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A formalization of one of the main claims of “Cost-effectiveness analysis of pharmacogenomics-guided clopidogrel treatment in Spanish patients undergoing percutaneous coronary intervention” by Fragoulakis et al. 20191

Issue title: Semantic Publishing with Formalization Papers

Guest editors: Cristina-Iulia Bucur and Tobias Kuhn

Article type: Formalization Paper

Authors: Patrinos, George P.; *

Affiliations: School of Health Sciences, Department of Pharmacy, University of Patras, Patras, Greece

Correspondence: [*] Corresponding author. E-mail: [email protected].

Note: [1] As RDF/nanopublication: http://purl.org/np/RAn15vsPJEVdJvjNKtBPo_oadtjeP9oc3Si-69FiJ4poQ

Keywords: Patient undergoing PCI, pharmacogenomics-guided clopidogrel therapy, cost-effective treatment

DOI: 10.3233/DS-210042

Journal: Data Science, vol. 5, no. 1, pp. 29-33, 2022

Received 5 July 2021
|
Accepted 17 November 2021
|
Published: 22 March 2022
Get PDF open access

Abstract

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.Introduction

Fragoulakis 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.Formalization

Our formalization looks as follows:

CONTEXT-CLASS (“in the context of all…”):patient undergoing PCI
SUBJECT-CLASS (“things of type…”):pharmacogenomics guided clopidogrel therapy
QUALIFIER:generally
RELATION-TYPE (“have a relation of type…”):enables
OBJECT-CLASS (“to things of type…”):cost-effective treatment

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 code

This 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> .
}

References

[1] 

C.I. Bucur, T. Kuhn, D. Ceolin and J. van Ossenbruggen, Expressing high-level scientific claims with formal semantics, in: Proceedings of the 11th Knowledge Capture Conference, (2021) . doi:10.1145/3460210.3493561.

[2] 

V. Fragoulakis, M. Bartsakoulia, X. Díaz-Villamarín, K. Chalikiopoulou, K. Kehagia, J.G.S. Ramos, L.J. Martínez-González, M. Gkotsi, E. Katrali, E. Skoufas, A. Vozikis, A. John, B.R. Ali, S. Wordsworth, C.L. Dávila-Fajardo, T. Katsila, G.P. Patrinos and C. Mitropoulou, Cost-effectiveness analysis of pharmacogenomics-guided clopidogrel treatment in Spanish patients undergoing percutaneous coronary intervention, Pharmacogenomics J. 19: (5) ((2019) ), 438–445. doi:10.1038/s41397-019-0069-1.

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