Release 4

This page is part of the FHIR Specification (v4.0.1: R4 - Mixed Normative and STU) 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-1base-example.ttl

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 1-based coordinatesystem

@prefix fhir: <http://hl7.org/fhir/> .
@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-1-base> a fhir:MolecularSequence;
  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "coord-1-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-1-base</p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 1</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>1</td><td>8</td></tr></table><blockquote><p><b>variant</b></p><p><b>start</b>: 2</p><p><b>end</b>: 3</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>: 5</p><p><b>end</b>: 5</p><p><b>observedAllele</b>: T</p><p><b>referenceAllele</b>: A</p><p><b>cigar</b>: 3I</p></blockquote><blockquote><p><b>variant</b></p><p><b>start</b>: 7</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 "1"^^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 "1"^^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 "3"^^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 "5"^^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 "3I" ]
  ], [
     fhir:index 2;
     fhir:MolecularSequence.variant.start [ fhir:value "7"^^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-1-base.ttl> a owl:Ontology;
  owl:imports fhir:fhir.ttl;
  owl:versionIRI <http://build.fhir.org/MolecularSequence/coord-1-base.ttl> .

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

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.