Genomics Reporting Implementation Guide
3.0.0 - STU3 International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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

Active as of 2024-12-12

Raw xml | Download


<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><a name="molecular-biomarker-ontology-cs-en-US"> </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>
  <url
       value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs"/>
  <version value="3.0.0"/>
  <name value="MolecularBiomarkerOntologyCS"/>
  <title value="Molecular Biomarker Ontology Codes"/>
  <status value="active"/>
  <experimental value="true"/>
  <date value="2024-12-12T20:13:16+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>