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Sequence-example.xml

Clinical Genomics Work GroupMaturity Level: N/ABallot Status: InformativeCompartments: Not linked to any defined compartments

Raw XML (canonical form + also see XML Format Specification)

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Simple sequence example (id = "example")

<Sequence xmlns="http://hl7.org/fhir">
    <id value="example"/> 
    <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p> <b> Generated Narrative with Details</b> </p> <p> <b> id</b> : example</p> <p> <b> type</b> : dna</p> <p> <b> coordinateSystem</b> : 0</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_000009.11 <span> (Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NC_000009.11' = 'NC_000009.11)</span> </td> <td> watson</td> <td> 22125500</td> <td> 22125510</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> 22125503</td> <td> 22125504</td> <td> C</td> <td> G</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> <td> <b> VariantsetId</b> </td> </tr> <tr> <td> *</td> <td> openapi</td> <td> <a> http://grch37.rest.ensembl.org/ga4gh/variants/3:rs1333049?content-type=application/json</a> </td> <td> GA4GH API</td> <td> 3:rs1333049</td> </tr> </table> </div> </text> <type value="dna"/> 
    <coordinateSystem value="0"/> 
    <patient> 
        <reference value="Patient/example"/> 
    </patient> 
    <referenceSeq> 
        <referenceSeqId> 
          <coding> 
            <system value="http://www.ncbi.nlm.nih.gov/nuccore"/> 
            <code value="NC_000009.11"/> 
          </coding> 
        </referenceSeqId> 
        <strand value="watson"/> 
        <windowStart value="22125500"/> 
        <windowEnd value="22125510"/> 
    </referenceSeq> 
    <variant> 
        <start value="22125503"/> 
        <end value="22125504"/> 
        <observedAllele value="C"/> 
        <referenceAllele value="G"/> 
    </variant> 
    <repository> 
        <type value="openapi"/> 
        <url value="http://grch37.rest.ensembl.org/ga4gh/variants/3:rs1333049?content-type=application/json"/> 
        <name value="GA4GH API"/> 
        <variantsetId value="3:rs1333049"/> 
    </repository> 
</Sequence> 

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.