Making NanoPub Template NanoPubs

makeNanoPub.groovy

@Grab(group='org.nanopub', module='nanopub', version='1.66')

import org.nanopub.Nanopub;
import org.nanopub.NanopubCreator;
import org.nanopub.NanopubUtils;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.model.vocabulary.FOAF;
import org.eclipse.rdf4j.model.vocabulary.RDF;
import org.eclipse.rdf4j.model.vocabulary.RDFS;
import org.eclipse.rdf4j.model.vocabulary.SKOS;
import org.eclipse.rdf4j.model.vocabulary.OWL;
import org.eclipse.rdf4j.rio.RDFFormat;

factory = SimpleValueFactory.getInstance()

externalUriPlaceholder = factory.createIRI("https://w3id.org/np/o/ntemplate/ExternalUriPlaceholder")
assertionTemplate = factory.createIRI("https://w3id.org/np/o/ntemplate/AssertionTemplate")
restrictedChoicePlaceholder = factory.createIRI("https://w3id.org/np/o/ntemplate/RestrictedChoicePlaceholder")
repeatableStatement = factory.createIRI("https://w3id.org/np/o/ntemplate/RepeatableStatement")
hasNanopubLabelPattern = factory.createIRI("https://w3id.org/np/o/ntemplate/hasNanopubLabelPattern")
hasStatement = factory.createIRI("https://w3id.org/np/o/ntemplate/hasStatement")
hasTag = factory.createIRI("https://w3id.org/np/o/ntemplate/hasTag")
hasTargetNanopubType = factory.createIRI("https://w3id.org/np/o/ntemplate/hasTargetNanopubType")
possibleValuesFrom = factory.createIRI("https://w3id.org/np/o/ntemplate/possibleValuesFrom")

wasAttributedTo = factory.createIRI("http://www.w3.org/ns/prov#wasAttributedTo")
description = factory.createIRI("http://purl.org/dc/terms/description")
license = factory.createIRI("http://purl.org/dc/terms/license")

citesIRI = factory.createIRI("http://purl.org/spar/cito/cites")
name = factory.createIRI("http://xmlns.com/foaf/0.1/name")

rdfObject = factory.createIRI("http://www.w3.org/1999/02/22-rdf-syntax-ns#object")
rdfPredicate = factory.createIRI("http://www.w3.org/1999/02/22-rdf-syntax-ns#predicate")
rdfSubject = factory.createIRI("http://www.w3.org/1999/02/22-rdf-syntax-ns#subject")

nanopubIRI = "http://purl.org/nanopub/temp/np1#"

creator = new NanopubCreator(nanopubIRI)
creator.addTimestamp(new Date())
creator.addNamespace("np", "http://www.nanopub.org/nschema#")
creator.addNamespace("dct", "http://purl.org/dc/terms/")
creator.addNamespace("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#")
creator.addNamespace("nt", "https://w3id.org/np/o/ntemplate/")
creator.addNamespace("npx", "http://purl.org/nanopub/x/")
creator.addNamespace("xsd", "http://www.w3.org/2001/XMLSchema#")
creator.addNamespace("rdfs", "http://www.w3.org/2000/01/rdf-schema#")
creator.addNamespace("orcid", "https://orcid.org/")
creator.addNamespace("ns1", "http://purl.org/np/")
creator.addNamespace("prov", "http://www.w3.org/ns/prov#")
creator.addNamespace("foaf", "http://xmlns.com/foaf/0.1/")
creator.addNamespace("owl", "http://www.w3.org/2002/07/owl#")
creator.addNamespace("pav", "http://purl.org/pav/")
creator.addNamespace("skos", "http://www.w3.org/2004/02/skos/core#")

creativeWork = factory.createIRI("http://purl.org/spar/fabio/ScholarlyWork")
creator.addAssertionStatement(creativeWork, RDFS.LABEL,
  factory.createLiteral("scholarly paper - any kind of scholarly work, such as an article, book, etc.")
)
creator.addAssertionStatement(RDF.TYPE, RDFS.LABEL, factory.createLiteral("is a"))

articleIRI = factory.createIRI("http://purl.org/nanopub/temp/np1#article")
creator.addAssertionStatement(articleIRI, RDF.TYPE, externalUriPlaceholder)
creator.addAssertionStatement(articleIRI, RDFS.LABEL,
  factory.createLiteral("DOI (https://doi.org/10...) or other URL of the citing article")
)

assertionIRI = creator.getAssertionUri()
creator.addAssertionStatement(assertionIRI, description,
  factory.createLiteral("Such a nanopublication expresses citation relations of a given article based on the CiTO relation types.")
)
creator.addAssertionStatement(assertionIRI, RDF.TYPE, assertionTemplate)
creator.addAssertionStatement(assertionIRI, RDFS.LABEL, factory.createLiteral("Declare citations with CiTO"))
creator.addAssertionStatement(assertionIRI, hasNanopubLabelPattern, factory.createLiteral("Citations for: \${article}"))
creator.addAssertionStatement(assertionIRI, hasTag, factory.createLiteral("Journals"))
creator.addAssertionStatement(assertionIRI, hasTargetNanopubType, citesIRI)
creator.addAssertionStatement(assertionIRI, hasTargetNanopubType, creativeWork)

st01IRI = factory.createIRI("http://purl.org/nanopub/temp/np1#st01")
st02IRI = factory.createIRI("http://purl.org/nanopub/temp/np1#st02")
creator.addAssertionStatement(assertionIRI, hasStatement, st01IRI)
creator.addAssertionStatement(assertionIRI, hasStatement, st02IRI)

citedIRI = factory.createIRI("http://purl.org/nanopub/temp/np1#cited")
creator.addAssertionStatement(citedIRI, RDF.TYPE, externalUriPlaceholder)
creator.addAssertionStatement(citedIRI, RDFS.LABEL,
  factory.createLiteral("DOI (https://doi.org/10...) or other URL of the cited article")
)

citesIRI = factory.createIRI("http://purl.org/nanopub/temp/np1#cites")
creator.addAssertionStatement(citesIRI, RDF.TYPE, restrictedChoicePlaceholder)
creator.addAssertionStatement(citesIRI, RDFS.LABEL, factory.createLiteral("select the citation type"))
creator.addAssertionStatement(citesIRI, possibleValuesFrom, factory.createIRI("https://w3id.org/np/RAZt5kzfoJg2m4dMRdMm2SP6JeUDD_GMzSq9xyRPMgP5k"))

creator.addAssertionStatement(st01IRI, rdfSubject, articleIRI)
creator.addAssertionStatement(st01IRI, rdfPredicate, RDF.TYPE)
creator.addAssertionStatement(st01IRI, rdfObject, creativeWork)

creator.addAssertionStatement(st02IRI, rdfSubject, articleIRI)
creator.addAssertionStatement(st02IRI, rdfPredicate, citesIRI)
creator.addAssertionStatement(st02IRI, rdfObject, citedIRI)
creator.addAssertionStatement(st02IRI, RDF.TYPE, repeatableStatement)

theCreator = factory.createIRI("https://orcid.org/0000-0002-1267-0234")
creator.addCreator(theCreator)
creator.addProvenanceStatement(assertionIRI, wasAttributedTo, theCreator)

nanopubIRI = creator.getNanopubUri()
creator.addPubinfoStatement(theCreator, name, factory.createLiteral("Tobias Kuhn"))
creator.addPubinfoStatement(nanopubIRI, RDFS.LABEL, factory.createLiteral("Template: Declare citations with CiTO"))
creator.addPubinfoStatement(nanopubIRI, license, factory.createIRI("https://creativecommons.org/licenses/by/4.0/"))
creator.addPubinfoStatement(nanopubIRI, factory.createIRI("http://purl.org/nanopub/x/supersedes"), factory.createIRI("https://w3id.org/np/RA6TJFuEfARzqg5NhFdhv-tE8q6v0DoY9rKYhw5WUMhTA"))
creator.addPubinfoStatement(nanopubIRI, factory.createIRI("http://purl.org/nanopub/x/wasCreatedAt"), factory.createIRI("https://nanodash.knowledgepixels.com/"))
creator.addPubinfoStatement(nanopubIRI, factory.createIRI("https://w3id.org/np/o/ntemplate/wasCreatedFromProvenanceTemplate"), factory.createIRI("http://purl.org/np/RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM"))
creator.addPubinfoStatement(nanopubIRI, factory.createIRI("https://w3id.org/np/o/ntemplate/wasCreatedFromPubinfoTemplate"), factory.createIRI("http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM"))
creator.addPubinfoStatement(nanopubIRI, factory.createIRI("https://w3id.org/np/o/ntemplate/wasCreatedFromPubinfoTemplate"), factory.createIRI("http://purl.org/np/RAh1gm83JiG5M6kDxXhaYT1l49nCzyrckMvTzcPn-iv90"))
creator.addPubinfoStatement(nanopubIRI, factory.createIRI("https://w3id.org/np/o/ntemplate/wasCreatedFromPubinfoTemplate"), factory.createIRI("http://purl.org/np/RAjpBMlw3owYhJUBo3DtsuDlXsNAJ8cnGeWAutDVjuAuI"))
creator.addPubinfoStatement(nanopubIRI, factory.createIRI("https://w3id.org/np/o/ntemplate/wasCreatedFromTemplate"), factory.createIRI("http://purl.org/np/RAJwu5sVubRqXY4t2gkSoGxWkMyZqnpkGTCPiTlmvi4so"))

// output everything
trustedPub = creator.finalizeTrustyNanopub()
outputBuffer = new StringBuffer();
outputBuffer.append(NanopubUtils.writeToString(trustedPub, RDFFormat.TRIG));
print outputBuffer.toString()

template.trig

@prefix this: <https://w3id.org/np/RAFYzuds9uDl0DcLD_T3sbiKDG2y9iL3OMPIg-dy7fOQc> .
@prefix sub: <https://w3id.org/np/RAFYzuds9uDl0DcLD_T3sbiKDG2y9iL3OMPIg-dy7fOQc#> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@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 ns1: <http://purl.org/np/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .

sub:Head {
  this: a np:Nanopublication;
    np:hasAssertion sub:assertion;
    np:hasProvenance sub:provenance;
    np:hasPublicationInfo sub:pubinfo .
}

sub:assertion {
  <http://purl.org/spar/fabio/ScholarlyWork> rdfs:label "scholarly paper - any kind of scholarly work, such as an article, book, etc." .
  
  rdf:type rdfs:label "is a" .
  
  sub:article a nt:ExternalUriPlaceholder;
    rdfs:label "DOI (https://doi.org/10...) or other URL of the citing article" .
  
  sub:assertion a nt:AssertionTemplate;
    dct:description "Such a nanopublication expresses citation relations of a given article based on the CiTO relation types.";
    rdfs:label "Declare citations with CiTO";
    nt:hasNanopubLabelPattern "Citations for: ${article}";
    nt:hasStatement sub:st01, sub:st02;
    nt:hasTag "Journals";
    nt:hasTargetNanopubType <http://purl.org/spar/cito/cites>, <http://purl.org/spar/fabio/ScholarlyWork> .
  
  sub:cited a nt:ExternalUriPlaceholder;
    rdfs:label "DOI (https://doi.org/10...) or other URL of the cited article" .
  
  sub:cites a nt:RestrictedChoicePlaceholder;
    rdfs:label "select the citation type";
    nt:possibleValuesFrom <https://w3id.org/np/RAZt5kzfoJg2m4dMRdMm2SP6JeUDD_GMzSq9xyRPMgP5k> .
  
  sub:st01 rdf:object <http://purl.org/spar/fabio/ScholarlyWork>;
    rdf:predicate rdf:type;
    rdf:subject sub:article .
  
  sub:st02 a nt:RepeatableStatement;
    rdf:object sub:cited;
    rdf:predicate sub:cites;
    rdf:subject sub:article .
}

sub:provenance {
  sub:assertion prov:wasAttributedTo orcid:0000-0002-1267-0234 .
}

sub:pubinfo {
  orcid:0000-0002-1267-0234 foaf:name "Tobias Kuhn" .
  
  this: dct:created "2024-12-29T11:54:06.411+01:00"^^xsd:dateTime;
    dct:creator orcid:0000-0002-1267-0234;
    dct:license <https://creativecommons.org/licenses/by/4.0/>;
    npx:supersedes <https://w3id.org/np/RA6TJFuEfARzqg5NhFdhv-tE8q6v0DoY9rKYhw5WUMhTA>;
    npx:wasCreatedAt <https://nanodash.knowledgepixels.com/>;
    rdfs:label "Template: Declare citations with CiTO";
    nt:wasCreatedFromProvenanceTemplate ns1:RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM;
    nt:wasCreatedFromPubinfoTemplate ns1:RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM,
      ns1:RAh1gm83JiG5M6kDxXhaYT1l49nCzyrckMvTzcPn-iv90, ns1:RAjpBMlw3owYhJUBo3DtsuDlXsNAJ8cnGeWAutDVjuAuI;
    nt:wasCreatedFromTemplate ns1:RAJwu5sVubRqXY4t2gkSoGxWkMyZqnpkGTCPiTlmvi4so .
}