@prefix this: <https://w3id.org/np/RAxh65i-lelMIAK3By-aVOElaEqosPBU-B4Um1Dy7Sgkw> .
@prefix sub: <https://w3id.org/np/RAxh65i-lelMIAK3By-aVOElaEqosPBU-B4Um1Dy7Sgkw/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix orcid: <https://orcid.org/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix mvikg: <http://example.org/mvikg/> .
@prefix gen: <https://w3id.org/kpxl/gen/terms/> .
@prefix unit: <http://qudt.org/vocab/unit/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix biolink: <https://w3id.org/biolink/vocab/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix sosa: <http://www.w3.org/ns/sosa/> .

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

sub:assertion {
  mvikg:alt rdfs:label "alternate allele" .
  
  mvikg:effect rdfs:label "variant effect" .
  
  mvikg:evidenceText rdfs:label "evidence text" .
  
  mvikg:frequencyUnit rdfs:label "frequency unit" .
  
  mvikg:frequencyValue rdfs:label "frequency value" .
  
  mvikg:length rdfs:label "variant length" .
  
  mvikg:ref rdfs:label "reference allele" .
  
  dcterms:isPartOf rdfs:label "is part of" .
  
  rdf:type rdfs:label "is a" .
  
  rdfs:label rdfs:label "label" .
  
  sosa:isFeatureOfInterestOf rdfs:label "is feature of interest of" .
  
  biolink:Gene rdfs:label "gene" .
  
  biolink:SequenceVariant rdfs:label "sequence variant" .
  
  biolink:end_coordinate rdfs:label "end coordinate" .
  
  biolink:has_sequence_variant rdfs:label "has sequence variant" .
  
  biolink:start_coordinate rdfs:label "start coordinate" .
  
  sub:alt a nt:LiteralPlaceholder;
    rdfs:label "alternate allele" .
  
  sub:effect a nt:LiteralPlaceholder;
    rdfs:label "variant effect" .
  
  sub:endCoordinate a nt:LiteralPlaceholder;
    rdfs:label "end coordinate (variant position)";
    nt:hasDatatype xsd:integer .
  
  sub:evidenceText a nt:LiteralPlaceholder;
    rdfs:label "evidence text (quote/description from the source)" .
  
  sub:freqUnit a nt:ExternalUriPlaceholder, nt:GuidedChoicePlaceholder;
    rdfs:label "frequency unit";
    nt:possibleValue unit:PERCENT, unit:UNITLESS .
  
  sub:freqValue a nt:LiteralPlaceholder;
    rdfs:label "frequency value";
    nt:hasDatatype xsd:decimal .
  
  sub:gene a nt:ExternalUriPlaceholder, nt:GuidedChoicePlaceholder;
    rdfs:label "the gene this variant belongs to (search existing genes, or enter an NCBI Gene ID)";
    nt:possibleValuesFromApi "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&retmode=json&id=",
      "https://w3id.org/np/l/nanopub-query-1.1/api/RAom4OoQ8U2K6A629YRXKo9-XU-ZJM7-KZs1h11OD6c1w/find-things?type=https://w3id.org/biolink/vocab/Gene" .
  
  sub:length a nt:LiteralPlaceholder;
    rdfs:label "variant length (free text — not all source rows give a clean integer)" .
  
  sub:ref a nt:LiteralPlaceholder;
    rdfs:label "reference allele" .
  
  sub:sample a nt:ExternalUriPlaceholder, nt:GuidedChoicePlaceholder;
    rdfs:label "the sample this gene was observed in (declared via the sample-context template)";
    nt:possibleValuesFromApi "https://w3id.org/np/l/nanopub-query-1.1/api/RAom4OoQ8U2K6A629YRXKo9-XU-ZJM7-KZs1h11OD6c1w/find-things?type=http://www.w3.org/ns/sosa/Sample" .
  
  sub:soType a nt:ExternalUriPlaceholder, nt:GuidedChoicePlaceholder;
    rdfs:label "sequence variant type (Sequence Ontology)";
    nt:possibleValuesFromApi "https://www.ebi.ac.uk/ols4/api/select?ontology=so&fieldList=iri,label,description&q=" .
  
  sub:st01 rdf:object sub:sample;
    rdf:predicate sosa:isFeatureOfInterestOf;
    rdf:subject sub:gene .
  
  sub:st02 rdf:object <https://w3id.org/spaces/mvikg/r/kg>;
    rdf:predicate dcterms:isPartOf;
    rdf:subject sub:variant .
  
  sub:st08 rdf:object biolink:Gene;
    rdf:predicate rdf:type;
    rdf:subject sub:gene .
  
  sub:st09 rdf:object sub:variant;
    rdf:predicate biolink:has_sequence_variant;
    rdf:subject sub:gene .
  
  sub:st10 rdf:object biolink:SequenceVariant;
    rdf:predicate rdf:type;
    rdf:subject sub:variant .
  
  sub:st11 rdf:object sub:variantName;
    rdf:predicate rdfs:label;
    rdf:subject sub:variant .
  
  sub:st12 a nt:OptionalStatement;
    rdf:object sub:soType;
    rdf:predicate rdf:type;
    rdf:subject sub:variant .
  
  sub:st13 a nt:OptionalStatement;
    rdf:object sub:effect;
    rdf:predicate mvikg:effect;
    rdf:subject sub:variant .
  
  sub:st14 a nt:OptionalStatement;
    rdf:object sub:length;
    rdf:predicate mvikg:length;
    rdf:subject sub:variant .
  
  sub:st15 a nt:OptionalStatement;
    rdf:object sub:alt;
    rdf:predicate mvikg:alt;
    rdf:subject sub:variant .
  
  sub:st16 a nt:OptionalStatement;
    rdf:object sub:ref;
    rdf:predicate mvikg:ref;
    rdf:subject sub:variant .
  
  sub:st17 a nt:OptionalStatement;
    rdf:object sub:startCoordinate;
    rdf:predicate biolink:start_coordinate;
    rdf:subject sub:variant .
  
  sub:st18 a nt:OptionalStatement;
    rdf:object sub:endCoordinate;
    rdf:predicate biolink:end_coordinate;
    rdf:subject sub:variant .
  
  sub:st19 a nt:OptionalStatement;
    rdf:object sub:evidenceText;
    rdf:predicate mvikg:evidenceText;
    rdf:subject sub:variant .
  
  sub:st20 a nt:GroupedStatement, nt:OptionalStatement;
    nt:hasStatement sub:st23, sub:st24 .
  
  sub:st23 rdf:object sub:freqValue;
    rdf:predicate mvikg:frequencyValue;
    rdf:subject sub:variant .
  
  sub:st24 rdf:object sub:freqUnit;
    rdf:predicate mvikg:frequencyUnit;
    rdf:subject sub:variant .
  
  sub:startCoordinate a nt:LiteralPlaceholder;
    rdfs:label "start coordinate (variant position)";
    nt:hasDatatype xsd:integer .
  
  sub:templateVersion a nt:AssertionTemplate, nt:UnlistedTemplate;
    dcterms:description "Declaring an MVIKG observation";
    dcterms:isVersionOf <https://w3id.org/np/RATaU30_DTYcbG3bqZQb4fLRktnxKyjASwI5fFFIumAeo/template>;
    rdfs:label "Declaring an MVIKG observation";
    gen:governedBy <https://w3id.org/spaces/mvikg>;
    nt:hasNanopubLabelPattern "${variantName}";
    nt:hasStatement sub:st01, sub:st02, sub:st08, sub:st09, sub:st10, sub:st11, sub:st12,
      sub:st13, sub:st14, sub:st15, sub:st16, sub:st17, sub:st18, sub:st19, sub:st20, sub:st23,
      sub:st24;
    nt:hasTag "Biology";
    nt:hasTargetNanopubType biolink:SequenceVariant .
  
  sub:variant a nt:IntroducedResource, nt:LocalResource;
    rdfs:label "this sequence variant" .
  
  sub:variantName a nt:LiteralPlaceholder;
    rdfs:label "variant name/notation (e.g. T77I)" .
}

sub:provenance {
  sub:assertion prov:wasAttributedTo orcid:0009-0005-5515-1230 .
}

sub:pubinfo {
  orcid:0000-0002-1267-0234 foaf:name "Tobias Kuhn" .
  
  this: dcterms:created "2026-11-11T05:57:23+00:00"^^xsd:dateTime;
    dcterms:creator orcid:0000-0002-1267-0234;
    dcterms:license <https://creativecommons.org/licenses/by/4.0/>;
    npx:embeds sub:templateVersion;
    npx:introduces <https://w3id.org/np/RATaU30_DTYcbG3bqZQb4fLRktnxKyjASwI5fFFIumAeo/template>;
    rdfs:label "Declaring an MVIKG observation";
    skos:changeNote "Corrects the template links in the publication info, with the template itself unchanged: the earlier version named the assertion templates for making provenance and publication info templates (RA-yPZEY..., RA4o9JqS...) as its own provenance and publication info templates. It now names the ones actually used (Attributed to myself/others; License, Creator, Change note, Derived) and the meta-template by its embedded IRI.";
    prov:wasDerivedFrom <https://w3id.org/np/RAnlONjGChImRjDeXxTwrTmndhfv1guES7EnXlp1CaE3g>;
    nt:wasCreatedFromProvenanceTemplate <https://w3id.org/np/RA7lSq6MuK_TIC6JMSHvLtee3lpLoZDOqLJCLXevnrPoU>;
    nt:wasCreatedFromPubinfoTemplate <https://w3id.org/np/RA-N4_kFxcruvBTlo1yJv29E4SLOXsx5KO_th69PprMrA>,
      <https://w3id.org/np/RA7NZ9N1vb-mbTo6pOyR14fdbQ8PpFtJHTY3UBPb6vMh4>, <https://w3id.org/np/RACJ58Gvyn91LqCKIO9zu1eijDQIeEff28iyDrJgjSJF8>,
      <https://w3id.org/np/RAKc76yHLDbloE6ObluzYQsfX37v6qrZXbYeIKpe8-YUo>;
    nt:wasCreatedFromTemplate <https://w3id.org/np/RAgeON_vGgJCt5E4DPMi0eOPaGwNv9tbfFTRZtBwdQL0w/templateVersion> .
  
  sub:sig npx:hasAlgorithm "RSA";
    npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCwUtewGCpT5vIfXYE1bmf/Uqu1ojqnWdYxv+ySO80ul8Gu7m8KoyPAwuvaPj0lvPtHrg000qMmkxzKhYknEjq8v7EerxZNYp5B3/3+5ZpuWOYAs78UnQVjbHSmDdmryr4D4VvvNIiUmd0yxci47dTFUj4DvfHnGd6hVe5+goqdcwIDAQAB";
    npx:hasSignature "q0EFXCV9X4RdbRchHw2A3XQNUJZxMH5egyuYTfA/LHQqZX+LzlOHUo0+opWGQyMrwXiyLN5mDZjcatn+ASX8GGWXtnMnE98VwrexjuyG0FvDGNUJt3gEFcS1KhZK2F3U8K08v64a89BmcXuNtpuNhsSzX5pD3t0i1759uCDxZz8=";
    npx:hasSignatureTarget this:;
    npx:signedBy orcid:0000-0002-1267-0234 .
}