Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions

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: NCBI Taxonomy (fragment)

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{
  "resourceType" : "CodeSystem",
  "id" : "ncbi-taxonomy-fragment",
  "language" : "en",
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: CodeSystem ncbi-taxonomy-fragment</b></p><a name=\"ncbi-taxonomy-fragment\"> </a><a name=\"hcncbi-taxonomy-fragment\"> </a><p>This case-insensitive code system <code>http://www.ncbi.nlm.nih.gov/taxonomy</code> provides <b>a fragment</b> that includes following codes:</p><table class=\"codes\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td></tr><tr><td style=\"white-space:nowrap\">9606<a name=\"ncbi-taxonomy-fragment-9606\"> </a></td><td>Homo sapiens</td></tr><tr><td style=\"white-space:nowrap\">10090<a name=\"ncbi-taxonomy-fragment-10090\"> </a></td><td>Mus musculus</td></tr><tr><td style=\"white-space:nowrap\">10116<a name=\"ncbi-taxonomy-fragment-10116\"> </a></td><td>Rattus norvegicus</td></tr><tr><td style=\"white-space:nowrap\">7955<a name=\"ncbi-taxonomy-fragment-7955\"> </a></td><td>Danio rerio</td></tr><tr><td style=\"white-space:nowrap\">2697049<a name=\"ncbi-taxonomy-fragment-2697049\"> </a></td><td>Severe acute respiratory syndrome coronavirus 2</td></tr><tr><td style=\"white-space:nowrap\">11520<a name=\"ncbi-taxonomy-fragment-11520\"> </a></td><td>Influenza B virus</td></tr><tr><td style=\"white-space:nowrap\">11320<a name=\"ncbi-taxonomy-fragment-11320\"> </a></td><td>Influenza A virus</td></tr><tr><td style=\"white-space:nowrap\">11234<a name=\"ncbi-taxonomy-fragment-11234\"> </a></td><td>Measles morbillivirus</td></tr><tr><td style=\"white-space:nowrap\">11250<a name=\"ncbi-taxonomy-fragment-11250\"> </a></td><td>Human orthopneumovirus</td></tr><tr><td style=\"white-space:nowrap\">12227<a name=\"ncbi-taxonomy-fragment-12227\"> </a></td><td>Human rhinovirus A</td></tr><tr><td style=\"white-space:nowrap\">11103<a name=\"ncbi-taxonomy-fragment-11103\"> </a></td><td>Hepacivirus C</td></tr><tr><td style=\"white-space:nowrap\">10359<a name=\"ncbi-taxonomy-fragment-10359\"> </a></td><td>Human cytomegalovirus</td></tr><tr><td style=\"white-space:nowrap\">10376<a name=\"ncbi-taxonomy-fragment-10376\"> </a></td><td>Human herpesvirus 4</td></tr></table></div>"
  },
  "extension" : [
    {
      "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
      "valueCode" : "cg"
    },
    {
      "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
      "valueInteger" : 1,
      "_valueInteger" : {
        "extension" : [
          {
            "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom",
            "valueCanonical" : "http://hl7.org/fhir/uv/cg-incubator/ImplementationGuide/hl7.fhir.uv.cg-incubator"
          }
        ]
      }
    },
    {
      "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
      "valueCode" : "trial-use",
      "_valueCode" : {
        "extension" : [
          {
            "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom",
            "valueCanonical" : "http://hl7.org/fhir/uv/cg-incubator/ImplementationGuide/hl7.fhir.uv.cg-incubator"
          }
        ]
      }
    }
  ],
  "url" : "http://www.ncbi.nlm.nih.gov/taxonomy",
  "version" : "0.1.0-ci-build",
  "name" : "NCBITaxonomyFragment",
  "title" : "NCBI Taxonomy (fragment)",
  "status" : "active",
  "experimental" : false,
  "date" : "2026-03-16",
  "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" : "clingenomics@lists.hl7.org"
        }
      ]
    }
  ],
  "description" : "A fragment of the NCBI Taxonomy database (https://www.ncbi.nlm.nih.gov/taxonomy) containing taxon IDs referenced by examples and profiles in this IG. Numeric taxon IDs are used as codes; scientific names are used as display text. This fragment covers commonly used research organisms and representative clinical viral pathogens. Add entries here as new examples reference additional taxon IDs.",
  "jurisdiction" : [
    {
      "coding" : [
        {
          "system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
          "code" : "001",
          "display" : "World"
        }
      ]
    }
  ],
  "copyright" : "NCBI Taxonomy data is a product of the National Center for Biotechnology Information (NCBI), part of the National Library of Medicine at the National Institutes of Health. The database is freely available in the public domain.",
  "caseSensitive" : false,
  "content" : "fragment",
  "concept" : [
    {
      "code" : "9606",
      "display" : "Homo sapiens"
    },
    {
      "code" : "10090",
      "display" : "Mus musculus"
    },
    {
      "code" : "10116",
      "display" : "Rattus norvegicus"
    },
    {
      "code" : "7955",
      "display" : "Danio rerio"
    },
    {
      "code" : "2697049",
      "display" : "Severe acute respiratory syndrome coronavirus 2"
    },
    {
      "code" : "11520",
      "display" : "Influenza B virus"
    },
    {
      "code" : "11320",
      "display" : "Influenza A virus"
    },
    {
      "code" : "11234",
      "display" : "Measles morbillivirus"
    },
    {
      "code" : "11250",
      "display" : "Human orthopneumovirus"
    },
    {
      "code" : "12227",
      "display" : "Human rhinovirus A"
    },
    {
      "code" : "11103",
      "display" : "Hepacivirus C"
    },
    {
      "code" : "10359",
      "display" : "Human cytomegalovirus"
    },
    {
      "code" : "10376",
      "display" : "Human herpesvirus 4"
    }
  ]
}