Merge pull request #647 from edmcouncil/GitHub-646

Updated 2 of the CMC UC CQs to reflect ontology revisions
edmcouncil · Jan 20, 2025 · 9d8e8fd · 9d8e8fd
2 parents ec5bca2 + 90f54c3
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diff --git a/etc/CQ/Example/uc2_cq2-1.sparql b/etc/CQ/Example/uc2_cq2-1.sparql
@@ -17,9 +17,10 @@ WHERE {
     BIND( uc2_cq2-1_parameter_1 AS $SellalbeArticle )
 
     $AuthorizedMedicinalProduct cmns-rlcmp:isPlayedBy $SellalbeArticle .
-    $AuthorizedMedicinalProduct idmp-mprd:hasAuthorization $Authorization .
+    ?hasAuthorization rdfs:subPropertyOf idmp-mprd:hasAuthorization .
+    $AuthorizedMedicinalProduct ?hasAuthorization $Authorization .
     $Authorization cmns-cxtdsg:isApplicableIn ?Jurisdiction . 
-    ?MarketingAuthorizationNumber cmns-id:identifies $Authorization 
+    ?MarketingAuthorizationNumber cmns-id:identifies $Authorization .
 
     # Optionally, get the name of the Authorization Number
     OPTIONAL{?MarketingAuthorizationNumber  rdfs:label  ?MarketingAuthorizationNumberLabel }

diff --git a/etc/CQ/Example/uc_cmc_cq2.sparql b/etc/CQ/Example/uc_cmc_cq2.sparql
@@ -1,19 +1,18 @@
-# UC-CMC-CQ 2: Which manufacturing site <site> is producing which medicinal product <m>? – FDA would ask for this in the application
-PREFIX cmns-dsg:     <https://www.omg.org/spec/Commons/Designators/>
-PREFIX cmns-rlcmp:  <https://www.omg.org/spec/Commons/RolesAndCompositions/>
-PREFIX cmns-txt:     <https://www.omg.org/spec/Commons/TextDatatype/>
-PREFIX idmp-mprd:   <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11615-MedicinalProducts/>
-PREFIX idmp-spor:   <https://spec.pistoiaalliance.org/idmp/ontology/ISO/EuropeanJurisdiction/SubstancesProductsOrganisationsReferentials/>
-PREFIX idmp-sub:     <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/>
-PREFIX rdf:              <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-PREFIX rdfs:             <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX owl:              <http://www.w3.org/2002/07/owl#>
-
-
-SELECT DISTINCT ?medicinalProduct ?site
-
-WHERE {
-    ?medicinalProduct a idmp-mprd:MedicinalProduct .
-    ?medicinalProduct idmp-mprd:isProducedAtManufacturingSite ?site .
-    ?site a idmp-mprd:ManufacturingSite .
+# UC-CMC-CQ 2: Which manufacturing site <site> is producing which medicinal product <m>? – FDA would ask for this in the application
+PREFIX cmns-doc:     <https://www.omg.org/spec/Commons/Documents/>
+PREFIX idmp-mprd:   <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11615-MedicinalProducts/>
+PREFIX rdf:              <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:             <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl:              <http://www.w3.org/2002/07/owl#>
+
+
+SELECT DISTINCT ?medicinalProduct ?physicalMedicinalProduct ?site
+
+WHERE {
+    ?medicinalProduct a idmp-mprd:MedicinalProduct .
+    ?medicinalProduct cmns-doc:specifies ?physicalMedicinalProduct .
+    ?physicalMedicinalProduct a idmp-mprd:PhysicalMedicinalProduct .
+    ?physicalMedicinalProduct idmp-mprd:isProducedAtManufacturingSite ?site .
+    ?site a idmp-mprd:ManufacturingSite .
+
 }
diff --git a/etc/CQ/Example/uc_cmc_cq3.sparql b/etc/CQ/Example/uc_cmc_cq3.sparql
@@ -1,27 +1,26 @@
-# UC-CMC-CQ 3: Which manufacturing site <site> is producing which substance <substance>?
-PREFIX cmns-dsg:    <https://www.omg.org/spec/Commons/Designators/>
-PREFIX cmns-rlcmp:  <https://www.omg.org/spec/Commons/RolesAndCompositions/>
-PREFIX cmns-txt:    <https://www.omg.org/spec/Commons/TextDatatype/>
-PREFIX idmp-mprd:   <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11615-MedicinalProducts/>
-PREFIX idmp-spor:   <https://spec.pistoiaalliance.org/idmp/ontology/ISO/EuropeanJurisdiction/SubstancesProductsOrganisationsReferentials/>
-PREFIX idmp-sub:    <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/>
-PREFIX rdf:         <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-PREFIX rdfs:        <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX owl:         <http://www.w3.org/2002/07/owl#>
-PREFIX cmns-col:    <https://www.omg.org/spec/Commons/Collections/>
-
-
-SELECT DISTINCT ?site ?substance
-
-WHERE {
-    # Bind Variable medicinal product <$medicinalProduct>
-	# Example for Norvasc: <https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/AmlodipineExample/NorvascMedicinalProduct>
-    BIND(uc_cmc_cq3_parameter_1 AS $medicinalProduct )
-
-    $medicinalProduct idmp-mprd:isProducedAtManufacturingSite ?site .
-    ?site a idmp-mprd:ManufacturingSite .
-
-    $medicinalProduct cmns-col:comprises ?pharmaceuticalOrManufacturedProduct.
-    ?pharmaceuticalOrManufacturedProduct cmns-col:comprises ?substance.
-    ?substance rdf:type/rdfs:subClassOf idmp-sub:Substance.
+# UC-CMC-CQ 3: Which manufacturing site <site> is producing which substance <substance>?
+PREFIX cmns-col:    <https://www.omg.org/spec/Commons/Collections/>
+PREFIX cmns-doc:    <https://www.omg.org/spec/Commons/Documents/>
+PREFIX idmp-mprd:   <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11615-MedicinalProducts/>
+PREFIX idmp-sub:    <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/>
+PREFIX rdf:         <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:        <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl:         <http://www.w3.org/2002/07/owl#>
+
+SELECT DISTINCT ?site ?substance
+
+WHERE {
+    # Bind Variable medicinal product <$medicinalProduct>
+	# Example for Norvasc: <https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/AmlodipineExample/NorvascMedicinalProduct>
+    BIND(uc_cmc_cq3_parameter_1 AS $medicinalProduct )
+
+     $medicinalProduct cmns-doc:specifies ?physicalMedicinalProduct .
+     ?physicalMedicinalProduct a idmp-mprd:PhysicalMedicinalProduct .
+     ?physicalMedicinalProduct idmp-mprd:isProducedAtManufacturingSite ?site .
+     ?site a idmp-mprd:ManufacturingSite .
+
+    $medicinalProduct cmns-col:comprises ?pharmaceuticalOrManufacturedProduct .
+    ?pharmaceuticalOrManufacturedProduct cmns-col:comprises ?substance .
+    ?substance rdf:type/rdfs:subClassOf idmp-sub:Substance .
+
 }
diff --git a/etc/CQ/Example/uc_cmc_cq4.sparql b/etc/CQ/Example/uc_cmc_cq4.sparql
@@ -0,0 +1,30 @@
+# UC-CMC-CQ 4: Which material ID <m> is used in which batch ID <b>?
+PREFIX cmns-col:    <https://www.omg.org/spec/Commons/Collections/>
+PREFIX cmns-doc:    <https://www.omg.org/spec/Commons/Documents/>
+PREFIX cmns-dsg:    <https://www.omg.org/spec/Commons/Designators/>
+PREFIX cmns-id: 	<https://www.omg.org/spec/Commons/Identifiers/>
+PREFIX cmns-txt:    <https://www.omg.org/spec/Commons/TextDatatype/>
+PREFIX idmp-mprd:   <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11615-MedicinalProducts/>
+PREFIX idmp-sub:    <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/>
+PREFIX rdf:         <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:        <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl:         <http://www.w3.org/2002/07/owl#>
+
+SELECT DISTINCT ?materialIdentifierValue ?productBatchIdentifierValue
+
+WHERE {
+    # Bind Variable medicinal product <$medicinalProduct>
+	# Example for Norvasc: <https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/AmlodipineExample/NorvascMedicinalProduct>
+    BIND(uc_cmc_cq4_parameter_1 AS $medicinalProduct )
+
+     $medicinalProduct cmns-doc:specifies ?physicalMedicinalProduct .
+     ?physicalMedicinalProduct a idmp-mprd:PhysicalMedicinalProduct .
+     ?productBatch cmns-col:isConstituentOf ?physicalMedicinalProduct .
+     ?productBatch rdf:type idmp-mprd:Batch .
+     ?productBatch cmns-dsg:isSignifiedBy ?productBatchId .
+     ?productBatchId cmns-txt:hasTextValue ?productBatchIdentifierValue.
+     ?productBatch cmns-col:comprises ?material .
+     ?material cmns-id:isIdentifiedBy ?materialIdentifierIRI .
+     ?materialIdentifierIRI rdf:type idmp-sub:MaterialIdentifier.
+     ?materialIdentifierIRI cmns-txt:hasTextValue ?materialIdentifierValue.
+}
diff --git a/etc/CQ/Example/uc_cmc_cq5.sparql b/etc/CQ/Example/uc_cmc_cq5.sparql
@@ -0,0 +1,36 @@
+# UC-CMC-CQ 5: Which material <m> is approved in which country <c> ? and what is the application ID?
+
+PREFIX cmns-col:    <https://www.omg.org/spec/Commons/Collections/>
+PREFIX cmns-doc:    <https://www.omg.org/spec/Commons/Documents/>
+PREFIX cmns-dsg:    <https://www.omg.org/spec/Commons/Designators/>
+PREFIX cmns-cxtdsg: <https://www.omg.org/spec/Commons/ContextualDesignators/>
+PREFIX cmns-id: 	<https://www.omg.org/spec/Commons/Identifiers/>
+PREFIX cmns-rlcmp:  <https://www.omg.org/spec/Commons/RolesAndCompositions/>
+PREFIX cmns-rga:    <https://www.omg.org/spec/Commons/RegulatoryAgencies/>
+PREFIX cmns-txt:    <https://www.omg.org/spec/Commons/TextDatatype/>
+PREFIX idmp-mprd:   <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11615-MedicinalProducts/>
+PREFIX idmp-sub:    <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/>
+PREFIX rdf:         <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:        <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl:         <http://www.w3.org/2002/07/owl#>
+
+SELECT DISTINCT ?materialIdentifierValue ?marketingAuthorisationId ?country
+
+WHERE {
+    # Bind Variable medicinal product <$medicinalProduct>
+	# Example for Norvasc: <https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/AmlodipineExample/NorvascMedicinalProduct>
+    BIND(uc_cmc_cq5_parameter_1 AS $medicinalProduct )
+
+     $medicinalProduct cmns-doc:specifies ?physicalMedicinalProduct .
+     ?physicalMedicinalProduct a idmp-mprd:PhysicalMedicinalProduct .
+     ?productBatch cmns-col:isConstituentOf ?physicalMedicinalProduct .
+     ?productBatch rdf:type idmp-mprd:Batch .
+     ?productBatch cmns-col:comprises ?material .
+     ?materialIdentifierIRI rdf:type idmp-sub:MaterialIdentifier.
+     ?materialIdentifierIRI cmns-txt:hasTextValue ?materialIdentifierValue.
+     ?authorisedMedicinalProduct cmns-rlcmp:isPlayedBy $medicinalProduct .
+     ?authorisedMedicinalProduct idmp-mprd:isAuthorizedForMarketingThrough ?marketingAuthorisation .
+     ?marketingAuthorisationId cmns-id:identifies ?marketingAuthorisation .
+     ?marketingAuthorisation cmns-cxtdsg:isApplicableIn ?jurisdiction .
+     ?jurisdiction cmns-rga:hasReach ?country.
+}
diff --git a/etc/CQ/Example/uc_cmc_cq6.sparql b/etc/CQ/Example/uc_cmc_cq6.sparql
@@ -0,0 +1,38 @@
+# UC-CMC-CQ 6: Which batch <b> is released for which country <c>?
+PREFIX cmns-col:    <https://www.omg.org/spec/Commons/Collections/>
+PREFIX cmns-doc:    <https://www.omg.org/spec/Commons/Documents/>
+PREFIX cmns-dsg:    <https://www.omg.org/spec/Commons/Designators/>
+PREFIX cmns-cxtdsg: <https://www.omg.org/spec/Commons/ContextualDesignators/>
+PREFIX cmns-id: 	<https://www.omg.org/spec/Commons/Identifiers/>
+PREFIX cmns-rlcmp:  <https://www.omg.org/spec/Commons/RolesAndCompositions/>
+PREFIX cmns-rga:    <https://www.omg.org/spec/Commons/RegulatoryAgencies/>
+PREFIX cmns-txt:    <https://www.omg.org/spec/Commons/TextDatatype/>
+PREFIX idmp-mprd:   <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11615-MedicinalProducts/>
+PREFIX idmp-sub:    <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/>
+PREFIX rdf:         <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:        <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl:         <http://www.w3.org/2002/07/owl#>
+
+SELECT DISTINCT ?productBatchIdentifierValue ?marketingAuthorisationId ?country
+
+WHERE {
+    # Bind Variable medicinal product <$medicinalProduct>
+	# Example for Norvasc: <https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/AmlodipineExample/NorvascMedicinalProduct>
+    BIND(uc_cmc_cq6_parameter_1 AS $medicinalProduct )
+
+     $medicinalProduct cmns-doc:specifies ?physicalMedicinalProduct .
+     ?physicalMedicinalProduct a idmp-mprd:PhysicalMedicinalProduct .
+
+     ?productBatch cmns-col:isConstituentOf ?physicalMedicinalProduct .
+     ?productBatch rdf:type idmp-mprd:Batch .
+     ?productBatch cmns-col:comprises ?material .
+     ?productBatch cmns-dsg:isSignifiedBy ?productBatchId .
+     ?productBatchId cmns-txt:hasTextValue ?productBatchIdentifierValue.
+
+     ?authorisedMedicinalProduct cmns-rlcmp:isPlayedBy $medicinalProduct .
+     ?authorisedMedicinalProduct idmp-mprd:isAuthorizedForMarketingThrough ?marketingAuthorisation .
+     ?marketingAuthorisationId cmns-id:identifies ?marketingAuthorisation .
+     ?marketingAuthorisation cmns-cxtdsg:isApplicableIn ?jurisdiction .
+
+     ?jurisdiction cmns-rga:hasReach ?country.
+}
diff --git a/etc/unit_tests/configs/idmp_tests_config.yaml b/etc/unit_tests/configs/idmp_tests_config.yaml
@@ -208,4 +208,22 @@ uc_cmc_cq3_tests:
   sparql_template: "cq_templates/uc_cmc_cq3.sparql"
   parameters:
     uc_cmc_cq3_parameter_1: "<https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/AmlodipineExample/NorvascMedicinalProduct>"
-  expected_output: "cq_expected_results/IDMP/uc_cmc_cq3_expected_results.json"    
+  expected_output: "cq_expected_results/IDMP/uc_cmc_cq3_expected_results.json"    
+
+uc_cmc_cq4_tests:
+  sparql_template: "cq_templates/uc_cmc_cq4.sparql"
+  parameters:
+    uc_cmc_cq4_parameter_1: "<https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/AmlodipineExample/NorvascMedicinalProduct>"
+  expected_output: "cq_expected_results/IDMP/uc_cmc_cq4_expected_results.json"    
+
+  uc_cmc_cq5_tests:
+  sparql_template: "cq_templates/uc_cmc_cq5.sparql"
+  parameters:
+    uc_cmc_cq5_parameter_1: "<https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/AmlodipineExample/NorvascMedicinalProduct>"
+  expected_output: "cq_expected_results/IDMP/uc_cmc_cq5_expected_results.json"    
+
+  uc_cmc_cq6_tests:
+  sparql_template: "cq_templates/uc_cmc_cq6.sparql"
+  parameters:
+    uc_cmc_cq6_parameter_1: "<https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/AmlodipineExample/NorvascMedicinalProduct>"
+  expected_output: "cq_expected_results/IDMP/uc_cmc_cq6_expected_results.json"    
diff --git a/etc/unit_tests/cq_expected_results/IDMP/uc2_cq2-1_amlodipine_expected_results.json b/etc/unit_tests/cq_expected_results/IDMP/uc2_cq2-1_amlodipine_expected_results.json
@@ -8,16 +8,33 @@
                 },
                 "Jurisdiction": {
                     "type": "uri",
-                    "value": "https://www.omg.org/spec/LCC/Countries/ISO3166-1-CountryCodes/Germany"
+                    "value": "https://www.omg.org/spec/Commons/EuropeanJurisdiction/WesternEuropeGovernmentEntitiesAndJurisdictions/JurisdictionOfGermany"
                 },
                 "MarketingAuthorizationNumberName": {
                     "type": "literal",
                     "value": "marketing authorization number EMEA/H/A-30/1288"
                 },
                 "JurisdictionName": {
                     "type": "literal",
-                    "value": "Deutschland",
-                    "xml:lang": "de"
+                    "value": "German jurisdiction"
+                }
+            },
+            {
+                "MarketingAuthorizationNumber": {
+                    "type": "uri",
+                    "value": "https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/AmlodipineExample/MarketingAuthorizationNumber-19787-S3"
+                },
+                "Jurisdiction": {
+                    "type": "uri",
+                    "value": "https://www.omg.org/spec/Commons/NorthAmericanJurisdiction/USGovernmentEntitiesAndJurisdictions/UnitedStatesJurisdiction"
+                },
+                "MarketingAuthorizationNumberName": {
+                    "type": "literal",
+                    "value": "marketing authorization number 19787 - S3"
+                },
+                "JurisdictionName": {
+                    "type": "literal",
+                    "value": "United States jurisdiction"
                 }
             }
         ]