Fragoulakis et al. claimed in previous work that pharmacogenomics-guided clopidogrel strategy represents a cost-effective treatment for patients undergoing PCI. We present here a formalization of that claim, stating that all things of class “pharmacogenomics guided clopidogrel therapy” that are in the context of a thing of class “patient undergoing PCI” generally have a relation of type “enables” to a thing of class “cost-effective treatment” in the same context.
1. IntroductionFragoulakis et al. [2 ] state that “Our data show that pharmacogenomics-guided clopidogrel treatment strategy may represent a cost-effective choice compared with non-pharmacogenomics-guided strategy for patients undergoing PCI.”. We present here a formalization of the main scientific claim from this quote by using a semantic template called the super-pattern [1 ].
2. FormalizationOur formalization looks as follows:
In the context class we use a new minted class “patient undergoing PCI” that is a subclass of “patient” (Q181600) from Wikidata and is related to the class “percutaneous coronary intervention” (Q2008344) from Wikidata. In the subject class, we use a new minted class “pharmacogenomics guided clopidogrel therapy” that is a subclass of “treatment” (Q179661) from Wikidata and is related to the class “pharmacogenomics” (Q1152227) and “clopidogrel” (Q410237) from Wikidata. In the object class we minted a new class “cost-effective treatment” that is a subclass of “treatment” (Q179661) from Wikidata and is related to the class “cost-effectiveness analysis” (Q1754768) from Wikidata.
3. RDF codeThis is our formalization as a nanopublication in TriG format:
@prefix this: <http://purl.org/np/RAn15vsPJEVdJvjNKtBPo_oadtjeP9oc3Si-69FiJ4poQ> .
@prefix sub: <http://purl.org/np/RAn15vsPJEVdJvjNKtBPo_oadtjeP9oc3Si-69FiJ4poQ#> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix sp: <https://w3id.org/linkflows/superpattern/terms/> .
sub:Head {
this: np:hasAssertion sub:assertion ;
np:hasProvenance sub:provenance ;
np:hasPublicationInfo sub:pubinfo ;
a np:Nanopublication .
}
sub:assertion {
sub:spi a sp:SuperPatternInstance ;
rdfs:label "Pharmacogenomics-guided clopidogrel strategy represents a cost-effective treatment for patients
undergoing PCI" ;
sp:hasContextClass <http://purl.org/np/RA9pwySo43TIfbvPuhK4ZuisvMsDvZ6TeR5N6MNKft8Nw#patient_undergoing_PCI> ;
sp:hasSubjectClass <http://purl.org/np/RAOxICL4ULhzr5mxC9cyzStCBtpoETQGin6Vr-
Ns7JNtA#pharmacogenomics_guided_clopidogrel_therapy> ;
sp:hasQualifier sp:generallyQualifier ;
sp:hasRelation sp:enables ;
sp:hasObjectClass <http://purl.org/np/RAlfRfPak2jsyyVy4knjOmxQSYtociP8Cc0O7gemMtqQY#cost-effective_treatment> .
}
sub:provenance {
sub:activity a sp:FormalizationActivity ;
prov:used sub:quote , <https://pubmed.ncbi.nlm.nih.gov/30647444/> ;
prov:wasAssociatedWith orcid:0000-0002-0519-7776 .
sub:assertion prov:wasGeneratedBy sub:activity .
sub:quote prov:value "Our data show that pharmacogenomics-guided clopidogrel treatment strategy may represent
a cost-effective choice compared with non-pharmacogenomics-guided strategy for patients undergoing PCI." ;
prov:wasQuotedFrom <https://pubmed.ncbi.nlm.nih.gov/30647444/> .
}
sub:pubinfo {
sub:sig npx:hasAlgorithm "RSA" ;
npx:hasPublicKey
"MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCJlM78d80R+gFMoQB1IG3f7AbqqGOCIv4HmZd1cx1KgEWMUUpPsojFNvx84fC/TltcJ8F8JafnbhDXW2HM2
MhdK4yC04ROEV1vIgSzjDicHfiqXvMqdPuMyQp4mmCEY7mUoeEW10mWZqjk+S9TnmiAQbFGcpExP8aosr2aTR7CSQIDAQAB" ;
npx:hasSignature
"cEQZgFxgTd99RYcmWsqM1LCUciLc1lXuy6mfjgKhn0BfsMcesqIKR+51xx6lfHD31tnz/bovIDh1YEPORGBe2PEvFMPvRRFd67B9s1awepEPll5tA7wmhkTOj
PrEUXISQaQu93NbpbYMYSGnRx+Shv7jNxE+hPrxQw7fD6EgJr8=" ;
npx:hasSignatureTarget this: .
this: dct:created "2021-11-17T21:22:59.625+02:00"^^xsd:dateTime ;
dct:creator orcid:0000-0002-0519-7776 , orcid:0000-0002-7114-6459 ;
npx:introduces sub:spi ;
npx:supersedes <http://purl.org/np/RAB_yY8X4BUuS9HMBso8SvvPfBX31cb8cCv41SgfyMBew> ;
<https://w3id.org/linkflows/reviews/isUpdateOf> <http://purl.org/np/RAWCmrfeUUoh1tOl_7qFYoWgrYeonmX4FzAFboCSEoL-s> ;
nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RAE1wniOy0yO39PlK9QkQ-wqbC3q-R2nXraP5huu8W39k> ;
nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RA2vCBXZf-icEcVRGhulJXugTGxpsV5yVr9yqCI1bQh4A> ,
<http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM> ,
<http://purl.org/np/RAjpBMlw3owYhJUBo3DtsuDlXsNAJ8cnGeWAutDVjuAuI> ;
nt:wasCreatedFromTemplate <http://purl.org/np/RAv68imZrEjfcp2rnEg1hzoBqEVc0cQMtp9_1Za0BxNM4> .
}
The following nanopublications introduce the newly minted classes in TriG format.
This is the class definition of “patient undergoing PCI”:
@prefix this: <http://purl.org/np/RA9pwySo43TIfbvPuhK4ZuisvMsDvZ6TeR5N6MNKft8Nw> .
@prefix sub: <http://purl.org/np/RA9pwySo43TIfbvPuhK4ZuisvMsDvZ6TeR5N6MNKft8Nw#> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
sub:Head {
this: np:hasAssertion sub:assertion ;
np:hasProvenance sub:provenance ;
np:hasPublicationInfo sub:pubinfo ;
a np:Nanopublication .
}
sub:assertion {
sub:patient_undergoing_PCI a <http://www.w3.org/2002/07/owl#Class> ;
rdfs:label "patient undergoing PCI" ;
rdfs:subClassOf <http://www.wikidata.org/entity/Q181600> ;
skos:definition "patient undergoing percutaneous coronary intervention" ;
skos:relatedMatch <http://www.wikidata.org/entity/Q2008344> .
}
sub:provenance {
sub:assertion prov:wasAttributedTo orcid:0000-0002-0519-7776 .
}
sub:pubinfo {
sub:sig npx:hasAlgorithm "RSA" ;
npx:hasPublicKey
"MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCJlM78d80R+gFMoQB1IG3f7AbqqGOCIv4HmZd1cx1KgEWMUUpPsojFNvx84fC/TltcJ8F8JafnbhDXW
2HM2MhdK4yC04ROEV1vIgSzjDicHfiqXvMqdPuMyQp4mmCEY7mUoeEW10mWZqjk+S9TnmiAQbFGcpExP8aosr2aTR7CSQIDAQAB" ;
npx:hasSignature
"Iv6wAp5BYaY+1tBEBIcPls8rQjacsBZifWaNxBQkJaoYJs5/ejUrEiMXVwul4D+4baebbEm8rkT6vp336uDcencmlDiZzHZGL1ioFQTG1Bc//XZYWBkO/jcGRB
3HNolScLz1Fo/dWaB94+qrW9MSTi6eVmIY9YqjH+3mGY6HJRk=" ;
npx:hasSignatureTarget this: .
this: dct:created "2021-11-04T10:24:46.053+02:00"^^xsd:dateTime ;
dct:creator orcid:0000-0002-0519-7776 , orcid:0000-0002-7114-6459 ;
npx:introduces sub:patient_undergoing_PCI ;
npx:supersedes <http://purl.org/np/RAuLZtfsHn3NGe0Md8lLNvYmBseEtW9v1rVUVfJCpJYUE> ;
<https://w3id.org/linkflows/reviews/isUpdateOf> <http://purl.org/np/RAuLZtfsHn3NGe0Md8lLNvYmBseEtW9v1rVUVfJCpJYUE> ;
nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RAi6zZAwhaJ23Hzg4lIjlPir6Take3ZQp-lS9skfBEwfQ> ;
nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RA2vCBXZf-icEcVRGhulJXugTGxpsV5yVr9yqCI1bQh4A> ,
<http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM> ,
<http://purl.org/np/RAOGu9Lh0BD4tbIRB9RG6RGRA_ObDh75NTbIqaWgxxs8M> ,
<http://purl.org/np/RAjpBMlw3owYhJUBo3DtsuDlXsNAJ8cnGeWAutDVjuAuI> ;
nt:wasCreatedFromTemplate <http://purl.org/np/RAdpgRpigXtt8iPV9uOPf3wIT3qzOI8Sg2Q72CNV8g-Yo> .
}
This is the class definition of “pharmacogenomics guided clopidogrel therapy”:
@prefix this: <http://purl.org/np/RAOxICL4ULhzr5mxC9cyzStCBtpoETQGin6Vr-Ns7JNtA> .
@prefix sub: <http://purl.org/np/RAOxICL4ULhzr5mxC9cyzStCBtpoETQGin6Vr-Ns7JNtA#> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
sub:Head {
this: np:hasAssertion sub:assertion ;
np:hasProvenance sub:provenance ;
np:hasPublicationInfo sub:pubinfo ;
a np:Nanopublication .
}
sub:assertion {
sub:pharmacogenomics_guided_clopidogrel_therapy a <http://www.w3.org/2002/07/owl#Class> ;
rdfs:label "pharmacogenomics guided clopidogrel therapy" ;
rdfs:subClassOf <http://www.wikidata.org/entity/Q179661> ;
skos:definition "A clopidogrel therapy assisted by pharmacogenomics." ;
skos:relatedMatch <http://www.wikidata.org/entity/Q1152227> , <http://www.wikidata.org/entity/Q410237> .
}
sub:provenance {
sub:assertion prov:wasAttributedTo orcid:0000-0002-0519-7776 .
}
sub:pubinfo {
sub:sig npx:hasAlgorithm "RSA" ;
npx:hasPublicKey
"MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCJlM78d80R+gFMoQB1IG3f7AbqqGOCIv4HmZd1cx1KgEWMUUpPsojFNvx84fC/TltcJ8F8JafnbhDXW2HM2
MhdK4yC04ROEV1vIgSzjDicHfiqXvMqdPuMyQp4mmCEY7mUoeEW10mWZqjk+S9TnmiAQbFGcpExP8aosr2aTR7CSQIDAQAB" ;
npx:hasSignature
"QNIcAE5wfsq1p8Z7J+KLQOwA1pbm5/VZFeRJe6JKkIB6TvXTdlO2OKOTDYMPZys15bU9yibaKOA/7YRQnaf6oTbgOmaT1mV5+zffRjl5SG+z+4A1R7HLIfr2G2x
9Z4kz55rQL+AQbvYgkDXiVMSsbdJdraQ5t/SBCJcEHOh2xuQ=" ;
npx:hasSignatureTarget this: .
this: dct:created "2021-11-04T11:02:34.246+02:00"^^xsd:dateTime ;
dct:creator orcid:0000-0002-0519-7776 , orcid:0000-0002-7114-6459 ;
npx:introduces sub:pharmacogenomics_guided_clopidogrel_therapy ;
npx:supersedes <http://purl.org/np/RA4BJq9pLse6z1BRbZIOgARyf1zOY9Qw33ix3lsHcazOE> ;
<https://w3id.org/linkflows/reviews/isUpdateOf> <http://purl.org/np/RAvOAyEg-J8ynmZNrkCgg5XqGuqRo-dXcGFvgDLxtY6ck> ;
nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RAi6zZAwhaJ23Hzg4lIjlPir6Take3ZQp-lS9skfBEwfQ> ;
nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RA2vCBXZf-icEcVRGhulJXugTGxpsV5yVr9yqCI1bQh4A> ,
<http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM> ,
<http://purl.org/np/RAjpBMlw3owYhJUBo3DtsuDlXsNAJ8cnGeWAutDVjuAuI> ;
nt:wasCreatedFromTemplate <http://purl.org/np/RAdpgRpigXtt8iPV9uOPf3wIT3qzOI8Sg2Q72CNV8g-Yo> .
}
This is the class definition of “cost-effective treatment”:
@prefix this: <http://purl.org/np/RAlfRfPak2jsyyVy4knjOmxQSYtociP8Cc0O7gemMtqQY> .
@prefix sub: <http://purl.org/np/RAlfRfPak2jsyyVy4knjOmxQSYtociP8Cc0O7gemMtqQY#> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
sub:Head {
this: np:hasAssertion sub:assertion ;
np:hasProvenance sub:provenance ;
np:hasPublicationInfo sub:pubinfo ;
a np:Nanopublication .
}
sub:assertion {
sub:cost-effective_treatment a <http://www.w3.org/2002/07/owl#Class> ;
rdfs:label "cost-effective treatment" ;
rdfs:subClassOf <http://www.wikidata.org/entity/Q179661> ;
skos:definition "cost-effective treatment" ;
skos:relatedMatch <http://www.wikidata.org/entity/Q1754768> .
}
sub:provenance {
sub:assertion prov:wasAttributedTo orcid:0000-0002-0519-7776 .
}
sub:pubinfo {
sub:sig npx:hasAlgorithm "RSA" ;
npx:hasPublicKey
"MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCJlM78d80R+gFMoQB1IG3f7AbqqGOCIv4HmZd1cx1KgEWMUUpPsojFNvx84fC/TltcJ8F8JafnbhDXW2HM2Mhd
K4yC04ROEV1vIgSzjDicHfiqXvMqdPuMyQp4mmCEY7mUoeEW10mWZqjk+S9TnmiAQbFGcpExP8aosr2aTR7CSQIDAQAB" ;
npx:hasSignature
"f+XJLoVxSGhXnuQYxbgd+cAl1jMEdNppqO11jalPaJlnUREFKwRB5A9mhsvEuV1TWGzHfzi1wEL8FiguHgg7YUTJlbA1pb8qA98/MFkWtXeYzIjwOgmuFUrSIBQF0
cEVX5OV8D3nzwwa+Y2glBes11pIkSRgAH4b3KMy8+PbNBg=" ;
npx:hasSignatureTarget this: .
this: dct:created "2021-11-04T10:28:39.058+02:00"^^xsd:dateTime ;
dct:creator orcid:0000-0002-0519-7776 , orcid:0000-0002-7114-6459 ;
npx:introduces sub:cost-effective_treatment ;
npx:supersedes <http://purl.org/np/RAjD4-Q2kO_cIUE52rde2uWbV3RtuCR90geXW90il2YX4> ;
<https://w3id.org/linkflows/reviews/isUpdateOf> <http://purl.org/np/RAjD4-Q2kO_cIUE52rde2uWbV3RtuCR90geXW90il2YX4> ;
nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RAi6zZAwhaJ23Hzg4lIjlPir6Take3ZQp-lS9skfBEwfQ> ;
nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RA2vCBXZf-icEcVRGhulJXugTGxpsV5yVr9yqCI1bQh4A> ,
<http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM> ,
<http://purl.org/np/RAOGu9Lh0BD4tbIRB9RG6RGRA_ObDh75NTbIqaWgxxs8M> ,
<http://purl.org/np/RAjpBMlw3owYhJUBo3DtsuDlXsNAJ8cnGeWAutDVjuAuI> ;
nt:wasCreatedFromTemplate <http://purl.org/np/RAdpgRpigXtt8iPV9uOPf3wIT3qzOI8Sg2Q72CNV8g-Yo> .
}
