FDA GSRS

Owned by Heiner Oberkampf
Last updated: Jul 11, 2024 by Ali Ariff
2 min read

General Information

Source Data Input

GSRS as RDF Knowledge Graph

https://pistoiaalliance.accurids.com/dataset/details/334

Transformation

The transformation script is available for Pistoia Alliance Members only. For more information please contact Pistoia Alliance Project Lead (Contact).

Alignment Specification

Data URI Assignment

IDMP Ontology ClassURI PatternComment
Substancehttps://gsrs.ncats.nih.gov/api/v1/substances/{ ?approvalID }
Molecular Structure

https://gsrs.ncats.nih.gov/api/v1/substances/{ ?structureID }/structure

Update later to https://data.pistoiaalliance.org/structure/{ ?structureID }
Registered Identifier

https://data.pistoiaalliance.org/id/{ ?CodeSystemWithoutSpace }/{ ?CodeWithoutSpace }


Contextual Namehttps://gsrs.ncats.nih.gov/api/v1/substances/{ ?approvalID }/{?NameUuid}
Moiety Role

https://data.pistoiaalliance.org/role/{?SourceSubstanceApprovalID}_MoietyRole_FDA_general_{?RelatedSubstanceApprovalID}


Class Mapping

GSRS ConceptTarget IDMP Ontology ClassComment
substanceClass: "chemical" https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/ChemicalSubstance
substanceClass: "protein" https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/ProteinSubstance
substanceClass: "nucleicAcid" https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/NucleicAcidSubstance
substanceClass: "mixture" https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Mixture
substanceClass: "polymer" https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/PolymerSubstance
substanceClass: "structurallyDiverse" https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/StructurallyDiverseSubstance
substanceClass: "specifiedSubstance" 

https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/SpecifiedSubstance

not included in data
substanceClass: "specifiedSubstanceG1" 
substanceClass: "specifiedSubstanceG2" not included in data
substanceClass: "specifiedSubstanceG3" not included in data
substanceClass: "specifiedSubstanceG4" not included in data
substanceClass: "concept"n.a. as still not in IDMP-O and no data in GSRSnot included in data

https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/SubstanceFallback if no substanceClass of the above matched

https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/MolecularStructure

https://www.omg.org/spec/Commons/RegistrationAuthorities/RegisteredIdentifier



https://www.omg.org/spec/Commons/ContextualDesignators/ContextualName
stereochemistry: "ABSOLUTE"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-Absolute
stereochemistry: "ACHIRAL"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-Achiral
stereochemistry: "AXIAL"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-Axial
stereochemistry: "AXIAL R"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-AxialR
stereochemistry: "AXIAL S"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-AxialS
stereochemistry: "CHIRAL"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-Chiral
stereochemistry: "CIS"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-Cis
stereochemistry: "EPIMERIC"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-Epimeric
stereochemistry: "MESO"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-Meso
stereochemistry: "MIXED"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-Mixed
stereochemistry: "OCTAHEDRAL 12"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-Octahedral12
stereochemistry: "OCTAHEDRAL 22"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-Octahedral22
stereochemistry: "OCTAHEDRAL 21"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-Octahedral21
stereochemistry: "RACEMIC"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-Racemic
stereochemistry: "SQUARE PLANAR 1"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-SquarePlanar1
stereochemistry: "SQUARE PLANAR 2"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-SquarePlanar2
stereochemistry: "SQUARE PLANAR 3"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-SquarePlanar3
stereochemistry: "SQUARE PLANAR 4"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-SquarePlanar4
stereochemistry: "TETRAHEDRAL"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-Tetrahedral
stereochemistry: "TRANS"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-Trans
stereochemistry: "UNKNOWN"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/Stereochemistry-Unknown
nameType: "bn"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/SubstanceNameClassifier-BrandName
nameType: "cd"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/SubstanceNameClassifier-CompanyCode
nameType: "cn"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/SubstanceNameClassifier-CommonName
nameType: "of"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/SubstanceNameClassifier-OfficialName
nameType: "sys"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/SubstanceNameClassifier-SystematicName
relationshipType: "ACTIVE MOIETY"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/RegulatoryContext-FoodAndDrugAdministrationGeneral
relationshipType: "ACTIVE MOIETY (FOR EXCLUSIVITY)"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/RegulatoryContext-FoodAndDrugAdministrationPatentExclusive
codeSystem: "CHEMBL"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/ChemblDatabase
codeSystem: "CAS"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/ChemicalAbstractsService
codeSystem: "WHO-ATC"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/AnatomicalTherapeuticChemicalClassificationSystem
codeSystem: "WHO-ESSENTIAL MEDICINES LIST"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/WorldHealthOrganizationRegistrationAuthority
codeSystem: "WHO-SDG"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/WorldHealthOrganizationRegistrationAuthority
codeSystem: "WHO-VATC"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/WorldHealthOrganizationRegistrationAuthority
codeSystem: "AUSTRALIAN PLANT NAME INDEX"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/AustralianPlantNameIndex
codeSystem: "CHEBI"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/ChemicalEntitiesOfBiologicalInterest
codeSystem: "CODEX ALIMENTARIUS (GSFA)"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/CodexGeneralStandardForFoodAdditivesOnlineDatabase
codeSystem: "DRUG BANK"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/DrugBank
codeSystem: "ECHA (EC/EINECS)"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/EuropeanInventoryOfExistingCommercialChemicalSubstances
codeSystem: "JECFA EVALUATION"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/EvaluationsOfTheJointExpertCommitteeOnFoodAdditives
codeSystem: "JECFA MONOGRAPH"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/EvaluationsOfTheJointExpertCommitteeOnFoodAdditives
codeSystem: "GRIN"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/GermplasmResourcesInformationNetwork
codeSystem: "ITIS"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/IntegratedTaxonomicInformationSystem
codeSystem: "KEGG"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/KyotoEncyclopediaOfGenesAndGenomes
codeSystem: "LIVERTOX"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/LiverTox
codeSystem: "MESH"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/MedicalSubjectHeadings
codeSystem: "MERCK"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/MerckIndexOnline
codeSystem: "NCI_THESAURUS"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/NationalCancerInstituteThesaurus
codeSystem: "GENE"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/NationalCenterForBiotechnologyInformationGeneDatabase
codeSystem: "NCBI TAXONOMY"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/NationalCenterForBiotechnologyInformationTaxonomyDatabase 
codeSystem: "NDF-RT"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/NationalDrugFileReferenceTerminology
codeSystem: "EPA PESTICIDE CODE"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/PesticideProductInformationSystem
codeSystem: "USDA PLANTS"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/PlantListOfAcceptedNomenclatureTaxonomyAndSymbols
codeSystem: "PUBCHEM"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/PubChem
codeSystem: "USP-MC MONOGRAPH"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/USPharmacopeiaMedicinesCompendium
codeSystem: "USP-MC VALIDATION RPT"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/USPharmacopeiaMedicinesCompendium
codeSystem: "UNIPROT"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/UniProt
codeSystem: "UCSF-FDA TRANSPORTAL"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/UniversityOfCaliforniaSanFrancisoFederalDrugAdministrationTransport
codeSystem: "WHO INTERNATIONAL PHARMACOPOEIA"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/WorldHealthOrganizationInternationalPharmacopoeia
codeSystem: "CLINICAL_TRIALS.GOV"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/ClinicalTrialsGov
codeSystem: "COSMETIC INGREDIENT REVIEW (CIR)"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/CosmeticIngredientReviewDatabase
codeSystem: "EVMPD"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/EuropeanMedicinesAgencyRegistrationAuthority
codeSystem: "EMA ASSESSMENT REPORTS"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/EuropeanMedicinesAgency
codeSystem: "EMA VETERINARY ASSESSMENT REPORTS"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/EuropeanMedicinesAgency
codeSystem: "FDA ORPHAN DRUG"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/FoodAndDrugAdministrationRegistrationAuthority
codeSystem: "FDA UNII"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/FoodAndDrugAdministrationRegistrationAuthority
codeSystem: "UNII"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/FoodAndDrugAdministrationRegistrationAuthority
codeSystem: "INN"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/InternationalNonproprietaryName

Relationship Alignment

GSRS contains more than 150 substance relationships. Below is the current alignment

GSRS RelationshipIDMP Ontology Property / PatternComment
chemical substance → approvalIDhttps://www.omg.org/spec/Commons/TextDatatype/hasTextValue
chemical substance → substanceClasshttp://www.w3.org/1999/02/22-rdf-syntax-ns#type
chemical substance → structure → smileshttps://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/hasSMILESValue
chemical substance → structure → ididmp-sub:hasDefiningStructure

Build structure URI with the ID

<https://data.pistoiaalliance.org/idmp/gsrs/structure/{ ?structureID }> a idmp-sub:MolecularStructure ;

chemical substance → structure → formulahttps://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/hasDefiningMolecularFormula
chemical substance → structure → formulahttps://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/hasDefiningMolecularFormulaByMoietywhen a structure formula contains ".". E.g., C9H7INO3.Na
chemical substance → structure → stereochemistryhttps://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/hasDefiningStereochemistry
chemical substance → structure → mwthttps://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/hasDefiningMolecularWeight
chemical substance → moieties → hashhttps://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/hasMoiety

Build URI with the hash

<https://gsrs.ncats.nih.gov/api/v1/substances/moieties({ ?moietyHash }>)

chemical substance → relationships → type: "ACTIVE MOIETY"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/hasActiveMoiety
chemical substance → relationships → type: "ACTIVE MOIETY (FOR EXCLUSIVITY)"https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/hasActiveMoiety
chemical substance → relationships → type: "INHIBITOR->TARGET"

https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/hasInhibitorTarget

(error) Property not defined in ontology

chemical substance → names → namehttps://www.omg.org/spec/Commons/TextDatatype/hasTextValue
chemical substance → names → typehttps://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/hasSubstanceNameType
chemical substance → names → displayNamehttp://www.w3.org/2004/02/skos/core#prefLabel
chemical substance → codes → code https://www.omg.org/spec/Commons/TextDatatype/hasTextValue
chemical substance → codes → codeSystemhttps://www.omg.org/spec/Commons/RegistrationAuthorities/isRegisteredIn
chemical substance → codes → urlhttp://www.w3.org/2000/01/rdf-schema#seeAslo
active moiety substance

idmp-sub:hasActiveMoiety

idmp-sub:hasInhibitorTarget

cmns-pts:playsRole

idmp-sub:isActiveMoietyOf

cmns-pts:realizes

cmns-id:isIdentifiedBy

cmns-dsg:hasName


active moiety role

cmns-cstdsg:isApplicableIn

cmns-pts:isPlayedBy

cmns-pts:isRealizedIn


molecular structure

idmp-sub:hasSimplifiedMolecularInputLineEntrySpecification

idmp-sub:hasMolecularFormula & idmp-sub:hasMolecularFormulaByMoiety

idmp-sub:hasStereochemistry

idmp-sub:hasMolecularWeight


registered identifier

cmns-txt:hasTextValue

cmns-ra:isRegisteredIn

rdfs:seeAslo

cmns-id:identifies


substance name

cmns-txt:hasTextValue

cmns-dsg:isNameOf

idmp-sub:hasSubstanceNameType


regulatory contextcmns-cstdsg:appliesTo

others

skos:related

Further Substance Relationships to be prioritized for alignment to IDMP-O

Many pharmacology relationships may be less relevant for IDMP now - maybe later in context of clinical and pharmacovigilance use cases.

Molfile Pattern