Genomics Reporting Implementation Guide
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This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

: Molecular Biomarker Ontology Codes - JSON Representation

Active as of 2023-12-18

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{
  "resourceType" : "CodeSystem",
  "id" : "molecular-biomarker-ontology-cs",
  "text" : {
    "status" : "generated",
    "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\">\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-ballot",
  "name" : "MolecularBiomarkerOntologyCS",
  "title" : "Molecular Biomarker Ontology Codes",
  "status" : "active",
  "experimental" : true,
  "date" : "2023-12-18T22:45:59+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."
        }
      ]
    }
  ]
}