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

endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml

@@ -1,7 +1,6 @@
 - model: endoreg_db.examination_indication_classification_choice
   fields:
     name: "colonoscopy_bleeding"
-    classification: "endoscopy_colonoscopy"
     name_de: "Koloskopie: Blutung"
     name_en: "Colonoscopy: Bleeding"
     subcategories:
@@ -15,19 +14,19 @@
 - 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",
-        ]
+        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
@@ -42,20 +41,20 @@
         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",
-        ]
+        choices:
+          [
+            "age",
+            "family_history_colorectal_cancer",
+            "family_history_polyposis_syndrome",
+          ]
         default: "age"
         probability: [0.8, 0.1, 0.1]
         required: true
@@ -64,38 +63,35 @@
 - 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",
-        ]
+        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]
+        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"
-        ]
-
-
+            "lesion_removal", # > 9mm
+            "hemostasis",
+            "dilatation",
+            "stent_placement",
+            "foreign_body_removal",
+          ]

endoreg_db/data/finding/00_generic.yaml

@@ -0,0 +1,35 @@
+- model: endoreg_db.finding
+  fields:
+    name: "examination_setting"
+    finding_types:
+      - baseline
+    description: "Settings related to the examination environment and conditions."
+    finding_classifications:
+      - examination_setting_generic_location
+
+- model: endoreg_db.finding
+  fields:
+    name: "sedation_endoscopy"
+    description: "Sedation during an examination"
+    finding_types:
+      - baseline
+    finding_classifications:
+      - sedation_performed
+      - examination_setting_generic_sedation
+
+- model: endoreg_db.finding
+  fields:
+    name: "post_resection_wound"
+    description: "Postresection Wound"
+    finding_types:
+      - observation
+      - iatrogenic
+    finding_interventions:
+      - endoscopy_injection_vasoactive
+      - endoscopy_hemoclip_generic
+      - endoscopy_over_the_scope_clip_generic
+    finding_classifications: [] #TODO active bleeding? macroscopically in sano?
+    caused_by_interventions:
+      - endoscopy_cold_snare_resection_generic
+      - endoscopy_diathermic_snare_resection_generic
+      - endoscopy_biopsy_foreceps_resection_generic

endoreg_db/data/finding/00_generic_complication.yaml

@@ -0,0 +1,9 @@
+- model: endoreg_db.finding
+  fields:
+    name: "complication_generic"
+    name_de: "Komplikation (generisch)"
+    name_en: "Complication (generic)"
+    finding_types:
+      - complication
+    finding_classifications:
+      - complication_generic_type

endoreg_db/data/finding/01_gastroscopy_baseline.yaml

@@ -0,0 +1,88 @@
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_esophagus_mucosa"
+    name_de: "Speiseröhren-Schleimhaut"
+    name_en: "Esophagus Mucosa"
+    finding_types:
+      - baseline
+    finding_classifications: [] #TODO
+    finding_interventions: []
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_gastroesophageal_junction"
+    name_de: "Gastroösophagealer Übergang"
+    name_en: "Gastroesophageal Junction"
+    finding_types:
+      - baseline
+    finding_classifications: []
+    finding_interventions: []
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_fundus_mucosa"
+    name_de: "Magenfundus-Schleimhaut"
+    name_en: "Gastric Fundus Mucosa"
+    finding_types:
+      - baseline
+    finding_classifications: []
+    finding_interventions: []
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_corpus_mucosa"
+    name_de: "Magenkörper-Schleimhaut"
+    name_en: "Gastric Corpus Mucosa"
+    finding_types:
+      - baseline
+    finding_classifications: []
+    finding_interventions: []
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_antrum_mucosa"
+    name_de: "Antrum-Schleimhaut"
+    name_en: "Antrum Mucosa"
+    finding_types:
+      - baseline
+    finding_classifications: []
+    finding_interventions: []
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_pylorus"
+    name_de: "Pylorus"
+    name_en: "Pylorus"
+    finding_types:
+      - baseline
+    finding_classifications: []
+    finding_interventions: []
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_angulus_flexure_mucosa"
+    name_de: "Angulusfalte"
+    name_en: "Angulus Flexure"
+    finding_types:
+      - baseline
+    finding_classifications: []
+    finding_interventions: []
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_duodenum_bulbus_mucosa"
+    name_de: "Duodenum-Bulbus"
+    name_en: "Duodenum Bulbus"
+    finding_types:
+      - baseline
+    finding_classifications: []
+    finding_interventions: []
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_duodenum_mucosa"
+    name_de: "Duodenum-Schleimhaut"
+    name_en: "Duodenum Mucosa"
+    finding_types:
+      - baseline
+    finding_classifications: []
+    finding_interventions: []

endoreg_db/data/finding/01_gastroscopy_observation.yaml

@@ -0,0 +1,113 @@
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_polyp"
+    description: "Polyp"
+    finding_types:
+      - observation
+      #TODO add finding_classifications and finding_interventions
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_ulcer"
+    description: "Ulcer"
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_erythema"
+    description: "Erythema"
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_subepithelial_tumor"
+    description: "Subepithelial Tumor"
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_stenosis"
+    description: "Stenosis"
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_varices_esophageal"
+    description: "Esophageal Varices"
+    finding_types:
+      - observation
+      - persisting
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_varices_gastric"
+    description: "Gastric Varices"
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_varices_duodenal"
+    description: "Duodenal Varices"
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_scar"
+    description: "Scar"
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_bleeding"
+    description: "Bleeding"
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_stenosis"
+    description: "Stenosis"
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_ectopic_gastric_mucosa"
+    description: "Ectopic Gastric Mucosa"
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_diverticulum_esophagus"
+    description: "Divertikel (Ösophagus)"
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_diverticulum_duodenum"
+    description: "Divertikel (Duodenum)"
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_ectopic_pancreatic_tissue"
+    description: "Ectopic Pancreatic Tissue"
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "gastroscopy_obstruction_generic"
+    description: "Generic Obstruction"
+    finding_types:
+      - observation

endoreg_db/data/finding/02_colonoscopy_baseline.yaml

@@ -0,0 +1,53 @@
+- model: endoreg_db.finding
+  fields:
+    name: "bowel_preparation_lc"
+    name_de: "Darmvorbereitung (Linkes Kolon)"
+    name_en: "Bowel Preparation (Left Colon)"
+    finding_types:
+      - baseline
+    finding_classifications:
+      - bowel_prep_boston
+      - bowel_prep_aronchick
+
+- model: endoreg_db.finding
+  fields:
+    name: "bowel_preparation_tc"
+    name_de: "Darmvorbereitung (Kolon Transversum)"
+    name_en: "Bowel Preparation (Transverse Colon)"
+    finding_types:
+      - baseline
+    finding_classifications:
+      - bowel_prep_boston
+      - bowel_prep_aronchick
+
+- model: endoreg_db.finding
+  fields:
+    name: "bowel_preparation_rc"
+    name_de: "Darmvorbereitung (Rechtes Kolon)"
+    name_en: "Bowel Preparation (Right Colon)"
+    finding_types:
+      - baseline
+    finding_classifications:
+      - bowel_prep_boston
+      - bowel_prep_aronchick
+
+- model: endoreg_db.finding
+  fields:
+    name: "bowel_preparation_simplified"
+    name_de: "Darmvorbereitung (Vereinfacht)"
+    name_en: "Bowel Preparation (Simplified)"
+    finding_types:
+      - baseline
+    finding_classifications:
+      - bowel_prep_boston_simplified
+
+- model: endoreg_db.finding
+  fields:
+    name: "colonoscopy_deepest_viewed_location"
+    name_de: "Tiefste betrachtete Stelle während einer Koloskopie"
+    name_en: "Deepest viewed location during colonoscopy"
+    finding_types:
+      - baseline
+    finding_classifications:
+      - colonoscopy_location_default
+      - colonoscopy_not_complete_reason #TODO Requirement should make sure, that a patientfindingclassification with reason is available if location is not cecum / appendix / terminal ileum

endoreg_db/data/finding/02_colonoscopy_hidden.yaml

@@ -0,0 +1,119 @@
+- model: endoreg_db.finding
+  fields:
+    name: "cecum"
+    description: "Anatomical structure: Cecum"
+    finding_types:
+      - anatomy
+      - hidden
+    finding_classifications:
+      - visualized
+
+- model: endoreg_db.finding
+  fields:
+    name: "terminal_ileum"
+    description: "Anatomical structure: Terminal ileum"
+    finding_types:
+      - anatomy
+      - hidden
+    finding_classifications:
+      - visualized
+
+- model: endoreg_db.finding
+  fields:
+    name: "appendiceal_orifice"
+    description: "Anatomical structure: Appendiceal orifice"
+    finding_types:
+      - anatomy
+      - hidden
+    finding_classifications:
+      - visualized
+
+- model: endoreg_db.finding
+  fields:
+    name: "ileocecal_valve"
+    description: "Anatomical structure: Ileocecal valve"
+    finding_types:
+      - anatomy
+      - hidden
+    finding_classifications:
+      - visualized
+
+- model: endoreg_db.finding
+  fields:
+    name: "ascending_colon"
+    description: "Anatomical structure: Ascending colon"
+    finding_types:
+      - anatomy
+      - hidden
+    finding_classifications:
+      - visualized
+
+- model: endoreg_db.finding
+  fields:
+    name: "right_flexure"
+    description: "Anatomical structure: Right flexure"
+    finding_types:
+      - anatomy
+      - hidden
+    finding_classifications:
+      - visualized
+
+- model: endoreg_db.finding
+  fields:
+    name: "transverse_colon"
+    description: "Anatomical structure: Transverse colon"
+    finding_types:
+      - anatomy
+      - hidden
+    finding_classifications:
+      - visualized
+
+- model: endoreg_db.finding
+  fields:
+    name: "left_flexure"
+    description: "Anatomical structure: Left flexure"
+    finding_types:
+      - anatomy
+      - hidden
+    finding_classifications:
+      - visualized
+
+- model: endoreg_db.finding
+  fields:
+    name: "descending_colon"
+    description: "Anatomical structure: Descending colon"
+    finding_types:
+      - anatomy
+      - hidden
+    finding_classifications:
+      - visualized
+
+- model: endoreg_db.finding
+  fields:
+    name: "sigmoid_colon"
+    description: "Anatomical structure: Sigmoid colon"
+    finding_types:
+      - anatomy
+      - hidden
+    finding_classifications:
+      - visualized
+
+- model: endoreg_db.finding
+  fields:
+    name: "rectum"
+    description: "Anatomical structure: Rectum"
+    finding_types:
+      - anatomy
+      - hidden
+    finding_classifications:
+      - visualized
+
+- model: endoreg_db.finding
+  fields:
+    name: "rectum_anus"
+    description: "Anatomical structure: Rectum and anus"
+    finding_types:
+      - anatomy
+      - hidden
+    finding_classifications:
+      - visualized

endoreg_db/data/finding/02_colonoscopy_observation.yaml

@@ -0,0 +1,152 @@
+- model: endoreg_db.finding
+  fields:
+    name: "colon_polyp"
+    name_de: "Kolonpolyp"
+    name_en: "Colon Polyp"
+    finding_types:
+      - observation
+    finding_interventions:
+      - endoscopy_biopsy_grasper_generic
+      - endoscopy_cold_snare_resection_generic
+      - endoscopy_diathermic_snare_resection_generic
+      - endoscopy_biopsy_foreceps_resection_generic
+      - endoscopy_emr_generic
+      - endoscopy_esd_generic
+      - endoscopy_eftr_generic
+      - endoscopy_injection_liftup
+      - endoscopy_hemoclip_generic
+      - endoscopy_over_the_scope_clip_generic
+    finding_classifications:
+      # Shared Models
+      ## size classifications
+      - lesion_size_mm
+      ## Morphology classifications
+      - lesion_circularity_default
+      - lesion_planarity_default
+      - lesion_surface_intact_default
+      ## Location
+      - colonoscopy_location_default
+      - colonoscopy_location_coarse
+      ## histology
+      - histology_dysplasia_default
+      - histology_dignity_default
+      - histology_in_sano_default
+
+      # More specific Models
+      ## size classifications
+      - colon_lesion_size_categorical
+      ## Morphology classifications
+      - colon_lesion_paris
+      - colon_lesion_nice
+      - colon_lesion_jnet
+      - colon_lesion_kudo
+      - colon_lesion_lst
+      ## histology
+      - colonoscopy_polyp_histology
+
+- model: endoreg_db.finding
+  fields:
+    name: "colon_diverticule"
+    name_de: "Kolondivertikel"
+    name_en: "Colon Diverticule"
+    finding_interventions:
+      - endoscopy_hemoclip_generic
+      - endoscopy_biopsy_grasper_generic
+      - endoscopy_injection_vasoactive
+    finding_types:
+      - observation
+    finding_classifications:
+      - colonoscopy_location_coarse
+      - colonoscopy_location_default
+      # - diverticule_inflammation_grade #TODO
+      # - diverticule_stenosis_degree_categorical #TODO
+
+- model: endoreg_db.finding
+  fields:
+    name: "anal_hemorrhoids"
+    name_de: "Hämorrhoiden"
+    name_en: "hemorrhoids"
+    finding_interventions: [] #TODO
+    finding_types:
+      - observation
+    finding_classifications:
+      - hemorrhoids_grade
+
+- model: endoreg_db.finding
+  fields:
+    name: "anal_fissure"
+    name_de: "Analfissur"
+    name_en: "Anal Fissure"
+    finding_interventions: [] #TODO
+    finding_types:
+      - observation
+    finding_classifications: [] #TODO
+
+- model: endoreg_db.finding
+  fields:
+    name: "colon_stenosis"
+    name_de: "Kolonstenose"
+    name_en: "Colon Stenosis"
+    finding_interventions:
+      - endoscopy_dilation_balloon #TODO
+      - endoscopy_stent_generic #TODO
+    finding_types:
+      - observation
+    finding_classifications:
+      # - colon_lesion_stenosis_degree_categorical #TODO
+      - colonoscopy_location_coarse
+      - colonoscopy_location_default
+      - lesion_circularity_default
+
+- model: endoreg_db.finding
+  fields:
+    name: "colon_post_intervention_wound"
+    name_de: "Postinterventionelle Wunde"
+    finding_interventions: ["endoscopy_hemoclip_generic"] #TODO
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "colon_tumor_mass"
+    name_de: "Tumor"
+    name_en: "Tumor"
+    finding_interventions: []
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "colon_inflammation"
+    name_de: "Entzündung"
+    name_en: "Inflammation"
+    finding_interventions: []
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "colon_erosion"
+    name_de: "Erosion"
+    name_en: "Erosion"
+    finding_interventions: []
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "colon_ulcer"
+    name_de: "Ulcus"
+    name_en: "Ulcer"
+    finding_interventions: []
+    finding_types:
+      - observation
+
+- model: endoreg_db.finding
+  fields:
+    name: "colon_scar"
+    name_de: "Narbe"
+    name_en: "Scar"
+    finding_interventions: []
+    finding_types:
+      - observation