valuesets 0.3.1__py3-none-any.whl

valuesets/schema/bio/sequence_alphabets.yaml

@@ -0,0 +1,1168 @@
+name: sequence_alphabets
+title: Biological Sequence Alphabet Value Sets
+description: 'Alphabets for biological sequences including DNA, RNA, and protein sequences. Includes standard alphabets and
+  extended versions with ambiguity codes following IUPAC nomenclature and common bioinformatics standards.
+
+  '
+id: https://w3id.org/valuesets/bio/sequence_alphabets
+imports:
+- linkml:types
+prefixes:
+  linkml: https://w3id.org/linkml/
+  SO: http://purl.obolibrary.org/obo/SO_
+  CHEBI: http://purl.obolibrary.org/obo/CHEBI_
+  EDAM: http://edamontology.org/
+  GENO: http://purl.obolibrary.org/obo/GENO_
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  dna_base:
+    description: Standard DNA nucleotide bases (canonical)
+    range: DNABaseEnum
+  dna_base_extended:
+    description: Extended DNA alphabet with IUPAC ambiguity codes
+    range: DNABaseExtendedEnum
+  rna_base:
+    description: Standard RNA nucleotide bases (canonical)
+    range: RNABaseEnum
+  rna_base_extended:
+    description: Extended RNA alphabet with IUPAC ambiguity codes
+    range: RNABaseExtendedEnum
+  amino_acid:
+    description: Standard amino acid single letter codes
+    range: AminoAcidEnum
+  amino_acid_extended:
+    description: Extended amino acid alphabet with ambiguity codes and special characters
+    range: AminoAcidExtendedEnum
+  codon:
+    description: Standard genetic code codons (DNA)
+    range: CodonEnum
+  nucleotide_modification:
+    description: Common nucleotide modifications
+    range: NucleotideModificationEnum
+  sequence_quality:
+    description: Sequence quality indicators (Phred scores)
+    range: SequenceQualityEnum
+enums:
+  DNABaseEnum:
+    description: Standard DNA nucleotide bases (canonical)
+    permissible_values:
+      A:
+        title: Adenine
+        aliases:
+        - adenine
+        meaning: CHEBI:16708
+        annotations:
+          complement: T
+          purine: 'true'
+          chemical_formula: C5H5N5
+      C:
+        title: Cytosine
+        aliases:
+        - cytosine
+        meaning: CHEBI:16040
+        annotations:
+          complement: G
+          pyrimidine: 'true'
+          chemical_formula: C4H5N3O
+      G:
+        title: Guanine
+        aliases:
+        - guanine
+        meaning: CHEBI:16235
+        annotations:
+          complement: C
+          purine: 'true'
+          chemical_formula: C5H5N5O
+      T:
+        title: Thymine
+        aliases:
+        - thymine
+        meaning: CHEBI:17821
+        annotations:
+          complement: A
+          pyrimidine: 'true'
+          chemical_formula: C5H6N2O2
+  DNABaseExtendedEnum:
+    description: Extended DNA alphabet with IUPAC ambiguity codes
+    permissible_values:
+      A:
+        title: Adenine
+        aliases:
+        - adenine
+        meaning: CHEBI:16708
+        annotations:
+          represents: A
+      C:
+        title: Cytosine
+        aliases:
+        - cytosine
+        meaning: CHEBI:16040
+        annotations:
+          represents: C
+      G:
+        title: Guanine
+        aliases:
+        - guanine
+        meaning: CHEBI:16235
+        annotations:
+          represents: G
+      T:
+        title: Thymine
+        aliases:
+        - thymine
+        meaning: CHEBI:17821
+        annotations:
+          represents: T
+      R:
+        title: Purine (A or G)
+        annotations:
+          represents: A,G
+          iupac: 'true'
+      Y:
+        title: Pyrimidine (C or T)
+        annotations:
+          represents: C,T
+          iupac: 'true'
+      S:
+        title: Strong (G or C)
+        annotations:
+          represents: G,C
+          iupac: 'true'
+          bond_strength: strong (3 H-bonds)
+      W:
+        title: Weak (A or T)
+        annotations:
+          represents: A,T
+          iupac: 'true'
+          bond_strength: weak (2 H-bonds)
+      K:
+        title: Keto (G or T)
+        annotations:
+          represents: G,T
+          iupac: 'true'
+      M:
+        title: Amino (A or C)
+        annotations:
+          represents: A,C
+          iupac: 'true'
+      B:
+        title: Not A (C, G, or T)
+        annotations:
+          represents: C,G,T
+          iupac: 'true'
+      D:
+        title: Not C (A, G, or T)
+        annotations:
+          represents: A,G,T
+          iupac: 'true'
+      H:
+        title: Not G (A, C, or T)
+        annotations:
+          represents: A,C,T
+          iupac: 'true'
+      V:
+        title: Not T (A, C, or G)
+        annotations:
+          represents: A,C,G
+          iupac: 'true'
+      N:
+        title: Any nucleotide (A, C, G, or T)
+        annotations:
+          represents: A,C,G,T
+          iupac: 'true'
+      GAP:
+        title: Gap character
+        annotations:
+          symbol: '-'
+          represents: gap
+  RNABaseEnum:
+    description: Standard RNA nucleotide bases (canonical)
+    permissible_values:
+      A:
+        title: Adenine
+        aliases:
+        - adenine
+        meaning: CHEBI:16708
+        annotations:
+          complement: U
+          purine: 'true'
+          chemical_formula: C5H5N5
+      C:
+        title: Cytosine
+        aliases:
+        - cytosine
+        meaning: CHEBI:16040
+        annotations:
+          complement: G
+          pyrimidine: 'true'
+          chemical_formula: C4H5N3O
+      G:
+        title: Guanine
+        aliases:
+        - guanine
+        meaning: CHEBI:16235
+        annotations:
+          complement: C
+          purine: 'true'
+          chemical_formula: C5H5N5O
+      U:
+        title: Uracil
+        aliases:
+        - uracil
+        meaning: CHEBI:17568
+        annotations:
+          complement: A
+          pyrimidine: 'true'
+          chemical_formula: C4H4N2O2
+  RNABaseExtendedEnum:
+    description: Extended RNA alphabet with IUPAC ambiguity codes
+    permissible_values:
+      A:
+        title: Adenine
+        aliases:
+        - adenine
+        meaning: CHEBI:16708
+        annotations:
+          represents: A
+      C:
+        title: Cytosine
+        aliases:
+        - cytosine
+        meaning: CHEBI:16040
+        annotations:
+          represents: C
+      G:
+        title: Guanine
+        aliases:
+        - guanine
+        meaning: CHEBI:16235
+        annotations:
+          represents: G
+      U:
+        title: Uracil
+        aliases:
+        - uracil
+        meaning: CHEBI:17568
+        annotations:
+          represents: U
+      R:
+        title: Purine (A or G)
+        annotations:
+          represents: A,G
+          iupac: 'true'
+      Y:
+        title: Pyrimidine (C or U)
+        annotations:
+          represents: C,U
+          iupac: 'true'
+      S:
+        title: Strong (G or C)
+        annotations:
+          represents: G,C
+          iupac: 'true'
+      W:
+        title: Weak (A or U)
+        annotations:
+          represents: A,U
+          iupac: 'true'
+      K:
+        title: Keto (G or U)
+        annotations:
+          represents: G,U
+          iupac: 'true'
+      M:
+        title: Amino (A or C)
+        annotations:
+          represents: A,C
+          iupac: 'true'
+      B:
+        title: Not A (C, G, or U)
+        annotations:
+          represents: C,G,U
+          iupac: 'true'
+      D:
+        title: Not C (A, G, or U)
+        annotations:
+          represents: A,G,U
+          iupac: 'true'
+      H:
+        title: Not G (A, C, or U)
+        annotations:
+          represents: A,C,U
+          iupac: 'true'
+      V:
+        title: Not U (A, C, or G)
+        annotations:
+          represents: A,C,G
+          iupac: 'true'
+      N:
+        title: Any nucleotide (A, C, G, or U)
+        annotations:
+          represents: A,C,G,U
+          iupac: 'true'
+      GAP:
+        title: Gap character
+        annotations:
+          symbol: '-'
+          represents: gap
+  AminoAcidEnum:
+    description: Standard amino acid single letter codes
+    permissible_values:
+      A:
+        title: Alanine
+        aliases:
+        - alanine
+        meaning: CHEBI:16449
+        annotations:
+          three_letter: Ala
+          polarity: nonpolar
+          essential: 'false'
+          molecular_weight: '89.09'
+      C:
+        title: Cysteine
+        aliases:
+        - L-cysteine
+        meaning: CHEBI:17561
+        annotations:
+          three_letter: Cys
+          polarity: polar
+          essential: 'false'
+          molecular_weight: '121.15'
+          special: forms disulfide bonds
+      D:
+        title: Aspartic acid
+        aliases:
+        - L-aspartic acid
+        meaning: CHEBI:17053
+        annotations:
+          three_letter: Asp
+          polarity: acidic
+          essential: 'false'
+          molecular_weight: '133.10'
+          charge: negative
+      E:
+        title: Glutamic acid
+        aliases:
+        - L-glutamic acid
+        meaning: CHEBI:16015
+        annotations:
+          three_letter: Glu
+          polarity: acidic
+          essential: 'false'
+          molecular_weight: '147.13'
+          charge: negative
+      F:
+        title: Phenylalanine
+        aliases:
+        - L-phenylalanine
+        meaning: CHEBI:17295
+        annotations:
+          three_letter: Phe
+          polarity: nonpolar
+          essential: 'true'
+          molecular_weight: '165.19'
+          aromatic: 'true'
+      G:
+        title: Glycine
+        aliases:
+        - glycine
+        meaning: CHEBI:15428
+        annotations:
+          three_letter: Gly
+          polarity: nonpolar
+          essential: 'false'
+          molecular_weight: '75.07'
+          special: smallest, most flexible
+      H:
+        title: Histidine
+        aliases:
+        - L-histidine
+        meaning: CHEBI:15971
+        annotations:
+          three_letter: His
+          polarity: basic
+          essential: 'true'
+          molecular_weight: '155.16'
+          charge: positive
+      I:
+        title: Isoleucine
+        aliases:
+        - L-isoleucine
+        meaning: CHEBI:17191
+        annotations:
+          three_letter: Ile
+          polarity: nonpolar
+          essential: 'true'
+          molecular_weight: '131.17'
+          branched: 'true'
+      K:
+        title: Lysine
+        aliases:
+        - L-lysine
+        meaning: CHEBI:18019
+        annotations:
+          three_letter: Lys
+          polarity: basic
+          essential: 'true'
+          molecular_weight: '146.19'
+          charge: positive
+      L:
+        title: Leucine
+        aliases:
+        - L-leucine
+        meaning: CHEBI:15603
+        annotations:
+          three_letter: Leu
+          polarity: nonpolar
+          essential: 'true'
+          molecular_weight: '131.17'
+          branched: 'true'
+      M:
+        title: Methionine
+        aliases:
+        - L-methionine
+        meaning: CHEBI:16643
+        annotations:
+          three_letter: Met
+          polarity: nonpolar
+          essential: 'true'
+          molecular_weight: '149.21'
+          special: start codon
+      N:
+        title: Asparagine
+        aliases:
+        - L-asparagine
+        meaning: CHEBI:17196
+        annotations:
+          three_letter: Asn
+          polarity: polar
+          essential: 'false'
+          molecular_weight: '132.12'
+      P:
+        title: Proline
+        aliases:
+        - L-proline
+        meaning: CHEBI:17203
+        annotations:
+          three_letter: Pro
+          polarity: nonpolar
+          essential: 'false'
+          molecular_weight: '115.13'
+          special: helix breaker, rigid
+      Q:
+        title: Glutamine
+        aliases:
+        - L-glutamine
+        meaning: CHEBI:18050
+        annotations:
+          three_letter: Gln
+          polarity: polar
+          essential: 'false'
+          molecular_weight: '146.15'
+      R:
+        title: Arginine
+        aliases:
+        - L-arginine
+        meaning: CHEBI:16467
+        annotations:
+          three_letter: Arg
+          polarity: basic
+          essential: 'false'
+          molecular_weight: '174.20'
+          charge: positive
+      S:
+        title: Serine
+        aliases:
+        - L-serine
+        meaning: CHEBI:17115
+        annotations:
+          three_letter: Ser
+          polarity: polar
+          essential: 'false'
+          molecular_weight: '105.09'
+          hydroxyl: 'true'
+      T:
+        title: Threonine
+        aliases:
+        - L-threonine
+        meaning: CHEBI:16857
+        annotations:
+          three_letter: Thr
+          polarity: polar
+          essential: 'true'
+          molecular_weight: '119.12'
+          hydroxyl: 'true'
+      V:
+        title: Valine
+        aliases:
+        - L-valine
+        meaning: CHEBI:16414
+        annotations:
+          three_letter: Val
+          polarity: nonpolar
+          essential: 'true'
+          molecular_weight: '117.15'
+          branched: 'true'
+      W:
+        title: Tryptophan
+        aliases:
+        - L-tryptophan
+        meaning: CHEBI:16828
+        annotations:
+          three_letter: Trp
+          polarity: nonpolar
+          essential: 'true'
+          molecular_weight: '204.23'
+          aromatic: 'true'
+          special: largest
+      Y:
+        title: Tyrosine
+        aliases:
+        - L-tyrosine
+        meaning: CHEBI:17895
+        annotations:
+          three_letter: Tyr
+          polarity: polar
+          essential: 'false'
+          molecular_weight: '181.19'
+          aromatic: 'true'
+          hydroxyl: 'true'
+  AminoAcidExtendedEnum:
+    description: Extended amino acid alphabet with ambiguity codes and special characters
+    permissible_values:
+      A:
+        title: Alanine
+        aliases:
+        - alanine
+        meaning: CHEBI:16449
+        annotations:
+          three_letter: Ala
+      C:
+        title: Cysteine
+        aliases:
+        - L-cysteine
+        meaning: CHEBI:17561
+        annotations:
+          three_letter: Cys
+      D:
+        title: Aspartic acid
+        aliases:
+        - L-aspartic acid
+        meaning: CHEBI:17053
+        annotations:
+          three_letter: Asp
+      E:
+        title: Glutamic acid
+        aliases:
+        - L-glutamic acid
+        meaning: CHEBI:16015
+        annotations:
+          three_letter: Glu
+      F:
+        title: Phenylalanine
+        aliases:
+        - L-phenylalanine
+        meaning: CHEBI:17295
+        annotations:
+          three_letter: Phe
+      G:
+        title: Glycine
+        aliases:
+        - glycine
+        meaning: CHEBI:15428
+        annotations:
+          three_letter: Gly
+      H:
+        title: Histidine
+        aliases:
+        - L-histidine
+        meaning: CHEBI:15971
+        annotations:
+          three_letter: His
+      I:
+        title: Isoleucine
+        aliases:
+        - L-isoleucine
+        meaning: CHEBI:17191
+        annotations:
+          three_letter: Ile
+      K:
+        title: Lysine
+        aliases:
+        - L-lysine
+        meaning: CHEBI:18019
+        annotations:
+          three_letter: Lys
+      L:
+        title: Leucine
+        aliases:
+        - L-leucine
+        meaning: CHEBI:15603
+        annotations:
+          three_letter: Leu
+      M:
+        title: Methionine
+        aliases:
+        - L-methionine
+        meaning: CHEBI:16643
+        annotations:
+          three_letter: Met
+      N:
+        title: Asparagine
+        aliases:
+        - L-asparagine
+        meaning: CHEBI:17196
+        annotations:
+          three_letter: Asn
+      P:
+        title: Proline
+        aliases:
+        - L-proline
+        meaning: CHEBI:17203
+        annotations:
+          three_letter: Pro
+      Q:
+        title: Glutamine
+        aliases:
+        - L-glutamine
+        meaning: CHEBI:18050
+        annotations:
+          three_letter: Gln
+      R:
+        title: Arginine
+        aliases:
+        - L-arginine
+        meaning: CHEBI:16467
+        annotations:
+          three_letter: Arg
+      S:
+        title: Serine
+        aliases:
+        - L-serine
+        meaning: CHEBI:17115
+        annotations:
+          three_letter: Ser
+      T:
+        title: Threonine
+        aliases:
+        - L-threonine
+        meaning: CHEBI:16857
+        annotations:
+          three_letter: Thr
+      V:
+        title: Valine
+        aliases:
+        - L-valine
+        meaning: CHEBI:16414
+        annotations:
+          three_letter: Val
+      W:
+        title: Tryptophan
+        aliases:
+        - L-tryptophan
+        meaning: CHEBI:16828
+        annotations:
+          three_letter: Trp
+      Y:
+        title: Tyrosine
+        aliases:
+        - L-tyrosine
+        meaning: CHEBI:17895
+        annotations:
+          three_letter: Tyr
+      B:
+        title: Aspartic acid
+        aliases:
+        - L-aspartic acid or Asparagine (D or N)
+        annotations:
+          three_letter: Asx
+          represents: D,N
+          ambiguity: 'true'
+      Z:
+        title: Glutamic acid
+        aliases:
+        - L-glutamic acid or Glutamine (E or Q)
+        annotations:
+          three_letter: Glx
+          represents: E,Q
+          ambiguity: 'true'
+      J:
+        title: Leucine
+        aliases:
+        - L-leucine or Isoleucine (L or I)
+        annotations:
+          three_letter: Xle
+          represents: L,I
+          ambiguity: 'true'
+      X:
+        title: Any amino acid
+        annotations:
+          three_letter: Xaa
+          represents: any
+          ambiguity: 'true'
+      STOP:
+        title: Translation stop/termination
+        annotations:
+          symbol: '*'
+          three_letter: Ter
+          represents: stop codon
+      GAP:
+        title: Gap character
+        annotations:
+          symbol: '-'
+          represents: gap
+      U:
+        title: Selenocysteine
+        aliases:
+        - L-selenocysteine
+        meaning: CHEBI:16633
+        annotations:
+          three_letter: Sec
+          special: 21st amino acid
+          codon: UGA with SECIS element
+      O:
+        title: Pyrrolysine (22nd amino acid)
+        meaning: CHEBI:21860
+        aliases:
+        - L-pyrrolysine
+        annotations:
+          three_letter: Pyl
+          special: 22nd amino acid
+          codon: UAG in certain archaea/bacteria
+  CodonEnum:
+    description: Standard genetic code codons (DNA)
+    permissible_values:
+      TTT:
+        title: Phenylalanine codon
+        annotations:
+          amino_acid: F
+          amino_acid_name: Phenylalanine
+      TTC:
+        title: Phenylalanine codon
+        annotations:
+          amino_acid: F
+          amino_acid_name: Phenylalanine
+      TTA:
+        title: Leucine codon
+        annotations:
+          amino_acid: L
+          amino_acid_name: Leucine
+      TTG:
+        title: Leucine codon
+        annotations:
+          amino_acid: L
+          amino_acid_name: Leucine
+      CTT:
+        title: Leucine codon
+        annotations:
+          amino_acid: L
+          amino_acid_name: Leucine
+      CTC:
+        title: Leucine codon
+        annotations:
+          amino_acid: L
+          amino_acid_name: Leucine
+      CTA:
+        title: Leucine codon
+        annotations:
+          amino_acid: L
+          amino_acid_name: Leucine
+      CTG:
+        title: Leucine codon
+        annotations:
+          amino_acid: L
+          amino_acid_name: Leucine
+      ATT:
+        title: Isoleucine codon
+        annotations:
+          amino_acid: I
+          amino_acid_name: Isoleucine
+      ATC:
+        title: Isoleucine codon
+        annotations:
+          amino_acid: I
+          amino_acid_name: Isoleucine
+      ATA:
+        title: Isoleucine codon
+        annotations:
+          amino_acid: I
+          amino_acid_name: Isoleucine
+      ATG:
+        title: Methionine codon (start codon)
+        annotations:
+          amino_acid: M
+          amino_acid_name: Methionine
+          special: start codon
+      GTT:
+        title: Valine codon
+        annotations:
+          amino_acid: V
+          amino_acid_name: Valine
+      GTC:
+        title: Valine codon
+        annotations:
+          amino_acid: V
+          amino_acid_name: Valine
+      GTA:
+        title: Valine codon
+        annotations:
+          amino_acid: V
+          amino_acid_name: Valine
+      GTG:
+        title: Valine codon
+        annotations:
+          amino_acid: V
+          amino_acid_name: Valine
+      TCT:
+        title: Serine codon
+        annotations:
+          amino_acid: S
+          amino_acid_name: Serine
+      TCC:
+        title: Serine codon
+        annotations:
+          amino_acid: S
+          amino_acid_name: Serine
+      TCA:
+        title: Serine codon
+        annotations:
+          amino_acid: S
+          amino_acid_name: Serine
+      TCG:
+        title: Serine codon
+        annotations:
+          amino_acid: S
+          amino_acid_name: Serine
+      AGT:
+        title: Serine codon
+        annotations:
+          amino_acid: S
+          amino_acid_name: Serine
+      AGC:
+        title: Serine codon
+        annotations:
+          amino_acid: S
+          amino_acid_name: Serine
+      CCT:
+        title: Proline codon
+        annotations:
+          amino_acid: P
+          amino_acid_name: Proline
+      CCC:
+        title: Proline codon
+        annotations:
+          amino_acid: P
+          amino_acid_name: Proline
+      CCA:
+        title: Proline codon
+        annotations:
+          amino_acid: P
+          amino_acid_name: Proline
+      CCG:
+        title: Proline codon
+        annotations:
+          amino_acid: P
+          amino_acid_name: Proline
+      ACT:
+        title: Threonine codon
+        annotations:
+          amino_acid: T
+          amino_acid_name: Threonine
+      ACC:
+        title: Threonine codon
+        annotations:
+          amino_acid: T
+          amino_acid_name: Threonine
+      ACA:
+        title: Threonine codon
+        annotations:
+          amino_acid: T
+          amino_acid_name: Threonine
+      ACG:
+        title: Threonine codon
+        annotations:
+          amino_acid: T
+          amino_acid_name: Threonine
+      GCT:
+        title: Alanine codon
+        annotations:
+          amino_acid: A
+          amino_acid_name: Alanine
+      GCC:
+        title: Alanine codon
+        annotations:
+          amino_acid: A
+          amino_acid_name: Alanine
+      GCA:
+        title: Alanine codon
+        annotations:
+          amino_acid: A
+          amino_acid_name: Alanine
+      GCG:
+        title: Alanine codon
+        annotations:
+          amino_acid: A
+          amino_acid_name: Alanine
+      TAT:
+        title: Tyrosine codon
+        annotations:
+          amino_acid: Y
+          amino_acid_name: Tyrosine
+      TAC:
+        title: Tyrosine codon
+        annotations:
+          amino_acid: Y
+          amino_acid_name: Tyrosine
+      TAA:
+        title: Stop codon (ochre)
+        annotations:
+          amino_acid: '*'
+          name: ochre
+          special: stop codon
+      TAG:
+        title: Stop codon (amber)
+        annotations:
+          amino_acid: '*'
+          name: amber
+          special: stop codon
+      TGA:
+        title: Stop codon (opal/umber)
+        annotations:
+          amino_acid: '*'
+          name: opal
+          special: stop codon or selenocysteine
+      CAT:
+        title: Histidine codon
+        annotations:
+          amino_acid: H
+          amino_acid_name: Histidine
+      CAC:
+        title: Histidine codon
+        annotations:
+          amino_acid: H
+          amino_acid_name: Histidine
+      CAA:
+        title: Glutamine codon
+        annotations:
+          amino_acid: Q
+          amino_acid_name: Glutamine
+      CAG:
+        title: Glutamine codon
+        annotations:
+          amino_acid: Q
+          amino_acid_name: Glutamine
+      AAT:
+        title: Asparagine codon
+        annotations:
+          amino_acid: N
+          amino_acid_name: Asparagine
+      AAC:
+        title: Asparagine codon
+        annotations:
+          amino_acid: N
+          amino_acid_name: Asparagine
+      AAA:
+        title: Lysine codon
+        annotations:
+          amino_acid: K
+          amino_acid_name: Lysine
+      AAG:
+        title: Lysine codon
+        annotations:
+          amino_acid: K
+          amino_acid_name: Lysine
+      GAT:
+        title: Aspartic acid codon
+        annotations:
+          amino_acid: D
+          amino_acid_name: Aspartic acid
+      GAC:
+        title: Aspartic acid codon
+        annotations:
+          amino_acid: D
+          amino_acid_name: Aspartic acid
+      GAA:
+        title: Glutamic acid codon
+        annotations:
+          amino_acid: E
+          amino_acid_name: Glutamic acid
+      GAG:
+        title: Glutamic acid codon
+        annotations:
+          amino_acid: E
+          amino_acid_name: Glutamic acid
+      TGT:
+        title: Cysteine codon
+        annotations:
+          amino_acid: C
+          amino_acid_name: Cysteine
+      TGC:
+        title: Cysteine codon
+        annotations:
+          amino_acid: C
+          amino_acid_name: Cysteine
+      TGG:
+        title: Tryptophan codon
+        annotations:
+          amino_acid: W
+          amino_acid_name: Tryptophan
+      CGT:
+        title: Arginine codon
+        annotations:
+          amino_acid: R
+          amino_acid_name: Arginine
+      CGC:
+        title: Arginine codon
+        annotations:
+          amino_acid: R
+          amino_acid_name: Arginine
+      CGA:
+        title: Arginine codon
+        annotations:
+          amino_acid: R
+          amino_acid_name: Arginine
+      CGG:
+        title: Arginine codon
+        annotations:
+          amino_acid: R
+          amino_acid_name: Arginine
+      AGA:
+        title: Arginine codon
+        annotations:
+          amino_acid: R
+          amino_acid_name: Arginine
+      AGG:
+        title: Arginine codon
+        annotations:
+          amino_acid: R
+          amino_acid_name: Arginine
+      GGT:
+        title: Glycine codon
+        annotations:
+          amino_acid: G
+          amino_acid_name: Glycine
+      GGC:
+        title: Glycine codon
+        annotations:
+          amino_acid: G
+          amino_acid_name: Glycine
+      GGA:
+        title: Glycine codon
+        annotations:
+          amino_acid: G
+          amino_acid_name: Glycine
+      GGG:
+        title: Glycine codon
+        annotations:
+          amino_acid: G
+          amino_acid_name: Glycine
+  NucleotideModificationEnum:
+    description: Common nucleotide modifications
+    permissible_values:
+      FIVE_METHYL_C:
+        title: 5-methylcytosine
+        description: 5-methylcytosine
+        meaning: CHEBI:27551
+        annotations:
+          symbol: m5C
+          type: DNA methylation
+          function: gene regulation
+      SIX_METHYL_A:
+        title: N(6)-methyladenosine
+        description: N6-methyladenosine
+        meaning: CHEBI:21891
+        annotations:
+          symbol: m6A
+          type: RNA modification
+          function: RNA stability, translation
+      PSEUDOURIDINE:
+        description: Pseudouridine
+        meaning: CHEBI:17802
+        annotations:
+          symbol: Ψ
+          type: RNA modification
+          function: RNA stability
+      INOSINE:
+        description: Inosine
+        meaning: CHEBI:17596
+        annotations:
+          symbol: I
+          type: RNA editing
+          pairs_with: A, C, U
+      DIHYDROURIDINE:
+        title: dihydrouridine
+        description: Dihydrouridine
+        meaning: CHEBI:23774
+        annotations:
+          symbol: D
+          type: tRNA modification
+      SEVEN_METHYL_G:
+        title: 7-methylguanosine
+        description: 7-methylguanosine
+        meaning: CHEBI:20794
+        annotations:
+          symbol: m7G
+          type: mRNA cap
+          function: translation initiation
+      FIVE_HYDROXY_METHYL_C:
+        title: 5-(hydroxymethyl)cytosine
+        description: 5-hydroxymethylcytosine
+        meaning: CHEBI:76792
+        annotations:
+          symbol: hmC
+          type: DNA modification
+          function: demethylation intermediate
+      EIGHT_OXO_G:
+        title: 8-oxoguanine
+        description: 8-oxoguanine
+        meaning: CHEBI:44605
+        annotations:
+          symbol: 8-oxoG
+          type: oxidative damage
+          pairs_with: A or C
+  SequenceQualityEnum:
+    description: Sequence quality indicators (Phred scores)
+    permissible_values:
+      Q0:
+        description: Phred quality 0 (100% error probability)
+        annotations:
+          phred_score: '0'
+          error_probability: '1.0'
+          ascii_char: '!'
+      Q10:
+        description: Phred quality 10 (10% error probability)
+        annotations:
+          phred_score: '10'
+          error_probability: '0.1'
+          ascii_char: +
+      Q20:
+        description: Phred quality 20 (1% error probability)
+        annotations:
+          phred_score: '20'
+          error_probability: '0.01'
+          ascii_char: '5'
+      Q30:
+        description: Phred quality 30 (0.1% error probability)
+        annotations:
+          phred_score: '30'
+          error_probability: '0.001'
+          ascii_char: '?'
+      Q40:
+        description: Phred quality 40 (0.01% error probability)
+        annotations:
+          phred_score: '40'
+          error_probability: '0.0001'
+          ascii_char: I
+      Q50:
+        description: Phred quality 50 (0.001% error probability)
+        annotations:
+          phred_score: '50'
+          error_probability: '0.00001'
+          ascii_char: S
+      Q60:
+        description: Phred quality 60 (0.0001% error probability)
+        annotations:
+          phred_score: '60'
+          error_probability: '0.000001'
+          ascii_char: ']'