Sequence-example-fda-comparisons.ttl

MolecularSequence example for vcf comparison on 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/MolecularSequence/fda-vcf-comparison> a fhir:MolecularSequence;
  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "fda-vcf-comparison"];
  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><p><b>coordinateSystem</b>: 1</p><p><b>patient</b>: <a>Generated Summary: Medical record number: 12345 (USUAL); active; Peter James Chalmers (OFFICIAL), Jim , Peter James Windsor (MAIDEN); , Phone: (03) 5555 6473, Phone: (03) 3410 5613, Phone: (03) 5555 8834; gender: male; birthDate: 1974-12-25; </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><span>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>Score</b></td><td><b>Method</b></td><td><b>TruthTP</b></td><td><b>TruthFN</b></td><td><b>QueryFP</b></td><td><b>GtFP</b></td><td><b>Precision</b></td><td><b>FScore</b></td></tr><tr><td>*</td><td>unknown</td><td><span>file-BkZxBZ00bpJVk2q6x43b1YBx</span></td><td>10453</td><td>101770080</td><td>5.000</td><td><span>VCF Comparison</span></td><td>129481</td><td>3168</td><td>1507</td><td>2186</td><td>0.9885</td><td>0.9823</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></tr><tr><td>*</td><td>login</td><td><a>https://precision.fda.gov/comparisons/1850</a></td><td>FDA</td></tr></table></div>"
  ];
  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: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: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:MolecularSequence.variant [
     fhir:index 0;
     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:MolecularSequence.quality [
     fhir:index 0;
     fhir:MolecularSequence.quality.type [ fhir:value "unknown" ];
     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-BkZxBZ00bpJVk2q6x43b1YBx" ]
       ]
     ];
     fhir:MolecularSequence.quality.start [ fhir:value "10453"^^xsd:integer ];
     fhir:MolecularSequence.quality.end [ fhir:value "101770080"^^xsd:integer ];
     fhir:MolecularSequence.quality.score [
       fhir:Quantity.value [ fhir:value "5.000"^^xsd:decimal ]
     ];
     fhir:MolecularSequence.quality.method [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "https://precision.fda.gov/apps/" ];
         fhir:Coding.code [ fhir:value "app-BqB9XZ8006ZZ2g5KzGXP3fpq" ]
       ];
       fhir:CodeableConcept.text [ fhir:value "VCF Comparison" ]
     ];
     fhir:MolecularSequence.quality.truthTP [ fhir:value "129481"^^xsd:decimal ];
     fhir:MolecularSequence.quality.truthFN [ fhir:value "3168"^^xsd:decimal ];
     fhir:MolecularSequence.quality.queryFP [ fhir:value "1507"^^xsd:decimal ];
     fhir:MolecularSequence.quality.gtFP [ fhir:value "2186"^^xsd:decimal ];
     fhir:MolecularSequence.quality.precision [ fhir:value "0.9885"^^xsd:decimal ];
     fhir:MolecularSequence.quality.fScore [ fhir:value "0.9823"^^xsd:decimal ]
  ];
  fhir:MolecularSequence.repository [
     fhir:index 0;
     fhir:MolecularSequence.repository.type [ fhir:value "login" ];
     fhir:MolecularSequence.repository.url [ fhir:value "https://precision.fda.gov/comparisons/1850" ];
     fhir:MolecularSequence.repository.name [ fhir:value "FDA" ]
  ] .

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

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

<http://hl7.org/fhir/MolecularSequence/fda-vcf-comparison.ttl> a owl:Ontology;
  owl:imports fhir:fhir.ttl;
  owl:versionIRI <http://build.fhir.org/MolecularSequence/fda-vcf-comparison.ttl> .

# -------------------------------------------------------------------------------------