Release 4B 5 Ballot

This page is part of the FHIR Specification (v4.3.0: R4B (v5.0.0-ballot: R5 Ballot - STU see ballot notes ). 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

Sequence-genetics-example-breastcancer.ttl

Example MolecularSequence/breastcancer (Turtle)

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

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

MolecularSequence example for patient with breast cancer gene variant 

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

<http://hl7.org/fhir/MolecularSequence/breastcancer> a fhir:MolecularSequence;

[a fhir:MolecularSequence;

  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "breastcancer"];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></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 &quot;breastcancer&quot; </p></div><p><b>type</b>: rna</p><p><b>coordinateSystem</b>: 0</p><p><b>patient</b>: <a href=\"todo.html\">Patient/brcapat</a></p><h3>ReferenceSeqs</h3><table class=\"grid\"><tr><td>-</td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>Homo sapiens BRCA2, DNA repair associated (BRCA2), mRNA <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#NM_000059.3)</span></td><td>101488058</td><td>101499444</td></tr></table><h3>Variants</h3><table class=\"grid\"><tr><td>-</td><td><b>Start</b></td><td><b>End</b></td><td><b>ObservedAllele</b></td><td><b>ReferenceAllele</b></td></tr><tr><td>*</td><td>32316186</td><td>32316187</td><td>A</td><td>C</td></tr></table></div>"

     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MolecularSequence</b><a name=\"breastcancer\"> </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;breastcancer&quot; </p></div><p><b>type</b>: rna</p><p><b>subject</b>: <a href=\"broken-link.html\">Patient/brcapat</a></p><blockquote><p><b>relative</b></p><p><b>coordinateSystem</b>: 0-based interval counting <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30100-4)</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></tr><tr><td>*</td><td>Homo sapiens BRCA2, DNA repair associated (BRCA2), mRNA <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#NM_000059.3)</span></td><td>101488058</td><td>101499444</td></tr></table><h3>Edits</h3><table class=\"grid\"><tr><td>-</td><td><b>Start</b></td><td><b>End</b></td><td><b>ReplacementSequence</b></td><td><b>ReplacedSequence</b></td></tr><tr><td>*</td><td>32316186</td><td>32316187</td><td>A</td><td>C</td></tr></table></blockquote></div>"

  ];
  fhir:MolecularSequence.type [ fhir:value "rna"];
  fhir:MolecularSequence.coordinateSystem [ fhir:value "0"^^xsd:integer];
  fhir:MolecularSequence.patient [
     fhir:link <http://hl7.org/fhir/Patient/brcapat>;

  fhir:MolecularSequence.subject [

     fhir:Reference.reference [ fhir:value "Patient/brcapat" ]
  ];
  fhir:MolecularSequence.referenceSeq [
     fhir:MolecularSequence.referenceSeq.referenceSeqId [

  fhir:MolecularSequence.relative [
     fhir:index 0;
     fhir:MolecularSequence.relative.coordinateSystem [

       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/nuccore/" ];
         fhir:Coding.code [ fhir:value "NM_000059.3" ];
         fhir:Coding.display [ fhir:value "Homo sapiens BRCA2, DNA repair associated (BRCA2), mRNA" ]

         a loinc:LA30100-4;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA30100-4" ];
         fhir:Coding.display [ fhir:value "0-based interval counting" ]

       ]
     ];
     fhir:MolecularSequence.referenceSeq.windowStart [ fhir:value "101488058"^^xsd:integer ];
     fhir:MolecularSequence.referenceSeq.windowEnd [ fhir:value "101499444"^^xsd:integer ]
  ];
  fhir:MolecularSequence.variant [
     fhir:index 0;
     fhir:MolecularSequence.variant.start [ fhir:value "32316186"^^xsd:integer ];
     fhir:MolecularSequence.variant.end [ fhir:value "32316187"^^xsd:integer ];
     fhir:MolecularSequence.variant.observedAllele [ fhir:value "A" ];
     fhir:MolecularSequence.variant.referenceAllele [ fhir:value "C" ]
  ] .

<http://hl7.org/fhir/Patient/brcapat> a fhir:Patient .

     fhir:MolecularSequence.relative.startingSequence [
       fhir:MolecularSequence.relative.startingSequence.sequenceCodeableConcept [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/nuccore/" ];
           fhir:Coding.code [ fhir:value "NM_000059.3" ];
           fhir:Coding.display [ fhir:value "Homo sapiens BRCA2, DNA repair associated (BRCA2), mRNA" ]
         ]
       ];
       fhir:MolecularSequence.relative.startingSequence.windowStart [ fhir:value "101488058"^^xsd:integer ];
       fhir:MolecularSequence.relative.startingSequence.windowEnd [ fhir:value "101499444"^^xsd:integer ]
     ];
     fhir:MolecularSequence.relative.edit [
       fhir:index 0;
       fhir:MolecularSequence.relative.edit.start [ fhir:value "32316186"^^xsd:integer ];
       fhir:MolecularSequence.relative.edit.end [ fhir:value "32316187"^^xsd:integer ];
       fhir:MolecularSequence.relative.edit.replacementSequence [ fhir:value "A" ];
       fhir:MolecularSequence.relative.edit.replacedSequence [ fhir:value "C" ]
     ]
  ]] .


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

<http://hl7.org/fhir/MolecularSequence/breastcancer.ttl> a owl:Ontology;
  owl:imports fhir:fhir.ttl;
  owl:versionIRI <http://build.fhir.org/MolecularSequence/breastcancer.ttl> .

[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.