Release 4B 5

This page is part of the FHIR Specification (v4.3.0: R4B (v5.0.0: R5 - STU ). The This is the current published version which supercedes in it's permanent home (it will always be available at this version is 5.0.0 . URL). For a full list of available versions, see the Directory of published versions . Page versions: R5 R4B R5 R4B R4 R3

Coord-1base-example.xml

Example MolecularSequence/coord-1-base (XML)

Clinical Genomics Work Group Maturity Level : N/A Standards Status : Informative Compartments : Patient

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

Jump past Narrative

Example of a record with 1-based coordinatesystem (id = "coord-1-base") 

<?xml version="1.0" encoding="UTF-8"?>


    
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<MolecularSequence xmlns="http://hl7.org/fhir">
    <id value="coord-1-base"/> 
    <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p> <b> Generated Narrative: MolecularSequence</b> <a name="coord-1-base"> </a> </p> <div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border:
       1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource MolecularSequence &quot;coord-1-base&quot; </p> </div> <p> <b> type</b> : dna</p> <blockquote> <p> <b> relative</b> </p> <p> <b> coordinateSystem</b> : 1-based character counting <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a> #LA30102-0)</span> </p> <h3> StartingSequences</h3> <table class="grid"><tr> <td> -</td> <td> <b> Sequence[x]</b> </td> <td> <b> WindowStart</b> </td> <td> <b> WindowEnd</b> </td> <td> <b> Strand</b> </td> </tr> <tr> <td> *</td> <td> ACGTAGTC</td> <td> 1</td> <td> 8</td> <td> watson</td> </tr> </table> <blockquote> <p> <b> edit</b> </p> <p> <b> start</b> : 2</p> <p> <b> end</b> : 3</p> <p> <b> replacementSequence</b> : ATG</p> <p> <b> replacedSequence</b> : -</p> </blockquote> <blockquote> <p> <b> edit</b> </p> <p> <b> start</b> : 5</p> <p> <b> end</b> : 5</p> <p> <b> replacementSequence</b> : T</p> <p> <b> replacedSequence</b> : A</p> </blockquote> <blockquote> <p> <b> edit</b> </p> <p> <b> start</b> : 7</p> <p> <b> end</b> : 7</p> <p> <b> replacementSequence</b> : -</p> <p> <b> replacedSequence</b> : T</p> </blockquote> </blockquote> </div> </text> <type value="dna"/> 
    <relative>         <coordinateSystem>             <coding>                 <system value="http://loinc.org"/>                 <code value="LA30102-0"/>                 <display value="1-based character counting"/>             </coding>         </coordinateSystem>         <startingSequence>             <sequenceString value="ACGTAGTC"/>             <windowStart value="1"/>             <windowEnd value="8"/>             <strand value="watson"/>         </startingSequence>         <edit>             <start value="2"/>             <end value="3"/>             <replacementSequence value="ATG"/>             <replacedSequence value="-"/>         </edit>         <edit>             <start value="5"/>             <end value="5"/>             <replacementSequence value="T"/>             <replacedSequence value="A"/>         </edit>         <edit>             <start value="7"/>             <end value="7"/>             <replacementSequence value="-"/>             <replacedSequence value="T"/>         </edit>       </relative> 


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MolecularSequence

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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.