Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide
3.0.0 - release
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
| Active as of 2024-11-24 |
<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="2024-11-24T13:22:27+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>
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-11-24
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