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Feb 2021 Error Fixes and New Mods #56

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merged 21 commits into from
Mar 10, 2021
Merged

Feb 2021 Error Fixes and New Mods #56

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379bdef
Updates MOD:01914
pmt706 Feb 10, 2021
2e89758
Cleanup of README and Adding in OWL Format
pmt706 Feb 10, 2021
ba503ef
Adding in two new mods from UniProt (PubMed 22504181)
pmt706 Feb 10, 2021
295cc18
Adding in AMP-Serine
pmt706 Feb 11, 2021
fca44ac
Adding in S-methylbutanedioic acid-L-cysteine
pmt706 Feb 11, 2021
828e18b
Adding HIB Lysine
pmt706 Feb 11, 2021
1b62f6a
Adding in betahydroxybutyryl lysine
pmt706 Feb 11, 2021
8485344
Adding in Glutaryl Lysine
pmt706 Feb 11, 2021
9d7bc5d
Updating Carbamoyl Lysine
pmt706 Feb 11, 2021
9559540
Adding methyl-d-asparagine
pmt706 Feb 11, 2021
6d06100
Fix MOD:00241
pmt706 Feb 11, 2021
7ccf523
Updating Date/Time/Version and adding in Geranylgeranyl L cysteine me…
pmt706 Mar 3, 2021
5a68a42
Removing Erroneous duplicate
pmt706 Mar 3, 2021
c454b0d
Syntax Error Fix
pmt706 Mar 10, 2021
327f7ac
Fixes MOD:02096
pmt706 Mar 10, 2021
5f93607
Fixing MOD:02094
pmt706 Mar 10, 2021
4f9a14a
Fixes MOD:02092
pmt706 Mar 10, 2021
b4c1f6a
Fixes MOD:02090 and MOD:02091
pmt706 Mar 10, 2021
5cdc06b
Updating Readme.md to indicate primacy of obo
pmt706 Mar 10, 2021
c637ddd
Fixes to MOD:01914
pmt706 Mar 10, 2021
8f7cc5d
Updating OWL for PR 56
pmt706 Mar 10, 2021
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189 changes: 180 additions & 9 deletions PSI-MOD.obo
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
format-version: 1.2
ontology: mod
date: 10:02:2021 14:33
date: 10:03:2021 14:36
saved-by: Paul M. Thomas
subsetdef: PSI-MOD-slim "subset of protein modifications"
synonymtypedef: DeltaMass-label "Label from MS DeltaMass" EXACT
Expand All @@ -17,9 +17,9 @@ synonymtypedef: Unimod-description "Description (full_name) from Unimod" RELATED
synonymtypedef: Unimod-interim "Interim label from Unimod" RELATED
synonymtypedef: UniProt-feature "Protein feature description from UniProtKB" EXACT
default-namespace: PSI-MOD
remark: PSI-MOD version: 1.030.0
remark: PSI-MOD version: 1.031.2
remark: RESID release: 75.00
remark: ISO-8601 date: 2021-02-10 14:33Z
remark: ISO-8601 date: 2021-03-10 14:36Z
remark: Annotation note 01 - "[PSI-MOD:ref]" has been replaced by PubMed:18688235.
remark: Annotation note 02 - When an entry in the RESID Database is annotated with different sources because the same modification can arise from different encoded amino acids, then the PSI-MOD definition for each different source instance carries the RESID cross-reference followed by a hash symbol "#" and a 3 or 4 character label. When an entry in the RESID Database is annotated as a general modification with the same enzymatic activity producing different chemical structures depending on natural variation in the nonproteinaceous substrate, on secondary modifications that do not change the nature of the primary modification, or on a combination of a primary and one or more secondary modifications on the same residue, then the PSI-MOD definition for each different instance carries the RESID cross-reference followed by the special tag "#var".
remark: Annotation note 03 - When an entry in the Unimod database is annotated as a general modification, and one or more instance sites are listed, then the PSI-MOD definition for each different site instance carries the Unimod cross-reference followed by a hash symbol and an amino acid code, "N-term" or "C-term".
Expand Down Expand Up @@ -5299,6 +5299,7 @@ xref: MassAvg: "114.10"
xref: MassMono: "114.042927"
xref: Origin: "N"
xref: Source: "natural"
xref: Source: "natural"
xref: TermSpec: "none"
xref: UniProt: "PTM-0115"
is_a: MOD:00664 ! stereoisomerized residue
Expand Down Expand Up @@ -6231,7 +6232,7 @@ xref: Origin: "N"
xref: Source: "artifact"
xref: TermSpec: "none"
xref: Unimod: "Unimod:414"
is_a: MOD:00160 ! N4-glycosyl-L-asparagine
is_a: MOD:00903 ! modified L-asparagine residue

[Term]
id: MOD:00242
Expand Down Expand Up @@ -21740,7 +21741,7 @@ xref: Formula: "C 6 H 10 N 2 O 2 S 1"
xref: MassAvg: "174.22"
xref: MassMono: "174.046299"
xref: Origin: "C"
xref: Source: "artifact
xref: Source: "artifact"
xref: Remap: "MOD:00417"
is_obsolete: true

Expand Down Expand Up @@ -33352,7 +33353,7 @@ relationship: contains MOD:01673 ! N-acetylaminohexosylated residue
[Term]
id: MOD:01678
name: N6-carbamoyl-L-lysine
def: "A protein modification that effectively coverts L-lysine to N6-carbamoyl-L-lysine." [DeltaMass:56, OMSSA:31, PubMed:10978403, PubMed:12203680, Unimod:5#K]
def: "A protein modification that effectively coverts L-lysine to N6-carbamoyl-L-lysine." [DeltaMass:56, OMSSA:31, PubMed:10978403, PubMed:12203680, Unimod:5#K, ChEBI:144369]
comment: This modification can be produced by hydrogen cyanate, either as a reagent or as released by urea degradation in solution [JSG].
subset: PSI-MOD-slim
synonym: "2-amino-6-ureido-hexanoic acid" EXACT PSI-MOD-alternate []
Expand All @@ -33362,6 +33363,7 @@ synonym: "carbamylk" EXACT OMSSA-label []
synonym: "homocitrulline" EXACT PSI-MOD-alternate []
synonym: "N6-(aminocarbonyl)-L-lysine" EXACT PSI-MOD-alternate []
synonym: "N6CbmLys" EXACT PSI-MOD-label []
synonym: "MOD_RES N6-carbamoyllysine" EXACT UniProt-feature []
xref: DiffAvg: "43.02"
xref: DiffFormula: "C 1 H 1 N 1 O 1"
xref: DiffMono: "43.005814"
Expand All @@ -33372,6 +33374,8 @@ xref: Origin: "K"
xref: Source: "artifact"
xref: TermSpec: "none"
xref: Unimod: "Unimod:5"
xref: UniProt: "PTM-0675"
is_a: MOD:00912 ! modified L-lysine residue
is_a: MOD:00398 ! carbamoylated residue

[Term]
Expand Down Expand Up @@ -38036,8 +38040,8 @@ xref: TermSpec: "none"
xref: Unimod: "Unimod:907"
xref: UniProt: "PTM-0556"
relationship: derives_from MOD:00037 ! 5-hydroxy-L-lysine
relationship: derives_from MOD:00476 ! monogalactosylated residue
is_a: MOD:00396 ! O-glycosylated residue
is_a: MOD:00476 ! monogalactosylated residue

[Term]
id: MOD:01915
Expand Down Expand Up @@ -40673,8 +40677,8 @@ name: crosslinked D-asparagine residue
def: "A protein modification that contains an D-asparagine residue crosslinked to one or more amino acid residues." [PubMed:18688235]
subset: PSI-MOD-slim
synonym: "XlnkDAsn" EXACT PSI-MOD-label []
xref: Origin: "N"
is_a: MOD:00203 ! D-asparagine
xref: Origin: "MOD:00203"
is_a: MOD:02097 ! modified D-asparagine residue

[Term]
id: MOD:02061
Expand Down Expand Up @@ -40993,6 +40997,173 @@ xref: TermSpec: "none"
is_a: MOD:00009 ! natural residue
is_a: MOD:01156 ! protein modification categorized by chemical process

[Term]
id: MOD:02089
name: O-(phospho-5'-uridine)-L-serine
def: "A protein modification that effectively crosslinks an L-serine residue and 5'-phosphouridine through a phosphodiester bond to form O-(phospho-5'-uridine)-L-serine." [DeltaMass:0, PubMed:22504181, Unimod:417#S, ChEBI:156051]
subset: PSI-MOD-slim
synonym: "MOD_RES O-UMP-serine" EXACT UniProt-feature []
synonym: "OUMPSer" EXACT PSI-MOD-label []
synonym: "PhosphoUridine" RELATED PSI-MS-label []
xref: DiffAvg: "306.17"
xref: DiffFormula: "C 9 H 11 N 2 O 8 P 1"
xref: DiffMono: "306.025302"
xref: Formula: "C 12 H 16 N 3 O 9 P 1"
xref: MassAvg: "377.24"
xref: MassMono: "377.062416"
xref: Origin: "S"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:417"
xref: UniProt: "PTM-0501"
is_a: MOD:00916 ! modified L-serine residue
is_a: MOD:01166 ! uridylated residue

[Term]
id: MOD:02090
name: O-(phospho-5'-uridine)-L-threonine
def: "A protein modification that effectively crosslinks an L-threonine residue and 5'-phosphouridine through a phosphodiester bond to form O-(phospho-5'-uridine)-L-threonine." [DeltaMass:0, PubMed:22504181, Unimod:417#T, ChEBI:156052]
subset: PSI-MOD-slim
synonym: "MOD_RES O-UMP-threonine" EXACT UniProt-feature []
synonym: "OUMPThr" EXACT PSI-MOD-label []
synonym: "PhosphoUridine" RELATED PSI-MS-label []
xref: DiffAvg: "306.17"
xref: DiffFormula: "C 9 H 11 N 2 O 8 P 1"
xref: DiffMono: "306.025302"
xref: Formula: "C 13 H 18 N 3 O 9 P 1"
xref: MassAvg: "391.27"
xref: MassMono: "391.078066"
xref: Origin: "T"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:417"
xref: UniProt: "PTM-0502"
is_a: MOD:00917 ! modified L-threonine residue
is_a: MOD:01166 ! uridylated residue

[Term]
id: MOD:02091
name: O-(phospho-5'-adenosine)-L-serine
def: "A protein modification that effectively crosslinks an L-serine residue and 5'-phosphoadenosine through a phosphodiester bond to form O-(phospho-5'-adenosine)-L-serine." [PubMed:21472612, Unimod:405#S]
subset: PSI-MOD-slim
synonym: "MOD_RES O-AMP-serine" EXACT UniProt-feature []
synonym: "Phosphoadenosine" RELATED PSI-MS-label []
xref: DiffAvg: "329.21"
xref: DiffFormula: "C 10 H 12 N 5 O 6 P 1"
xref: DiffMono: "329.052520"
xref: Formula: "C 13 H 17 N 6 O 8 P 1"
xref: MassAvg: "416.28"
xref: MassMono: "416.084549"
xref: Origin: "S"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:405"
xref: UniProt: "PTM-0651"
is_a: MOD:00916 ! modified L-serine residue
is_a: MOD:01165 ! adenylated residue

[Term]
id: MOD:02092
name: S-methylbutanedioic acid-L-cysteine
def: "A protein modification that effectively converts an L-cysteine residue to form S-methylbutanedioic acid-L-cysteine through a thioether bond." [PubMed:29590092]
subset: PSI-MOD-slim
synonym: "MOD_RES S-(2,3-dicarboxypropyl)cysteine" EXACT UniProt-feature []
xref: DiffAvg: "130.10"
xref: DiffFormula: "C 5 H 6 N 0 O 4 P 0 S 0"
xref: DiffMono: "130.026609"
xref: Formula: "C 8 H 11 N 1 O 5 P 0 S 1"
xref: MassAvg: "233.24"
xref: MassMono: "233.035793"
xref: Origin: "C"
xref: Source: "natural"
xref: TermSpec: "none"
xref: UniProt: "PTM-0676"
is_a: MOD:00905 ! modified L-cysteine residue
is_a: MOD:00001 ! alkylated residue

[Term]
id: MOD:02093
name: N6-(2-hydroxyisobutanoyl)-L-lysine
def: "A protein modification that effectively converts an L-lysine residue to N6-(2-hydroxyisobutanoyl)-L-lysine." [PubMed:29775581, PubMed:24681537, ChEBI:144968, Unimod:1849]
synonym: "MOD_RES N6-(2-hydroxyisobutyryl)lysine" EXACT UniProt-feature []
xref: DiffAvg: "86.09"
xref: DiffFormula: "C 4 H 6 N 0 O 2"
xref: DiffMono: "86.036779"
xref: Formula: "C 10 H 18 N 2 O 3"
xref: MassAvg: "214.27"
xref: MassMono: "214.131742"
xref: Origin: "K"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:1849"
xref: UniProt: "PTM-0638"
is_a: MOD:01875 ! N6-acylated L-lysine

[Term]
id: MOD:02094
name: N6-((3R)-3-hydroxybutanoyl)-L-lysine
def: "A protein modification that effectively converts an L-lysine residue to N6-((3R)-3-hydroxybutanoyl)-L-lysine." [PubMed:27105115, ChEBI:149490]
synonym: "MOD_RES N6-(beta-hydroxybutyryl)lysine" EXACT UniProt-feature []
xref: DiffAvg: "87.10"
xref: DiffFormula: "C 4 H 7 N 0 O 2"
xref: DiffMono: "87.044604"
xref: Formula: "C 10 H 19 N 2 O 3"
xref: MassAvg: "215.27"
xref: MassMono: "215.139567"
xref: Origin: "K"
xref: Source: "natural"
xref: TermSpec: "none"
xref: UniProt: "PTM-0499"
is_a: MOD:01875 ! N6-acylated L-lysine

[Term]
id: MOD:02095
name: N6-glutaryl-L-lysine
def: "A protein modification that effectively converts an L-lysine residue to N6-glutaryl-L-lysine." [PubMed:24703693, ChEBI:87828]
synonym: "MOD_RES N6-glutaryllysine" EXACT UniProt-feature []
xref: DiffAvg: "114.10"
xref: DiffFormula: "C 5 H 6 N 0 O 3"
xref: DiffMono: "114.031694"
xref: Formula: "C 11 H 18 N 2 O 4"
xref: MassAvg: "242.28"
xref: MassMono: "242.126657"
xref: Origin: "K"
xref: Source: "natural"
xref: TermSpec: "none"
xref: UniProt: "PTM-0487"
is_a: MOD:01875 ! N6-acylated L-lysine

[Term]
id: MOD:02096
name: N4-methyl-D-asparagine
def: "A protein modification that effectively converts a D-asparagine residue to N4-methyl-D-asparagine." [PubMed:22983711, ChEBI:149514]
subset: PSI-MOD-slim
synonym: "MOD_RES N4-methyl-D-asparagine" EXACT UniProt-feature []
synonym: "N4-methylated D-asparagine" EXACT PSI-MOD-alternate []
xref: DiffAvg: "14.03"
xref: DiffFormula: "C 1 H 2 N 0 O 0"
xref: DiffMono: "14.015650"
xref: Formula: "C 5 H 8 N 2 O 2"
xref: MassAvg: "128.13"
xref: MassMono: "128.058578"
xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: UniProt: "PTM-0691"
is_a: MOD:00599 ! monomethylated residue
is_a: MOD:00602 ! N-methylated residue
is_a: MOD:00673 ! methylated asparagine
is_a: MOD:02097 ! modified D-asparagine residue
is_a: MOD:00894 ! residues isobaric at 128.058578 Da

[Term]
id: MOD:02097
name: modified D-asparagine residue
def: "A protein modification that modifies a D-asparagine residue." [PubMed:18688235]
subset: PSI-MOD-slim
synonym: "ModDAsn" EXACT PSI-MOD-label []
is_a: MOD:00203 ! D-asparagine
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[Typedef]
id: contains
name: contains
Expand Down
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