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Clinical Genomics Work Group | Maturity Level: N/A | Standards Status: Informative | Compartments: Patient |
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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 with Details</b></p><p><b>id</b>: fda-vcf-comparison</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>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>file-BkZxBZ00bpJVk2q6x43b1YBx <span>(Details : {https://precision.fda.gov/files/ code 'file-BkZxBZ00bpJVk2q6x43b1YBx' = 'file-BkZxBZ00bpJVk2q6x43b1YBx)</span></td><td>10453</td><td>101770080</td><td>5.000</td><td>VCF Comparison <span>(Details : {https://precision.fda.gov/apps/ code 'app-BqB9XZ8006ZZ2g5KzGXP3fpq' = 'app-BqB9XZ8006ZZ2g5KzGXP3fpq)</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> . # -------------------------------------------------------------------------------------
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.