Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

## : Molecular Biomarker Ontology Codes - XML Representation

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    <CodeSystem xmlns="http://hl7.org/fhir">
      <id value="molecular-biomarker-ontology-cs"/>
      <text>
        <status value="generated"/>
        <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: CodeSystem molecular-biomarker-ontology-cs</b></p><a name="molecular-biomarker-ontology-cs"> </a><a name="hcmolecular-biomarker-ontology-cs"> </a><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs</code> defines the following codes in a Is-A hierarchy:</p><table class="codes"><tr><td><b>Lvl</b></td><td style="white-space:nowrap"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td>1</td><td style="white-space:nowrap">_physiologyBiomarkerCategory<a name="molecular-biomarker-ontology-cs-_physiologyBiomarkerCategory"> </a></td><td>Molecular biomarker physiologic role category</td><td>A category based on the normal bodily function of the biomarker.</td></tr><tr><td>2</td><td style="white-space:nowrap">  antibody<a name="molecular-biomarker-ontology-cs-antibody"> </a></td><td>antibody category</td><td>Molecular biomarker physiologic role is an antibody.</td></tr><tr><td>2</td><td style="white-space:nowrap">  antgen<a name="molecular-biomarker-ontology-cs-antgen"> </a></td><td>antigen category</td><td>Molecular biomarker physiologic role is an antigen.</td></tr><tr><td>2</td><td style="white-space:nowrap">  cellReceptor<a name="molecular-biomarker-ontology-cs-cellReceptor"> </a></td><td>cell receptor category</td><td>Molecular biomarker physiologic role is a cell receptor.</td></tr><tr><td>2</td><td style="white-space:nowrap">  cellReceptorLigand<a name="molecular-biomarker-ontology-cs-cellReceptorLigand"> </a></td><td>cell receptor ligand category</td><td>Molecular biomarker physiologic role is a cell receptor ligand.</td></tr><tr><td>1</td><td style="white-space:nowrap">_moleculeTypeBiomarkerCategory<a name="molecular-biomarker-ontology-cs-_moleculeTypeBiomarkerCategory"> </a></td><td>Molecular biomarker molecular type category</td><td>A category based on the type of biomarker molecule.</td></tr><tr><td>2</td><td style="white-space:nowrap">  carbohydrate<a name="molecular-biomarker-ontology-cs-carbohydrate"> </a></td><td>carbohydrate category</td><td>Molecular biomarker molecule type is a carbohydrate.</td></tr><tr><td>2</td><td style="white-space:nowrap">  lipid<a name="molecular-biomarker-ontology-cs-lipid"> </a></td><td>lipid category</td><td>Molecular biomarker molecule type is a lipid.</td></tr><tr><td>2</td><td style="white-space:nowrap">  nucleicAcid<a name="molecular-biomarker-ontology-cs-nucleicAcid"> </a></td><td>nucleic acid category</td><td>Molecular biomarker molecule type is a nucleic acid.</td></tr><tr><td>2</td><td style="white-space:nowrap">  protein<a name="molecular-biomarker-ontology-cs-protein"> </a></td><td>protein category</td><td>Molecular biomarker molecule type is a protein. Includes single or multi-subunit proteins with or without post-translational modifications.</td></tr><tr><td>1</td><td style="white-space:nowrap">_methodBiomarkerCategory<a name="molecular-biomarker-ontology-cs-_methodBiomarkerCategory"> </a></td><td>Molecular biomarker method type category</td><td>A category based on the measurement ascertainment method of the biomarker. (Methods are drawn from LOINC (https://loinc.org/kb/users-guide/major-parts-of-a-loinc-term/#type-of-method-6th-part) and NCBI Genetic Testing Registry (https://www.ncbi.nlm.nih.gov/gtr/)).</td></tr><tr><td>2</td><td style="white-space:nowrap">  enzymeAssay<a name="molecular-biomarker-ontology-cs-enzymeAssay"> </a></td><td>enzyme assay category</td><td>Molecular biomarker method is enzyme assay.</td></tr><tr><td>2</td><td style="white-space:nowrap">  flowCytometry<a name="molecular-biomarker-ontology-cs-flowCytometry"> </a></td><td>flow cytometry category</td><td>Molecular biomarker method is flow cytometry.</td></tr><tr><td>2</td><td style="white-space:nowrap">  immuneStain<a name="molecular-biomarker-ontology-cs-immuneStain"> </a></td><td>immune stain category</td><td>Molecular biomarker method is immune stain.</td></tr><tr><td>2</td><td style="white-space:nowrap">  immunoassay<a name="molecular-biomarker-ontology-cs-immunoassay"> </a></td><td>immunoassay category</td><td>Molecular biomarker method is immunoassay.</td></tr><tr><td>2</td><td style="white-space:nowrap">  methylationAnalysis<a name="molecular-biomarker-ontology-cs-methylationAnalysis"> </a></td><td>methylation analysis category</td><td>Molecular biomarker method is methylation analysis.</td></tr><tr><td>2</td><td style="white-space:nowrap">  molgen<a name="molecular-biomarker-ontology-cs-molgen"> </a></td><td>molecular sequence adjacent category</td><td>Molecular biomarker method is molecular sequence adjacent observation.</td></tr></table></div>
      </text>
      <extension
                 url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
        <valueCode value="cg"/>
      </extension>
      <extension
                 url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
        <valueCode value="informative">
          <extension
                     url="http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom">
            <valueCanonical
                            value="http://hl7.org/fhir/uv/genomics-reporting/ImplementationGuide/genomics-reporting"/>
          </extension>
        </valueCode>
      </extension>
      <url
           value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs"/>
      <version value="4.0.0-cibuild"/>
      <name value="MolecularBiomarkerOntologyCS"/>
      <title value="Molecular Biomarker Ontology Codes"/>
      <status value="active"/>
      <experimental value="true"/>
      <date value="2025-11-08T00:09:50+00:00"/>
      <publisher value="HL7 International / Clinical Genomics"/>
      <contact>
        <name value="HL7 International / Clinical Genomics"/>
        <telecom>
          <system value="url"/>
          <value value="http://www.hl7.org/Special/committees/clingenomics"/>
        </telecom>
        <telecom>
          <system value="email"/>
          <value value="cg@lists.HL7.org"/>
        </telecom>
      </contact>
      <description
                   value="This (experimental) code system provides for a draft categorization of biomarkers along several axes. Based on ballot feedback, the committee anticipates significant revisions."/>
      <jurisdiction>
        <coding>
          <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
          <code value="001"/>
          <display value="World"/>
        </coding>
      </jurisdiction>
      <caseSensitive value="true"/>
      <hierarchyMeaning value="is-a"/>
      <content value="complete"/>
      <count value="17"/>
      <concept>
        <code value="_physiologyBiomarkerCategory"/>
        <display value="Molecular biomarker physiologic role category"/>
        <definition
                    value="A category based on the normal bodily function of the biomarker."/>
        <concept>
          <code value="antibody"/>
          <display value="antibody category"/>
          <definition
                      value="Molecular biomarker physiologic role is an antibody."/>
        </concept>
        <concept>
          <code value="antgen"/>
          <display value="antigen category"/>
          <definition
                      value="Molecular biomarker physiologic role is an antigen."/>
        </concept>
        <concept>
          <code value="cellReceptor"/>
          <display value="cell receptor category"/>
          <definition
                      value="Molecular biomarker physiologic role is a cell receptor."/>
        </concept>
        <concept>
          <code value="cellReceptorLigand"/>
          <display value="cell receptor ligand category"/>
          <definition
                      value="Molecular biomarker physiologic role is a cell receptor ligand."/>
        </concept>
      </concept>
      <concept>
        <code value="_moleculeTypeBiomarkerCategory"/>
        <display value="Molecular biomarker molecular type category"/>
        <definition value="A category based on the type of biomarker molecule."/>
        <concept>
          <code value="carbohydrate"/>
          <display value="carbohydrate category"/>
          <definition
                      value="Molecular biomarker molecule type is a carbohydrate."/>
        </concept>
        <concept>
          <code value="lipid"/>
          <display value="lipid category"/>
          <definition value="Molecular biomarker molecule type is a lipid."/>
        </concept>
        <concept>
          <code value="nucleicAcid"/>
          <display value="nucleic acid category"/>
          <definition
                      value="Molecular biomarker molecule type is a nucleic acid."/>
        </concept>
        <concept>
          <code value="protein"/>
          <display value="protein category"/>
          <definition
                      value="Molecular biomarker molecule type is a protein. Includes single or multi-subunit proteins with or without post-translational modifications."/>
        </concept>
      </concept>
      <concept>
        <code value="_methodBiomarkerCategory"/>
        <display value="Molecular biomarker method type category"/>
        <definition
                    value="A category based on the measurement ascertainment method of the biomarker. (Methods are drawn from LOINC (https://loinc.org/kb/users-guide/major-parts-of-a-loinc-term/#type-of-method-6th-part) and NCBI Genetic Testing Registry (https://www.ncbi.nlm.nih.gov/gtr/))."/>
        <concept>
          <code value="enzymeAssay"/>
          <display value="enzyme assay category"/>
          <definition value="Molecular biomarker method is enzyme assay."/>
        </concept>
        <concept>
          <code value="flowCytometry"/>
          <display value="flow cytometry category"/>
          <definition value="Molecular biomarker method is flow cytometry."/>
        </concept>
        <concept>
          <code value="immuneStain"/>
          <display value="immune stain category"/>
          <definition value="Molecular biomarker method is immune stain."/>
        </concept>
        <concept>
          <code value="immunoassay"/>
          <display value="immunoassay category"/>
          <definition value="Molecular biomarker method is immunoassay."/>
        </concept>
        <concept>
          <code value="methylationAnalysis"/>
          <display value="methylation analysis category"/>
          <definition
                      value="Molecular biomarker method is methylation analysis."/>
        </concept>
        <concept>
          <code value="molgen"/>
          <display value="molecular sequence adjacent category"/>
          <definition
                      value="Molecular biomarker method is molecular sequence adjacent observation."/>
        </concept>
      </concept>
    </CodeSystem>