Clinical Genomics Resource Incubator
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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

: Molecular Definition Literal Encoding

Page standards status: Informative Maturity Level: 1

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{
  "resourceType" : "CodeSystem",
  "id" : "moleculardefinition-literal-encoding",
  "meta" : {
    "lastUpdated" : "2025-01-30T00:00:00Z",
    "profile" : [
      🔗 "http://hl7.org/fhir/StructureDefinition/shareablecodesystem"
    ]
  },
  "language" : "en",
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: CodeSystem moleculardefinition-literal-encoding</b></p><a name=\"moleculardefinition-literal-encoding\"> </a><a name=\"hcmoleculardefinition-literal-encoding\"> </a><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Last updated: 2025-01-30 00:00:00+0000</p><p style=\"margin-bottom: 0px\">Profile: <a href=\"http://hl7.org/fhir/R5/shareablecodesystem.html\">Shareable CodeSystem</a></p></div><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/cg-incubator/CodeSystem/moleculardefinition-literal-encoding</code> defines the following codes:</p><table class=\"codes\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td style=\"white-space:nowrap\">nuc-dna-1-noamb<a name=\"moleculardefinition-literal-encoding-nuc-dna-1-noamb\"> </a></td><td>Nucleotide, 1-letter, no ambiguity, DNA residues</td><td>Single-letter DNA nucleotide codes (A, C, G, T) without ambiguity codes. Based on IUPAC symbols.</td></tr><tr><td style=\"white-space:nowrap\">nuc-rna-1-noamb<a name=\"moleculardefinition-literal-encoding-nuc-rna-1-noamb\"> </a></td><td>Nucleotide, 1-letter, no ambiguity, RNA residues</td><td>Single-letter RNA nucleotide codes (A, C, G, U) without ambiguity codes. Based on IUPAC symbols.</td></tr><tr><td style=\"white-space:nowrap\">nuc-dna-1-noamb-n<a name=\"moleculardefinition-literal-encoding-nuc-dna-1-noamb-n\"> </a></td><td>Nucleotide, 1-letter, no ambiguity except N, DNA residues</td><td>Single-letter DNA nucleotide codes (A, C, G, T, N) where N represents any nucleotide. Based on IUPAC symbols.</td></tr><tr><td style=\"white-space:nowrap\">nuc-dna-1-amb<a name=\"moleculardefinition-literal-encoding-nuc-dna-1-amb\"> </a></td><td>Nucleotide, 1-letter, with ambiguity, DNA residues</td><td>Single-letter DNA nucleotide codes with ambiguity codes (A, C, G, T, R, Y, M, K, S, W, H, B, V, D, N). Based on IUPAC symbols.</td></tr><tr><td style=\"white-space:nowrap\">nuc-rna-1-amb<a name=\"moleculardefinition-literal-encoding-nuc-rna-1-amb\"> </a></td><td>Nucleotide, 1-letter, with ambiguity, RNA residues</td><td>Single-letter RNA nucleotide codes with ambiguity codes. Based on IUPAC symbols.</td></tr><tr><td style=\"white-space:nowrap\">aa-1-noamb-20common<a name=\"moleculardefinition-literal-encoding-aa-1-noamb-20common\"> </a></td><td>Amino acid, 1-letter, no ambiguity, 20 common</td><td>Standard single-letter amino acid codes for the 20 common amino acids without ambiguity codes (A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y). Based on IUPAC symbols.</td></tr><tr><td style=\"white-space:nowrap\">aa-3-noamb-20common<a name=\"moleculardefinition-literal-encoding-aa-3-noamb-20common\"> </a></td><td>Amino acid, 3-letter, no ambiguity, 20 common</td><td>Three-letter amino acid codes for the 20 common amino acids without ambiguity codes (Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, Val). Based on IUPAC symbols.</td></tr><tr><td style=\"white-space:nowrap\">aa-1-amb<a name=\"moleculardefinition-literal-encoding-aa-1-amb\"> </a></td><td>Amino acid, 1-letter, with ambiguity</td><td>Single-letter amino acid codes with ambiguity codes (A, B, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, U, V, W, X, Y, Z). Based on IUPAC symbols.</td></tr><tr><td style=\"white-space:nowrap\">aa-3-amb<a name=\"moleculardefinition-literal-encoding-aa-3-amb\"> </a></td><td>Amino acid, 3-letter, with ambiguity</td><td>Three-letter amino acid codes with ambiguity codes (Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, Val, Asx, Sec, Xaa, Glx). Based on IUPAC symbols.</td></tr></table></div>"
  },
  "extension" : [
    {
      "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
      "valueCode" : "cg"
    },
    {
      "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
      "valueCode" : "informative"
    },
    {
      "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
      "valueInteger" : 1
    }
  ],
  "url" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/moleculardefinition-literal-encoding",
  "identifier" : [
    {
      "system" : "urn:ietf:rfc:3986",
      "value" : "urn:oid:2.16.840.1.113883.4.642.4.2051"
    }
  ],
  "version" : "0.1.0-ci-build",
  "name" : "MolecularDefinitionLiteralEncoding",
  "title" : "Molecular Definition Literal Encoding",
  "status" : "draft",
  "experimental" : true,
  "date" : "2025-01-30",
  "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" : "Codes for the encoding used in molecular definition literal representations, based on IUPAC standards for nucleotide and amino acid sequences.",
  "jurisdiction" : [
    {
      "coding" : [
        {
          "system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
          "code" : "001",
          "display" : "World"
        }
      ]
    }
  ],
  "caseSensitive" : true,
  "valueSet" : "http://hl7.org/fhir/uv/cg-incubator/ValueSet/moleculardefinition-literal-encoding",
  "content" : "complete",
  "concept" : [
    {
      "code" : "nuc-dna-1-noamb",
      "display" : "Nucleotide, 1-letter, no ambiguity, DNA residues",
      "definition" : "Single-letter DNA nucleotide codes (A, C, G, T) without ambiguity codes. Based on IUPAC symbols."
    },
    {
      "code" : "nuc-rna-1-noamb",
      "display" : "Nucleotide, 1-letter, no ambiguity, RNA residues",
      "definition" : "Single-letter RNA nucleotide codes (A, C, G, U) without ambiguity codes. Based on IUPAC symbols."
    },
    {
      "code" : "nuc-dna-1-noamb-n",
      "display" : "Nucleotide, 1-letter, no ambiguity except N, DNA residues",
      "definition" : "Single-letter DNA nucleotide codes (A, C, G, T, N) where N represents any nucleotide. Based on IUPAC symbols."
    },
    {
      "code" : "nuc-dna-1-amb",
      "display" : "Nucleotide, 1-letter, with ambiguity, DNA residues",
      "definition" : "Single-letter DNA nucleotide codes with ambiguity codes (A, C, G, T, R, Y, M, K, S, W, H, B, V, D, N). Based on IUPAC symbols."
    },
    {
      "code" : "nuc-rna-1-amb",
      "display" : "Nucleotide, 1-letter, with ambiguity, RNA residues",
      "definition" : "Single-letter RNA nucleotide codes with ambiguity codes. Based on IUPAC symbols."
    },
    {
      "code" : "aa-1-noamb-20common",
      "display" : "Amino acid, 1-letter, no ambiguity, 20 common",
      "definition" : "Standard single-letter amino acid codes for the 20 common amino acids without ambiguity codes (A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y). Based on IUPAC symbols."
    },
    {
      "code" : "aa-3-noamb-20common",
      "display" : "Amino acid, 3-letter, no ambiguity, 20 common",
      "definition" : "Three-letter amino acid codes for the 20 common amino acids without ambiguity codes (Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, Val). Based on IUPAC symbols."
    },
    {
      "code" : "aa-1-amb",
      "display" : "Amino acid, 1-letter, with ambiguity",
      "definition" : "Single-letter amino acid codes with ambiguity codes (A, B, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, U, V, W, X, Y, Z). Based on IUPAC symbols."
    },
    {
      "code" : "aa-3-amb",
      "display" : "Amino acid, 3-letter, with ambiguity",
      "definition" : "Three-letter amino acid codes with ambiguity codes (Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, Val, Asx, Sec, Xaa, Glx). Based on IUPAC symbols."
    }
  ]
}