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Example MolecularDefinition/example-sequence1 (Turtle)

Clinical Genomics Work GroupMaturity Level: N/AStandards Status: InformativeCompartments: No defined compartments

Raw Turtle (+ also see Turtle/RDF Format Specification)

Simple Sequence example 1

@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <https://loinc.org/rdf/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

# - resource -------------------------------------------------------------------

[a fhir:MolecularDefinition ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "example-sequence1"] ; # 
  fhir:meta [
     fhir:profile ( [
       fhir:v "http://hl7.org/fhir/StructureDefinition/sequence"^^xsd:anyURI ;
       fhir:link <http://hl7.org/fhir/StructureDefinition/sequence>
     ] )
  ] ; # 
  fhir:type [ fhir:v "dna"] ; # 
  fhir:representation ( [
     fhir:literal [
       fhir:value [ fhir:v "ATGAACAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTC TTTTACTAAGTGTTCAAATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAA GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGACCCCAAAGATCTCATGTTAAGTGGAG AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTATGG CACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT GTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATG ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAGAAATGGA AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCYG TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC AAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGA" ]
     ] ;
     fhir:resolvable [
       fhir:contentType [ fhir:v "text/html" ] ;
       fhir:url [ fhir:v "https://www.ncbi.nlm.nih.gov/nuccore/MW716256.1?report=fasta"^^xsd:anyURI ]
     ] ;
     fhir:extracted [
       fhir:startingMolecule [
         fhir:reference [ fhir:v "MolecularDefinition/example-starting-sequence-2b-extracted" ] ;
         fhir:type [ fhir:v "MolecularDefinition"^^xsd:anyURI ] ;
         fhir:display [ fhir:v "Starting Sequence Resource:                 ATGAACAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTC                 TTTTACTAAGTGTTCAAATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAA                 GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGACCCCAAAGATCTCATGTTAAGTGGAG                 AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTATGG                 CACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT                 GTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATG                 ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAGAAATGGA                 AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCYG                 TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC                 AAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA                 GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGAGCCTGTACAGACAGTT                 AATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGA" ]
       ] ;
       fhir:start [ fhir:v "0"^^xsd:integer ] ;
       fhir:end [ fhir:v "754"^^xsd:integer ] ;
       fhir:coordinateSystem [
         fhir:coding ( [
           a loinc:LA30100-4 ;
           fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
           fhir:code [ fhir:v "LA30100-4" ] ;
           fhir:display [ fhir:v "0-based interval counting" ]
         ] ) ;
         fhir:text [ fhir:v "0-based interval counting" ]
       ] ;
       fhir:reverseComplement [ fhir:v "false"^^xsd:boolean ]
     ] ;
     fhir:concatenated [
       fhir:sequenceElement ( [
         fhir:sequence [
           fhir:reference [ fhir:v "MolecularDefinition/example-sequence0-2b-concatenated" ] ;
           fhir:type [ fhir:v "MolecularDefinition"^^xsd:anyURI ] ;
           fhir:display [ fhir:v "Sequence-of index 0-Resource for concatenated sequence example:                     ATGAACAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTC TTTTACTAAGTGTTCAAATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAA GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGACCCCAAAGATCTCATGTTAAGTGGAG" ]
         ] ;
         fhir:ordinalIndex [ fhir:v "0"^^xsd:integer ]
       ] [
         fhir:sequence [
           fhir:reference [ fhir:v "MolecularDefinition/example-sequence1-2b-concatenated" ] ;
           fhir:type [ fhir:v "MolecularDefinition"^^xsd:anyURI ] ;
           fhir:display [ fhir:v "Sequence-of index 1-Resource for concatenated sequence example:                     AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTATGG CACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT GTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATG ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAGAAATGGA AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCYG" ]
         ] ;
         fhir:ordinalIndex [ fhir:v "1"^^xsd:integer ]
       ] [
         fhir:sequence [
           fhir:reference [ fhir:v "MolecularDefinition/example-sequence2-2b-concatenated" ] ;
           fhir:type [ fhir:v "MolecularDefinition"^^xsd:anyURI ] ;
           fhir:display [ fhir:v "Sequence-of index 2-Resource for concatenated sequence example:                     TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC AAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGA" ]
         ] ;
         fhir:ordinalIndex [ fhir:v "2"^^xsd:integer ]
       ] )
     ] ;
     fhir:relative [
       fhir:startingMolecule [
         fhir:reference [ fhir:v "MolecularDefinition/example-starting-sequence-2b-relative" ] ;
         fhir:type [ fhir:v "MolecularDefinition"^^xsd:anyURI ] ;
         fhir:display [ fhir:v "Starting Sequence Resource" ]
       ] ;
       fhir:edit ( [
         fhir:coordinateSystem [
           fhir:coding ( [
             a loinc:LA30100-4 ;
             fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
             fhir:code [ fhir:v "LA30100-4" ] ;
             fhir:display [ fhir:v "0-based interval counting" ]
           ] ) ;
           fhir:text [ fhir:v "0-based interval counting" ]
         ] ;
         fhir:start [ fhir:v "0"^^xsd:integer ] ;
         fhir:end [ fhir:v "5"^^xsd:integer ] ;
         fhir:replacementMolecule [
           fhir:reference [ fhir:v "MolecularDefinition/example-replacement-sequence" ] ;
           fhir:type [ fhir:v "MolecularDefinition"^^xsd:anyURI ] ;
           fhir:display [ fhir:v "Replacement Sequence Resource: ATGAA" ]
         ] ;
         fhir:replacedMolecule [
           fhir:reference [ fhir:v "MolecularDefinition/example-replaced-sequence" ] ;
           fhir:type [ fhir:v "MolecularDefinition"^^xsd:anyURI ] ;
           fhir:display [ fhir:v "Replaced Sequence Resource: CCCCC" ]
         ]
       ] )
     ]
  ] )] . # 

# -------------------------------------------------------------------------------------

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.