Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build
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
| Page standards status: Informative |
@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 -------------------------------------------------------------------
<http://hl7.org/fhir/CodeSystem/molecular-biomarker-ontology-cs> a fhir:CodeSystem ;
fhir:nodeRole fhir:treeRoot ;
fhir:Resource.id [ fhir:value "molecular-biomarker-ontology-cs"] ;
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ] ;
fhir:Narrative.div "<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>"
] ;
fhir:DomainResource.extension [
fhir:index 0 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg" ] ;
fhir:Extension.valueCode [ fhir:value "cg" ]
], [
fhir:index 1 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status" ] ;
fhir:Extension.valueCode [
fhir:value "informative" ;
fhir:Element.extension [
fhir:index 0 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom" ] ;
fhir:Extension.valueCanonical [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/ImplementationGuide/genomics-reporting" ;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/ImplementationGuide/genomics-reporting>
]
]
]
] ;
fhir:CodeSystem.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs"] ;
fhir:CodeSystem.version [ fhir:value "4.0.0-cibuild"] ;
fhir:CodeSystem.name [ fhir:value "MolecularBiomarkerOntologyCS"] ;
fhir:CodeSystem.title [ fhir:value "Molecular Biomarker Ontology Codes"] ;
fhir:CodeSystem.status [ fhir:value "active"] ;
fhir:CodeSystem.experimental [ fhir:value "true"^^xsd:boolean] ;
fhir:CodeSystem.date [ fhir:value "2026-09-21T13:24:35+00:00"^^xsd:dateTime] ;
fhir:CodeSystem.publisher [ fhir:value "HL7 International / Clinical Genomics"] ;
fhir:CodeSystem.contact [
fhir:index 0 ;
fhir:ContactDetail.name [ fhir:value "HL7 International / Clinical Genomics" ] ;
fhir:ContactDetail.telecom [
fhir:index 0 ;
fhir:ContactPoint.system [ fhir:value "url" ] ;
fhir:ContactPoint.value [ fhir:value "http://www.hl7.org/Special/committees/clingenomics" ]
], [
fhir:index 1 ;
fhir:ContactPoint.system [ fhir:value "email" ] ;
fhir:ContactPoint.value [ fhir:value "cg@lists.HL7.org" ]
]
] ;
fhir:CodeSystem.description [ fhir:value "This (experimental) code system provides for a draft categorization of biomarkers along several axes. Based on ballot feedback, the committee anticipates significant revisions."] ;
fhir:CodeSystem.jurisdiction [
fhir:index 0 ;
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://unstats.un.org/unsd/methods/m49/m49.htm" ] ;
fhir:Coding.code [ fhir:value "001" ] ;
fhir:Coding.display [ fhir:value "World" ]
]
] ;
fhir:CodeSystem.caseSensitive [ fhir:value "true"^^xsd:boolean] ;
fhir:CodeSystem.hierarchyMeaning [ fhir:value "is-a"] ;
fhir:CodeSystem.content [ fhir:value "complete"] ;
fhir:CodeSystem.count [ fhir:value "17"^^xsd:nonNegativeInteger] ;
fhir:CodeSystem.concept [
fhir:index 0 ;
fhir:CodeSystem.concept.code [ fhir:value "_physiologyBiomarkerCategory" ] ;
fhir:CodeSystem.concept.display [ fhir:value "Molecular biomarker physiologic role category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "A category based on the normal bodily function of the biomarker." ] ;
fhir:CodeSystem.concept.concept [
fhir:index 0 ;
fhir:CodeSystem.concept.code [ fhir:value "antibody" ] ;
fhir:CodeSystem.concept.display [ fhir:value "antibody category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Molecular biomarker physiologic role is an antibody." ]
], [
fhir:index 1 ;
fhir:CodeSystem.concept.code [ fhir:value "antgen" ] ;
fhir:CodeSystem.concept.display [ fhir:value "antigen category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Molecular biomarker physiologic role is an antigen." ]
], [
fhir:index 2 ;
fhir:CodeSystem.concept.code [ fhir:value "cellReceptor" ] ;
fhir:CodeSystem.concept.display [ fhir:value "cell receptor category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Molecular biomarker physiologic role is a cell receptor." ]
], [
fhir:index 3 ;
fhir:CodeSystem.concept.code [ fhir:value "cellReceptorLigand" ] ;
fhir:CodeSystem.concept.display [ fhir:value "cell receptor ligand category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Molecular biomarker physiologic role is a cell receptor ligand." ]
]
], [
fhir:index 1 ;
fhir:CodeSystem.concept.code [ fhir:value "_moleculeTypeBiomarkerCategory" ] ;
fhir:CodeSystem.concept.display [ fhir:value "Molecular biomarker molecular type category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "A category based on the type of biomarker molecule." ] ;
fhir:CodeSystem.concept.concept [
fhir:index 0 ;
fhir:CodeSystem.concept.code [ fhir:value "carbohydrate" ] ;
fhir:CodeSystem.concept.display [ fhir:value "carbohydrate category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Molecular biomarker molecule type is a carbohydrate." ]
], [
fhir:index 1 ;
fhir:CodeSystem.concept.code [ fhir:value "lipid" ] ;
fhir:CodeSystem.concept.display [ fhir:value "lipid category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Molecular biomarker molecule type is a lipid." ]
], [
fhir:index 2 ;
fhir:CodeSystem.concept.code [ fhir:value "nucleicAcid" ] ;
fhir:CodeSystem.concept.display [ fhir:value "nucleic acid category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Molecular biomarker molecule type is a nucleic acid." ]
], [
fhir:index 3 ;
fhir:CodeSystem.concept.code [ fhir:value "protein" ] ;
fhir:CodeSystem.concept.display [ fhir:value "protein category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Molecular biomarker molecule type is a protein. Includes single or multi-subunit proteins with or without post-translational modifications." ]
]
], [
fhir:index 2 ;
fhir:CodeSystem.concept.code [ fhir:value "_methodBiomarkerCategory" ] ;
fhir:CodeSystem.concept.display [ fhir:value "Molecular biomarker method type category" ] ;
fhir:CodeSystem.concept.definition [ fhir: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/))." ] ;
fhir:CodeSystem.concept.concept [
fhir:index 0 ;
fhir:CodeSystem.concept.code [ fhir:value "enzymeAssay" ] ;
fhir:CodeSystem.concept.display [ fhir:value "enzyme assay category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Molecular biomarker method is enzyme assay." ]
], [
fhir:index 1 ;
fhir:CodeSystem.concept.code [ fhir:value "flowCytometry" ] ;
fhir:CodeSystem.concept.display [ fhir:value "flow cytometry category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Molecular biomarker method is flow cytometry." ]
], [
fhir:index 2 ;
fhir:CodeSystem.concept.code [ fhir:value "immuneStain" ] ;
fhir:CodeSystem.concept.display [ fhir:value "immune stain category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Molecular biomarker method is immune stain." ]
], [
fhir:index 3 ;
fhir:CodeSystem.concept.code [ fhir:value "immunoassay" ] ;
fhir:CodeSystem.concept.display [ fhir:value "immunoassay category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Molecular biomarker method is immunoassay." ]
], [
fhir:index 4 ;
fhir:CodeSystem.concept.code [ fhir:value "methylationAnalysis" ] ;
fhir:CodeSystem.concept.display [ fhir:value "methylation analysis category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Molecular biomarker method is methylation analysis." ]
], [
fhir:index 5 ;
fhir:CodeSystem.concept.code [ fhir:value "molgen" ] ;
fhir:CodeSystem.concept.display [ fhir:value "molecular sequence adjacent category" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Molecular biomarker method is molecular sequence adjacent observation." ]
]
] .
# - ontology header ------------------------------------------------------------
<http://hl7.org/fhir/CodeSystem/molecular-biomarker-ontology-cs.ttl> a owl:Ontology ;
owl:imports fhir:fhir.ttl ;
owl:versionIRI <http://build.fhir.org/CodeSystem/molecular-biomarker-ontology-cs.ttl> .
IG © 2025+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#4.0.0-cibuild based on FHIR 4.0.1. Generated 2026-09-21
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