This page is part of the FHIR Specification ~~(v3.0.2:~~ (v4.0.1: R4 - Mixed Normative and STU ~~3).~~ ) 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: R4B R4 R3 R4 R3
Sequence-example-fda.ttl

Clinical Genomics Work Group
Maturity Level : N/A
~~Ballot~~ Standards Status : Informative
Compartments : ~~Not linked to any defined compartments~~ Patient
Raw Turtle ~~, JSON-LD~~ (+ also see Turtle/RDF Format Specification )
~~Sequence~~ MolecularSequence example from precisionFDA
@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/fda-example> a fhir:Sequence;

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

  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "fda-example"];
  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>: fda-example</p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 1</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>NC_000001.11 <span>(Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NC_000001.11' = 'NC_000001.11)</span></td><td>1</td><td>10453</td><td>101770080</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></tr><tr><td>*</td><td>13116</td><td>13117</td><td>T</td><td>G</td></tr></table><h3>Qualities</h3><table><tr><td>-</td><td><b>Type</b></td><td><b>StandardSequence</b></td><td><b>Start</b></td><td><b>End</b></td><td><b>Method</b></td><td><b>TruthTP</b></td><td><b>QueryTP</b></td><td><b>TruthFN</b></td><td><b>QueryFP</b></td><td><b>GtFP</b></td><td><b>Precision</b></td><td><b>Recall</b></td><td><b>FScore</b></td></tr><tr><td>*</td><td>snp</td><td>file-Bk50V4Q0qVb65P0v2VPbfYPZ <span>(Details : {https://precision.fda.gov/files/ code 'file-Bk50V4Q0qVb65P0v2VPbfYPZ' = 'file-Bk50V4Q0qVb65P0v2VPbfYPZ)</span></td><td>10453</td><td>101770080</td><td>Vcfeval + Hap.py Comparison <span>(Details : {https://precision.fda.gov/jobs/ code 'job-ByxYPx809jFVy21KJG74Jg3Y' = 'job-ByxYPx809jFVy21KJG74Jg3Y)</span></td><td>7749</td><td>7984</td><td>2554</td><td>10670</td><td>2186</td><td>0.428005</td><td>0.752111</td><td>0.545551</td></tr></table><h3>Repositories</h3><table><tr><td>-</td><td><b>Type</b></td><td><b>Url</b></td><td><b>Name</b></td><td><b>VariantsetId</b></td></tr><tr><td>*</td><td>login</td><td><a>https://precision.fda.gov/files/file-Bx37ZK009P4bX5g3qjkFZV38</a></td><td>FDA</td><td>file-Bx37ZK009P4bX5g3qjkFZV38</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>: fda-example</p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 1</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>NC_000001.11 <span>(Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NC_000001.11' = 'NC_000001.11)</span></td><td>watson</td><td>10453</td><td>101770080</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></tr><tr><td>*</td><td>13116</td><td>13117</td><td>T</td><td>G</td></tr></table><h3>Qualities</h3><table><tr><td>-</td><td><b>Type</b></td><td><b>StandardSequence</b></td><td><b>Start</b></td><td><b>End</b></td><td><b>Method</b></td><td><b>TruthTP</b></td><td><b>QueryTP</b></td><td><b>TruthFN</b></td><td><b>QueryFP</b></td><td><b>GtFP</b></td><td><b>Precision</b></td><td><b>Recall</b></td><td><b>FScore</b></td></tr><tr><td>*</td><td>snp</td><td>file-Bk50V4Q0qVb65P0v2VPbfYPZ <span>(Details : {https://precision.fda.gov/files/ code 'file-Bk50V4Q0qVb65P0v2VPbfYPZ' = 'file-Bk50V4Q0qVb65P0v2VPbfYPZ)</span></td><td>10453</td><td>101770080</td><td>Vcfeval + Hap.py Comparison <span>(Details : {https://precision.fda.gov/jobs/ code 'job-ByxYPx809jFVy21KJG74Jg3Y' = 'job-ByxYPx809jFVy21KJG74Jg3Y)</span></td><td>7749</td><td>7984</td><td>2554</td><td>10670</td><td>2186</td><td>0.428005</td><td>0.752111</td><td>0.545551</td></tr></table><h3>Repositories</h3><table><tr><td>-</td><td><b>Type</b></td><td><b>Url</b></td><td><b>Name</b></td><td><b>VariantsetId</b></td></tr><tr><td>*</td><td>login</td><td><a>https://precision.fda.gov/files/file-Bx37ZK009P4bX5g3qjkFZV38</a></td><td>FDA</td><td>file-Bx37ZK009P4bX5g3qjkFZV38</td></tr></table></div>"

  ];
  fhir:Sequence.type [ fhir:value "dna"];
  fhir:Sequence.coordinateSystem [ fhir:value "1"^^xsd:integer];
  fhir:Sequence.patient [

  fhir:MolecularSequence.type [ fhir:value "dna"];
  fhir:MolecularSequence.coordinateSystem [ fhir:value "1"^^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.referenceSeqId [

       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/nuccore" ];
         fhir:Coding.code [ fhir:value "NC_000001.11" ]
       ]
     ];
     fhir:Sequence.referenceSeq.strand [ fhir:value "1"^^xsd:integer ];
     fhir:Sequence.referenceSeq.windowStart [ fhir:value "10453"^^xsd:integer ];
     fhir:Sequence.referenceSeq.windowEnd [ fhir:value "101770080"^^xsd:integer ]

     fhir:MolecularSequence.referenceSeq.strand [ fhir:value "watson" ];
     fhir:MolecularSequence.referenceSeq.windowStart [ fhir:value "10453"^^xsd:integer ];
     fhir:MolecularSequence.referenceSeq.windowEnd [ fhir:value "101770080"^^xsd:integer ]

  ];
  fhir:Sequence.variant [

  fhir:MolecularSequence.variant [

     fhir:index 0;
     fhir:Sequence.variant.start [ fhir:value "13116"^^xsd:integer ];
     fhir:Sequence.variant.end [ fhir:value "13117"^^xsd:integer ];
     fhir:Sequence.variant.observedAllele [ fhir:value "T" ];
     fhir:Sequence.variant.referenceAllele [ fhir:value "G" ]

     fhir:MolecularSequence.variant.start [ fhir:value "13116"^^xsd:integer ];
     fhir:MolecularSequence.variant.end [ fhir:value "13117"^^xsd:integer ];
     fhir:MolecularSequence.variant.observedAllele [ fhir:value "T" ];
     fhir:MolecularSequence.variant.referenceAllele [ fhir:value "G" ]

  ];
  fhir:Sequence.quality [

  fhir:MolecularSequence.quality [

     fhir:index 0;
     fhir:Sequence.quality.type [ fhir:value "snp" ];
     fhir:Sequence.quality.standardSequence [

     fhir:MolecularSequence.quality.type [ fhir:value "snp" ];
     fhir:MolecularSequence.quality.standardSequence [

       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "https://precision.fda.gov/files/" ];
         fhir:Coding.code [ fhir:value "file-Bk50V4Q0qVb65P0v2VPbfYPZ" ]
       ]
     ];
     fhir:Sequence.quality.start [ fhir:value "10453"^^xsd:integer ];
     fhir:Sequence.quality.end [ fhir:value "101770080"^^xsd:integer ];
     fhir:Sequence.quality.method [

     fhir:MolecularSequence.quality.start [ fhir:value "10453"^^xsd:integer ];
     fhir:MolecularSequence.quality.end [ fhir:value "101770080"^^xsd:integer ];
     fhir:MolecularSequence.quality.method [

       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "https://precision.fda.gov/jobs/" ];
         fhir:Coding.code [ fhir:value "job-ByxYPx809jFVy21KJG74Jg3Y" ]
       ];
       fhir:CodeableConcept.text [ fhir:value "Vcfeval + Hap.py Comparison" ]
     ];
     fhir:Sequence.quality.truthTP [ fhir:value "7749"^^xsd:decimal ];
     fhir:Sequence.quality.queryTP [ fhir:value "7984"^^xsd:decimal ];
     fhir:Sequence.quality.truthFN [ fhir:value "2554"^^xsd:decimal ];
     fhir:Sequence.quality.queryFP [ fhir:value "10670"^^xsd:decimal ];
     fhir:Sequence.quality.gtFP [ fhir:value "2186"^^xsd:decimal ];
     fhir:Sequence.quality.precision [ fhir:value "0.428005"^^xsd:decimal ];
     fhir:Sequence.quality.recall [ fhir:value "0.752111"^^xsd:decimal ];
     fhir:Sequence.quality.fScore [ fhir:value "0.545551"^^xsd:decimal ]

     fhir:MolecularSequence.quality.truthTP [ fhir:value "7749"^^xsd:decimal ];
     fhir:MolecularSequence.quality.queryTP [ fhir:value "7984"^^xsd:decimal ];
     fhir:MolecularSequence.quality.truthFN [ fhir:value "2554"^^xsd:decimal ];
     fhir:MolecularSequence.quality.queryFP [ fhir:value "10670"^^xsd:decimal ];
     fhir:MolecularSequence.quality.gtFP [ fhir:value "2186"^^xsd:decimal ];
     fhir:MolecularSequence.quality.precision [ fhir:value "0.428005"^^xsd:decimal ];
     fhir:MolecularSequence.quality.recall [ fhir:value "0.752111"^^xsd:decimal ];
     fhir:MolecularSequence.quality.fScore [ fhir:value "0.545551"^^xsd:decimal ]

  ];
  fhir:Sequence.repository [

  fhir:MolecularSequence.repository [

     fhir:index 0;
     fhir:Sequence.repository.type [ fhir:value "login" ];
     fhir:Sequence.repository.url [ fhir:value "https://precision.fda.gov/files/file-Bx37ZK009P4bX5g3qjkFZV38" ];
     fhir:Sequence.repository.name [ fhir:value "FDA" ];
     fhir:Sequence.repository.variantsetId [ fhir:value "file-Bx37ZK009P4bX5g3qjkFZV38" ]

     fhir:MolecularSequence.repository.type [ fhir:value "login" ];
     fhir:MolecularSequence.repository.url [ fhir:value "https://precision.fda.gov/files/file-Bx37ZK009P4bX5g3qjkFZV38" ];
     fhir:MolecularSequence.repository.name [ fhir:value "FDA" ];
     fhir:MolecularSequence.repository.variantsetId [ fhir:value "file-Bx37ZK009P4bX5g3qjkFZV38" ]

  ] .

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

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

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

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

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

  owl:versionIRI <http://build.fhir.org/MolecularSequence/fda-example.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.