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Example MolecularSequence/coord-0-base (Turtle)

Clinical Genomics Work GroupMaturity Level: N/AStandards Status: InformativeCompartments: 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: <http://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: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: 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:MolecularSequence.type [ fhir:value "dna"];
  fhir:MolecularSequence.relative [
     fhir:index 0;
     fhir:MolecularSequence.relative.coordinateSystem [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA30101-2;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA30101-2" ];
         fhir:Coding.display [ fhir:value "0-based character counting" ]
       ]
     ];
     fhir:MolecularSequence.relative.startingSequence [
       fhir:MolecularSequence.relative.startingSequence.sequenceString [ fhir:value "ACGTAGTC" ];
       fhir:MolecularSequence.relative.startingSequence.windowStart [ fhir:value "0"^^xsd:integer ];
       fhir:MolecularSequence.relative.startingSequence.windowEnd [ fhir:value "8"^^xsd:integer ];
       fhir:MolecularSequence.relative.startingSequence.strand [ fhir:value "watson" ]
     ];
     fhir:MolecularSequence.relative.edit [
       fhir:index 0;
       fhir:MolecularSequence.relative.edit.start [ fhir:value "2"^^xsd:integer ];
       fhir:MolecularSequence.relative.edit.end [ fhir:value "2"^^xsd:integer ];
       fhir:MolecularSequence.relative.edit.replacementSequence [ fhir:value "ATG" ];
       fhir:MolecularSequence.relative.edit.replacedSequence [ fhir:value "-" ]
     ], [
       fhir:index 1;
       fhir:MolecularSequence.relative.edit.start [ fhir:value "4"^^xsd:integer ];
       fhir:MolecularSequence.relative.edit.end [ fhir:value "5"^^xsd:integer ];
       fhir:MolecularSequence.relative.edit.replacementSequence [ fhir:value "T" ];
       fhir:MolecularSequence.relative.edit.replacedSequence [ fhir:value "A" ]
     ], [
       fhir:index 2;
       fhir:MolecularSequence.relative.edit.start [ fhir:value "6"^^xsd:integer ];
       fhir:MolecularSequence.relative.edit.end [ fhir:value "7"^^xsd:integer ];
       fhir:MolecularSequence.relative.edit.replacementSequence [ fhir:value "-" ];
       fhir:MolecularSequence.relative.edit.replacedSequence [ fhir:value "T" ]
     ]
  ]] .

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

[a owl:Ontology;
  owl:imports fhir:fhir.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.