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Gno cross reference terms added #39

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merged 5 commits into from
Dec 5, 2020
Merged

Gno cross reference terms added #39

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6cb6215
Added GNO Terms to all glycans
pmt706 Dec 2, 2020
d4d56eb
Merge pull request #5 from pmt706/missingmassValues-Issue20
pmt706 Dec 3, 2020
327d38d
Merge pull request #7 from pmt706/missingmassValues-Issue20
pmt706 Dec 3, 2020
be703f3
Merge pull request #8 from HUPO-PSI/master
pmt706 Dec 4, 2020
6543591
updating release
pmt706 Dec 4, 2020
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47 changes: 44 additions & 3 deletions PSI-MOD.obo
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
format-version: 1.2
date: 03:12:2020 16:58
date: 04:12:2020 23:31
saved-by: Paul M. Thomas
subsetdef: PSI-MOD-slim "subset of protein modifications"
synonymtypedef: DeltaMass-label "Label from MS DeltaMass" EXACT
Expand All @@ -16,9 +16,9 @@ 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: 1.022.0
remark: PSI-MOD version: 1.023.0
remark: RESID release: 75.00
remark: ISO-8601 date: 2020-12-03 16:58Z
remark: ISO-8601 date: 2020-12-04 23:31Z
remark: Annotation note 1 - "[PSI-MOD:ref]" has been replaced by PubMed:18688235.
remark: Annotation note 2 - 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 3 - 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 All @@ -28,6 +28,7 @@ remark: Annotation note 6 - For cross-link modifications, the number following "
remark: Annotation note 7 - The synonym cross-reference "MOD:old name" has been replaced by "MOD:alternate name".
remark: Annotation note 8 - The DeltaMass listings for free amino acids have been removed. Most Unimod entries that have not been "approved" have by general agreement not been incorporated unless there has been a request for a specific term by a PRIDE submitter.
remark: Annotation note 9 - The Open Mass Spectrometry Search Algorithm, OMSSA, enumerated list of modifications are being incorporated. The string values are synonyms with the synonymtypedef "OMSSA-label", and their integer values (which are supposed to be stable) are definition cross-references.
remark: Annotation note 10 - GNOme is the Glycan Naming and Subsumption Ontology (https://gnome.glyomics.org/), an ontology for the support of glycomics. PSI-MOD does not have all possible glycans in its entries, just the ones that are noted to be on proteins and have been requested for addition. GNOme uses GlyTouCan (http://glytoucan.org/) to provide stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations).

[Term]
id: MOD:00000
Expand Down Expand Up @@ -10619,6 +10620,7 @@ xref: MassMono: "none"
xref: Origin: "X"
xref: Source: "none"
xref: TermSpec: "none"
xref: GNOme: "GNO:G29068FM"
is_a: MOD:00693 ! glycosylated residue

[Term]
Expand Down Expand Up @@ -11979,6 +11981,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:137"
xref: GNOme: "GNO:G02815KT"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand Down Expand Up @@ -12057,6 +12060,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:142"
xref: GNOme: "GNO:G00194GV"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -12076,6 +12080,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:143"
xref: GNOme: "GNO:G27391WQ"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -12095,6 +12100,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:144"
xref: GNOme: "GNO:G39365VM"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -12114,6 +12120,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:145"
xref: GNOme: "GNO:G74392IM"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -12133,6 +12140,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:146"
xref: GNOme: "GNO:G54129SE"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -12152,6 +12160,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:147"
xref: GNOme: "GNO:G06042JP"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -12171,6 +12180,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:148"
xref: GNOme: "GNO:G58001LT"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -12191,6 +12201,7 @@ xref: MassMono: "none"
xref: Origin: "X"
xref: Source: "natural"
xref: TermSpec: "none"
xref: GNOme: "GNO:G17015OC"
is_a: MOD:00725 ! complex glycosylation

[Term]
Expand All @@ -12209,6 +12220,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:150"
xref: GNOme: "GNO:G90423UY"
is_a: MOD:00725 ! complex glycosylation

[Term]
Expand All @@ -12227,6 +12239,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:151"
xref: GNOme: "GNO:G54968WM"
is_a: MOD:00725 ! complex glycosylation

[Term]
Expand All @@ -12245,6 +12258,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:152"
xref: GNOme: "GNO:G94583DZ"
is_a: MOD:00725 ! complex glycosylation

[Term]
Expand All @@ -12263,6 +12277,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:153"
xref: GNOme: "GNO:G53434XO"
is_a: MOD:00725 ! complex glycosylation

[Term]
Expand All @@ -12281,6 +12296,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:154"
xref: GNOme: "GNO:G64686LL"
is_a: MOD:00725 ! complex glycosylation

[Term]
Expand All @@ -12299,6 +12315,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:155"
xref: GNOme: "GNO:G84825UQ"
is_a: MOD:00725 ! complex glycosylation

[Term]
Expand All @@ -12317,6 +12334,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:156"
xref: GNOme: "GNO:G05460KC"
is_a: MOD:00725 ! complex glycosylation

[Term]
Expand All @@ -12335,6 +12353,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:157"
xref: GNOme: "GNO:G18999EB"
is_a: MOD:00725 ! complex glycosylation

[Term]
Expand All @@ -12353,6 +12372,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:158"
xref: GNOme: "GNO:G93579XB"
is_a: MOD:00725 ! complex glycosylation

[Term]
Expand All @@ -12373,6 +12393,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:159"
xref: GNOme: "GNO:G28681TP"
is_a: MOD:00725 ! complex glycosylation

[Term]
Expand All @@ -12391,6 +12412,7 @@ xref: Origin: "X"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:160"
xref: GNOme: "GNO:G23729WG"
is_a: MOD:00725 ! complex glycosylation

[Term]
Expand All @@ -12409,6 +12431,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:161"
xref: GNOme: "GNO:G88520YF"
is_a: MOD:00725 ! complex glycosylation

[Term]
Expand Down Expand Up @@ -13930,6 +13953,7 @@ xref: Origin: "X"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:295"
xref: GNOme: "GNO:G49112ZN"
is_a: MOD:00736 ! deoxyhexosylated

[Term]
Expand Down Expand Up @@ -14087,6 +14111,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:305"
xref: GNOme: "GNO:G25987BV"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand Down Expand Up @@ -14168,6 +14193,7 @@ xref: MassMono: "none"
xref: Origin: "X"
xref: Source: "natural"
xref: TermSpec: "none"
xref: GNOme: "GNO:G90627TW"
is_a: MOD:00725 ! complex glycosylation

[Term]
Expand Down Expand Up @@ -15780,6 +15806,7 @@ xref: MassMono: "none"
xref: Origin: "X"
xref: Source: "natural"
xref: TermSpec: "none"
xref: GNOme: "GNO:G02438LG"
is_a: MOD:00693 ! glycosylated residue

[Term]
Expand All @@ -15798,6 +15825,7 @@ xref: MassMono: "none"
xref: Origin: "X"
xref: Source: "natural"
xref: TermSpec: "none"
xref: GNOme: "GNO:G76685HR"
is_a: MOD:00693 ! glycosylated residue

[Term]
Expand Down Expand Up @@ -16040,6 +16068,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:307"
xref: GNOme: "GNO:G59937CP"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -16059,6 +16088,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:311"
xref: GNOme: "GNO:G10486CT"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -16076,6 +16106,7 @@ xref: MassMono: "none"
xref: Origin: "X"
xref: Source: "natural"
xref: TermSpec: "none"
xref: GNOme: "GNO:G81399MY"
is_a: MOD:00434 ! hexosylated residue

[Term]
Expand All @@ -16094,6 +16125,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:309"
xref: GNOme: "GNO:G35029YA"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -16113,6 +16145,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:310"
xref: GNOme: "GNO:G72787SB"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand Down Expand Up @@ -22810,6 +22843,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:308"
xref: GNOme: "GNO:G83555HU"
is_a: MOD:00725 ! complex glycosylation

[Term]
Expand Down Expand Up @@ -39876,6 +39910,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:1519"
xref: GNOme: "GNO:G03382KH"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -39894,6 +39929,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:1785"
xref: GNOme: "GNO:G70418MS"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -39912,6 +39948,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:1484"
xref: GNOme: "GNO:G82119TF"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -39930,6 +39967,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:1781"
xref: GNOme: "GNO:G50757KG"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -39948,6 +39986,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:1509"
xref: GNOme: "GNO:G84820NF"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -39966,6 +40005,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:1531"
xref: GNOme: "GNO:G70101JE"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand All @@ -39984,6 +40024,7 @@ xref: Origin: "N"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:1480"
xref: GNOme: "GNO:G05724UK"
is_a: MOD:00725 ! complex glycosylation
is_a: MOD:00903 ! modified L-asparagine residue

Expand Down