endoreg-db 0.8.5.1__py3-none-any.whl

endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml

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+- 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

endoreg_db/data/finding_intervention/endoscopy_egd.yaml

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+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_biopsy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_hp_biopsy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_injection_vasoactive
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_clip
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_over_the_scope_clip
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_varice_band_ligation
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_varice_sclerotherapy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_argon_plasma_coagulation
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_percutaneous_gastroenterostomy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_percutaneous_jejunostomy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_clip
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_varicosis_band_ligation
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_varicosis_sclerotherapy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_injection_vasoactive
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_injection_varicosis
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_polypectomy_cold_snare
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_polypectomy_hot_snare
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_polypectomy_forceps
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_injection_liftup
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_emr
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_esd
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_eftr
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_poem
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_stepwise_biopsy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_esophagus_injection_botox
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_stenosis_dilation
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_stenosis_bougie
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_stenosis_balloon
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_stenosis_stent
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_radiofrequency_ablation
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_lesion_cryotherapy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_stenosis_laser
+    # ...existing code...

endoreg_db/data/finding_intervention/endoscopy_ercp.yaml

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+- model: endoreg_db.finding_intervention
+  fields:
+    name: ercp
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: ercp_sphincterotomy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: ercp_stent
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: ercp_extraction
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: ercp_biopsy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: erc
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: erp
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: ercp_radiofrequency_ablation
+    # ...existing code...

endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml

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+# (currently no interventions)
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_lower_gi_solid_lesion_fna
+
+# endosonography_lower_gi_lymph_node_fna
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_lower_gi_lymph_node_fna

endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml

@@ -0,0 +1,36 @@
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_solid_lesion_fna
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_cyst_fna
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_pseudocyst_fna
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_biliary_drainage
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_pancreatic_drainage
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_cyst_gastrostomy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_pancreaticogastrostomy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_cholangioduodenostomy
+    # ...existing code...
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_upper_gi_pancreaticoduodenostomy
+    # ...existing code...

endoreg_db/data/finding_intervention_type/endoscopy.yaml

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+- 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_morphology_classification_type/colonoscopy.yaml

@@ -0,0 +1,79 @@
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colon_lesion_size"
+    name_de: "Größenklassifikation Kolonläsion"
+    name_en: "Colon Lesion Size Classification"
+
+    required_by_findings: [
+      "colon_polyp"
+    ]
+    optional_for_findings: [
+      "tumor"
+    ]
+
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colon_lesion_shape"
+    name_de: "Formklassifikation Kolonläsion"
+    name_en: "Colon Lesion Shape Classification"
+
+    required_by_findings: [
+      "colon_polyp"
+    ]
+    optional_for_findings: [
+      "tumor"
+    ]
+
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colon_lesion_surface_intact"
+    name_de: "Oberflächenklassifikation Kolonläsion"
+    name_en: "Colon Lesion Surface Classification"
+
+    required_by_findings: [
+      "colon_polyp"
+    ]
+    optional_for_findings: [
+      "tumor"
+    ]
+
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colon_lesion_planarity"
+    name_de: "Planaritätsklassifikation Kolonläsion"
+    name_en: "Colon Lesion Planarity Classification"
+
+    required_by_findings: [
+      "colon_polyp"
+    ]
+    optional_for_findings: [
+
+    ]
+
+# Circularity
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colon_lesion_circularity"
+    name_de: "Kolonläsion - Zirkularität"
+    name_en: "Colon lesion - circularity"
+
+    required_by_findings: [
+      "colon_polyp"
+    ]
+    optional_for_findings: [
+      "tumor"
+    ]
+
+# colon_lesion_advanced_imaging
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colon_lesion_advanced_imaging"
+    name_de: "Kolonläsion - Advanced Imaging"
+    name_en: "Colon lesion - Advanced Imaging"
+
+    required_by_findings: [
+      "colon_polyp"
+    ]
+    optional_for_findings: [
+      "tumor"
+    ]

endoreg_db/data/finding_type/data.yaml

@@ -0,0 +1,43 @@
+- model: endoreg_db.finding_type
+  fields:
+    name: "macroscopic"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "iatrogenic"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "postinterventional_immediate"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "postinterventional_delayed"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "bleeding"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "endoscopy_baseline"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "medication_related"
+    
+- model: endoreg_db.finding_type
+  fields:
+    name: "anatomy"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "anatomy_colon"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "summary"
+
+- model: endoreg_db.finding_type
+  fields:
+    name: "complication"

endoreg_db/data/gender/data.yaml

@@ -0,0 +1,42 @@
+- model: endoreg_db.gender
+  fields:
+    name: "male"
+    name_de: "männlich"
+    name_en: "male"
+    abbreviation: "m"
+- model: endoreg_db.gender
+  fields:
+    name: "mostly_male"
+    name_de: "überwiegend männlich"
+    name_en: "mostly male"
+- model: endoreg_db.gender
+  fields:
+    name: "female"
+    name_de: "weiblich"
+    name_en: "female"
+    abbreviation: "f"
+- model: endoreg_db.gender
+  fields:
+    name: "mostly_female"
+    name_de: "überwiegend weiblich"
+    name_en: "mostly female"
+    abbreviation: "mf"
+- model: endoreg_db.gender
+  fields:
+    name: "andy"
+    name_de: "andy"
+    name_en: "andy"
+    abbreviation: "andy"
+- model: endoreg_db.gender
+  fields:
+    name: "other"
+    name_de: "andere"
+    name_en: "other"
+    abbreviation: "x"
+- model: endoreg_db.gender
+  fields:
+    name: "unknown"
+    name_de: "unbekannt"
+    name_en: "unknown"
+    abbreviation: "?"
+

endoreg_db/data/information_source/annotation.yaml

@@ -0,0 +1,6 @@
+- model: endoreg_db.InformationSource
+  fields:
+    name: "default_annotation"
+    information_source_types: [
+      "annotation"
+    ]

endoreg_db/data/information_source/data.yaml

@@ -0,0 +1,30 @@
+- model: endoreg_db.InformationSource
+  fields:
+    name: treating_physician
+- model: endoreg_db.InformationSource
+  fields:
+    name: treating_physician_anamnestic
+- model: endoreg_db.InformationSource
+  fields:
+    name: physicians_note_anamnestic
+- model: endoreg_db.InformationSource
+  fields:
+    name: patient_anamnestic
+- model: endoreg_db.InformationSource
+  fields:
+    name: physical_measurement
+- model: endoreg_db.InformationSource
+  fields:
+    name: family_anamnestic
+- model: endoreg_db.InformationSource
+  fields:
+    name: physical_examination
+- model: endoreg_db.InformationSource
+  fields:
+    name: unknown
+- model: endoreg_db.InformationSource
+  fields:
+    name: prediction
+- model: endoreg_db.InformationSource
+  fields:
+    name: annotation

endoreg_db/data/information_source/endoscopy_guidelines.yaml

@@ -0,0 +1,7 @@
+- model: endoreg_db.InformationSource
+  fields:
+    name: "guideline_quality_in_gi"
+    name_de: "Qualitätsanforderungen in der gastrointestinalen Endoskopie v2.0"
+    name_en: "Quality requirements in gastrointestinal endoscopy v2.0"
+    date: "2025-01-01" # not final
+    #TODO Implement information_source

endoreg_db/data/information_source/medication.yaml

@@ -0,0 +1,6 @@
+- model: endoreg_db.InformationSource
+  fields:
+    name: "fachinformation-apixaban-eliquis_2.5mg-bristol_meyer_squibbs"
+    name_de: "Fachinformation Apixaban (Eliquis) 2.5mg, Bristol Meyer Squibbs"
+    name_en: "Apixaban (Eliquis) 2.5mg, Bristol Meyer Squibbs"
+    date: "2024-04-28"

endoreg_db/data/information_source/prediction.yaml

@@ -0,0 +1,7 @@
+- model: endoreg_db.InformationSource
+  fields:
+    name: "default_prediction"
+    information_source_types: [
+      "prediction"
+    ]
+    

endoreg_db/data/information_source_type/data.yaml

@@ -0,0 +1,8 @@
+- model: endoreg_db.InformationSourceType
+  fields:
+    name: "annotation"
+
+- model: endoreg_db.InformationSourceType
+  fields:
+    name: "prediction"
+    

endoreg_db/data/lab_value/cardiac_enzymes.yaml

@@ -0,0 +1,37 @@
+# Creatine kinase: Female: 30–135 U/L; male: 55–170 U/L 
+# Creatine kinase MB (CKMB): ˂5% of total 
+# Troponin: ≤0.04 ng/mL
+
+- model: endoreg_db.lab_value
+  fields:
+    name: "creatine_kinase"
+    name_de: "Kreatinkinase"
+    name_en: "Creatine Kinase"
+    abbreviation: "CK"
+    default_unit: "units per liter"
+    normal_range_gender_dependent: true
+    default_normal_range: {
+      "female": {
+        "min": 30,
+        "max": 135
+      },
+      "male": {
+        "min": 55,
+        "max": 170
+      }
+    }
+    default_numerical_value_distribution: "uniform_default"
+
+- model: endoreg_db.lab_value
+  fields:
+    name: "creatine_kinase_mb_fraction"
+    name_de: "Kreatinkinase MB"
+    name_en: "Creatine Kinase MB"
+    abbreviation: "CKMB%"
+    default_unit: "percent"
+    default_normal_range: {
+      "min": 0.01,
+      "max": 5
+    }
+    default_numerical_value_distribution: "uniform_default"
+