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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Typo in def of "amine-lyase activity"? #15291

Closed sjm41 closed 6 years ago

sjm41 commented 6 years ago

amine-lyase activity ; GO:0016843 Def: Catalysis of the release of amides by the cleavage of a carbon-nitrogen bond or the reverse reaction with an amine as a substrate. (EC: 4.3.3.-)

Should "release of amides" be changed to "release of amines"?

Compare to: amidine-lyase activity ; GO:0016842 Def: Catalysis of the release of amides or amidines by the cleavage of a carbon-nitrogen bond or the reverse reaction with an amide or amidine as a substrate. (EC: 4.3.2.-)

krchristie commented 6 years ago

Seems reasonable based on the page for EC 4.3, http://www.sbcs.qmul.ac.uk/iubmb/enzyme/EC4/3/ which says:

This subclass contains the enzymes that release ammonia or one of its derivatives, with the formation of a double bond or ring. Some catalyse the actual elimination of the ammonia, amine or amide, e.g. [snipped rest since structures won't paste well]

@hdrabkin - Does this suggestion look OK to you?

Also, I wanted to check about the fact that these two terms have database cross-references to incomplete EC numbers, though in the format of EC:4.3.2, rather than the EC:4.3.2.- format which if I remember correctly, you were trying to get rid of. Or are you OK with these ones that are explicitly the grouping terms that match the EC grouping terms?

hdrabkin commented 6 years ago

a .- will be spit out in Travis at the moment; if a grouping term but in as EC:4.3.2 as an xref; you could use a .- in the definition reference I think, but have not tried it with a new term.

krchristie commented 6 years ago

@hdrabkin - I'm not sure my questions were clear. I'll rephrase.

  1. Do you agree with the submitter's suggestion to change the definition of amine-lyase activity (GO:0016843) from "Catalysis of the release of amides" to "release of amines"

  2. I am asking about existing EC dbxrefs in the form of EC:1.2.3, rather than EC:1.2.3.-, i.e. EC numbers that only have 3 digits, but do NOT include the dash. Are you trying to remove these?

hdrabkin commented 6 years ago

yes, am removing 3 digits but not from grouping terms; only the children (more specific) of the grouping terms.

hdrabkin commented 6 years ago

His suggestion seems reasonable yes.

krchristie commented 6 years ago

Thanks @hdrabkin !!

sjm41 commented 6 years ago

Thanks Karen!

krchristie commented 6 years ago

@sjm41 - Thanks for pointing out the typo! Sorry so slow to fix it.