PTHR11559

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This is a list of questions that arose while PAINTing PTHR11559.

Questions for ontology curators

Molecular Function

  • Question: Shouldn't GO:0003990 "acetylcholinesterase activity" be a child of GO:0004104 "cholinesterase activity"? (SF# 3220868)
    • GO:0004104 "cholinesterase activity" is defined as "Catalysis of the reaction: an acylcholine + H2O = choline + a carboxylic acid anion."
      • Acylcholine (CHEBI:35287) is defined as "A choline ester formed from choline and a carboxylic acid."
    • GO:0003990 "acetylcholinesterase activity" is defined as "Catalysis of the reaction: acetylcholine + H2O = choline + acetate."
      • Acetylcholine (CHEBI:15355) "is an ester of acetic acid and choline..."
    • Since acetic acid is a carboxylic acid, acetylcholine is an acylcholine.
    • Curator answer: "I just checked with ChEBI. I think the [above] is true, but not the [BP assertion below], as long as cholinesterase really does only work on acylcholines. A choline ester is not a choline in ChEBI, so the latter is not true. [We] are starting to work through the GO-ChEBI misalignements. We will put this one at the top of the list."
  • Question: GO:0017171 "serine hydrolase activity" is defined as "Catalysis of the hydrolysis of a substrate by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile ..." In other words, the definition specifies a reaction mechanism. Is this a valid use of GO?
    • Curator answer: I think it's a valid way to define a function. Most of the other catalytic activities are defined based on the EC definition of catalysis of <reaction spelled out>, which is why you see so many in that type of format. However, this does not mean that definitions of functions based on mechanism are not equally valid. -TB

Biological Process

  • Question: Similar to the MF annotations above, shouldn't GO:0008291 "acetylcholine metabolic process" be a child of GO:0019695 "choline metabolic process"? (SF# 3220868)
    • Curator answer: Probably not. See above.