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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<CodeSystem xmlns="http://hl7.org/fhir">
  <id value="moleculardefinition-literal-encoding"/>
  <meta>
    <lastUpdated value="2025-01-30T00:00:00Z"/>
    <profile
             value="http://hl7.org/fhir/StructureDefinition/shareablecodesystem"/>
  </meta>
  <language value="en"/>
  <text>
    <status value="generated"/>
    <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>
  </text>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
    <valueCode value="cg"/>
  </extension>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
    <valueCode value="informative"/>
  </extension>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm">
    <valueInteger value="1"/>
  </extension>
  <url
       value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/moleculardefinition-literal-encoding"/>
  <identifier>
    <system value="urn:ietf:rfc:3986"/>
    <value value="urn:oid:2.16.840.1.113883.4.642.4.2051"/>
  </identifier>
  <version value="0.1.0-ci-build"/>
  <name value="MolecularDefinitionLiteralEncoding"/>
  <title value="Molecular Definition Literal Encoding"/>
  <status value="draft"/>
  <experimental value="true"/>
  <date value="2025-01-30"/>
  <publisher value="HL7 International / Clinical Genomics"/>
  <contact>
    <name value="HL7 International / Clinical Genomics"/>
    <telecom>
      <system value="url"/>
      <value value="http://www.hl7.org/Special/committees/clingenomics"/>
    </telecom>
    <telecom>
      <system value="email"/>
      <value value="clingenomics@lists.hl7.org"/>
    </telecom>
  </contact>
  <description
               value="Codes for the encoding used in molecular definition literal representations, based on IUPAC standards for nucleotide and amino acid sequences."/>
  <jurisdiction>
    <coding>
      <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
      <code value="001"/>
      <display value="World"/>
    </coding>
  </jurisdiction>
  <caseSensitive value="true"/>
  <valueSet
            value="http://hl7.org/fhir/uv/cg-incubator/ValueSet/moleculardefinition-literal-encoding"/>
  <content value="complete"/>
  <concept>
    <code value="nuc-dna-1-noamb"/>
    <display value="Nucleotide, 1-letter, no ambiguity, DNA residues"/>
    <definition
                value="Single-letter DNA nucleotide codes (A, C, G, T) without ambiguity codes. Based on IUPAC symbols."/>
  </concept>
  <concept>
    <code value="nuc-rna-1-noamb"/>
    <display value="Nucleotide, 1-letter, no ambiguity, RNA residues"/>
    <definition
                value="Single-letter RNA nucleotide codes (A, C, G, U) without ambiguity codes. Based on IUPAC symbols."/>
  </concept>
  <concept>
    <code value="nuc-dna-1-noamb-n"/>
    <display
             value="Nucleotide, 1-letter, no ambiguity except N, DNA residues"/>
    <definition
                value="Single-letter DNA nucleotide codes (A, C, G, T, N) where N represents any nucleotide. Based on IUPAC symbols."/>
  </concept>
  <concept>
    <code value="nuc-dna-1-amb"/>
    <display value="Nucleotide, 1-letter, with ambiguity, DNA residues"/>
    <definition
                value="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."/>
  </concept>
  <concept>
    <code value="nuc-rna-1-amb"/>
    <display value="Nucleotide, 1-letter, with ambiguity, RNA residues"/>
    <definition
                value="Single-letter RNA nucleotide codes with ambiguity codes. Based on IUPAC symbols."/>
  </concept>
  <concept>
    <code value="aa-1-noamb-20common"/>
    <display value="Amino acid, 1-letter, no ambiguity, 20 common"/>
    <definition
                value="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."/>
  </concept>
  <concept>
    <code value="aa-3-noamb-20common"/>
    <display value="Amino acid, 3-letter, no ambiguity, 20 common"/>
    <definition
                value="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."/>
  </concept>
  <concept>
    <code value="aa-1-amb"/>
    <display value="Amino acid, 1-letter, with ambiguity"/>
    <definition
                value="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."/>
  </concept>
  <concept>
    <code value="aa-3-amb"/>
    <display value="Amino acid, 3-letter, with ambiguity"/>
    <definition
                value="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."/>
  </concept>
</CodeSystem>