Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide
3.0.0 - STU3
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 2024-12-12 |
{
"resourceType" : "CodeSystem",
"id" : "molecular-biomarker-ontology-cs",
"text" : {
"status" : "generated",
"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><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\">\u00a0\u00a0antibody<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\">\u00a0\u00a0antgen<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\">\u00a0\u00a0cellReceptor<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\">\u00a0\u00a0cellReceptorLigand<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\">\u00a0\u00a0carbohydrate<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\">\u00a0\u00a0lipid<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\">\u00a0\u00a0nucleicAcid<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\">\u00a0\u00a0protein<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\">\u00a0\u00a0enzymeAssay<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\">\u00a0\u00a0flowCytometry<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\">\u00a0\u00a0immuneStain<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\">\u00a0\u00a0immunoassay<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\">\u00a0\u00a0methylationAnalysis<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\">\u00a0\u00a0molgen<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>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
"valueCode" : "cg"
}
],
"url" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs",
"version" : "3.0.0",
"name" : "MolecularBiomarkerOntologyCS",
"title" : "Molecular Biomarker Ontology Codes",
"status" : "active",
"experimental" : true,
"date" : "2024-12-12T20:13:16+00:00",
"publisher" : "HL7 International / Clinical Genomics",
"contact" : [
{
"name" : "HL7 International / Clinical Genomics",
"telecom" : [
{
"system" : "url",
"value" : "http://www.hl7.org/Special/committees/clingenomics"
},
{
"system" : "email",
"value" : "cg@lists.HL7.org"
}
]
}
],
"description" : "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" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code" : "001",
"display" : "World"
}
]
}
],
"caseSensitive" : true,
"hierarchyMeaning" : "is-a",
"content" : "complete",
"count" : 17,
"concept" : [
{
"code" : "_physiologyBiomarkerCategory",
"display" : "Molecular biomarker physiologic role category",
"definition" : "A category based on the normal bodily function of the biomarker.",
"concept" : [
{
"code" : "antibody",
"display" : "antibody category",
"definition" : "Molecular biomarker physiologic role is an antibody."
},
{
"code" : "antgen",
"display" : "antigen category",
"definition" : "Molecular biomarker physiologic role is an antigen."
},
{
"code" : "cellReceptor",
"display" : "cell receptor category",
"definition" : "Molecular biomarker physiologic role is a cell receptor."
},
{
"code" : "cellReceptorLigand",
"display" : "cell receptor ligand category",
"definition" : "Molecular biomarker physiologic role is a cell receptor ligand."
}
]
},
{
"code" : "_moleculeTypeBiomarkerCategory",
"display" : "Molecular biomarker molecular type category",
"definition" : "A category based on the type of biomarker molecule.",
"concept" : [
{
"code" : "carbohydrate",
"display" : "carbohydrate category",
"definition" : "Molecular biomarker molecule type is a carbohydrate."
},
{
"code" : "lipid",
"display" : "lipid category",
"definition" : "Molecular biomarker molecule type is a lipid."
},
{
"code" : "nucleicAcid",
"display" : "nucleic acid category",
"definition" : "Molecular biomarker molecule type is a nucleic acid."
},
{
"code" : "protein",
"display" : "protein category",
"definition" : "Molecular biomarker molecule type is a protein. Includes single or multi-subunit proteins with or without post-translational modifications."
}
]
},
{
"code" : "_methodBiomarkerCategory",
"display" : "Molecular biomarker method type category",
"definition" : "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" : "enzymeAssay",
"display" : "enzyme assay category",
"definition" : "Molecular biomarker method is enzyme assay."
},
{
"code" : "flowCytometry",
"display" : "flow cytometry category",
"definition" : "Molecular biomarker method is flow cytometry."
},
{
"code" : "immuneStain",
"display" : "immune stain category",
"definition" : "Molecular biomarker method is immune stain."
},
{
"code" : "immunoassay",
"display" : "immunoassay category",
"definition" : "Molecular biomarker method is immunoassay."
},
{
"code" : "methylationAnalysis",
"display" : "methylation analysis category",
"definition" : "Molecular biomarker method is methylation analysis."
},
{
"code" : "molgen",
"display" : "molecular sequence adjacent category",
"definition" : "Molecular biomarker method is molecular sequence adjacent observation."
}
]
}
]
}
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-12-12
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