Release 4 5

This page is part of the FHIR Specification (v4.0.1: R4 (v5.0.0: R5 - Mixed Normative and STU ) ). This is the current published version in it's permanent home (it will always be available at this URL). The current version which supercedes this version is 5.0.0 . For a full list of available versions, see the Directory of published versions . Page versions: R5 R4B R4 R3

Coord-0base-example.ttl

Example MolecularSequence/coord-0-base (Turtle)

Clinical Genomics Work Group Maturity Level : N/A Standards Status : Informative Compartments : Patient

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

Example of a record with 0-based coordinatesystem 

@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 -------------------------------------------------------------------

<http://hl7.org/fhir/MolecularSequence/coord-0-base> a fhir:MolecularSequence;
  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "coord-0-base"];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: coord-0-base</p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table><tr><td>-</td><td><b>ReferenceSeqString</b></td><td><b>Strand</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>ACGTAGTC</td><td>watson</td><td>0</td><td>8</td></tr></table><blockquote><p><b>variant</b></p><p><b>start</b>: 2</p><p><b>end</b>: 2</p><p><b>observedAllele</b>: ATG</p><p><b>referenceAllele</b>: -</p><p><b>cigar</b>: 3I</p></blockquote><blockquote><p><b>variant</b></p><p><b>start</b>: 4</p><p><b>end</b>: 5</p><p><b>observedAllele</b>: T</p><p><b>referenceAllele</b>: A</p><p><b>cigar</b>: 1M</p></blockquote><blockquote><p><b>variant</b></p><p><b>start</b>: 6</p><p><b>end</b>: 7</p><p><b>observedAllele</b>: -</p><p><b>referenceAllele</b>: T</p><p><b>cigar</b>: 1D</p></blockquote><p><b>observedSeq</b>: ACATGGTAGC</p></div>"
  ];
  fhir:MolecularSequence.type [ fhir:value "dna"];
  fhir:MolecularSequence.coordinateSystem [ fhir:value "0"^^xsd:integer];
  fhir:MolecularSequence.referenceSeq [
     fhir:MolecularSequence.referenceSeq.referenceSeqString [ fhir:value "ACGTAGTC" ];
     fhir:MolecularSequence.referenceSeq.strand [ fhir:value "watson" ];
     fhir:MolecularSequence.referenceSeq.windowStart [ fhir:value "0"^^xsd:integer ];
     fhir:MolecularSequence.referenceSeq.windowEnd [ fhir:value "8"^^xsd:integer ]
  ];
  fhir:MolecularSequence.variant [
     fhir:index 0;
     fhir:MolecularSequence.variant.start [ fhir:value "2"^^xsd:integer ];
     fhir:MolecularSequence.variant.end [ fhir:value "2"^^xsd:integer ];
     fhir:MolecularSequence.variant.observedAllele [ fhir:value "ATG" ];
     fhir:MolecularSequence.variant.referenceAllele [ fhir:value "-" ];
     fhir:MolecularSequence.variant.cigar [ fhir:value "3I" ]
  ], [
     fhir:index 1;
     fhir:MolecularSequence.variant.start [ fhir:value "4"^^xsd:integer ];
     fhir:MolecularSequence.variant.end [ fhir:value "5"^^xsd:integer ];
     fhir:MolecularSequence.variant.observedAllele [ fhir:value "T" ];
     fhir:MolecularSequence.variant.referenceAllele [ fhir:value "A" ];
     fhir:MolecularSequence.variant.cigar [ fhir:value "1M" ]
  ], [
     fhir:index 2;
     fhir:MolecularSequence.variant.start [ fhir:value "6"^^xsd:integer ];
     fhir:MolecularSequence.variant.end [ fhir:value "7"^^xsd:integer ];
     fhir:MolecularSequence.variant.observedAllele [ fhir:value "-" ];
     fhir:MolecularSequence.variant.referenceAllele [ fhir:value "T" ];
     fhir:MolecularSequence.variant.cigar [ fhir:value "1D" ]
  ];
  fhir:MolecularSequence.observedSeq [ fhir:value "ACATGGTAGC"] .

# - ontology header ------------------------------------------------------------

<http://hl7.org/fhir/MolecularSequence/coord-0-base.ttl> a owl:Ontology;
  owl:imports fhir:fhir.ttl;
  owl:versionIRI <http://build.fhir.org/MolecularSequence/coord-0-base.ttl> .

[a fhir:MolecularSequence ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "coord-0-base"] ; # 
  fhir:text [
     fhir:status [ fhir:v "generated" ] ;
     fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MolecularSequence</b><a name=\"coord-0-base\"> </a></p><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\">Resource MolecularSequence &quot;coord-0-base&quot; </p></div><p><b>type</b>: dna</p><blockquote><p><b>relative</b></p><p><b>coordinateSystem</b>: 0-based character counting <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30101-2)</span></p><h3>StartingSequences</h3><table class=\"grid\"><tr><td>-</td><td><b>Sequence[x]</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td><td><b>Strand</b></td></tr><tr><td>*</td><td>ACGTAGTC</td><td>0</td><td>8</td><td>watson</td></tr></table><blockquote><p><b>edit</b></p><p><b>start</b>: 2</p><p><b>end</b>: 2</p><p><b>replacementSequence</b>: ATG</p><p><b>replacedSequence</b>: -</p></blockquote><blockquote><p><b>edit</b></p><p><b>start</b>: 4</p><p><b>end</b>: 5</p><p><b>replacementSequence</b>: T</p><p><b>replacedSequence</b>: A</p></blockquote><blockquote><p><b>edit</b></p><p><b>start</b>: 6</p><p><b>end</b>: 7</p><p><b>replacementSequence</b>: -</p><p><b>replacedSequence</b>: T</p></blockquote></blockquote></div>"
  ] ; # 
  fhir:type [ fhir:v "dna"] ; # 
  fhir:relative ( [
     fhir:coordinateSystem [
       fhir:coding ( [
         a loinc:LA30101-2 ;
         fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
         fhir:code [ fhir:v "LA30101-2" ] ;
         fhir:display [ fhir:v "0-based character counting" ]
       ] )
     ] ;
     fhir:startingSequence [
       fhir:sequence [ fhir:v "ACGTAGTC" ] ;
       fhir:windowStart [ fhir:v "0"^^xsd:integer ] ;
       fhir:windowEnd [ fhir:v "8"^^xsd:integer ] ;
       fhir:strand [ fhir:v "watson" ]
     ] ;
     fhir:edit ( [
       fhir:start [ fhir:v "2"^^xsd:integer ] ;
       fhir:end [ fhir:v "2"^^xsd:integer ] ;
       fhir:replacementSequence [ fhir:v "ATG" ] ;
       fhir:replacedSequence [ fhir:v "-" ]
     ] [
       fhir:start [ fhir:v "4"^^xsd:integer ] ;
       fhir:end [ fhir:v "5"^^xsd:integer ] ;
       fhir:replacementSequence [ fhir:v "T" ] ;
       fhir:replacedSequence [ fhir:v "A" ]
     ] [
       fhir:start [ fhir:v "6"^^xsd:integer ] ;
       fhir:end [ fhir:v "7"^^xsd:integer ] ;
       fhir:replacementSequence [ fhir:v "-" ] ;
       fhir:replacedSequence [ fhir:v "T" ]
     ] )
  ] )] . # 


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

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.