Update schemas

cidgoh · Oct 4, 2024 · 36a5e71 · 36a5e71
1 parent ae5a9d3
commit 36a5e71
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Showing 3 changed files with 29 additions and 19 deletions.
diff --git a/web/templates/grdi/schema.json b/web/templates/grdi/schema.json
@@ -5653,14 +5653,14 @@
           "text": "Intermediate antimicrobial phenotype [ARO:3004300]",
           "is_a": "Antibiotic resistance not defined [GENEPIO:0002040]",
           "exact_mappings": [
-            "NCBI_ANTIBIOGRAM:not%20defined"
+            "NCBI_ANTIBIOGRAM:intermediate"
           ]
         },
         "Indeterminate antimicrobial phenotype [GENEPIO:0100585]": {
           "text": "Indeterminate antimicrobial phenotype [GENEPIO:0100585]",
           "is_a": "Antibiotic resistance not defined [GENEPIO:0002040]",
           "exact_mappings": [
-            "NCBI_ANTIBIOGRAM:not%20defined"
+            "NCBI_ANTIBIOGRAM:indeterminate"
           ]
         },
         "Nonsusceptible antimicrobial phenotype [ARO:3004303]": {
@@ -5764,10 +5764,7 @@
         },
         "Antimicrobial gradient (E-test) [NCIT:85596]": {
           "text": "Antimicrobial gradient (E-test) [NCIT:85596]",
-          "is_a": "Agar diffusion [NCIT:85595]",
-          "exact_mappings": [
-            "NCBI_ANTIBIOGRAM:disk%20diffusion"
-          ]
+          "is_a": "Agar diffusion [NCIT:85595]"
         },
         "Agar dilution [ARO:3004411]": {
           "text": "Agar dilution [ARO:3004411]",
@@ -5776,7 +5773,10 @@
           ]
         },
         "Broth dilution [ARO:3004397]": {
-          "text": "Broth dilution [ARO:3004397]"
+          "text": "Broth dilution [ARO:3004397]",
+          "exact_mappings": [
+            "NCBI_ANTIBIOGRAM:broth%20dilution"
+          ]
         }
       }
     },
@@ -5787,7 +5787,10 @@
       "from_schema": "https://example.com/GRDI",
       "permissible_values": {
         "BIOMIC Microbiology System [ARO:3007569]": {
-          "text": "BIOMIC Microbiology System [ARO:3007569]"
+          "text": "BIOMIC Microbiology System [ARO:3007569]",
+          "exact_mappings": [
+            "NCBI_ANTIBIOGRAM:BIOMIC"
+          ]
         },
         "Microscan [ARO:3004400]": {
           "text": "Microscan [ARO:3004400]",
@@ -5834,7 +5837,10 @@
           ]
         },
         "Omron [ARO:3004408]": {
-          "text": "Omron [ARO:3004408]"
+          "text": "Omron [ARO:3004408]",
+          "exact_mappings": [
+            "NCBI_ANTIBIOGRAM:Omron"
+          ]
         },
         "Siemens [ARO:3004407]": {
           "text": "Siemens [ARO:3004407]",

diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi/schema.yaml
@@ -16593,12 +16593,12 @@ enums:
       Intermediate antimicrobial phenotype [ARO:3004300]:
         text: Intermediate antimicrobial phenotype [ARO:3004300]
         exact_mappings:
-        - NCBI_ANTIBIOGRAM:not%20defined
+        - NCBI_ANTIBIOGRAM:intermediate
         is_a: Antibiotic resistance not defined [GENEPIO:0002040]
       Indeterminate antimicrobial phenotype [GENEPIO:0100585]:
         text: Indeterminate antimicrobial phenotype [GENEPIO:0100585]
         exact_mappings:
-        - NCBI_ANTIBIOGRAM:not%20defined
+        - NCBI_ANTIBIOGRAM:indeterminate
         is_a: Antibiotic resistance not defined [GENEPIO:0002040]
       Nonsusceptible antimicrobial phenotype [ARO:3004303]:
         text: Nonsusceptible antimicrobial phenotype [ARO:3004303]
@@ -16667,22 +16667,24 @@ enums:
         - NCBI_ANTIBIOGRAM:disk%20diffusion
       Antimicrobial gradient (E-test) [NCIT:85596]:
         text: Antimicrobial gradient (E-test) [NCIT:85596]
-        exact_mappings:
-        - NCBI_ANTIBIOGRAM:disk%20diffusion
         is_a: Agar diffusion [NCIT:85595]
       Agar dilution [ARO:3004411]:
         text: Agar dilution [ARO:3004411]
         exact_mappings:
         - NCBI_ANTIBIOGRAM:agar%20dilution
       Broth dilution [ARO:3004397]:
         text: Broth dilution [ARO:3004397]
+        exact_mappings:
+        - NCBI_ANTIBIOGRAM:broth%20dilution
   AntimicrobialLaboratoryTypingPlatformMenu:
     name: AntimicrobialLaboratoryTypingPlatformMenu
     title: antimicrobial_laboratory_typing_platform menu
     description: ''
     permissible_values:
       BIOMIC Microbiology System [ARO:3007569]:
         text: BIOMIC Microbiology System [ARO:3007569]
+        exact_mappings:
+        - NCBI_ANTIBIOGRAM:BIOMIC
       Microscan [ARO:3004400]:
         text: Microscan [ARO:3004400]
         exact_mappings:
@@ -16714,6 +16716,8 @@ enums:
         - NCBI_ANTIBIOGRAM:Biom%C3%A9rieux
       Omron [ARO:3004408]:
         text: Omron [ARO:3004408]
+        exact_mappings:
+        - NCBI_ANTIBIOGRAM:Omron
       Siemens [ARO:3004407]:
         text: Siemens [ARO:3004407]
         exact_mappings:

diff --git a/web/templates/grdi/schema_enums.tsv b/web/templates/grdi/schema_enums.tsv
@@ -1486,8 +1486,8 @@ AMR_testing_by menu	AmrTestingByMenu		Public Health Agency of Canada (PHAC) [GEN
 
 
 antimicrobial_phenotype menu	AntimicrobialPhenotypeMenu		Antibiotic resistance not defined [GENEPIO:0002040]							not defined	
-				Intermediate antimicrobial phenotype [ARO:3004300]						not defined	
-				Indeterminate antimicrobial phenotype [GENEPIO:0100585]						not defined	
+				Intermediate antimicrobial phenotype [ARO:3004300]						intermediate	
+				Indeterminate antimicrobial phenotype [GENEPIO:0100585]						indeterminate	
 			Nonsusceptible antimicrobial phenotype [ARO:3004303]							nonsusceptible	
 			Resistant antimicrobial phenotype [ARO:3004301]							resistant	
 			Susceptible antimicrobial phenotype [ARO:3004302]							susceptible	
@@ -1507,12 +1507,12 @@ antimicrobial_measurement_sign menu	AntimicrobialMeasurementSignMenu		less than
 
 
 antimicrobial_laboratory_typing_method menu	AntimicrobialLaboratoryTypingMethodMenu		Agar diffusion [NCIT:85595]							disk diffusion	
-				Antimicrobial gradient (E-test) [NCIT:85596]						disk diffusion	
+				Antimicrobial gradient (E-test) [NCIT:85596]							
 			Agar dilution [ARO:3004411]							agar dilution	
-			Broth dilution [ARO:3004397]								
+			Broth dilution [ARO:3004397]							broth dilution	
 
 
-antimicrobial_laboratory_typing_platform menu	AntimicrobialLaboratoryTypingPlatformMenu		BIOMIC Microbiology System [ARO:3007569]								
+antimicrobial_laboratory_typing_platform menu	AntimicrobialLaboratoryTypingPlatformMenu		BIOMIC Microbiology System [ARO:3007569]							BIOMIC	
 			Microscan [ARO:3004400]							Microscan	
 			Phoenix [ARO:3004401]							Phoenix	
 			Sensititre [ARO:3004402]							Sensititre	
@@ -1521,7 +1521,7 @@ antimicrobial_laboratory_typing_platform menu	AntimicrobialLaboratoryTypingPlatf
 
 antimicrobial_vendor_name menu	AntimicrobialVendorNameMenu		Becton Dickinson [ARO:3004405]							Becton Dickinson	
 			bioMérieux [ARO:3004406]							Biomérieux	
-			Omron [ARO:3004408]								
+			Omron [ARO:3004408]							Omron	
 			Siemens [ARO:3004407]							Siemens	
 			Trek [ARO:3004409]							Trek