This page is part of the FHIR Specification (v4.4.0: R5 Preview #2). 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
Clinical Genomics Work Group | Maturity Level: N/A | Standards Status: Informative | Compartments: Patient |
Raw XML (canonical form + also see XML Format Specification)
MolecularSequence example for vcf comparison on precisionFDA (id = "fda-vcf-comparison")
<?xml version="1.0" encoding="UTF-8"?> <MolecularSequence xmlns="http://hl7.org/fhir"> <id value="fda-vcf-comparison"/> <text> <status value="generated"/> <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-BkZxBZ00bp JVk2q6x43b1YBx)</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-BqB9XZ8006ZZ2 g5KzGXP3fpq)</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> </text> <coordinateSystem value="1"/> <patient> <reference value="Patient/example"/> </patient> <referenceSeq> <referenceSeqId> <coding> <system value="http://www.ncbi.nlm.nih.gov/nuccore"/> <code value="NC_000001.11"/> </coding> </referenceSeqId> <strand value="watson"/> <windowStart value="10453"/> <windowEnd value="101770080"/> </referenceSeq> <variant> <start value="13116"/> <end value="13117"/> <observedAllele value="T"/> <referenceAllele value="G"/> </variant> <quality> <type value="unknown"/> <standardSequence> <coding> <system value="https://precision.fda.gov/files/"/> <code value="file-BkZxBZ00bpJVk2q6x43b1YBx"/> </coding> </standardSequence> <start value="10453"/> <end value="101770080"/> <score> <value value="5.000"/> </score> <method> <coding> <system value="https://precision.fda.gov/apps/"/> <code value="app-BqB9XZ8006ZZ2g5KzGXP3fpq"/> </coding> <text value="VCF Comparison"/> </method> <truthTP value="129481"/> <truthFN value="3168"/> <queryFP value="1507"/> <gtFP value="2186"/> <precision value="0.9885"/> <fScore value="0.9823"/> </quality> <repository> <type value="login"/> <url value="https://precision.fda.gov/comparisons/1850"/> <name value="FDA"/> </repository> </MolecularSequence>
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.