@prefix this: <https://w3id.org/np/RAInHt3ngomYe6YObDAZwqYKtWdi12RFuaaJ5I8G6DM5U> .
@prefix sub: <https://w3id.org/np/RAInHt3ngomYe6YObDAZwqYKtWdi12RFuaaJ5I8G6DM5U/> .
@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/> .

<https://w3id.org/np/RAInHt3ngomYe6YObDAZwqYKtWdi12RFuaaJ5I8G6DM5U> a np:Nanopublication;
  np:hasAssertion sub:assertion;
  np:hasProvenance sub:provenance;
  np:hasPublicationInfo sub:pubinfo;
  dct:created "2025-11-06T08:45:04.817Z"^^xsd:dateTime;
  dct:creator orcid:0000-0002-1267-0234;
  dct:license <https://creativecommons.org/licenses/by/4.0/>;
  npx:supersedes <https://w3id.org/np/RARhEnvsUzWmW9AzNfZoPFU05rMpsy1Tj02grJWohM8Bs>;
  npx:wasCreatedAt <https://nanodash.knowledgepixels.com/>;
  rdfs:label "Expressing an association between an organism and a nucleotide sequence (extended)";
  prov:wasDerivedFrom ns1:RACPgaoRptG1W-IZpNk6r-MBSMgcdZlaMrAtli9GkmKaE;
  nt:wasCreatedFromProvenanceTemplate ns1:RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM;
  nt:wasCreatedFromPubinfoTemplate <https://w3id.org/np/RA0J4vUn_dekg-U1kK3AOEt02p9mT2WO03uGxLDec1jLw>,
    <https://w3id.org/np/RARW4MsFkHuwjycNElvEVtuMjpf4yWDL10-0C5l2MqqRQ>, <https://w3id.org/np/RAoTD7udB2KtUuOuAe74tJi1t3VzK0DyWS7rYVAq1GRvw>,
    <https://w3id.org/np/RAukAcWHRDlkqxk7H2XNSegc1WnHI569INvNr-xdptDGI>;
  nt:wasCreatedFromTemplate <https://w3id.org/np/RA1XuAdO6LOtlPJgWiytJHFuK4BFHjQK5x7d9FVymzFnc> .

<http://purl.obolibrary.org/obo/BTO_0000487> rdfs:label "fruit body" .

<http://purl.obolibrary.org/obo/BTO_0001171> rdfs:label "spore" .

rdf:type rdfs:label "is an instance of" .

rdfs:comment rdfs:label "has the free-text comment" .

<http://www.w3.org/2002/07/owl#sameAs> rdfs:label "is the same as" .

<http://www.w3.org/2003/01/geo/wgs84_pos#location> rdfs:label "has the location" .

<https://w3id.org/biolink/vocab/object> rdfs:label "links the organism to the nucleotide sequence" .

<https://w3id.org/biolink/vocab/predicate> rdfs:label "refers to the relation" .

<https://w3id.org/biolink/vocab/subject> rdfs:label "refers to" .

<https://w3id.org/biolink/vocab/timepoint> rdfs:label "has the time stamp - points to the date and time associated with this relation or organism (e.g. date of collection); if occurrence URI is given, this is redundant and does not need to be filled in" .

<https://w3id.org/kpxl/biodiv/terms/OrganismToNucleotideSequenceAssociation> rdfs:label
    "an association of an organism to a nucleotide sequence" .

<https://w3id.org/kpxl/biodiv/terms/hasAssembledNucleotideSequence> rdfs:label "assembled nucleotide sequence" .

<https://w3id.org/kpxl/biodiv/terms/hasIsolationProtocol> rdfs:label "has the isolation protocol" .

<https://w3id.org/kpxl/biodiv/terms/hasLifeCycleStage> rdfs:label "has the life cycle stage" .

<https://w3id.org/kpxl/biodiv/terms/hasLocationCoordinates> rdfs:label "has the location coordinates - points to the location coordinates associated with this relation or organism (e.g. place of collection); if occurrence URI is given, this is redundant and does not need to be filled in" .

<https://w3id.org/kpxl/biodiv/terms/hasObservedNucleotideSequence> rdfs:label "observed nucleotide sequence" .

<https://w3id.org/kpxl/biodiv/terms/hasOccurrence> rdfs:label "has the occurrence - links an organism to a record of a specific occurrence of it" .

<https://w3id.org/kpxl/biodiv/terms/hasSampleType> rdfs:label "has the sample type" .

<https://w3id.org/kpxl/biodiv/terms/hasSequencedNucleotideSequence> rdfs:label "sequenced nucleotide sequence" .

<https://w3id.org/kpxl/biodiv/terms/hasStrainID> rdfs:label "has the strain ID" .

<https://w3id.org/kpxl/biodiv/terms/hasTaxonConceptDefinition> rdfs:label "is used as defined in" .

<https://w3id.org/kpxl/biodiv/terms/hasTaxonName> rdfs:label "has the name - links a taxon usage to a taxon name" .

<https://w3id.org/kpxl/biodiv/terms/isIdentifiedByNuceotideSequence> rdfs:label "identified by nucleotide sequence" .

sub:assertion a nt:AssertionTemplate;
  dct:description "<p>Such a nanopublication expresses an association between an organism (normally identified as belonging to a certain taxon concept) and a nucleotide sequence (that can correspond to a gene or subunit of a gene), for example expressing that Sequence ID (INSDC / Genbank accession number or BOLD Process ID) identifies Organism X as belonging to a Taxon Concept Y.</p>";
  rdfs:label "Expressing an association between an organism and a nucleotide sequence (extended)";
  nt:hasDefaultProvenance ns1:RAYfEAP8KAu9qhBkCtyq_hshOvTAJOcdfIvGhiGwUqB-M;
  nt:hasNanopubLabelPattern "Organism of ${taxonname} - ${relation} - ${nucleotidesequence}";
  nt:hasStatement sub:st00, sub:st05, sub:st09, sub:st10, sub:st11, sub:st12, sub:st20,
    sub:st25, sub:st30, sub:st80, sub:st81, sub:st82, sub:st83, sub:st85, sub:st86, sub:st87,
    sub:st90;
  nt:hasTag "Biodiversity";
  nt:hasTargetNanopubType <https://w3id.org/kpxl/biodiv/terms/BiodivNanopub>;
  prov:wasAttributedTo orcid:0000-0002-1267-0234 .

sub:association a nt:IntroducedResource, nt:LocalResource;
  rdfs:label "this association" .

sub:comment a nt:LongLiteralPlaceholder;
  rdfs:label "short explanation related to the above statement" .

sub:coordinates a nt:LiteralPlaceholder;
  rdfs:label "lat/long e.g. '+47.37+8.54' or with altitude '+47.37+8.54+410.5'";
  nt:hasRegex "[+-][0-9]+(\\.[0-9]+)?[+-][0-9]+(\\.[0-9]+)?([+-][0-9]+(\\.[0-9]+)?)?" .

sub:isolationProtocol a nt:ExternalUriPlaceholder;
  rdfs:label "DOI of isolation protocol document";
  nt:hasRegex "https://doi\\.org/.+" .

sub:lifecyclestage a nt:RestrictedChoicePlaceholder;
  rdfs:label "select the life cycle stage of the organism; leave blank if unknown";
  nt:possibleValue <http://purl.obolibrary.org/obo/BTO_0000487>, <http://purl.obolibrary.org/obo/BTO_0001171>;
  nt:possibleValuesFrom ns1:RAVZS2MV-siFEqsgFTtgSoKA5qJkp7r1nM_n-MqPkvgdE .

sub:location a nt:ExternalUriPlaceholder;
  rdfs:label "GeoNames location ID (https://sws.geonames.org/.../)";
  nt:hasRegex "https://sws\\.geonames\\.org/[0-9]+/" .

sub:nucleotidesequence a nt:ExternalUriPlaceholder;
  rdfs:label "INSDC/Genbank # (e.g. https://www.ncbi.nlm.nih.gov/nuccore/...)" .

sub:occurrence a nt:ExternalUriPlaceholder;
  rdfs:label "occurrence URI from GBIF (https://www.gbif.org/occurrence/...) or iDigBio, BOLD, PlutoF, etc." .

sub:organism a nt:LocalResource;
  rdfs:label "the organism" .

sub:organismAlt a nt:ExternalUriPlaceholder;
  rdfs:label "any existing URI identifier of organism (e.g. of digital collection specimen or observation in nature)" .

sub:relation a nt:RestrictedChoicePlaceholder;
  rdfs:label "the relation between the organism and the nucleotide sequence";
  nt:hasDefaultValue <https://w3id.org/kpxl/biodiv/terms/hasObservedNucleotideSequence>;
  nt:possibleValue <https://w3id.org/kpxl/biodiv/terms/hasAssembledNucleotideSequence>,
    <https://w3id.org/kpxl/biodiv/terms/hasObservedNucleotideSequence>, <https://w3id.org/kpxl/biodiv/terms/hasSequencedNucleotideSequence>,
    <https://w3id.org/kpxl/biodiv/terms/isIdentifiedByNuceotideSequence> .

sub:sampleType a nt:GuidedChoicePlaceholder;
  rdfs:label "choose the type of sample";
  nt:possibleValuesFromApi "https://www.ebi.ac.uk/ols/api/select?ontology=uberon&q=" .

sub:st00 rdf:object <https://w3id.org/kpxl/biodiv/terms/OrganismToNucleotideSequenceAssociation>;
  rdf:predicate rdf:type;
  rdf:subject sub:association .

sub:st05 rdf:object sub:relation;
  rdf:predicate <https://w3id.org/biolink/vocab/predicate>;
  rdf:subject sub:association .

sub:st09 rdf:object sub:organism;
  rdf:predicate <https://w3id.org/biolink/vocab/subject>;
  rdf:subject sub:association .

sub:st10 rdf:object sub:taxon;
  rdf:predicate rdf:type;
  rdf:subject sub:organism .

sub:st11 rdf:object sub:taxonname;
  rdf:predicate <https://w3id.org/kpxl/biodiv/terms/hasTaxonName>;
  rdf:subject sub:taxon .

sub:st12 a nt:OptionalStatement;
  rdf:object sub:taxondef;
  rdf:predicate <https://w3id.org/kpxl/biodiv/terms/hasTaxonConceptDefinition>;
  rdf:subject sub:taxon .

sub:st20 a nt:OptionalStatement;
  rdf:object sub:lifecyclestage;
  rdf:predicate <https://w3id.org/kpxl/biodiv/terms/hasLifeCycleStage>;
  rdf:subject sub:organism .

sub:st25 a nt:OptionalStatement;
  rdf:object sub:occurrence;
  rdf:predicate <https://w3id.org/kpxl/biodiv/terms/hasOccurrence>;
  rdf:subject sub:organism .

sub:st30 a nt:OptionalStatement, nt:RepeatableStatement;
  rdf:object sub:organismAlt;
  rdf:predicate <http://www.w3.org/2002/07/owl#sameAs>;
  rdf:subject sub:organism .

sub:st80 a nt:OptionalStatement;
  rdf:object sub:location;
  rdf:predicate <http://www.w3.org/2003/01/geo/wgs84_pos#location>;
  rdf:subject sub:association .

sub:st81 a nt:OptionalStatement;
  rdf:object sub:coordinates;
  rdf:predicate <https://w3id.org/kpxl/biodiv/terms/hasLocationCoordinates>;
  rdf:subject sub:association .

sub:st82 a nt:OptionalStatement;
  rdf:object sub:timepoint;
  rdf:predicate <https://w3id.org/biolink/vocab/timepoint>;
  rdf:subject sub:association .

sub:st83 a nt:OptionalStatement;
  rdf:object sub:sampleType;
  rdf:predicate <https://w3id.org/kpxl/biodiv/terms/hasSampleType>;
  rdf:subject sub:association .

sub:st85 rdf:object sub:nucleotidesequence;
  rdf:predicate <https://w3id.org/biolink/vocab/object>;
  rdf:subject sub:association .

sub:st86 a nt:OptionalStatement, nt:RepeatableStatement;
  rdf:object sub:strainid;
  rdf:predicate <https://w3id.org/kpxl/biodiv/terms/hasStrainID>;
  rdf:subject sub:association .

sub:st87 a nt:OptionalStatement;
  rdf:object sub:isolationProtocol;
  rdf:predicate <https://w3id.org/kpxl/biodiv/terms/hasIsolationProtocol>;
  rdf:subject sub:association .

sub:st90 a nt:OptionalStatement;
  rdf:object sub:comment;
  rdf:predicate rdfs:comment;
  rdf:subject nt:ASSERTION .

sub:strainid a nt:LiteralPlaceholder;
  rdfs:label "Strain ID string (e.g. DSMZ, ATCC)" .

sub:taxon a nt:LocalResource;
  rdfs:label "the taxon concept" .

sub:taxondef a nt:ExternalUriPlaceholder;
  rdfs:label "DOI (https://doi.org/...) or treatment ID (https://treatment.plazi.org/id/...)";
  nt:hasRegex "(https://doi\\.org/|https://treatment\\.plazi\\.org/id/).+" .

sub:taxonname a nt:GuidedChoicePlaceholder;
  rdfs:label "search and select from list (if not found, paste identifying URI from IPNI, MycoBank, Index Fungorum, or Zoobank)";
  nt:possibleValuesFromApi "https://vodex.petapico.org/nidx/query?rows=100&q=label:" .

sub:timepoint a nt:LiteralPlaceholder;
  rdfs:label "time expressed in XSD DateTime format, e.g. '2023-03-30T22:17:11Z'";
  nt:hasRegex "-?([1-9]\\d\\d\\d+|0\\d\\d\\d)-(0[1-9]|1[0-2])-(0[1-9]|[12]\\d|3[01])T(([01]\\d|2[0-3]):[0-5]\\d:[0-5]\\d(\\.\\d+)?|24:00:00(\\.0+)?)(Z|[+-](0\\d|1[0-4]):[0-5]\\d)?" .

orcid:0000-0002-1267-0234 foaf:name "Tobias Kuhn" .

sub:sig npx:hasAlgorithm "RSA";
  npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQD4Wj537OijfOWVtsHMznuXKISqBhtGDQZfdO6pbb4hg9EHMcUFGTLbWaPrP783PHv8HMAAPjvEkHLaOHMIknqhaIa5236lfBO3r+ljVdYBElBcLvROmwG+ZGtmPNZf7lMhI15xf5TfoaSa84AFRd5J2EXekK6PhaFQhRm1IpSYtwIDAQAB";
  npx:hasSignature "7zizA+9r3gQf5sEZhyJN4qLZBwJPv21heDLqgSPELUVu/xqsylf15d6m1lMhTHoNT5jYeW5M0BtiBLU5/DcME4SHJEbv1Biy3ChyZUbPQRJClKrzNN7kRpmjAqQQBKAhWmnkjKVtJPh3V30NQVrAgrQuq022ahgEdlY/TthyOqA=";
  npx:hasSignatureTarget <https://w3id.org/np/RAInHt3ngomYe6YObDAZwqYKtWdi12RFuaaJ5I8G6DM5U>;
  npx:signedBy orcid:0000-0002-1267-0234 .