MolecularSequence example for patient with breast cancer gene variant

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

# - 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 fhir:MolecularSequence ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "breastcancer"] ; # 
  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=\"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:type [ fhir:v "rna"] ; # 
  fhir:subject [
     fhir:reference [ fhir:v "Patient/brcapat" ]
  ] ; # 
  fhir:relative ( [
     fhir:coordinateSystem [
       fhir:coding ( [
         a loinc:LA30100-4 ;
         fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
         fhir:code [ fhir:v "LA30100-4" ] ;
         fhir:display [ fhir:v "0-based interval counting" ]
       ] )
     ] ;
     fhir:startingSequence [
       fhir:sequence [
         a fhir:CodeableConcept ;
         fhir:coding ( [
           fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/nuccore/"^^xsd:anyURI ] ;
           fhir:code [ fhir:v "NM_000059.3" ] ;
           fhir:display [ fhir:v "Homo sapiens BRCA2, DNA repair associated (BRCA2), mRNA" ]
         ] )
       ] ;
       fhir:windowStart [ fhir:v "101488058"^^xsd:integer ] ;
       fhir:windowEnd [ fhir:v "101499444"^^xsd:integer ]
     ] ;
     fhir:edit ( [
       fhir:start [ fhir:v "32316186"^^xsd:integer ] ;
       fhir:end [ fhir:v "32316187"^^xsd:integer ] ;
       fhir:replacementSequence [ fhir:v "A" ] ;
       fhir:replacedSequence [ fhir:v "C" ]
     ] )
  ] )] . # 


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