Sequence-example-fda-vcfeval.ttl

MolecularSequence example for vcf and Hap.py 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-vcfeval-comparison> a fhir:MolecularSequence;
  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "fda-vcfeval-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><blockquote><p><b>quality</b></p><p><b>type</b>: indel</p><p><b>standardSequence</b>: <span>file-BkZxBZ00bpJVk2q6x43b1YBx</span></p><p><b>start</b>: 10453</p><p><b>end</b>: 101770080</p><p><b>method</b>: <span>Vcfeval + Hap.py Comparison</span></p><p><b>truthTP</b>: 7749</p><p><b>truthFN</b>: 2554</p><p><b>queryFP</b>: 10670</p><p><b>gtFP</b>: 2186</p><p><b>precision</b>: 0.428005</p><p><b>recall</b>: 0.752111</p></blockquote><blockquote><p><b>quality</b></p><p><b>type</b>: snp</p><p><b>standardSequence</b>: <span>file-BkZxBZ00bpJVk2q6x43b1YBx</span></p><p><b>start</b>: 10453</p><p><b>end</b>: 101770080</p><p><b>method</b>: <span>Vcfeval + Hap.py Comparison</span></p><p><b>truthTP</b>: 92106</p><p><b>truthFN</b>: 1247</p><p><b>queryFP</b>: 21744</p><p><b>gtFP</b>: 493</p><p><b>precision</b>: 0.808602</p><p><b>recall</b>: 0.986642</p></blockquote><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/jobs/job-ByxYPx809jFVy21KJG74Jg3Y</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 "indel" ];
     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.method [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "https://precision.fda.gov/apps/" ];
         fhir:Coding.code [ fhir:value "app-BxfGF8j02pBZzZxbzZxP725P" ]
       ];
       fhir:CodeableConcept.text [ fhir:value "Vcfeval + Hap.py Comparison" ]
     ];
     fhir:MolecularSequence.quality.truthTP [ fhir:value "7749"^^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:index 1;
     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-BkZxBZ00bpJVk2q6x43b1YBx" ]
       ]
     ];
     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/apps/" ];
         fhir:Coding.code [ fhir:value "app-BxfGF8j02pBZzZxbzZxP725P" ]
       ];
       fhir:CodeableConcept.text [ fhir:value "Vcfeval + Hap.py Comparison" ]
     ];
     fhir:MolecularSequence.quality.truthTP [ fhir:value "92106"^^xsd:decimal ];
     fhir:MolecularSequence.quality.truthFN [ fhir:value "1247"^^xsd:decimal ];
     fhir:MolecularSequence.quality.queryFP [ fhir:value "21744"^^xsd:decimal ];
     fhir:MolecularSequence.quality.gtFP [ fhir:value "493"^^xsd:decimal ];
     fhir:MolecularSequence.quality.precision [ fhir:value "0.808602"^^xsd:decimal ];
     fhir:MolecularSequence.quality.recall [ fhir:value "0.986642"^^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/jobs/job-ByxYPx809jFVy21KJG74Jg3Y" ];
     fhir:MolecularSequence.repository.name [ fhir:value "FDA" ]
  ] .

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

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

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

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