@prefix ns1: <http://purl.org/np/> .
@prefix this: <http://purl.org/np/RAU9t6bWj3QVoTwNttzAvB7a_lnHe0nFC-XJue8o_GeIo> .
@prefix sub: <http://purl.org/np/RAU9t6bWj3QVoTwNttzAvB7a_lnHe0nFC-XJue8o_GeIo#> .
@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 prov: <http://www.w3.org/ns/prov#> .

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

sub:assertion {
  sub:assertion 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>";
    a nt:AssertionTemplate;
    rdfs:label "Expressing an association between an organism (source specimen) and a nucleotide sequence";
    nt:hasDefaultProvenance ns1:RA2VjRiJ5AsNnPHDXuOqvsEJwTwqtj5rBb-OFkpPOzd9s;
    nt:hasNanopubLabelPattern "${taxonname} - ${relation} - ${nucleotidesequence}";
    nt:hasStatement sub:st00, sub:st05, sub:st09, sub:st10, sub:st11, sub:st12, sub:st20,
      sub:st25, sub:st30, sub:st39, sub:st81, sub:st82, sub:st90;
    nt:hasTag "Biodiversity" .
  
  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 coordinates in format like '+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:lifecyclestage a nt:RestrictedChoicePlaceholder;
    rdfs:label "select the life cycle stage of the organism; leave blank if unknown";
    nt:possibleValuesFrom ns1:RAVZS2MV-siFEqsgFTtgSoKA5qJkp7r1nM_n-MqPkvgdE .
  
  sub:nucleotidesequence a nt:ExternalUriPlaceholder;
    rdfs:label "INSDC / Genbank accession number (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> .
  
  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 rdf:object sub:taxondef;
    rdf:predicate <https://w3id.org/kpxl/biodiv/terms/hasTaxonConceptDefinition>;
    rdf:subject sub:taxon;
    a nt:OptionalStatement .
  
  sub:st20 rdf:object sub:lifecyclestage;
    rdf:predicate <https://w3id.org/kpxl/biodiv/terms/hasCycleStage>;
    rdf:subject sub:organism;
    a nt:OptionalStatement .
  
  sub:st25 rdf:object sub:occurrence;
    rdf:predicate <https://w3id.org/kpxl/biodiv/terms/hasOccurrence>;
    rdf:subject sub:organism;
    a nt:OptionalStatement .
  
  sub:st30 rdf:object sub:organismAlt;
    rdf:predicate <http://www.w3.org/2002/07/owl#sameAs>;
    rdf:subject sub:organism;
    a nt:OptionalStatement, nt:RepeatableStatement .
  
  sub:st39 rdf:object sub:nucleotidesequence;
    rdf:predicate <https://w3id.org/biolink/vocab/object>;
    rdf:subject sub:association .
  
  sub:st81 rdf:object sub:coordinates;
    rdf:predicate <https://w3id.org/kpxl/biodiv/terms/hasLocationCoordinates>;
    rdf:subject sub:association;
    a nt:OptionalStatement .
  
  sub:st82 rdf:object sub:timepoint;
    rdf:predicate <https://w3id.org/biolink/vocab/timepoint>;
    rdf:subject sub:association;
    a nt:OptionalStatement .
  
  sub:st90 rdf:object sub:comment;
    rdf:predicate rdfs:comment;
    rdf:subject nt:ASSERTION;
    a nt:OptionalStatement .
  
  sub:taxon a nt:LocalResource;
    rdfs:label "the taxon concept" .
  
  sub:taxondef a nt:ExternalUriPlaceholder;
    rdfs:label "publication DOI (https://doi.org/...) or taxon 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, you may paste URL 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)?" .
  
  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" .
  
  <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 "occurred at the time - points to time when this association happened" .
  
  <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/hasCycleStage> rdfs:label "has the life cycle stage" .
  
  <https://w3id.org/kpxl/biodiv/terms/hasLocationCoordinates> rdfs:label "has the location coordinates - points to the coordinates of the location where the association took place" .
  
  <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/hasSequencedNucleotideSequence> rdfs:label "sequenced nucleotide sequence" .
  
  <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" .
}

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

sub:pubinfo {
  sub:sig npx:hasAlgorithm "RSA";
    npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCjDGQCS1S+SRnERDuYDXOugdYUP0efEquHJEEHAbU/uLzBVlga89zqrNPCS7fBE6lArBUWEmT8eLKdMapyqvAzI1J3jUWTMhDJF+XFBkUiuiFfNSc4vJJcmi0yujtnuzXsRIG202jyaP4f5ULoskFwaZOSBZJfiE0dsB3D7DTIAQIDAQAB";
    npx:hasSignature "POX23lESjl9Eby6B5rlCTG0pPcit+tqy1FWxlNfEbH1/2HT5Am+DyXOaHRO0TDetXZ68s2Xn9UkFa6aiErYOQXnuNYTsPN63GZ0su4wsUDC7WA/1UNovK8D7Q7nVTj4sXq0zCLI/WpeO+yZ/3FHjHju1nmnkCydkZTnWu00bBeY=";
    npx:hasSignatureTarget this: .
  
  this: dct:created "2023-08-09T07:28:43.713Z"^^xsd:dateTime;
    dct:creator orcid:0000-0002-1267-0234;
    dct:license <https://creativecommons.org/licenses/by/4.0/>;
    npx:supersedes ns1:RAgtd3aIdF2e5dkgSNfhx-har1xvQec9iKAltf06lUd5c;
    nt:wasCreatedFromProvenanceTemplate ns1:RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM;
    nt:wasCreatedFromPubinfoTemplate ns1:RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM,
      ns1:RAh1gm83JiG5M6kDxXhaYT1l49nCzyrckMvTzcPn-iv90, ns1:RAjpBMlw3owYhJUBo3DtsuDlXsNAJ8cnGeWAutDVjuAuI;
    nt:wasCreatedFromTemplate ns1:RAcWdTxuDiVS_r3AtyI1TlF6_0oiGqUs75JsK6JTfQzsQ .
}