_ifobt",
+        ]
+        default: "unknown"
+        probability: [0.5, 0.1, 0.1, 0.1, 0.2]
+        required: true
+        description: "Reason for surveillance"
+    numerical_descriptors:
+      months_since_last_colonoscopy:
+        unit: "month"
+        min: 3
+        max: 120
+        mean: 24
+        std: 12
+        distribution: "normal"
+        description: "Months since last colonoscopy"
+        required: true
+        
+- model: endoreg_db.examination_indication_classification_choice
+  fields:
+    name: "colonoscopy_screening"
+    classification: "endoscopy_colonoscopy"
+    name_de: "Koloskopie: Screening"
+    name_en: "Colonoscopy: Screening"
+    subcategories:
+      reason:
+        choices: [
+          "age",
+          "family_history_colorectal_cancer",
+          "family_history_polyposis_syndrome",
+        ]
+        default: "age"
+        probability: [0.8, 0.1, 0.1]
+        required: true
+        description: "Reason for screening"
+
+- model: endoreg_db.examination_indication_classification_choice
+  fields:
+    name: "colonoscopy_diagnostic"
+    classification: "endoscopy_colonoscopy"
+    name_de: "Koloskopie: Diagnostik"
+    name_en: "Colonoscopy: Diagnostic"
+    subcategories:
+      reason:
+        choices: [
+          "abdominal_pain",
+          "diarrhea",
+          "constipation",
+          "weight_loss",
+          "anemia",
+          "positive_ifobt",
+          "suspected_inflammatory_bowel_disease",
+        ]
+        default: "abdominal_pain"
+        probability: [0.2,0.2,0.2,0.0.5,0.1,0.1,0.05]
+        required: true
+
+- model: endoreg_db.examination_indication_classification_choice
+  fields:
+    name: "colonoscopy_therapeutic"
+    classification: "endoscopy_colonoscopy"
+    name_de: "Koloskopie: therapeutisch"
+    name_en: "Colonoscopy: Therapeutic"
+    subcategories:
+      reason:
+        choices: [
+          "lesion_removal", # > 9mm
+          "hemostasis",
+          "dilatation",
+          "stent_placement",
+          "foreign_body_removal"
+        ]
+
+

endoreg_db/data/finding/data.yaml

@@ -0,0 +1,141 @@
+- model: endoreg_db.finding
+  fields:
+    name: "colon_polyp"
+    name_de: "Kolonpolyp"
+    name_en: "Colon Polyp"
+
+    finding_interventions:
+      [
+        "colon-lesion-polypectomy-cold-snare",
+        "colon-lesion-polypectomy-hot-snare",
+        "colon-lesion-injection-liftup",
+        "colon-lesion-injection-vasoactive",
+        "colon-lesion-biopsy",
+        "colon-lesion-emr",
+        "colon-lesion-esd",
+        "colon-lesion-clip",
+      ]
+
+    causing_finding_interventions: []
+    opt_causing_finding_interventions: []
+
+    examinations: ["colonoscopy"]
+
+    finding_types: ["macroscopic"]
+
+- model: endoreg_db.finding
+  fields:
+    name: "post-intervention-wound"
+    name_de: "Postinterventionelle Wunde"
+
+    finding_interventions: ["colon-lesion-clip"]
+
+    causing_finding_interventions: ["colon-lesion-polypectomy-cold-snare"]
+
+    opt_causing_finding_interventions: []
+
+    examinations: ["colonoscopy"]
+
+    finding_types: ["macroscopic"]
+
+- model: endoreg_db.finding
+  fields:
+    name: "tumor"
+    name_de: "Tumor"
+    name_en: "Tumor"
+
+    finding_interventions: []
+    causing_finding_interventions: []
+    opt_causing_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: []
+    causing_finding_interventions: []
+    opt_causing_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: []
+    causing_finding_interventions: []
+    opt_causing_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: []
+    causing_finding_interventions: []
+    opt_causing_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: []
+    causing_finding_interventions: []
+    opt_causing_finding_interventions: ["colon-lesion-polypectomy-cold-snare"]
+
+    examinations:
+      [
+        "colonoscopy",
+        "endosonography_upper_gi",
+        "endosonography_lower_gi",
+        "ercp",
+        "small_bowel_endoscopy",
+        "capsule_endoscopy",
+      ]
+
+    finding_types: ["macroscopic"]

endoreg_db/data/finding_intervention/endoscopy.yaml

@@ -0,0 +1,138 @@
+- 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: []
+

endoreg_db/data/finding_intervention_type/endoscopy.yaml

@@ -0,0 +1,15 @@
+- model: endoreg_db.finding_intervention_type
+  fields:
+    name: "therapeutic"
+
+- model: endoreg_db.finding_intervention_type
+  fields:
+    name: "invasive"
+
+- model: endoreg_db.finding_intervention_type
+  fields:
+    name: "diagnostic"
+
+- model: endoreg_db.finding_intervention_type
+  fields:
+    name: "foreign_body"

endoreg_db/data/finding_location_classification/colonoscopy.yaml

@@ -0,0 +1,46 @@
+- model: endoreg_db.finding_location_classification
+  fields:
+    name: "colonoscopy_default"
+    name_de: "Koloskopie Standard"
+    name_en: "Colonoscopy Default"
+    examinations: [
+      "colonoscopy"
+    ]
+    finding_types: [
+      "macroscopic"
+    ]
+    findings: [
+      "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_location_classification_choice
+  fields:
+    name: "colonoscopy_coarse"
+    name_de: "Koloskopie Grob"
+    name_en: "Colonoscopy Coarse"
+    examinations: [
+      "colonoscopy"
+    ]
+    finding_types: [
+      "macroscopic"
+    ]
+    findings: []
+    choices: [
+      "left_colon",
+      "right_colon",
+      "rectum"
+    ]