Phenomics Exchange for Research and Diagnostics
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Phenomics Exchange for Research and Diagnostics, published by HL7 International / Clinical Interoperability Council. This guide is not an authorized publication; it is the continuous build for version 0.1.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/phenomics-exchange-ig/ and changes regularly. See the Directory of published versions

: An INVALID phenotypic abnormality Observation example. - XML Representation

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<Observation xmlns="http://hl7.org/fhir">
  <id value="phenotypic-abnormality-invalid-1"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative: Observation </b><a name="phenotypic-abnormality-invalid-1"> </a><a name="hcphenotypic-abnormality-invalid-1"> </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">ResourceObservation &quot;phenotypic-abnormality-invalid-1&quot; </p></div><p><b>status</b>: final</p><p><b>code</b>: Intellectual disability <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0001249)</span></p><p><b>value</b>: true</p><blockquote><p><b>component</b></p><p><b>code</b>: Severity <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0012824)</span></p><p><b>value</b>: Mild <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0012825)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Severity <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0012824)</span></p><p><b>value</b>: Mild <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0012825)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Clinical modifier <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0012823)</span></p><p><b>value</b>: Worse in evening <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0410401)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Clinical modifier <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0012823)</span></p><p><b>value</b>: Refractory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0031375)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Clinical modifier <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0012823)</span></p><p><b>value</b>: Non existant modifier <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:999999999)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Onset <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0003674)</span></p><p><b>value</b>: Congenital onset <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0003577)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Onset <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0003674)</span></p><p><b>value</b>: 0 Day<span style="background: LightGoldenRodYellow"> (Details: system  codeDay = 'Day')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Severity <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (OTHER#OTHER)</span></p><p><b>value</b>: Mild <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (OTHER#OTHERTHING)</span></p></blockquote></div>
  </text>
  <status value="final"/>
  <code>
    <coding>
      <system value="http://human-phenotype-ontology.org"/>
      <code value="HP:0001249"/>
      <display value="Intellectual disability"/>
    </coding>
    <text value="Intellectual disability"/>
  </code>
  <valueBoolean value="true"/>
  <component>
    <code>
      <coding>
        <system value="http://human-phenotype-ontology.org"/>
        <code value="HP:0012824"/>
        <display value="Severity"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://human-phenotype-ontology.org"/>
        <code value="HP:0012825"/>
        <display value="Mild"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://human-phenotype-ontology.org"/>
        <code value="HP:0012824"/>
        <display value="Severity"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://human-phenotype-ontology.org"/>
        <code value="HP:0012825"/>
        <display value="Mild"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://human-phenotype-ontology.org"/>
        <code value="HP:0012823"/>
        <display value="Clinical modifier"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://human-phenotype-ontology.org"/>
        <code value="HP:0410401"/>
        <display value="Worse in evening"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://human-phenotype-ontology.org"/>
        <code value="HP:0012823"/>
        <display value="Clinical modifier"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://human-phenotype-ontology.org"/>
        <code value="HP:0031375"/>
        <display value="Refractory"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://human-phenotype-ontology.org"/>
        <code value="HP:0012823"/>
        <display value="Clinical modifier"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://human-phenotype-ontology.org"/>
        <code value="HP:999999999"/>
        <display value="Non existant modifier"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://human-phenotype-ontology.org"/>
        <code value="HP:0003674"/>
        <display value="Onset"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://human-phenotype-ontology.org"/>
        <code value="HP:0003577"/>
        <display value="Congenital onset"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://human-phenotype-ontology.org"/>
        <code value="HP:0003674"/>
        <display value="Onset"/>
      </coding>
    </code>
    <valueQuantity>
      <value value="0"/>
      <unit value="Day"/>
      <system value="http://some/unit/system"/>
      <code value="Day"/>
    </valueQuantity>
  </component>
  <component>
    <code>
      <coding>
        <system
                value="http://github.com/phenopackets/core-ig/CodeSystem/OTHER"/>
        <code value="OTHER"/>
        <display value="Severity"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system
                value="http://github.com/phenopackets/core-ig/CodeSystem/OTHER"/>
        <code value="OTHERTHING"/>
        <display value="Mild"/>
      </coding>
    </valueCodeableConcept>
  </component>
</Observation>