FHIR Release 3 (STU) Snapshot 3: Connectathon 32 Base

This page is part of the Snapshot #3 for FHIR Specification (v3.0.2: STU 3). The current version which supercedes this version is 5.0.0 R5 , released to support Connectathon 32 . For a full list of available versions, see the Directory of published versions . Page versions: R4B R4 R3

Sequence-example-fda-vcfeval.json

Example ValueSet/device-category (XML)

Clinical Genomics Vocabulary Work Group Maturity Level : N/A Ballot Standards Status : Informative Compartments : Not linked to any defined compartments

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

Sequence example Definition for vcf and Hap.py comparison on precisionFDA Value SetFHIRDeviceCategory

{ "resourceType": "Sequence", "id": "fda-vcfeval-comparison", "text": { "status": "generated", "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: fda-vcfeval-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>1</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><blockquote><p><b>quality</b></p><p><b>type</b>: indel</p><p><b>standardSequence</b>: file-BkZxBZ00bpJVk2q6x43b1YBx <span>(Details : {https://precision.fda.gov/files/ code 'file-BkZxBZ00bpJVk2q6x43b1YBx' = 'file-BkZxBZ00bpJVk2q6x43b1YBx)</span></p><p><b>start</b>: 10453</p><p><b>end</b>: 101770080</p><p><b>method</b>: Vcfeval + Hap.py Comparison <span>(Details : {https://precision.fda.gov/apps/ code 'app-BxfGF8j02pBZzZxbzZxP725P' = 'app-BxfGF8j02pBZzZxbzZxP725P)</span></p><p><b>truthTP</b>: 7749</p><p><b>truthFN</b>: 2554</p><p><b>queryFP</b>: 10670</p><p><b>gtFP</b>: 2186</p><p><b>precision</b>: 0.428005</p><p><b>recall</b>: 0.752111</p></blockquote><blockquote><p><b>quality</b></p><p><b>type</b>: snp</p><p><b>standardSequence</b>: file-BkZxBZ00bpJVk2q6x43b1YBx <span>(Details : {https://precision.fda.gov/files/ code 'file-BkZxBZ00bpJVk2q6x43b1YBx' = 'file-BkZxBZ00bpJVk2q6x43b1YBx)</span></p><p><b>start</b>: 10453</p><p><b>end</b>: 101770080</p><p><b>method</b>: Vcfeval + Hap.py Comparison <span>(Details : {https://precision.fda.gov/apps/ code 'app-BxfGF8j02pBZzZxbzZxP725P' = 'app-BxfGF8j02pBZzZxbzZxP725P)</span></p><p><b>truthTP</b>: 92106</p><p><b>truthFN</b>: 1247</p><p><b>queryFP</b>: 21744</p><p><b>gtFP</b>: 493</p><p><b>precision</b>: 0.808602</p><p><b>recall</b>: 0.986642</p></blockquote><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/jobs/job-ByxYPx809jFVy21KJG74Jg3Y</a></td><td>FDA</td></tr></table></div>" }, "coordinateSystem": 1, "patient": { "reference": "Patient/example" }, "referenceSeq": { "referenceSeqId": { "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", "code": "NC_000001.11" } ] }, "strand": 1, "windowStart": 10453, "windowEnd": 101770080 }, "variant": [ { "start": 13116, "end": 13117, "observedAllele": "T", "referenceAllele": "G" } ], "quality": [ { "type": "indel", "standardSequence": { "coding": [ { "system": "https://precision.fda.gov/files/", "code": "file-BkZxBZ00bpJVk2q6x43b1YBx" } ] }, "start": 10453, "end": 101770080, "method": { "coding": [ { "system": "https://precision.fda.gov/apps/", "code": "app-BxfGF8j02pBZzZxbzZxP725P" } ], "text": "Vcfeval + Hap.py Comparison" }, "truthTP": 7749, "truthFN": 2554, "queryFP": 10670, "gtFP": 2186, "precision": 0.428005, "recall": 0.752111 }, { "type": "snp", "standardSequence": { "coding": [ { "system": "https://precision.fda.gov/files/", "code": "file-BkZxBZ00bpJVk2q6x43b1YBx" } ] }, "start": 10453, "end": 101770080, "method": { "coding": [ { "system": "https://precision.fda.gov/apps/", "code": "app-BxfGF8j02pBZzZxbzZxP725P" } ], "text": "Vcfeval + Hap.py Comparison" }, "truthTP": 92106, "truthFN": 1247, "queryFP": 21744, "gtFP": 493, "precision": 0.808602, "recall": 0.986642 } ], "repository": [ { "type": "login", "url": "https://precision.fda.gov/jobs/job-ByxYPx809jFVy21KJG74Jg3Y", "name": "FDA" } ] } 
<?xml version="1.0" encoding="UTF-8"?>

<ValueSet xmlns="http://hl7.org/fhir">
  <id value="device-category"/> 
  <meta> 
    <lastUpdated value="2022-12-14T07:12:54.019+11:00"/> 
    <profile value="http://hl7.org/fhir/StructureDefinition/shareablevalueset"/> 
  </meta> 
  <text> 
    <status value="generated"/> 
    <div xmlns="http://www.w3.org/1999/xhtml">
      <ul> 
        <li> Include all codes defined in 
          <a href="codesystem-device-category.html">
            <code> http://hl7.org/fhir/device-category</code> 
          </a> 
        </li> 
      </ul> 
    </div> 
  </text> 
  <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
    <valueCode value="oo"/> 
  </extension> 
  <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-state">
    <valueCode value="trial-use"/> 
  </extension> 
  <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm">
    <valueInteger value="1"/> 
  </extension> 
  <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
    <valueCode value="draft"/> 
  </extension> 
  <url value="http://hl7.org/fhir/ValueSet/device-category"/> 
  <identifier> 
    <system value="urn:ietf:rfc:3986"/> 
    <value value="urn:oid:2.16.840.1.113883.4.642.3.3307"/> 
  </identifier> 
  <version value="5.0.0-snapshot3"/> 
  <name value="FHIRDeviceCategory"/> 
  <title value="FHIRDeviceCategory"/> 
  <status value="draft"/> 
  <experimental value="true"/> 
  <date value="2020-12-28T16:55:11+11:00"/> 
  <publisher value="HL7 (FHIR Project)"/> 
  <contact> 
    <telecom> 
      <system value="url"/> 
      <value value="http://hl7.org/fhir"/> 
    </telecom> 
    <telecom> 
      <system value="email"/> 
      <value value="fhir@lists.hl7.org"/> 
    </telecom> 
  </contact> 
  <description value="The association state of the device."/> 
  <jurisdiction> 
    <coding> 
      <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/> 
      <code value="001"/> 
      <display value="World"/> 
    </coding> 
  </jurisdiction> 
  <immutable value="true"/> 
  <compose> 
    <include> 
      <system value="http://hl7.org/fhir/device-category"/> 
    </include> 
  </compose> 

</

ValueSet

>

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.