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Add additional terms beyond hydroxyl-phenalanine #79

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Merged
mobiusklein merged 9 commits into from
Nov 21, 2025
Merged

Add additional terms beyond hydroxyl-phenalanine #79

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0cfb7dc
add additional terms
mobiusklein Oct 3, 2025
b95f3e5
version bump
mobiusklein Oct 23, 2025
43d9a7b
Merge remote-tracking branch 'origin' into feature/hydroxy-tryptophan
mobiusklein Oct 23, 2025
b13cf04
response to review comments
mobiusklein Oct 23, 2025
d7bbb24
resolve merge'
mobiusklein Oct 31, 2025
f484c08
Remove carbon-oxygenated residues, future PR to add to hierarchy
mobiusklein Oct 31, 2025
614cdc6
feature: add qualifiers for synonyms, bump version
mobiusklein Nov 21, 2025
24840a5
Merge branch 'master' into feature/hydroxy-tryptophan
mobiusklein Nov 21, 2025
c92bf38
fix: fix validator errors
mobiusklein Nov 21, 2025
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188 changes: 188 additions & 0 deletions PSI-MOD.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -41165,6 +41165,194 @@ subset: PSI-MOD-slim
synonym: "ModDAsn" EXACT PSI-MOD-label []
is_a: MOD:00203 ! D-asparagine

[Term]
id: MOD:02106
name: 4-hydroxy-L-tryptophan
def: "A protein modification that effectively converts an L-tryptophan residue to a 4-hydroxy-L-tryptophan." [PMID:32911085]
synonym: "(S)-2-Amino-3-(4-hydroxy-1H-indol-3-yl)propanoic acid"
xref: DiffAvg: "16.00"
xref: DiffFormula: "C 0 H 0 N 0 O 1"
xref: DiffMono: "15.994915"
xref: Formula: "C 11 H 10 N 2 O 2"
xref: MassAvg: "202.21"
xref: MassMono: "202.074228"
xref: Origin: "W"
xref: Source: "hypothetical"
xref: TermSpec: "none"
is_a: MOD:01622 ! monohydroxylated tryptophan

[Term]
id: MOD:02107
name: 5-hydroxy-L-tryptophan
def: "A protein modification that effectively converts an L-tryptophan residue to a 5-hydroxy-L-tryptophan." [PMID:32911085]
synonym: "(S)-2-Amino-3-(5-hydroxy-1H-indol-3-yl)propanoic acid"
xref: DiffAvg: "16.00"
xref: DiffFormula: "C 0 H 0 N 0 O 1"
xref: DiffMono: "15.994915"
xref: Formula: "C 11 H 10 N 2 O 2"
xref: MassAvg: "202.21"
xref: MassMono: "202.074228"
xref: Origin: "W"
xref: Source: "hypothetical"
xref: TermSpec: "none"
is_a: MOD:01622 ! monohydroxylated tryptophan

[Term]
id: MOD:02108
name: 6-hydroxy-L-tryptophan
def: "A protein modification that effectively converts an L-tryptophan residue to a 6-hydroxy-L-tryptophan." [PMID:32911085]
synonym: "(S)-2-Amino-3-(4-hydroxy-1H-indol-3-yl)propanoic acid"
xref: DiffAvg: "16.00"
xref: DiffFormula: "C 0 H 0 N 0 O 1"
xref: DiffMono: "15.994915"
xref: Formula: "C 11 H 10 N 2 O 2"
xref: MassAvg: "202.21"
xref: MassMono: "202.074228"
xref: Origin: "W"
xref: Source: "hypothetical"
xref: TermSpec: "none"
is_a: MOD:01622 ! monohydroxylated tryptophan

[Term]
id: MOD:02109
name: oxindolylalanine
def: "A protein modification that effectively converts an L-tryptophan residue to a oxindolylalanine." [PMID:32911085]
synonym: "Oxindolyl-L-alanine"
synonym:"2-amino-3-(2-oxoindolin-3-yl)propanoic acid"
xref: DiffAvg: "16.00"
xref: DiffFormula: "C 0 H 0 N 0 O 1"
xref: DiffMono: "15.994915"
xref: Formula: "C 11 H 10 N 2 O 2"
xref: MassAvg: "202.21"
xref: MassMono: "202.074228"
xref: Origin: "W"
xref: Source: "hypothetical"
xref: TermSpec: "none"
is_a: MOD:01622 ! monohydroxylated tryptophan

[Term]
id: MOD:02110
name: 5-hydroxy-L-proline
def: "A protein modification that effectively converts an L-proline residue to 5-hydroxy-L-proline" [ChEBI:18095, PubMed:11292863, PubMed:2400108, PubMed:3734192, RESID:AA0030]
subset: PSI-MOD-slim
synonym: "(2S,5S)-5-hydroxypyrrolidine-2-carboxylic acid"
xref: DiffAvg: "16.00"
xref: DiffFormula: "C 0 H 0 N 0 O 1"
xref: DiffMono: "15.994915"
xref: Formula: "C 5 H 7 N 1 O 2"
xref: MassAvg: "113.12"
xref: MassMono: "113.047678"
xref: Origin: "P"
xref: Source: "natural"
xref: TermSpec: "none"
is_a: MOD:01024 ! monohydroxylated proline

[Term]
id: MOD:02111
name: (2S,4S)-5-hydroxyleucine
def: "A protein modification that effectively converts an L-leucine residue to a (2S,4S)-5-hydroxyleucine." [PubMed:9164839]
synonym: "(2S,4S)-2-amino-5-hydroxy-4-methylpentanoic acid"
xref: DiffAvg: "16.00"
xref: DiffFormula: "C 0 H 0 N 0 O 1"
xref: DiffMono: "15.994915"
xref: Formula: "C 6 H 11 N 1 O 2"
xref: MassAvg: "129.16"
xref: MassMono: "129.078979"
xref: Origin: "L"
xref: Source: "artifact"
xref: TermSpec: "none"
is_a: MOD:01411 ! monohydroxylated leucine

[Term]
id: MOD:02112
name: 4,5-Dihydroxytryptophan
def: "A protein modification that converts an L-tryptophan residue to 4,5-Dihydroxytryptophan." [PubMed:16046449, PubMed:30267362]
subset: PSI-MOD-slim
synonym: "dihydroxy" RELATED Unimod-description []
synonym: "Dioxidation" RELATED PSI-MS-label []
synonym: "Double oxidation of Trp" EXACT DeltaMass-label []
synonym: "(2S)-2-amino-3-(4,5-dihydroxy-1H-indol-3-yl)propanoic acid"
xref: DiffAvg: "32.00"
xref: DiffFormula: "O 2"
xref: DiffMono: "31.989829"
xref: Formula: "C 11 H 10 N 2 O 3"
xref: MassAvg: "218.21"
xref: MassMono: "218.069142"
xref: Origin: "W"
xref: Source: "hypothetical"
xref: TermSpec: "none"
xref: Unimod: "Unimod:425"
is_a: MOD:00679 ! carbon oxygenated residue
is_a: MOD:00918 ! modified L-tryptophan residue

[Term]
id: MOD:02113
name: 5,6-Dihydroxytryptophan
def: "A protein modification that converts an L-tryptophan residue to 5,6-Dihydroxytryptophan." [PubMed:16046449, PubMed:30267362]
subset: PSI-MOD-slim
synonym: "dihydroxy" RELATED Unimod-description []
synonym: "Dioxidation" RELATED PSI-MS-label []
synonym: "Double oxidation of Trp" EXACT DeltaMass-label []
synonym: "(2S)-2-amino-3-(5,6-dihydroxy-1H-indol-3-yl)propanoic acid"
xref: DiffAvg: "32.00"
xref: DiffFormula: "O 2"
xref: DiffMono: "31.989829"
xref: Formula: "C 11 H 10 N 2 O 3"
xref: MassAvg: "218.21"
xref: MassMono: "218.069142"
xref: Origin: "W"
xref: Source: "hypothetical"
xref: TermSpec: "none"
xref: Unimod: "Unimod:425"
is_a: MOD:00679 ! carbon oxygenated residue
is_a: MOD:00918 ! modified L-tryptophan residue

[Term]
id: MOD:02114
name: 5,7-Dihydroxytryptophan
def: "A protein modification that converts an L-tryptophan residue to 5,7-Dihydroxytryptophan." [PubMed:16046449, PubMed:30267362]
subset: PSI-MOD-slim
synonym: "dihydroxy" RELATED Unimod-description []
synonym: "Dioxidation" RELATED PSI-MS-label []
synonym: "Double oxidation of Trp" EXACT DeltaMass-label []
synonym: "(2S)-2-amino-3-(5,7-dihydroxy-1H-indol-3-yl)propanoic acid"
xref: DiffAvg: "32.00"
xref: DiffFormula: "O 2"
xref: DiffMono: "31.989829"
xref: Formula: "C 11 H 10 N 2 O 3"
xref: MassAvg: "218.21"
xref: MassMono: "218.069142"
xref: Origin: "W"
xref: Source: "hypothetical"
xref: TermSpec: "none"
xref: Unimod: "Unimod:425"
is_a: MOD:00679 ! carbon oxygenated residue
is_a: MOD:00918 ! modified L-tryptophan residue

[Term]
id: MOD:02115
name: Dioxindolylalanine
def: "A protein modification that converts an L-tryptophan residue to dioxindolylalanine." [PubMed:10554268, PubMed:32911085]
subset: PSI-MOD-slim
synonym: "dihydroxy" RELATED Unimod-description []
synonym: "Dioxidation" RELATED PSI-MS-label []
synonym: "Double oxidation of Trp" EXACT DeltaMass-label []
synonym: "(alphaS)-alpha-Amino-2,3-dihydro-3-hydroxy-2-oxo-1H-indole-3-propanoic acid"
synonym: "(2S)-2-amino-3-(3-hydroxy-2-oxo-1H-indol-3-yl)propanoic acid"
synonym: "Dioxindolyl-L-alanine"
xref: DiffAvg: "32.00"
xref: DiffFormula: "O 2"
xref: DiffMono: "31.989829"
xref: Formula: "C 11 H 10 N 2 O 3"
xref: MassAvg: "218.21"
xref: MassMono: "218.069142"
xref: Origin: "W"
xref: Source: "artifact"
xref: TermSpec: "none"
xref: Unimod: "Unimod:425"
is_a: MOD:00679 ! carbon oxygenated residue
is_a: MOD:00918 ! modified L-tryptophan residue

[Typedef]
id: contains
name: contains
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