Clinical Genomics Resource Incubator
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Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions

: Molecular Definition Sequence 1

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@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <https://loinc.org/rdf/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

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

 a fhir:MolecularDefinition ;
  fhir:resourceDefinition http://hl7.org/fhir/StructureDefinition/MolecularDefinition|0.1.0-ci-build ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "example-sequence1"] ; # 
  fhir:language [ fhir:v "en"] ; # 
  fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div [ fhir:v "<div xmlns=\"http://www.w3.org/1999/xhtml\" xml:lang=\"en\" lang=\"en\"><p class=\"res-header-id\"><b>Generated Narrative: MolecularDefinition example-sequence1</b></p><a name=\"example-sequence1\"> </a><a name=\"hcexample-sequence1\"> </a><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Language: en</p></div><p><b>moleculeType</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/moleculardefinition-moleculetype dna}\">DNA sequence</span></p><blockquote><p><b>representation</b></p><h3>Literals</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Value</b></td></tr><tr><td style=\"display: none\">*</td><td>ATGAACAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTC TTTTACTAAGTGTTCAAATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAA GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGACCCCAAAGATCTCATGTTAAGTGGAG AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTATGG CACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT GTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATG ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAGAAATGGA AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCYG TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC AAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGA</td></tr></table><p><b>resolvable</b>: <a href=\"DocumentReference-example-genomicFile-mw7162561.html\">DocumentReference: identifier = http://example.org/identifiers/files#11111; status = current; docStatus = preliminary; description = A sample Document Reference instance representing Homo sapiens isolate 7 BRCA1 (BRCA1) gene, exon 10 and partial cds.</a></p><blockquote><p><b>extracted</b></p><p><b>startingMolecule</b>: <a href=\"MolecularDefinition-example-starting-sequence-2b-extracted.html\">Starting Sequence Resource:                 ATGAACAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTC                 TTTTACTAAGTGTTCAAATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAA                 GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGACCCCAAAGATCTCATGTTAAGTGGAG                 AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTATGG                 CACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT                 GTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATG                 ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAGAAATGGA                 AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCYG                 TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC                 AAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA                 GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGAGCCTGTACAGACAGTT                 AATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGA</a></p><blockquote><p><b>coordinateInterval</b></p><h3>CoordinateSystems</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>System</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://loinc.org LA30100-4}\">0-based interval counting</span></td></tr></table><p><b>start</b>: 0</p><p><b>end</b>: 754</p></blockquote><p><b>reverseComplement</b>: false</p></blockquote><blockquote><p><b>concatenated</b></p><blockquote><p><b>sequenceElement</b></p><p><b>sequence</b>: <a href=\"MolecularDefinition-example-sequence0-2b-concatenated.html\">Sequence-of index 0-Resource for concatenated sequence example:                     ATGAACAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTC TTTTACTAAGTGTTCAAATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAA GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGACCCCAAAGATCTCATGTTAAGTGGAG</a></p><p><b>ordinalIndex</b>: 0</p></blockquote><blockquote><p><b>sequenceElement</b></p><p><b>sequence</b>: <a href=\"MolecularDefinition-example-sequence1-2b-concatenated.html\">Sequence-of index 1-Resource for concatenated sequence example:                     AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTATGG CACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT GTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATG ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAGAAATGGA AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCYG</a></p><p><b>ordinalIndex</b>: 1</p></blockquote><blockquote><p><b>sequenceElement</b></p><p><b>sequence</b>: <a href=\"MolecularDefinition-example-sequence2-2b-concatenated.html\">Sequence-of index 2-Resource for concatenated sequence example:                     TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC AAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGA</a></p><p><b>ordinalIndex</b>: 2</p></blockquote></blockquote><blockquote><p><b>relative</b></p><p><b>startingMolecule</b>: <a href=\"MolecularDefinition-example-starting-sequence-2b-relative.html\">Starting Sequence Resource</a></p><blockquote><p><b>edit</b></p><blockquote><p><b>coordinateInterval</b></p><h3>CoordinateSystems</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>System</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://loinc.org LA30100-4}\">0-based interval counting</span></td></tr></table><p><b>start</b>: 0</p><p><b>end</b>: 5</p></blockquote><p><b>replacementMolecule</b>: <a href=\"MolecularDefinition-example-replacement-sequence.html\">Replacement Sequence Resource: ATGAA</a></p><p><b>replacedMolecule</b>: <a href=\"MolecularDefinition-example-replaced-sequence.html\">Replaced Sequence Resource: CCCCC</a></p></blockquote></blockquote></blockquote></div>"^^rdf:XMLLiteral ]
  ] ; # 
  fhir:moleculeType [
    ( fhir:coding [
fhir:system [
fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/moleculardefinition-moleculetype"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/moleculardefinition-moleculetype>       ] ;
fhir:code [ fhir:v "dna" ] ;
fhir:display [ fhir:v "DNA sequence" ]     ] )
  ] ; # 
  fhir:representation ( [
fhir:literal [
fhir:value [ fhir:v "ATGAACAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTC TTTTACTAAGTGTTCAAATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAA GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGACCCCAAAGATCTCATGTTAAGTGGAG AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTATGG CACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT GTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATG ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAGAAATGGA AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCYG TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC AAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGA" ]     ] ;
fhir:resolvable [
fhir:l fhir:DocumentReference/example-genomicFile-mw7162561 ;
fhir:reference [ fhir:v "DocumentReference/example-genomicFile-mw7162561" ]     ] ;
fhir:extracted [
fhir:startingMolecule [
fhir:l fhir:MolecularDefinition/example-starting-sequence-2b-extracted ;
fhir:reference [ fhir:v "MolecularDefinition/example-starting-sequence-2b-extracted" ] ;
fhir:type [
fhir:v "MolecularDefinition"^^xsd:anyURI ;
fhir:l fhir:MolecularDefinition         ] ;
fhir:display [ fhir:v "Starting Sequence Resource:                 ATGAACAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTC                 TTTTACTAAGTGTTCAAATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAA                 GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGACCCCAAAGATCTCATGTTAAGTGGAG                 AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTATGG                 CACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT                 GTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATG                 ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAGAAATGGA                 AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCYG                 TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC                 AAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA                 GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGAGCCTGTACAGACAGTT                 AATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGA" ]       ] ;
fhir:coordinateInterval [
fhir:coordinateSystem [
fhir:system [
            ( fhir:coding [
a loinc:LA30100-4 ;
fhir:system [
fhir:v "http://loinc.org"^^xsd:anyURI ;
fhir:l <http://loinc.org>               ] ;
fhir:code [ fhir:v "LA30100-4" ] ;
fhir:display [ fhir:v "0-based interval counting" ]             ] ) ;
fhir:text [ fhir:v "0-based interval counting" ]           ]         ] ;
fhir:start [
a fhir:Quantity ;
fhir:value [ fhir:v "0"^^xsd:decimal ]         ] ;
fhir:end [
a fhir:Quantity ;
fhir:value [ fhir:v "754"^^xsd:decimal ]         ]       ] ;
fhir:reverseComplement [ fhir:v false ]     ] ;
fhir:concatenated [
      ( fhir:sequenceElement [
fhir:sequence [
fhir:l fhir:MolecularDefinition/example-sequence0-2b-concatenated ;
fhir:reference [ fhir:v "MolecularDefinition/example-sequence0-2b-concatenated" ] ;
fhir:type [
fhir:v "MolecularDefinition"^^xsd:anyURI ;
fhir:l fhir:MolecularDefinition           ] ;
fhir:display [ fhir:v "Sequence-of index 0-Resource for concatenated sequence example:                     ATGAACAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTC TTTTACTAAGTGTTCAAATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAA GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGACCCCAAAGATCTCATGTTAAGTGGAG" ]         ] ;
fhir:ordinalIndex [ fhir:v 0 ]       ] [
fhir:sequence [
fhir:l fhir:MolecularDefinition/example-sequence1-2b-concatenated ;
fhir:reference [ fhir:v "MolecularDefinition/example-sequence1-2b-concatenated" ] ;
fhir:type [
fhir:v "MolecularDefinition"^^xsd:anyURI ;
fhir:l fhir:MolecularDefinition           ] ;
fhir:display [ fhir:v "Sequence-of index 1-Resource for concatenated sequence example:                     AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTATGG CACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT GTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATG ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAGAAATGGA AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCYG" ]         ] ;
fhir:ordinalIndex [ fhir:v 1 ]       ] [
fhir:sequence [
fhir:l fhir:MolecularDefinition/example-sequence2-2b-concatenated ;
fhir:reference [ fhir:v "MolecularDefinition/example-sequence2-2b-concatenated" ] ;
fhir:type [
fhir:v "MolecularDefinition"^^xsd:anyURI ;
fhir:l fhir:MolecularDefinition           ] ;
fhir:display [ fhir:v "Sequence-of index 2-Resource for concatenated sequence example:                     TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC AAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGA" ]         ] ;
fhir:ordinalIndex [ fhir:v 2 ]       ] )     ] ;
fhir:relative [
fhir:startingMolecule [
fhir:l fhir:MolecularDefinition/example-starting-sequence-2b-relative ;
fhir:reference [ fhir:v "MolecularDefinition/example-starting-sequence-2b-relative" ] ;
fhir:type [
fhir:v "MolecularDefinition"^^xsd:anyURI ;
fhir:l fhir:MolecularDefinition         ] ;
fhir:display [ fhir:v "Starting Sequence Resource" ]       ] ;
      ( fhir:edit [
fhir:coordinateInterval [
fhir:coordinateSystem [
fhir:system [
              ( fhir:coding [
a loinc:LA30100-4 ;
fhir:system [
fhir:v "http://loinc.org"^^xsd:anyURI ;
fhir:l <http://loinc.org>                 ] ;
fhir:code [ fhir:v "LA30100-4" ] ;
fhir:display [ fhir:v "0-based interval counting" ]               ] ) ;
fhir:text [ fhir:v "0-based interval counting" ]             ]           ] ;
fhir:start [
a fhir:Quantity ;
fhir:value [ fhir:v "0"^^xsd:decimal ]           ] ;
fhir:end [
a fhir:Quantity ;
fhir:value [ fhir:v "5"^^xsd:decimal ]           ]         ] ;
fhir:replacementMolecule [
fhir:l fhir:MolecularDefinition/example-replacement-sequence ;
fhir:reference [ fhir:v "MolecularDefinition/example-replacement-sequence" ] ;
fhir:type [
fhir:v "MolecularDefinition"^^xsd:anyURI ;
fhir:l fhir:MolecularDefinition           ] ;
fhir:display [ fhir:v "Replacement Sequence Resource: ATGAA" ]         ] ;
fhir:replacedMolecule [
fhir:l fhir:MolecularDefinition/example-replaced-sequence ;
fhir:reference [ fhir:v "MolecularDefinition/example-replaced-sequence" ] ;
fhir:type [
fhir:v "MolecularDefinition"^^xsd:anyURI ;
fhir:l fhir:MolecularDefinition           ] ;
fhir:display [ fhir:v "Replaced Sequence Resource: CCCCC" ]         ]       ] )     ]
  ] ) . #