Deorphanize or Deprecate Terms Rooted at MOD:00003 and MOD:00947

[pmt706]

There are are large number of orphan terms that only have root in the base that brought them in. UniMod (MOD:00003) and DeltaMass (MOD:00947).

In PSI-MOD 1.029.0, this amounts to

• MOD:00003 (UniMod): 28 orphans
• MOD:00947 (DeltaMass): 60 orphans

My proposal is to deprecate orphan terms that are:

• abiological (e.g. MOD:00508, a UniMod orphan term for gas-phase ions generated in the mass spectrometry process)
• unsupported by literature reference (MOD:00958, a DeltaMass orphan term for a crosslink between Arg and His sidechains with loss of "5"

And to properly fix terms that are incomplete such as:

• DeltaMass orphan MOD:00971 that describes oxohistidine from a properly referenced manuscript
• Unimod Orphan MOD:00576 that described crotonylation... here I will convert to something like "crotonylated residue" on amino acid X. The addition of child terms for each modified residue will come in the future.

Does anyone have strong reasons why I shouldn't do this? I assume that answer will be no, but always good to throw the question out into the ether.

[pabinz]

Litterature for crotonylated Lysine:
PMID: 31475443
you can complete the MOD:01278 with
id: MOD:01278
name: crotonylated L-lysine
def: "A protein modification that effectively converts an L-lysine residue to a crotonylated-L-Lysine to" [PubMed:31475443, Unimod:253#K]
synonym: "Crotonaldehyde" RELATED PSI-MS-label []
synonym: "Crotonaldehyde" RELATED Unimod-description []
xref: DiffAvg: "70.09"
xref: DiffFormula: "C 4 H 6 O 1"
xref: DiffMono: "70.041865"
xref: Formula: "C 10 H 18 N 2 O 2"
xref: MassAvg: "198.27"
xref: MassMono: "198.136828"
xref: Origin: "K"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:253"
is_a: MOD:00576 ! crotonylated residue
is_a: MOD:00912 ! modified L-lysine residue