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Example Illustration of Patterns for Names and IDs

Example Illustration of Patterns for Names and IDs

Owned by Heiner Oberkampf
Last updated: Jun 03, 2022

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 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.

Amlodipine example 
@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/AnnotationVocabulary/>.
@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: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" .

gsrs:1J444QC288
	rdf:type            	idmp-sub:ChemicalSubstance ;        
	rdfs:label				"AMLODIPINE" ;
	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: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     	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" .


Substance

Substance 
@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     "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" .
 
gsrs:1J444QC288
    rdf:type            idmp-sub:ChemicalSubstance ;       
    rdfs:label          "AMLODIPINE" .


Substance Names

Substance Names 
@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		<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" .


Substance Identifiers

Substance Identifiers 
@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/AnnotationVocabulary/>.
@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" .






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