@prefix this: <https://w3id.org/np/RALRRzcTp2-0bwxqsE6K3G_NZVZ_QO529mQ7O236SUWaU> .
@prefix sub: <https://w3id.org/np/RALRRzcTp2-0bwxqsE6K3G_NZVZ_QO529mQ7O236SUWaU/> .
@prefix qudt: <http://qudt.org/schema/qudt/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix dcmitype: <http://purl.org/dc/dcmitype/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix mvikg: <http://example.org/mvikg/> .
@prefix gen: <https://w3id.org/kpxl/gen/terms/> .
@prefix unit: <http://qudt.org/vocab/unit/> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix biolink: <https://w3id.org/biolink/vocab/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@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:comparedTo rdfs:label "compared to" .
  
  mvikg:effect rdfs:label "variant effect" .
  
  mvikg:frequency rdfs:label "frequency" .
  
  mvikg:has_biome rdfs:label "has biome" .
  
  mvikg:length rdfs:label "variant length" .
  
  mvikg:ref rdfs:label "reference allele" .
  
  <http://purl.obolibrary.org/obo/ECO_0000305> rdfs:label "evidence" .
  
  dcmitype:Dataset rdfs:label "dataset" .
  
  dct:description rdfs:label "description" .
  
  dct:isPartOf rdfs:label "is part of" .
  
  qudt:QuantityValue rdfs:label "quantity value" .
  
  qudt:hasUnit rdfs:label "unit" .
  
  qudt:numericValue rdfs:label "numeric value" .
  
  rdf:type rdfs:label "is a" .
  
  rdfs:label rdfs:label "label" .
  
  sosa:isFeatureOfInterestOf rdfs:label "is feature of interest of" .
  
  sosa:isSampleOf rdfs:label "is sample of" .
  
  biolink:Gene rdfs:label "gene" .
  
  biolink:PhenotypicFeature rdfs:label "phenotypic feature" .
  
  biolink:SequenceVariant rdfs:label "sequence variant" .
  
  biolink:end_coordinate rdfs:label "end coordinate" .
  
  biolink:has_evidence rdfs:label "has evidence" .
  
  biolink:has_phenotype rdfs:label "has phenotype" .
  
  biolink:has_sequence_variant rdfs:label "has sequence variant" .
  
  biolink:in_taxon rdfs:label "in taxon" .
  
  biolink:start_coordinate rdfs:label "start coordinate" .
  
  sub:alt a nt:LiteralPlaceholder;
    rdfs:label "alternate allele" .
  
  sub:biome a nt:ExternalUriPlaceholder, nt:GuidedChoicePlaceholder;
    rdfs:label "the biome the taxon was sampled from (GOLD biome recommended)";
    nt:possibleValuesFromApi "https://www.ebi.ac.uk/ols4/api/select?ontology=gold&fieldList=iri,label,description&q=" .
  
  sub:comparedTo a nt:LiteralPlaceholder;
    rdfs:label "compared to (the baseline/control the phenotype outcome was compared against)" .
  
  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:evidence a nt:EmbeddedResource, nt:LocalResource;
    rdfs:label "evidence for this variant" .
  
  sub:evidenceText a nt:LiteralPlaceholder;
    rdfs:label "evidence text (quote/description from the source)" .
  
  sub:freq a nt:EmbeddedResource, nt:LocalResource;
    rdfs:label "the variant's frequency" .
  
  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:AgentPlaceholder, nt:ExternalUriPlaceholder, nt:GuidedChoicePlaceholder;
    rdfs:label "the gene this variant and (optionally) phenotype belong to";
    nt:possibleValuesFromApi "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:organism a nt:EmbeddedResource, nt:LocalResource;
    rdfs:label "the strain/organism this sample was taken from" .
  
  sub:phenotype a nt:EmbeddedResource, nt:LocalResource;
    rdfs:label "the phenotype associated with this gene" .
  
  sub:phenotypeDescription a nt:LiteralPlaceholder;
    rdfs:label "phenotype description (prose, e.g. \"DeltarfaH mutant elicited ROS production...\")" .
  
  sub:project a nt:ExternalUriPlaceholder;
    rdfs:label "the PMC article/dataset this record is derived from (PMC URI, e.g. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079231/)" .
  
  sub:ref a nt:LiteralPlaceholder;
    rdfs:label "reference allele" .
  
  sub:sample a nt:EmbeddedResource, nt:LocalResource;
    rdfs:label "the sample this gene was observed in" .
  
  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 a nt:GroupedStatement, nt:OptionalStatement;
    nt:hasStatement sub:st03, sub:st04 .
  
  sub:st03 rdf:object sub:project;
    rdf:predicate dct:isPartOf;
    rdf:subject sub:sample .
  
  sub:st04 rdf:object dcmitype:Dataset;
    rdf:predicate rdf:type;
    rdf:subject sub:project .
  
  sub:st05 rdf:object sub:organism;
    rdf:predicate sosa:isSampleOf;
    rdf:subject sub:sample .
  
  sub:st06 rdf:object sub:taxon;
    rdf:predicate biolink:in_taxon;
    rdf:subject sub:organism .
  
  sub:st07 a nt:OptionalStatement;
    rdf:object sub:biome;
    rdf:predicate mvikg:has_biome;
    rdf:subject sub:taxon .
  
  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:GroupedStatement, nt:OptionalStatement;
    nt:hasStatement sub:st20, sub:st21, sub:st22 .
  
  sub:st20 rdf:object sub:evidence;
    rdf:predicate biolink:has_evidence;
    rdf:subject sub:variant .
  
  sub:st21 rdf:object <http://purl.obolibrary.org/obo/ECO_0000305>;
    rdf:predicate rdf:type;
    rdf:subject sub:evidence .
  
  sub:st22 rdf:object sub:evidenceText;
    rdf:predicate dct:description;
    rdf:subject sub:evidence .
  
  sub:st23 a nt:GroupedStatement, nt:OptionalStatement;
    nt:hasStatement sub:st24, sub:st25, sub:st26, sub:st27 .
  
  sub:st24 rdf:object sub:freq;
    rdf:predicate mvikg:frequency;
    rdf:subject sub:variant .
  
  sub:st25 rdf:object qudt:QuantityValue;
    rdf:predicate rdf:type;
    rdf:subject sub:freq .
  
  sub:st26 rdf:object sub:freqValue;
    rdf:predicate qudt:numericValue;
    rdf:subject sub:freq .
  
  sub:st27 rdf:object sub:freqUnit;
    rdf:predicate qudt:hasUnit;
    rdf:subject sub:freq .
  
  sub:st28 a nt:GroupedStatement, nt:OptionalStatement;
    nt:hasStatement sub:st29, sub:st30, sub:st31, sub:st32 .
  
  sub:st29 rdf:object sub:phenotype;
    rdf:predicate biolink:has_phenotype;
    rdf:subject sub:gene .
  
  sub:st30 rdf:object biolink:PhenotypicFeature;
    rdf:predicate rdf:type;
    rdf:subject sub:phenotype .
  
  sub:st31 rdf:object sub:phenotypeDescription;
    rdf:predicate rdfs:label;
    rdf:subject sub:phenotype .
  
  sub:st32 rdf:object sub:comparedTo;
    rdf:predicate mvikg:comparedTo;
    rdf:subject sub:phenotype .
  
  sub:startCoordinate a nt:LiteralPlaceholder;
    rdfs:label "start coordinate (variant position)";
    nt:hasDatatype xsd:integer .
  
  sub:taxon a nt:ExternalUriPlaceholder, nt:GuidedChoicePlaceholder;
    rdfs:label "the organism taxon the strain belongs to (NCBITaxon)";
    nt:possibleValuesFromApi "https://www.ebi.ac.uk/ols/api/select?ontology=ncbitaxon&fieldList=iri,label,description&q=" .
  
  sub:templateVersion a nt:AssertionTemplate, nt:UnlistedTemplate;
    dct:description "Declaring an MVIKG observation";
    dct:isVersionOf sub:template;
    rdfs:label "Declaring an MVIKG observation";
    gen:governedBy <https://w3id.org/spaces/mvikg>;
    nt:hasNanopubLabelPattern "${variantName}";
    nt:hasStatement sub:st01, sub:st02, sub:st03, sub:st04, sub:st05, sub:st06, sub:st07,
      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:st21, sub:st22, sub:st23, sub:st24, sub:st25,
      sub:st26, sub:st27, sub:st28, sub:st29, sub:st30, sub:st31, sub:st32;
    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 {
  this: dct:created "2026-11-04T12:15:21Z"^^xsd:dateTime;
    dct:creator orcid:0009-0005-5515-1230;
    dct:license <https://creativecommons.org/licenses/by/4.0/>;
    npx:embeds sub:templateVersion;
    npx:introduces sub:template;
    rdfs:label "Declaring an MVIKG observation";
    nt:wasCreatedFromProvenanceTemplate <https://w3id.org/np/RA-yPZEYODCS39dWOWm7NA_ClOGFHzPi8iYhLzoZf19GI>;
    nt:wasCreatedFromPubinfoTemplate <https://w3id.org/np/RA4o9JqSxNO2Z47itbAcxvpVfdR97t_7usxmdR90URXQs>;
    nt:wasCreatedFromTemplate <https://w3id.org/np/RAgeON_vGgJCt5E4DPMi0eOPaGwNv9tbfFTRZtBwdQL0w> .
  
  sub:sig npx:hasAlgorithm "RSA";
    npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAjO3oH8Lq/l1oZIUY3FlCz5DnndybGvAhBdmEJ/yq7Nv3GZEYPrEro23rCBCp0GiriOXlVbk61pA/7JFE6tqzTresINW6QQMxE9sIhCBlX4cG66JFD8ud6bMvUyzCR8LQA6zfrSbafGE06rvglJd4MDUcTwvUKqtL9UCnOaowVfnZ3sPOe9EqlmJuO3iHGxBSXMPOPEJZUzMXsFDWFuMZTnrR8gY3r5nVF5a8L/MD135ZH8qW5yGXOB28CmVYCAbw2o07QEKzyzFKN+W1gfnprYZvuKzwGexnzcdzc1S8N/M5bzhWQ40EKCEqgUE8c81OzEMm1HUlUKEJ/o5I/FKKAwIDAQAB";
    npx:hasSignature "ChSF6c0V/t7cmQmsRqXEYzTq9LnmmdAeGtEIjTUQiaHZVxfGYAaRhZrm2pcTEQofgMppSO2KZHPYO9/LN8fg7vWQlcy1CELQaPzJpOX1rPvQcSVMsrjhTO+r2Xlkv1HoW2Gbe5JdYeVJAEFED5nvMzwdBp0pBjVLKEqZuUFKH0Nf9mdHIzOFk95nVGMxhZo67WArSjbrFaxGFH4AVfZ+hO2mUZnHvakVAvWd95WEJN4lYdRQDuv62ZooJhrqE+EJUmxlwK3BsnBLffXUghT1JOEV+4Z4iotVRxapj7FMSjxiFTMmhU/iF6Vq8qpidTRGp38uJgScM3XT7MjlCVOXWQ==";
    npx:hasSignatureTarget this:;
    npx:signedBy orcid:0009-0005-5515-1230 .
}