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

endoreg_db/data/finding_classification_choice/02_colonoscopy_polyp_advanced_imaging.yaml

@@ -0,0 +1,76 @@
+# JNET
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_jnet_1"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_jnet_2a"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_jnet_2b"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_jnet_3"
+
+# NICE
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_NICE_type_1"
+    name_de: "Kolonläsion - NICE Typ 1"
+    name_en: "Colon lesion - NICE type 1"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_NICE_type_2"
+    name_de: "Kolonläsion - NICE Typ 2"
+    name_en: "Colon lesion - NICE type 2"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_NICE_type_3"
+    name_de: "Kolonläsion - NICE Typ 3"
+    name_en: "Colon lesion - NICE type 3"
+
+# Kudo
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_kudo_1"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_kudo_2"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_kudo_3s"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_kudo_3l"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_kudo_4"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_kudo_5i"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_kudo_5n"
+
+# Sano
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_sano_1"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_sano_2"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_sano_3a"
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_sano_3b"

endoreg_db/data/{_examples/finding_classification_choice/colon_lesion_paris.yaml → finding_classification_choice/02_colonoscopy_polyp_morphology.yaml}

@@ -1,41 +1,42 @@
+# Paris
 - model: endoreg_db.finiding_morphology_classification_choice
   fields:
-    name: "colon_paris_Is"
+    name: "colon_lesion_paris_Is"
     name_de: "Kolonläsion Formklassifikation (Paris Is)"
     name_en: "Colon Lesion Shape Classification (Paris Is)"
     description: "Shape classification for colon lesions (Paris Is)"
 
 - model: endoreg_db.finiding_morphology_classification_choice
   fields:
-    name: "colon_paris_Ip"
+    name: "colon_lesion_paris_Ip"
     name_de: "Kolonläsion Formklassifikation (Paris Ip)"
     name_en: "Colon Lesion Shape Classification (Paris Ip)"
     description: "Shape classification for colon lesions (Paris Ip)"
 
 - model: endoreg_db.finiding_morphology_classification_choice
   fields:
-    name: "colon_paris_IIa"
+    name: "colon_lesion_paris_IIa"
     name_de: "Kolonläsion Formklassifikation (Paris IIa)"
     name_en: "Colon Lesion Shape Classification (Paris IIa)"
     description: "Shape classification for colon lesions (Paris IIa)"
 
 - model: endoreg_db.finiding_morphology_classification_choice
   fields:
-    name: "colon_paris_IIb"
+    name: "colon_lesion_paris_IIb"
     name_de: "Kolonläsion Formklassifikation (Paris IIb)"
     name_en: "Colon Lesion Shape Classification (Paris IIb)"
     description: "Shape classification for colon lesions (Paris IIb)"
 
 - model: endoreg_db.finiding_morphology_classification_choice
   fields:
-    name: "colon_paris_IIc"
+    name: "colon_lesion_paris_IIc"
     name_de: "Kolonläsion Formklassifikation (Paris IIc)"
     name_en: "Colon Lesion Shape Classification (Paris IIc)"
     description: "Shape classification for colon lesions (Paris IIc)"
 
 - model: endoreg_db.finiding_morphology_classification_choice
   fields:
-    name: "colon_paris_III"
+    name: "colon_lesion_paris_III"
     name_de: "Kolonläsion Formklassifikation (Paris III)"
     name_en: "Colon Lesion Shape Classification (Paris III)"
     description: "Shape classification for colon lesions (Paris III)"
@@ -43,7 +44,7 @@
 # IIa+IIc
 - model: endoreg_db.finiding_morphology_classification_choice
   fields:
-    name: "colon_paris_IIa_IIc"
+    name: "colon_lesion_paris_IIa_IIc"
     name_de: "Kolonläsion Formklassifikation (Paris IIa+IIc)"
     name_en: "Colon Lesion Shape Classification (Paris IIa+IIc)"
     description: "Shape classification for colon lesions (Paris IIa+IIc)"
@@ -51,7 +52,24 @@
 # IIb+IIc
 - model: endoreg_db.finiding_morphology_classification_choice
   fields:
-    name: "colon_paris_IIb_IIc"
+    name: "colon_lesion_paris_IIb_IIc"
     name_de: "Kolonläsion Formklassifikation (Paris IIb+IIc)"
     name_en: "Colon Lesion Shape Classification (Paris IIb+IIc)"
     description: "Shape classification for colon lesions (Paris IIb+IIc)"
+
+# LST
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_lst_granular_homogeneous"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_lst_granular_nodular_mixed"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_lst_non_granular_flat_elevated"
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colon_lesion_lst_non_granular_pseudodepressed"

endoreg_db/data/finding_classification_choice/02_colonoscopy_size.yaml

@@ -0,0 +1,27 @@
+- 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)"

endoreg_db/data/finding_classification_type/{colonoscopy_basic.yaml → 00_generic.yaml}

@@ -1,48 +1,53 @@
-#####
-# Base types for distinguishing morphology and location
-# Related Fields
 - model: endoreg_db.finding_classification_type
   fields:
     name: "location"
     name_de: "Lokalisation"
     name_en: "Location"
-  
+
 - model: endoreg_db.finding_classification_type
   fields:
     name: "morphology"
     name_de: "Morphologie"
     name_en: "Morphology"
 
-#####
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "histology"
+    name_de: "Histologie"
+    name_en: "Histology"
 
 - model: endoreg_db.finding_classification_type
   fields:
-    name: "bowel_prep"
+    name: "size"
 
 - model: endoreg_db.finding_classification_type
   fields:
-    name: "colon_lesion_size"
+    name: "surface_integrity"
 
 - model: endoreg_db.finding_classification_type
   fields:
-    name: "colon_lesion_surface_intact"
+    name: "planarity"
 
 - model: endoreg_db.finding_classification_type
   fields:
-    name: "colon_lesion_planarity"
+    name: "circularity"
 
 - model: endoreg_db.finding_classification_type
   fields:
-    name: "colon_lesion_circularity"
+    name: "shape"
 
 - model: endoreg_db.finding_classification_type
   fields:
-    name: "colon_lesion_advanced_imaging"
+    name: "capillary_pattern"
 
 - model: endoreg_db.finding_classification_type
   fields:
-    name: "colon_lesion_shape"
+    name: "inferrable"
 
 - model: endoreg_db.finding_classification_type
   fields:
-    name: "colon_lesion_capillary_pattern"
+    name: "bowel_prep"
+
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colon_lesion_advanced_imaging"

endoreg_db/data/finding_classification_type/02_colonoscopy.yaml

@@ -0,0 +1,9 @@
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colonoscopy_bowel_prep"
+    name_de: "Darmvorbereitung"
+    name_en: "Bowel Preparation"
+
+- model: endoreg_db.finding_classification_type
+  fields:
+    name: "colonoscopy_advanced_imaging"

endoreg_db/data/finding_intervention/00_generic_endoscopy.yaml

@@ -0,0 +1,59 @@
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_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
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_foreign_body_removal_generic
+    description:
+      Foreign body removal is a technique used to remove objects that have
+      been accidentally swallowed and are stuck in the colon.
+    intervention_types:
+      - therapeutic
+      - invasive
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_foreign_body_removal_grasper
+    description:
+      Foreign body removal with grasper is a technique used to remove objects
+      that have been accidentally swallowed and are stuck in the colon using a grasper tool.
+    intervention_types:
+      - therapeutic
+      - invasive
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_foreign_body_removal_net
+    description:
+      Foreign body removal with net is a technique used to remove objects
+      that have been accidentally swallowed and are stuck in the colon using a net tool.
+    intervention_types:
+      - therapeutic
+      - invasive
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_foreign_body_removal_snare
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_biopsy_grasper_generic
+    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

endoreg_db/data/finding_intervention/00_generic_endoscopy_ablation.yaml

@@ -0,0 +1,44 @@
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_ablation_radiofrequency
+    description:
+      Radiofrequency ablation is a technique used to destroy abnormal tissue
+      in the colon using heat generated by radiofrequency energy.
+    intervention_types:
+      - therapeutic
+      - invasive
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_ablation_cryotherapy
+    description:
+      Cryotherapy is a technique used to destroy abnormal tissue in the
+      colon using extreme cold.
+    intervention_types:
+      - therapeutic
+      - invasive
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_ablation_laser
+    description:
+      Laser ablation is a technique used to destroy abnormal tissue in the
+      colon using focused light energy.
+    intervention_types:
+      - therapeutic
+      - invasive
+
+# argon_plasma_coagulation
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_ablation_argon_plasma_coagulation
+    description:
+      Argon plasma coagulation (APC) is a non-contact thermal ablation
+      technique used to treat various lesions in the colon. It involves the use of ionized
+      argon gas to deliver electrical energy to the target tissue, causing coagulation and
+      devitalization of the lesion. APC is commonly used for the treatment of bleeding
+      lesions, such as angiodysplasia, as well as for the ablation of residual adenomatous
+      tissue following polypectomy.
+    intervention_types:
+      - therapeutic
+      - invasive

endoreg_db/data/finding_intervention/00_generic_endoscopy_bleeding.yaml

@@ -0,0 +1,55 @@
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_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
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_hemoclip_generic
+    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
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_sclerotherapy_generic
+    description: Sclerotherapy is a technique used to treat bleeding lesions.
+    intervention_types:
+      - therapeutic
+      - invasive
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_rubber_band_ligation_generic
+    description:
+      Rubber band ligation is a technique used to treat bleeding lesions
+      in the colon.
+    intervention_types:
+      - therapeutic
+      - invasive
+      - foreign_body
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_over_the_scope_clip_generic
+    description:
+      Over-the-scope clip (OTSC) is a clipping system used to close defects
+      in the GI tract.
+    intervention_types:
+      - therapeutic
+      - invasive
+      - foreign_body

endoreg_db/data/finding_intervention/00_generic_endoscopy_resection.yaml

@@ -0,0 +1,85 @@
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_cold_snare_resection_generic
+    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:
+      - diagnostic
+      - therapeutic
+      - invasive
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_diathermic_snare_resection_generic
+    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:
+      - diagnostic
+      - therapeutic
+      - invasive
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_biopsy_foreceps_resection_generic
+    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
+      - therapeutic
+      - invasive
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_emr_generic
+    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:
+      - diagnostic
+      - therapeutic
+      - invasive
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_esd_generic
+    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
+      - diagnostic
+      - invasive
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_eftr_generic
+    description:
+      Endoscopic full-thickness resection (EFTR) is a technique used to
+      remove lesions in the colon.
+    intervention_types:
+      - therapeutic
+      - invasive
+      - diagnostic
+      - foreign_body

endoreg_db/data/finding_intervention/00_generic_endoscopy_stenosis.yaml

@@ -0,0 +1,17 @@
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_dilation_balloon
+    description: Balloon dilation is a technique used to widen a narrowed area
+      in the colon.
+    intervention_types:
+      - therapeutic
+      - invasive
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_dilation_bougie
+    description: Bougie dilation is a technique used to widen a narrowed area
+      in the colon.
+    intervention_types:
+      - therapeutic
+      - invasive

endoreg_db/data/finding_intervention/00_generic_endoscopy_stent.yaml

@@ -0,0 +1,9 @@
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endoscopy_stent_generic
+    description: Stent placement is a technique used to keep a narrowed area
+      in the colon open.
+    intervention_types:
+      - therapeutic
+      - invasive
+      - foreign_body

endoreg_db/data/finding_intervention/01_gastroscopy.yaml

@@ -0,0 +1,19 @@
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_percutaneous_gastroenterostomy
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_percutaneous_jejunostomy
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_poem
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_stepwise_biopsy
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: egd_esophagus_injection_botox

endoreg_db/data/finding_intervention/04_eus.yaml

@@ -0,0 +1,39 @@
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_solid_lesion_fna
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_lymph_node_fna
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_cyst_fna
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_pseudocyst_fna
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_biliary_drainage
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_pancreatic_drainage
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_cyst_gastrostomy
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_pancreaticogastrostomy
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_cholangioduodenostomy
+
+- model: endoreg_db.finding_intervention
+  fields:
+    name: endosonography_pancreaticoduodenostomy

endoreg_db/data/finding_intervention/05_ercp.yaml

@@ -0,0 +1,3 @@
+- model: endoreg_db.finding_intervention
+  fields:
+    name: ercp_sphincterotomy

endoreg_db/data/finding_type/data.yaml

@@ -1,10 +1,10 @@
 - model: endoreg_db.finding_type
   fields:
-    name: "macroscopic"
+    name: "observation"
 
 - model: endoreg_db.finding_type
   fields:
-    name: "iatrogenic"
+    name: "baseline"
 
 - model: endoreg_db.finding_type
   fields:
@@ -16,28 +16,24 @@
 
 - model: endoreg_db.finding_type
   fields:
-    name: "bleeding"
+    name: "anatomy"
 
 - model: endoreg_db.finding_type
   fields:
-    name: "endoscopy_baseline"
+    name: "hidden"
 
 - model: endoreg_db.finding_type
   fields:
-    name: "medication_related"
-    
-- model: endoreg_db.finding_type
-  fields:
-    name: "anatomy"
+    name: "summary"
 
 - model: endoreg_db.finding_type
   fields:
-    name: "anatomy_colon"
+    name: "complication"
 
 - model: endoreg_db.finding_type
   fields:
-    name: "summary"
+    name: "iatrogenic"
 
 - model: endoreg_db.finding_type
   fields:
-    name: "complication"
+    name: "persisting"