@prefix ns1: . @prefix this: . @prefix sub: . @prefix np: . @prefix dct: . @prefix rdf: . @prefix nt: . @prefix npx: . @prefix xsd: . @prefix rdfs: . @prefix orcid: . @prefix 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 "

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.

"; a nt:AssertionTemplate; rdfs:label "Expressing an association between an organism (source specimen) and a nucleotide sequence"; nt:hasDefaultProvenance ns1:RA2VjRiJ5AsNnPHDXuOqvsEJwTwqtj5rBb-OFkpPOzd9s; 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: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 ; nt:possibleValue , , . sub:st00 rdf:object ; rdf:predicate rdf:type; rdf:subject sub:association . sub:st05 rdf:object sub:relation; rdf:predicate ; rdf:subject sub:association . sub:st09 rdf:object sub:organism; rdf:predicate ; 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 ; rdf:subject sub:taxon . sub:st12 rdf:object sub:taxondef; rdf:predicate ; rdf:subject sub:taxon; a nt:OptionalStatement . sub:st20 rdf:object sub:lifecyclestage; rdf:predicate ; rdf:subject sub:organism; a nt:OptionalStatement . sub:st25 rdf:object sub:occurrence; rdf:predicate ; rdf:subject sub:organism; a nt:OptionalStatement . sub:st30 rdf:object sub:organismAlt; rdf:predicate ; rdf:subject sub:organism; a nt:OptionalStatement, nt:RepeatableStatement . sub:st39 rdf:object sub:nucleotidesequence; rdf:predicate ; rdf:subject sub:association . sub:st81 rdf:object sub:coordinates; rdf:predicate ; rdf:subject sub:association; a nt:OptionalStatement . sub:st82 rdf:object sub:timepoint; rdf:predicate ; 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" . rdfs:label "is the same as" . rdfs:label "links the organism to the nucleotide sequence" . rdfs:label "refers to the relation" . rdfs:label "refers to" . rdfs:label "has the time stamp - points to the date and time associated with this relation or organism (e.g. date of collection)" . rdfs:label "an association of an organism to a nucleotide sequence" . rdfs:label "assembled nucleotide sequence" . rdfs:label "has the life cycle stage" . rdfs:label "has the location coordinates - points to the location coordinates associated with this relation or organism (e.g. place of collection)" . rdfs:label "observed nucleotide sequence" . rdfs:label "has the occurrence - links an organism to a record of a specific occurrence of it" . rdfs:label "sequenced nucleotide sequence" . rdfs:label "is used as defined in" . 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 "FyFZcClVM9qDZQUGZeN4m/7MHd+omJCQiPA35lEjupCzYSXvKydk8IIIMN+eYYBRVBBNqwb6f968bJWknn3xZ85oZU0AkvRc6IiUiVXJ79MsCdw2uu+J0NCyROns3yARf8WNOqrLbDmSNXvuPWbAhMoEGeBON1N440snZeKcx5w="; npx:hasSignatureTarget this: . this: dct:created "2023-08-15T04:53:46.148Z"^^xsd:dateTime; dct:creator orcid:0000-0002-1267-0234; dct:license ; npx:supersedes ns1:RA3kgvKf_8HHLSYHPzFZB7HCr35cC60p46qZVxhhSZnnI; rdfs:label "Template: Expressing an association between an organism (source specimen) and a nucleotide sequence"; nt:wasCreatedFromProvenanceTemplate ns1:RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM; nt:wasCreatedFromPubinfoTemplate ns1:RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM, ns1:RAh1gm83JiG5M6kDxXhaYT1l49nCzyrckMvTzcPn-iv90, ns1:RAjpBMlw3owYhJUBo3DtsuDlXsNAJ8cnGeWAutDVjuAuI; nt:wasCreatedFromTemplate ns1:RANjqEfLnGSzLuq0heRSXN0psYWW0oX4v3W8w7osb3xfs . }