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

CodeSystem: Molecular Definition Literal Encoding (Experimental)

Official URL: http://hl7.org/fhir/uv/cg-incubator/CodeSystem/moleculardefinition-literal-encoding Version: 0.1.0-ci-build
Standards status: Informative Draft as of 2025-01-30 Maturity Level: 1 Computable Name: MolecularDefinitionLiteralEncoding
Other Identifiers: OID:2.16.840.1.113883.4.642.4.2051

Codes for the encoding used in molecular definition literal representations, based on IUPAC standards for nucleotide and amino acid sequences.

This Code system is referenced in the definition of the following value sets:

Last updated: 2025-01-30 00:00:00+0000

Profile: Shareable CodeSystem

This case-sensitive code system http://hl7.org/fhir/uv/cg-incubator/CodeSystem/moleculardefinition-literal-encoding defines the following codes:

CodeDisplayDefinition
nuc-dna-1-noamb Nucleotide, 1-letter, no ambiguity, DNA residues Single-letter DNA nucleotide codes (A, C, G, T) without ambiguity codes. Based on IUPAC symbols.
nuc-rna-1-noamb Nucleotide, 1-letter, no ambiguity, RNA residues Single-letter RNA nucleotide codes (A, C, G, U) without ambiguity codes. Based on IUPAC symbols.
nuc-dna-1-noamb-n Nucleotide, 1-letter, no ambiguity except N, DNA residues Single-letter DNA nucleotide codes (A, C, G, T, N) where N represents any nucleotide. Based on IUPAC symbols.
nuc-dna-1-amb Nucleotide, 1-letter, with ambiguity, DNA residues 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.
nuc-rna-1-amb Nucleotide, 1-letter, with ambiguity, RNA residues Single-letter RNA nucleotide codes with ambiguity codes. Based on IUPAC symbols.
aa-1-noamb-20common Amino acid, 1-letter, no ambiguity, 20 common 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.
aa-3-noamb-20common Amino acid, 3-letter, no ambiguity, 20 common 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.
aa-1-amb Amino acid, 1-letter, with ambiguity 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.
aa-3-amb Amino acid, 3-letter, with ambiguity 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.

Description of the above table(s).