Sequence-example-fda-comparisons.xml

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</b> </p> <p> <b> id</b> : fda-vcf-comparison</p> <p> <b> coordinateSystem</b> : 1</p> <p> <b> patient</b> : <a> Generated Summary: id: example; Medical record number: 12345 (USUAL); active; Peter James
           Chalmers (OFFICIAL), Jim , Peter James Windsor (MAIDEN); -unknown-(HOME), ph: (03) 5555
           6473(WORK), ph: (03) 3410 5613(MOBILE), ph: (03) 5555 8834(OLD); 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> </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>