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 thus demonstrates how established modeling patterns can be represented in the structure of the IDMP Ontology, using the names and IDs of 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 | ||||||
|---|---|---|---|---|---|---|
| ||||||
@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:SingleSubstance gsrs:1J444QC288 rdf:type owl:Class ; rdfs:subClassOf idmp-sub:SubstanceChemicalSubstance ; rdfs:label "single substance" ; skos:definition "substance that can be described by a single representation or set of descriptive elements" . idmp-sub:Substance 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 rdfs:label "AMLODIPINE" ; cmns-dsg:hasName gsrs:1J444QC288\/62fae2dd-eca3-4985-899b-79154991441a<https://gsrs.ncats.nih.gov/api/v1/substances/1J444QC288/f7a0a700-a9e5-4be8-a615-7f4e271c8f00> ; cmns-id:isIdentifiedBy <https://data.pistoiaalliance.org/EVMPD/SUB05467MIG> . gsrs:1J444QC288\/62fae2dd-eca3-4985-899b-79154991441a<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" . |
...
| Code Block | ||||||
|---|---|---|---|---|---|---|
| ||||||
@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
| Code Block | ||||||
|---|---|---|---|---|---|---|
| ||||||
@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" . |
...
Substance Identifiers
| Code Block | ||||||
|---|---|---|---|---|---|---|
| ||||||
@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" . |
Substance Codes
clearly describe difference to "Substance Identifiers"
...
...
