muthuvenkat
commented
15 years ago Hi Chris,
As you probably know, ChEBI doesn't internally maintain a distinction between exact and related synonyms. We create these for the OBO export. It would be great to have this added but we're a bit short of resources at the moment.
So, as you rightly observe, a formula is very likely to be shared between multiple entities. In the case of H2O, water is the only entity which also lists H2O as a synonym (not of type formula):
[Term] id: CHEBI:15377 name: water synonym: "H2O" RELATED [KEGG COMPOUND:]
while in the other cases H2O only appears as the formula,
[Term] id: CHEBI:29375 name: diprotium oxide synonym: "H2O" RELATED FORMULA [ChEBI:]
[Term] id: CHEBI:33813 name: ((18)O)water synonym: "H2O" RELATED FORMULA [ChEBI:]
Hope that covers most of the cases that are giving you trouble.
Original comment by: jannahastings
GO uses the string "H2O" in the text definitions for many reactions. This would seem to be a perfectly acceptable and unambiguous abbreviation for CHEBI:15377
However, CHEBI does not provide this information. The string "H2O" is on equal footing as a related synonym for 3 terms. Can we please have this is an exact synonym for CHEBI:15377
Failing that, is there a heuristic for finding the best ID for a non-unique related synonym? For example, FORMULAs appear to be shared most frequently.
CHEBI:15377 ! water [SYNONYM: "H(2)O" (related)] [SYNONYM: "HOH" (related)] [SYNONYM: "Wasser" (related)] [SYNONYM: "[OH2]" (related)] [SYNONYM: "acqua" (related)] [SYNONYM: "agua" (related)] [SYNONYM: "aqua" (related)] [SYNONYM: "dihydridooxygen" (related)] [SYNONYM: "dihydrogen oxide" (related)] [SYNONYM: "eau" (related)] [SYNONYM: "oxidane" (exact)] [SYNONYM: "water" (exact)] [SYNONYM: "H2O" (related)] [SYNONYM: "Water" (exact)] [SYNONYM: "WATER" (exact)] [SYNONYM: "H2O" (related)] [SYNONYM: "H2O" (related)] [SYNONYM: "[H]O[H]" (related)] [SYNONYM: "InChI=1/H2O/h1H2" (related)] [SYNONYM: "InChIKey=XLYOFNOQVPJJNP-UHFFFAOYAF" (related)]
CHEBI:29375 ! diprotium oxide [SYNONYM: "((1)H2)water" (related)] [SYNONYM: "diprotium oxide" (exact)] [SYNONYM: "H2O" (related)] [SYNONYM: "[1H]O[1H]" (related)] [SYNONYM: "InChI=1/H2O/h1H2/i/hH2/f/i1H2" (related)] [SYNONYM: "InChIKey=XLYOFNOQVPJJNP-ZPNZTUNVGW" (related)]
CHEBI:33813 ! ((18)O)water [SYNONYM: "((18)O)water" (exact)] [SYNONYM: "(18)OH2" (related)] [SYNONYM: "H2(18)O" (related)] [SYNONYM: "heavy-oxygen water" (related)] [SYNONYM: "water-(18)O" (related)] [SYNONYM: "H2O" (related)] [SYNONYM: "[H][18O][H]" (related)] [SYNONYM: "InChI=1/H2O/h1H2/i1+2" (related)] [SYNONYM: "InChIKey=XLYOFNOQVPJJNP-NJFSPNSNET" (related)]
Reported by: cmungall