Modeling patterns, developed in response to recurring design problems, provide a well-proven, common solution for encapsulating knowledge, achieved through the use of effective naming, organizing and reasoning of knowledge. The example below explains how the Names and IDs from the public GSRS Data on Amlodipine is demonstrates how established modeling patterns can be represented in the structure of the IDMP Ontology., using the publicly available GSRS data on Amlodipine (https://gsrs.ncats.nih.gov/ginas/app/beta/substances/1J444QC288).

Note: To keep things simple, in this example Amlodipine is modelled as an instance of idmp:Substance (i.e., with a rdf:type relationship).

Amlodipine example

The following block of code combines those that are shown in the substance, substance names, and substance identifiers sections below, which give a better depiction of how the different entities are related.

Code Block

language	text
title	Amlodipine example
collapse	true

@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-av:	<https://www.omg.org/spec/Commons/AbbreviationsAnnotationVocabulary/>.
@prefix cmns-cls: 	<https://www.omg.org/spec/Commons/Classifiers/> .
@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 cmns-ra: 	<https://www.omg.org/spec/Commons/RegistrationAuthorities/> .
@prefix idmp-sub: 	<https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/> .
@prefix idmp-ra: 	<https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/> .
@prefix skos: 		<http://www.w3.org/2004/02/skos/core#> .
@prefix gsrs:		<https://gsrs.ncats.nih.gov/api/v1/substances/> .


idmp-sub:ChemicalSubstance
    rdf:type            owl:Class ;     rdfs:subClassOf     idmp-sub:SingleSubstance ;       
    rdfs:label          "chemical substance" ;
    skos:definition     "single substance that can be described as a stoichiometric or non-stoichiometric single molecular entity and is not a protein, nucleic acid or polymer substance" .


idmp-sub:SingleSubstancegsrs:1J444QC288
	rdf:type      rdf:type            owl:Class ;
    rdfs:subClassOf     	idmp-sub:SubstanceChemicalSubstance ;        
   	rdfs:label          "single substance				"AMLODIPINE" ;
    skos:definition     "substance that can be described by a single representation or set of descriptive elements" .
 	cmns-dsg:hasName		<https://gsrs.ncats.nih.gov/api/v1/substances/1J444QC288/f7a0a700-a9e5-4be8-a615-7f4e271c8f00> ;
	cmns-id:isIdentifiedBy  <https://data.pistoiaalliance.org/EVMPD/SUB05467MIG> .
	
<https://gsrs.ncats.nih.gov/api/v1/substances/1J444QC288/f7a0a700-a9e5-4be8-a615-7f4e271c8f00>
	rdf:type            	 idmp-sub:SubstanceSubstanceName ;
	cmns-txt:hasTextValue	   rdf:type            owl:Class ;       
    rdfs:label          "substance" ;
    skos:definition     "matter of defined composition that has discrete existence, whose origin may be biological, mineral or chemical" .
 
gsrs:1J444QC288
	rdf:type            	idmp-sub:ChemicalSubstance ;        
	rdfs:label				"AMLODIPINE" ;
	cmns-dsg:hasName		gsrs:1J444QC288\/62fae2dd-eca3-4985-899b-79154991441a ;
	cmns-id:isIdentifiedBy <https://data.pistoiaalliance.org/EVMPD/SUB05467MIG> .
	
gsrs:1J444QC288\/62fae2dd-eca3-4985-899b-79154991441a
	rdf:type            	 idmp-sub:SubstanceName ;
	cmns-txt:hasTextValue	 "3-ETHYL 5-METHYL (+/-)-2-((2-AMINOETHOXY)METHYL)-4-(O-CHLOROPHENYL)-1,4-DIHYDRO-6-METHYL-3,5-PYRIDINEDICARBOXYLATE" ;
	cmns-cls:isClassifiedBy	 idmp-ra:IUPACName .
	
idmp-sub:SubstanceName
	rdf:type            	owl:Class ; 
	rdfs:label 				"substance name" ;
	skos:definition			"name or company code associated with the substance" .
	
idmp-ra:IUPACName
	rdf:type				idmp-sub:SubstanceNameClassifier ;
	rdfs:label 				"IUPAC name" .
	
idmp-sub:SubstanceNameClassifier
	rdf:type            	owl:Class ; 
	rdfs:label 				"substance name classifier" .

<https://data.pistoiaalliance.org/EVMPD/SUB05467MIG>
	rdf:type            				idmp-ra:EudraVigilanceCode ;        
	cmns-txt:hasTextValue				"SUB05467MIG" ;
	cmns-ra:isRegisteredIn				idmp-ra:ExtendedEudraVigilanceMedicinalProductDictionary ;
	cmns-ra:hasRegistrationAuthority	idmp-ra:EuropeanMedicinesAgencyRegistrationAuthority .

idmp-ra:EudraVigilanceCode
	rdfs:subClassOf"3-ETHYL 5-METHYL (+/-)-2-((2-AMINOETHOXY)METHYL)-4-(O-CHLOROPHENYL)-1,4-DIHYDRO-6-METHYL-3,5-PYRIDINEDICARBOXYLATE" ;
	cmns-cls:isClassifiedBy	 idmp-ra:IUPACName .
	
idmp-sub:SubstanceName
	rdf:type            	owl:Class ; 	rdfs:subClassOf			idmp-sub:SubstanceCode
;
	rdfs:label 				"EudraVigilancesubstance codename" ;
	cmns-av:abbreviation	"EV codeskos:definition			"name or company code associated with the substance" .
	
idmp-subra:SubstanceCodeIUPACName
	rdf:type				owl:Class ;
	rdfs:subClassOf			cmns-ra:RegisteredIdentifieridmp-sub:SubstanceNameClassifier ;
	rdfs:label 				"substanceIUPAC codename" .
	
cmnsidmp-rasub:RegisteredIdentifierSubstanceNameClassifier
	rdf:type		            		owl:Class ; 	rdfs:label				"registered identifier" ;
	skosrdfs:definitionlabel 				"contextual identifier that is registered in a registry by, or on behalf of, a registration authority according to some registration scheme" .

idmp-ra:ExtendedEudraVigilanceMedicinalProductDictionary
	rdf:type				idmp-ra:Registry ;
	rdfs:label				"eXtended EudraVigilance Medicinal Product Dictionary""substance name classifier" .

<https://data.pistoiaalliance.org/EVMPD/SUB05467MIG>
	rdf:type            				idmp-ra:EudraVigilanceCode ;        
	cmns-txt:hasTextValue				"SUB05467MIG" ;
	cmns-ra:isRegisteredIn				idmp-ra:ExtendedEudraVigilanceMedicinalProductDictionary ;
	cmns-avra:abbreviation	"XEVMPD"hasRegistrationAuthority	idmp-ra:EuropeanMedicinesAgencyRegistrationAuthority .
	
idmp-ra:RegistryEudraVigilanceCode
	rdfrdfs:type		subClassOf     	owl:Class ;
	rdfs:label	subClassOf			"registry" .
	
idmp-rasub:EuropeanMedicinesAgencyRegistrationAuthority
	rdf:type				idmp-ra:RegistrationAuthority SubstanceCode ;
	rdfs:label				"EuropeanEudraVigilance Medicinescode" Agency Registration Authority;
	cmns-av:abbreviation	"EV code" .
	
idmp-rasub:RegistrationAuthoritySubstanceCode
	rdf:type			    	owl:Class ;
	rdfs:labelsubClassOf				"registration authority" .

Substance

Code Block

language	text
title	Substance
collapse	true

@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 idmp-sub:	<https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/> .
@prefix skos:		<http://www.w3.org/2004/02/skos/core#> .
@prefix gsrs:		<https://gsrs.ncats.nih.gov/api/v1/substances/> .

idmp-sub:ChemicalSubstance
    rdf:type            owl:Class ;
    rdfs:subClassOf     idmp-sub:SingleSubstance ;       
    rdfs:label          "chemical substance" ;
    skos:definition     "single substance that can be described as a stoichiometric or non-stoichiometric single molecular entity and is not a protein, nucleic acid or polymer substance" .
 
idmp-sub:SingleSubstance
    rdf:type            owl:Class ;
    rdfs:subClassOf     idmp-sub:Substance ;       
    rdfs:label          "single substance" ;
    skos:definition     "substance that can be described by a single representation or set of descriptive elements" .
 
idmp-sub:Substancecmns-ra:RegisteredIdentifier ;
	rdfs:label				"substance code" .

cmns-ra:RegisteredIdentifier
	rdf:type		   		owl:Class ;
	rdfs:label				"registered identifier" ;
	skos:definition			"contextual identifier that is registered in a registry by, or on behalf of, a registration authority according to some registration scheme" .

idmp-ra:ExtendedEudraVigilanceMedicinalProductDictionary
	rdf:type				idmp-ra:Registry ;
	rdfs:label				"eXtended EudraVigilance Medicinal Product Dictionary" ;
	cmns-av:abbreviation	"XEVMPD" .
	
idmp-ra:Registry
	rdf:type		     	owl:Class ;
	rdfs:label				"registry" .
	
idmp-ra:EuropeanMedicinesAgencyRegistrationAuthority
	rdf:type				idmp-ra:RegistrationAuthority ;
	rdfs:label				"European Medicines Agency Registration Authority" .
	
idmp-ra:RegistrationAuthority
	rdf:type		    	owl:Class ;
	rdfs:label				"registration authority" .

Substance

Code Block

language	text
title	Substance
collapse	true

@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 idmp-sub:	<https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/> .
@prefix skos:		<http://www.w3.org/2004/02/skos/core#> .
@prefix gsrs:		<https://gsrs.ncats.nih.gov/api/v1/substances/> .

idmp-sub:ChemicalSubstance
    rdf:type            owl:Class ;       
    rdfs:label          "chemical substance" ;
    skos:definition     "matter of defined composition that has discrete existence, whose origin may be biological, mineral or chemicalsingle substance that can be described as a stoichiometric or non-stoichiometric single molecular entity and is not a protein, nucleic acid or polymer substance" .
 
gsrs:1J444QC288
    rdf:type            idmp-sub:ChemicalSubstance ;       
    rdfs:label          "AMLODIPINE" .

...

Image Added

Substance Names

Code Block

language	text
title	Substance Names
collapse	true

@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 skos: 		<http://www.w3.org/2004/02/skos/core#> .
@prefix cmns-cls: 	<https://www.omg.org/spec/Commons/Classifiers/> .
@prefix cmns-dsg: 	<https://www.omg.org/spec/Commons/Designators/> .
@prefix cmns-txt: 	<https://www.omg.org/spec/Commons/TextDatatype/> .
@prefix idmp-sub: 	<https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/> .
@prefix idmp-ra: 	<https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/> .
@prefix gsrs:		<https://gsrs.ncats.nih.gov/api/v1/substances/> .


gsrs:1J444QC288
	rdf:type            	idmp-sub:ChemicalSubstance ;        
	rdfs:label				"AMLODIPINE" ;
	cmns-dsg:hasName		gsrs:1J444QC288\/62fae2dd-eca3-4985-899b-79154991441a .
	
gsrs:1J444QC288\/62fae2dd-eca3-4985-899b-79154991441a<https://gsrs.ncats.nih.gov/api/v1/substances/1J444QC288/f7a0a700-a9e5-4be8-a615-7f4e271c8f00> .
	
<https://gsrs.ncats.nih.gov/api/v1/substances/1J444QC288/f7a0a700-a9e5-4be8-a615-7f4e271c8f00>
	rdf:type            	 idmp-sub:SubstanceName ;
	cmns-txt:hasTextValue	 "3-ETHYL 5-METHYL (+/-)-2-((2-AMINOETHOXY)METHYL)-4-(O-CHLOROPHENYL)-1,4-DIHYDRO-6-METHYL-3,5-PYRIDINEDICARBOXYLATE" ;
	cmns-cls:isClassifiedBy	 idmp-ra:IUPACName .
	
idmp-sub:SubstanceName
	rdf:type            	owl:Class ; 
	rdfs:label 				"substance name" ;
	skos:definition			"name or company code associated with the substance" .
	
idmp-ra:IUPACName
	rdf:type				idmp-sub:SubstanceNameClassifier ;
	rdfs:label 				"IUPAC name" .
	
idmp-sub:SubstanceNameClassifier
	rdf:type            	owl:Class ; 
	rdfs:label 				"substance name classifier" .

...

Image Added

Substance Identifiers

Code Block

language	text
title	Substance Identifiers
collapse	true

@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-av:	<https://www.omg.org/spec/Commons/AbbreviationsAnnotationVocabulary/>.
@prefix cmns-id:	<https://www.omg.org/spec/Commons/Identifiers/> .
@prefix cmns-txt: 	<https://www.omg.org/spec/Commons/TextDatatype/> .
@prefix cmns-ra: 	<https://www.omg.org/spec/Commons/RegistrationAuthorities/> .
@prefix idmp-sub: 	<https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/> .
@prefix idmp-ra: 	<https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/> .
@prefix skos: 		<http://www.w3.org/2004/02/skos/core#> .
@prefix gsrs:		<https://gsrs.ncats.nih.gov/api/v1/substances/> .


gsrs:1J444QC288
	rdf:type            	idmp-sub:ChemicalSubstance ;        
	rdfs:label				"AMLODIPINE" ;
	cmns-id:isIdentifiedBy <https://data.pistoiaalliance.org/EVMPD/SUB05467MIG> .
	
<https://data.pistoiaalliance.org/EVMPD/SUB05467MIG>
	rdf:type            				idmp-ra:EudraVigilanceCode ;        
	cmns-txt:hasTextValue				"SUB05467MIG" ;
	cmns-ra:isRegisteredIn				idmp-ra:ExtendedEudraVigilanceMedicinalProductDictionary ;
	cmns-ra:hasRegistrationAuthority	idmp-ra:EuropeanMedicinesAgencyRegistrationAuthority .

idmp-ra:EudraVigilanceCode
	rdfs:subClassOf     	owl:Class ;
	rdfs:subClassOf			idmp-sub:SubstanceCode ;
	rdfs:label				"EudraVigilance code" ;
	cmns-av:abbreviation	"EV code" .

idmp-sub:SubstanceCode
	rdf:type				owl:Class ;
	rdfs:subClassOf			cmns-ra:RegisteredIdentifier ;
	rdfs:label				"substance code" .

cmns-ra:RegisteredIdentifier
	rdf:type		   		owl:Class ;
	rdfs:label				"registered identifier" ;
	skos:definition			"contextual identifier that is registered in a registry by, or on behalf of, a registration authority according to some registration scheme" .

idmp-ra:ExtendedEudraVigilanceMedicinalProductDictionary
	rdf:type				idmp-ra:Registry ;
	rdfs:label				"eXtended EudraVigilance Medicinal Product Dictionary" ;
	cmns-av:abbreviation	"XEVMPD" .
	
idmp-ra:Registry
	rdf:type		     	owl:Class ;
	rdfs:label				"registry" .
	
idmp-ra:EuropeanMedicinesAgencyRegistrationAuthority
	rdf:type				idmp-ra:RegistrationAuthority ;
	rdfs:label				"European Medicines Agency Registration Authority" .
	
idmp-ra:RegistrationAuthority
	rdf:type		    	owl:Class ;
	rdfs:label				"registration authority" .

Image Removed

Substance Codes

clearly describe difference to "Substance Identifiers"

...

Version	Old Version 24	New Version Current
Changes made by	Li Ming Gooi	Heiner Oberkampf
Saved on	Jun 02, 2022	Jun 03, 2022

Versions Compared

Key

Amlodipine example

Substance

Substance

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Substance Names

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Substance Identifiers

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Substance Codes

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Content Comparison

Versions Compared

Key

Amlodipine example

Substance

Substance

Image Added

Substance Names

Image Added

Substance Identifiers

Image Removed

Substance Codes

Image Added