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Merge branch 'master' of https://github.com/edmcouncil/idmp into IDMP…
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@ElisaKendall
ElisaKendall committed Sep 25, 2023
2 parents c9647ce + ba9f260 commit 5aebc58
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39 changes: 20 additions & 19 deletions etc/transformation/GSRS/gsrs-public-data-identifiers.rqg
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX cmns-id: <https://www.omg.org/spec/Commons/Identifiers/>
PREFIX cmns-ra: <https://www.omg.org/spec/Commons/RegistrationAuthorities/>
PREFIX idmp-nara: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/NorthAmericanJurisdiction/NorthAmericanRegistrationAuthorities/>
PREFIX cmns-txt: <https://www.omg.org/spec/Commons/TextDatatype/>
PREFIX idmp-eura: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/EuropeanJurisdiction/EuropeanRegistrationAuthorities/>
PREFIX idmp-sub: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/>
Expand Down Expand Up @@ -55,44 +56,44 @@ BIND(str(?CodeUrl) AS ?SeeAlsoIdentifier)

BIND(
IF(str(?CodeCodeSystem) = "CHEMBL", idmp-eura:ChemblDatabase ,
IF(str(?CodeCodeSystem) = "CAS", idmp-ra:ChemicalAbstractsService ,
IF(str(?CodeCodeSystem) = "CAS", idmp-nara:ChemicalAbstractsService ,
IF(str(?CodeCodeSystem) = "WHO-ATC", idmp-ra:AnatomicalTherapeuticChemicalClassificationSystem ,
IF(str(?CodeCodeSystem) = "WHO-ESSENTIAL MEDICINES LIST", idmp-ra:ModelListOfEssentialMedicines ,
IF(str(?CodeCodeSystem) = "WHO-SDG", idmp-ra:UnitedNationsSustainableDevelopmentGoals ,
IF(str(?CodeCodeSystem) = "WHO-VATC", idmp-ra:AnatomicalTherapeuticChemicalClassificationSystem ,
IF(str(?CodeCodeSystem) = "AUSTRALIAN PLANT NAME INDEX", idmp-ra:AustralianPlantNameIndex ,
IF(str(?CodeCodeSystem) = "CHEBI", idmp-eura:ChemicalEntitiesOfBiologicalInterest ,
IF(str(?CodeCodeSystem) = "CODEX ALIMENTARIUS (GSFA)", idmp-ra:CodexGeneralStandardForFoodAdditivesOnlineDatabase ,
IF(str(?CodeCodeSystem) = "DRUG BANK", idmp-ra:DrugBank ,
IF(str(?CodeCodeSystem) = "DRUG BANK", idmp-nara:DrugBank ,
IF(str(?CodeCodeSystem) = "ECHA (EC/EINECS)", idmp-eura:EuropeanInventoryOfExistingCommercialChemicalSubstances ,
IF(str(?CodeCodeSystem) = "JECFA EVALUATION", idmp-ra:EvaluationsOfTheJointExpertCommitteeOnFoodAdditives ,
IF(str(?CodeCodeSystem) = "JECFA MONOGRAPH", idmp-ra:EvaluationsOfTheJointExpertCommitteeOnFoodAdditives ,
IF(str(?CodeCodeSystem) = "GRIN", idmp-ra:GermplasmResourcesInformationNetwork ,
IF(str(?CodeCodeSystem) = "ITIS", idmp-ra:IntegratedTaxonomicInformationSystem ,
IF(str(?CodeCodeSystem) = "GRIN", idmp-nara:GermplasmResourcesInformationNetwork ,
IF(str(?CodeCodeSystem) = "ITIS", idmp-nara:IntegratedTaxonomicInformationSystem ,
IF(str(?CodeCodeSystem) = "KEGG", idmp-ra:KyotoEncyclopediaOfGenesAndGenomes ,
IF(str(?CodeCodeSystem) = "LIVERTOX", idmp-ra:LiverTox ,
IF(str(?CodeCodeSystem) = "MESH", idmp-ra:MedicalSubjectHeadings ,
IF(str(?CodeCodeSystem) = "LIVERTOX", idmp-nara:LiverTox ,
IF(str(?CodeCodeSystem) = "MESH", idmp-nara:MedicalSubjectHeadings ,
IF(str(?CodeCodeSystem) = "MERCK INDEX", idmp-ra:MerckIndexOnline ,
IF(str(?CodeCodeSystem) = "NCI_THESAURUS", idmp-ra:NationalCancerInstituteThesaurus ,
IF(str(?CodeCodeSystem) = "GENE", idmp-ra:NationalCenterForBiotechnologyInformationGeneDatabase ,
IF(str(?CodeCodeSystem) = "NCBI TAXONOMY", idmp-ra:NationalCenterForBiotechnologyInformationTaxonomyDatabase ,
IF(str(?CodeCodeSystem) = "NDF-RT", idmp-ra:NationalDrugFileReferenceTerminology ,
IF(str(?CodeCodeSystem) = "EPA PESTICIDE CODE", idmp-ra:PesticideProductInformationSystem ,
IF(str(?CodeCodeSystem) = "USDA PLANTS", idmp-ra:PlantListOfAcceptedNomenclatureTaxonomyAndSymbols ,
IF(str(?CodeCodeSystem) = "PUBCHEM", idmp-ra:PubChem ,
IF(str(?CodeCodeSystem) = "USP-MC MONOGRAPH", idmp-ra:USPharmacopeiaMedicinesCompendium ,
IF(str(?CodeCodeSystem) = "NCI_THESAURUS", idmp-nara:NationalCancerInstituteThesaurus ,
IF(str(?CodeCodeSystem) = "GENE", idmp-nara:NationalCenterForBiotechnologyInformationGeneDatabase ,
IF(str(?CodeCodeSystem) = "NCBI TAXONOMY", idmp-nara:NationalCenterForBiotechnologyInformationTaxonomyDatabase ,
IF(str(?CodeCodeSystem) = "NDF-RT", idmp-nara:NationalDrugFileReferenceTerminology ,
IF(str(?CodeCodeSystem) = "EPA PESTICIDE CODE", idmp-nara:PesticideProductInformationSystem ,
IF(str(?CodeCodeSystem) = "USDA PLANTS", idmp-nara:PlantListOfAcceptedNomenclatureTaxonomyAndSymbols ,
IF(str(?CodeCodeSystem) = "PUBCHEM", idmp-nara:PubChem ,
IF(str(?CodeCodeSystem) = "USP-MC MONOGRAPH", idmp-nara:USPharmacopeiaMedicinesCompendium ,
IF(str(?CodeCodeSystem) = "USP-MC VALIDATION RPT", idmp-ra:USPharmacopeiaMedicinesCompendium ,
IF(str(?CodeCodeSystem) = "UNIPROT", idmp-eura:UniProt ,
IF(str(?CodeCodeSystem) = "UCSF-FDA TRANSPORTAL", idmp-ra:UniversityOfCaliforniaSanFrancisoFederalDrugAdministrationTransport ,
IF(str(?CodeCodeSystem) = "UCSF-FDA TRANSPORTAL", idmp-nara:UniversityOfCaliforniaSanFrancisoFederalDrugAdministrationTransport ,
IF(str(?CodeCodeSystem) = "WHO INTERNATIONAL PHARMACOPOEIA", idmp-ra:WorldHealthOrganizationInternationalPharmacopoeia ,
IF(str(?CodeCodeSystem) = "CLINICAL_TRIALS.GOV", idmp-ra:ClinicalTrialsGov ,
IF(str(?CodeCodeSystem) = "COSMETIC INGREDIENT REVIEW (CIR)", idmp-ra:CosmeticIngredientReviewDatabase ,
IF(str(?CodeCodeSystem) = "COSMETIC INGREDIENT REVIEW (CIR)", idmp-nara:CosmeticIngredientReviewDatabase ,
IF(str(?CodeCodeSystem) = "EVMPD", idmp-eura:ExtendedEudraVigilanceMedicinalProductDictionary ,
IF(str(?CodeCodeSystem) = "EMA ASSESSMENT REPORTS", idmp-eura:EuropeanPublicAssessmentReports ,
IF(str(?CodeCodeSystem) = "EMA VETERINARY ASSESSMENT REPORTS", idmp-eura:EuropeanPublicAssessmentReports ,
IF(str(?CodeCodeSystem) = "FDA ORPHAN DRUG", idmp-ra:OrphanDrugProductDesignationDatabase ,
IF(str(?CodeCodeSystem) = "FDA UNII", idmp-ra:GlobalSubstanceRegistrationSystem ,
IF(str(?CodeCodeSystem) = "UNII", idmp-ra:GlobalSubstanceRegistrationSystem ,
IF(str(?CodeCodeSystem) = "FDA ORPHAN DRUG", idmp-nara:OrphanDrugProductDesignationDatabase ,
IF(str(?CodeCodeSystem) = "FDA UNII", idmp-nara:GlobalSubstanceRegistrationSystem ,
IF(str(?CodeCodeSystem) = "UNII", idmp-nara:GlobalSubstanceRegistrationSystem ,
IF(str(?CodeCodeSystem) = "INN", idmp-ra:MedNetINN,
?CodeCodeSystem ))))))))))))))))))))))))))))))))))))))))
AS ?Registry)
Expand Down
4 changes: 2 additions & 2 deletions etc/unit_tests/configs/gsrs_tests_config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,5 +14,5 @@ uc1_cq4_tests:
sparql_template: "cq_templates/uc1_cq4.sparql"
parameters:
uc1_cq4_parameter_1: "<https://gsrs.ncats.nih.gov/api/v1/substances/1J444QC288>"
uc1_cq4_parameter_2: "<https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/GlobalSubstanceRegistrationSystem>"
expected_output: "cq_expected_results/GSRS/uc1_cq4_expected_results.json"
uc1_cq4_parameter_2: "<https://spec.pistoiaalliance.org/idmp/ontology/ISO/NorthAmericanJurisdiction/NorthAmericanRegistrationAuthorities/GlobalSubstanceRegistrationSystem>"
expected_output: "cq_expected_results/GSRS/uc1_cq4_expected_results.json"

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