Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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 - TTL Representation
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@prefix fhir: <http://hl7.org/fhir/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
# - resource -------------------------------------------------------------------
a fhir:CodeSystem ;
fhir:nodeRole fhir:treeRoot ;
fhir:id [ fhir:v "molecular-biomarker-ontology-cs"] ; #
fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><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 heirarchy:</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>"
] ; #
fhir:extension ( [
fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg"^^xsd:anyURI ] ;
fhir:value [ fhir:v "cg" ]
] ) ; #
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs"^^xsd:anyURI] ; #
fhir:version [ fhir:v "3.0.1-SNAPSHOT"] ; #
fhir:name [ fhir:v "MolecularBiomarkerOntologyCS"] ; #
fhir:title [ fhir:v "Molecular Biomarker Ontology Codes"] ; #
fhir:status [ fhir:v "active"] ; #
fhir:experimental [ fhir:v "true"^^xsd:boolean] ; #
fhir:date [ fhir:v "2024-04-09T13:57:55+00:00"^^xsd:dateTime] ; #
fhir:publisher [ fhir:v "HL7 International / Clinical Genomics"] ; #
fhir:contact ( [
fhir:name [ fhir:v "HL7 International / Clinical Genomics" ] ;
( fhir:telecom [
fhir:system [ fhir:v "url" ] ;
fhir:value [ fhir:v "http://www.hl7.org/Special/committees/clingenomics" ] ] [
fhir:system [ fhir:v "email" ] ;
fhir:value [ fhir:v "cg@lists.HL7.org" ] ] )
] ) ; #
fhir:description [ fhir:v "This (experimental) code system provides for a draft categorization of biomarkers along several axes. Based on ballot feedback, the committee anticipates significant revisions."] ; #
fhir:jurisdiction ( [
( fhir:coding [
fhir:system [ fhir:v "http://unstats.un.org/unsd/methods/m49/m49.htm"^^xsd:anyURI ] ;
fhir:code [ fhir:v "001" ] ;
fhir:display [ fhir:v "World" ] ] )
] ) ; #
fhir:caseSensitive [ fhir:v "true"^^xsd:boolean] ; #
fhir:hierarchyMeaning [ fhir:v "is-a"] ; #
fhir:content [ fhir:v "complete"] ; #
fhir:count [ fhir:v "17"^^xsd:nonNegativeInteger] ; #
fhir:concept ( [
fhir:code [ fhir:v "_physiologyBiomarkerCategory" ] ;
fhir:display [ fhir:v "Molecular biomarker physiologic role category" ] ;
fhir:definition [ fhir:v "A category based on the normal bodily function of the biomarker." ] ;
( fhir:concept [
fhir:code [ fhir:v "antibody" ] ;
fhir:display [ fhir:v "antibody category" ] ;
fhir:definition [ fhir:v "Molecular biomarker physiologic role is an antibody." ] ] [
fhir:code [ fhir:v "antgen" ] ;
fhir:display [ fhir:v "antigen category" ] ;
fhir:definition [ fhir:v "Molecular biomarker physiologic role is an antigen." ] ] [
fhir:code [ fhir:v "cellReceptor" ] ;
fhir:display [ fhir:v "cell receptor category" ] ;
fhir:definition [ fhir:v "Molecular biomarker physiologic role is a cell receptor." ] ] [
fhir:code [ fhir:v "cellReceptorLigand" ] ;
fhir:display [ fhir:v "cell receptor ligand category" ] ;
fhir:definition [ fhir:v "Molecular biomarker physiologic role is a cell receptor ligand." ] ] )
] [
fhir:code [ fhir:v "_moleculeTypeBiomarkerCategory" ] ;
fhir:display [ fhir:v "Molecular biomarker molecular type category" ] ;
fhir:definition [ fhir:v "A category based on the type of biomarker molecule." ] ;
( fhir:concept [
fhir:code [ fhir:v "carbohydrate" ] ;
fhir:display [ fhir:v "carbohydrate category" ] ;
fhir:definition [ fhir:v "Molecular biomarker molecule type is a carbohydrate." ] ] [
fhir:code [ fhir:v "lipid" ] ;
fhir:display [ fhir:v "lipid category" ] ;
fhir:definition [ fhir:v "Molecular biomarker molecule type is a lipid." ] ] [
fhir:code [ fhir:v "nucleicAcid" ] ;
fhir:display [ fhir:v "nucleic acid category" ] ;
fhir:definition [ fhir:v "Molecular biomarker molecule type is a nucleic acid." ] ] [
fhir:code [ fhir:v "protein" ] ;
fhir:display [ fhir:v "protein category" ] ;
fhir:definition [ fhir:v "Molecular biomarker molecule type is a protein. Includes single or multi-subunit proteins with or without post-translational modifications." ] ] )
] [
fhir:code [ fhir:v "_methodBiomarkerCategory" ] ;
fhir:display [ fhir:v "Molecular biomarker method type category" ] ;
fhir:definition [ fhir:v "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/))." ] ;
( fhir:concept [
fhir:code [ fhir:v "enzymeAssay" ] ;
fhir:display [ fhir:v "enzyme assay category" ] ;
fhir:definition [ fhir:v "Molecular biomarker method is enzyme assay." ] ] [
fhir:code [ fhir:v "flowCytometry" ] ;
fhir:display [ fhir:v "flow cytometry category" ] ;
fhir:definition [ fhir:v "Molecular biomarker method is flow cytometry." ] ] [
fhir:code [ fhir:v "immuneStain" ] ;
fhir:display [ fhir:v "immune stain category" ] ;
fhir:definition [ fhir:v "Molecular biomarker method is immune stain." ] ] [
fhir:code [ fhir:v "immunoassay" ] ;
fhir:display [ fhir:v "immunoassay category" ] ;
fhir:definition [ fhir:v "Molecular biomarker method is immunoassay." ] ] [
fhir:code [ fhir:v "methylationAnalysis" ] ;
fhir:display [ fhir:v "methylation analysis category" ] ;
fhir:definition [ fhir:v "Molecular biomarker method is methylation analysis." ] ] [
fhir:code [ fhir:v "molgen" ] ;
fhir:display [ fhir:v "molecular sequence adjacent category" ] ;
fhir:definition [ fhir:v "Molecular biomarker method is molecular sequence adjacent observation." ] ] )
] ) . #
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