endoreg-db 0.5.3__py3-none-any.whl → 0.6.1__py3-none-any.whl

endoreg_db/data/center/data.yaml

@@ -22,12 +22,15 @@
       "Kathrin",
       "Florian",
       "Philip",
-      "Laura"
+      "Laura",
+      "Tanja",
     ]
+    
     last_names: [
       "Kozielski",
       "Reiter",
       "Purrer",
+      "Hossner",
       "Kudlich",
       "Brand",
       "Weich",
@@ -40,7 +43,7 @@
       "Weich",
       "Dela Cruz",
       "Wiesemann",
-      "Weise",
+      "Wiese",
       "Sodmann"
     ]
 - model: endoreg_db.center
@@ -51,10 +54,37 @@
     first_names: [] # many to many; if foreign key, we would just have a string; strings represent "name" attribute
     last_names: []
 
+# bbk_regensburg
 - model: endoreg_db.center
   fields:
-    name: "gplay_case_generator"
-    name_de: "GPlay Case Generator"
-    name_en: "GPlay Case Generator"
+    name: "bbk_regensburg"
+    name_de: "Barmherzige  Brüder Krankenhaus Regensburg"
+    name_en: "Barmherzige Brüder Hospital Regensburg"
+    first_names: []
+    last_names: []
+
+# uke_hamburg
+- model: endoreg_db.center
+  fields:
+    name: "uke_hamburg"
+    name_de: "Universitätsklinikum Hamburg-Eppendorf"
+    name_en: "University Hospital Hamburg-Eppendorf"
+    first_names: []
+    last_names: []
+
+# rkh_ludwigsburg
+- model: endoreg_db.center
+  fields:
+    name: "rkh_ludwigsburg"
+    name_de: "RKH Krankenhaus Ludwigsburg"
+    name_en: "RKH Hospital Ludwigsburg"
+    first_names: []
+    last_names: []
+
+- model: endoreg_db.center
+  fields:
+    name: "endoreg_db_demo"
+    name_de: "Demo Center"
+    name_en: "Demo Center"
     first_names: []
     last_names: []

endoreg_db/data/contraindication/bleeding.yaml

@@ -0,0 +1,11 @@
+- model: endoreg_db.contraindication
+  fields:
+    name: "anticoagulation-therapeutic"
+    description: "Therapeutic anticoagulation"
+
+- model: endoreg_db.contraindication
+  fields:
+    name: "thrombocytopenia-severe"
+    description: "Thrombocyte count < 50.000/µl"
+
+

endoreg_db/data/distribution/numeric/data.yaml

@@ -0,0 +1,14 @@
+- model: endoreg_db.numeric_value_distribution
+  fields:
+    name: "uniform_default"
+    distribution_type: "uniform"
+    min_descriptor: "min_x_1"
+    max_descriptor: "max_x_1"
+
+
+- model: endoreg_db.numeric_value_distribution
+  fields:
+    name: "uniform_high_x1.5"
+    distribution_type: "uniform"
+    min_descriptor: "max_x_1"
+    max_descriptor: "max_x_1.5"

endoreg_db/data/endoscope/data.yaml

@@ -0,0 +1,93 @@
+- model: endoreg_db.endoscope
+  fields:
+    name: "default_colonoscope_ukw"
+    name_de: "Standard Koloskop UKW"
+    name_en: "Default Colonoscope UKW"
+    sn: "1"
+    center: "university_hospital_wuerzburg"
+    endoscope_type: "colonoscope"
+
+- model: endoreg_db.endoscope
+  fields:
+    name: "default_gastroscope_ukw"
+    name_de: "Standard Gastroskop UKW"
+    name_en: "Default Gastroscope UKW"
+    sn: "2"
+    center: "university_hospital_wuerzburg"
+    endoscope_type: "gastroscope"
+
+- model: endoreg_db.endoscope
+  fields:
+    name: "default_colonoscope_rbk"
+    name_de: "Standard Koloskop RBK"
+    name_en: "Default Colonoscope RBK"
+    sn: "3"
+    center: "rbk_stuttgart"
+    endoscope_type: "colonoscope"
+
+- model: endoreg_db.endoscope
+  fields:
+    name: "default_gastroscope_rbk"
+    name_de: "Standard Gastroskop RBK"
+    name_en: "Default Gastroscope RBK"
+    sn: "4"
+    center: "rbk_stuttgart"
+    endoscope_type: "gastroscope"
+
+- model: endoreg_db.endoscope
+  fields:
+    name: "default_colonoscope_bbk"
+    name_de: "Standard Koloskop BBK"
+    name_en: "Default Colonoscope BBK"
+    sn: "5"
+    center: "bbk_regensburg"
+    endoscope_type: "colonoscope"
+
+- model: endoreg_db.endoscope
+  fields:
+    name: "default_gastroscope_bbk"
+    name_de: "Standard Gastroskop BBK"
+    name_en: "Default Gastroscope BBK"
+    sn: "6"
+    center: "bbk_regensburg"
+    endoscope_type: "gastroscope"
+
+# UKE
+- model: endoreg_db.endoscope
+  fields:
+    name: "default_colonoscope_uke"
+    name_de: "Standard Koloskop UKE"
+    name_en: "Default Colonoscope UKE"
+    sn: "7"
+    center: "uke_hamburg"
+    endoscope_type: "colonoscope"
+
+- model: endoreg_db.endoscope
+  fields:
+    name: "default_gastroscope_uke"
+    name_de: "Standard Gastroskop UKE"
+    name_en: "Default Gastroscope UKE"
+    sn: "8"
+    center: "uke_hamburg"
+    endoscope_type: "gastroscope"
+
+# rkh_ludwigsburg
+- model: endoreg_db.endoscope
+  fields:
+    name: "default_colonoscope_rkh"
+    name_de: "Standard Koloskop RKH"
+    name_en: "Default Colonoscope RKH"
+    sn: "9"
+    center: "rkh_ludwigsburg"
+    endoscope_type: "colonoscope"
+
+- model: endoreg_db.endoscope 
+  fields:
+    name: "default_gastroscope_rkh"
+    name_de: "Standard Gastroskop RKH"
+    name_en: "Default Gastroscope RKH"
+    sn: "10"
+    center: "rkh_ludwigsburg"
+    endoscope_type: "gastroscope"
+
+

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

@@ -0,0 +1,101 @@
+- 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"
+    ]