Sequence-example-pgx-1.ttl

Example of a single varaint on a reference Sequence MolecularSequence related to a haplotype observation in PGx example

@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/Sequence/example-pgx-1> a fhir:Sequence;

<http://hl7.org/fhir/MolecularSequence/example-pgx-1> a fhir:MolecularSequence;

  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "example-pgx-1"];
  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>: example-pgx-1</p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 0</p><p><b>patient</b>: <a>Patient/example</a></p><h3>ReferenceSeqs</h3><table><tr><td>-</td><td><b>ReferenceSeqId</b></td><td><b>Strand</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>NG_007726.3 <span>(Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NG_007726.3' = 'NG_007726.3)</span></td><td>1</td><td>55227970</td><td>55227980</td></tr></table><h3>Variants</h3><table><tr><td>-</td><td><b>Start</b></td><td><b>End</b></td><td><b>ObservedAllele</b></td><td><b>ReferenceAllele</b></td><td><b>VariantPointer</b></td></tr><tr><td>*</td><td>55227976</td><td>55227977</td><td>G</td><td>T</td><td><a>Target Haplotype Observation</a></td></tr></table></div>"

     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: example-pgx-1</p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 0</p><p><b>patient</b>: <a>Patient/example</a></p><h3>ReferenceSeqs</h3><table><tr><td>-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>Strand</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>sense</td><td>NG_007726.3 <span>(Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NG_007726.3' = 'NG_007726.3)</span></td><td>watson</td><td>55227970</td><td>55227980</td></tr></table><h3>Variants</h3><table><tr><td>-</td><td><b>Start</b></td><td><b>End</b></td><td><b>ObservedAllele</b></td><td><b>ReferenceAllele</b></td><td><b>VariantPointer</b></td></tr><tr><td>*</td><td>55227976</td><td>55227977</td><td>G</td><td>T</td><td><a>Target Haplotype Observation</a></td></tr></table></div>"

  ];
  fhir:Sequence.type [ fhir:value "dna"];
  fhir:Sequence.coordinateSystem [ fhir:value "0"^^xsd:integer];
  fhir:Sequence.patient [

  fhir:MolecularSequence.type [ fhir:value "dna"];
  fhir:MolecularSequence.coordinateSystem [ fhir:value "0"^^xsd:integer];
  fhir:MolecularSequence.patient [

     fhir:link <http://hl7.org/fhir/Patient/example>;
     fhir:Reference.reference [ fhir:value "Patient/example" ]
  ];
  fhir:Sequence.referenceSeq [
     fhir:Sequence.referenceSeq.referenceSeqId [

  fhir:MolecularSequence.referenceSeq [
     fhir:MolecularSequence.referenceSeq.orientation [ fhir:value "sense" ];
     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 "NG_007726.3" ]
       ]
     ];
     fhir:Sequence.referenceSeq.strand [ fhir:value "1"^^xsd:integer ];
     fhir:Sequence.referenceSeq.windowStart [ fhir:value "55227970"^^xsd:integer ];
     fhir:Sequence.referenceSeq.windowEnd [ fhir:value "55227980"^^xsd:integer ]

     fhir:MolecularSequence.referenceSeq.strand [ fhir:value "watson" ];
     fhir:MolecularSequence.referenceSeq.windowStart [ fhir:value "55227970"^^xsd:integer ];
     fhir:MolecularSequence.referenceSeq.windowEnd [ fhir:value "55227980"^^xsd:integer ]

  ];
  fhir:Sequence.variant [

  fhir:MolecularSequence.variant [

     fhir:index 0;
     fhir:Sequence.variant.start [ fhir:value "55227976"^^xsd:integer ];
     fhir:Sequence.variant.end [ fhir:value "55227977"^^xsd:integer ];
     fhir:Sequence.variant.observedAllele [ fhir:value "G" ];
     fhir:Sequence.variant.referenceAllele [ fhir:value "T" ];
     fhir:Sequence.variant.variantPointer [

     fhir:MolecularSequence.variant.start [ fhir:value "55227976"^^xsd:integer ];
     fhir:MolecularSequence.variant.end [ fhir:value "55227977"^^xsd:integer ];
     fhir:MolecularSequence.variant.observedAllele [ fhir:value "G" ];
     fhir:MolecularSequence.variant.referenceAllele [ fhir:value "T" ];
     fhir:MolecularSequence.variant.variantPointer [

       fhir:link <http://hl7.org/fhir/Observation/example-haplotype1>;
       fhir:Reference.reference [ fhir:value "Observation/example-haplotype1" ];
       fhir:Reference.display [ fhir:value "Target Haplotype Observation" ]
     ]
  ] .

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

<http://hl7.org/fhir/Observation/example-haplotype1> a fhir:Observation .

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

<http://hl7.org/fhir/Sequence/example-pgx-1.ttl> a owl:Ontology;

<http://hl7.org/fhir/MolecularSequence/example-pgx-1.ttl> a owl:Ontology;

  owl:imports fhir:fhir.ttl;
  owl:versionIRI <http://hl7.org/fhir/STU3/Sequence/example-pgx-1.ttl> .

  owl:versionIRI <http://build.fhir.org/MolecularSequence/example-pgx-1.ttl> .


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