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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Non-specific mentions of EC:6.2.1.3 #23296

Closed sjm41 closed 2 years ago

sjm41 commented 2 years ago

Please remove mentions (attributions) of EC:6.2.1.3 (Long-chain-fatty-acid--CoA ligase) from the definitions of these two terms:

id: GO:0031955 name: short-chain fatty acid-CoA ligase activity def: "Catalysis of the reaction: ATP + a short-chain fatty acid + CoA = AMP + diphosphate + an acyl-CoA; short-chain fatty acids are fatty acids with a chain length of less than C6." [EC:6.2.1.3, GOC:mah]

id: GO:0031957 name: very long-chain fatty acid-CoA ligase activity def: "Catalysis of the reaction: ATP + a very-long-chain fatty acid + CoA = AMP + diphosphate + an acyl-CoA; a very long-chain fatty acid is a fatty acid which has a chain length greater than C22." [EC:6.2.1.3, GOC:mah]

I'm not sure if there's agreement on what the cut-offs are for short/medium/long/very long fatty acids, but the EC entry for EC:6.2.1.3 (Long-chain-fatty-acid--CoA ligase) doesn't really help/support with the GO defs above - it just says "The liver enzyme acts on acids from C(6) to C(20); that from brain shows high activity up to C(24)."

EC:6.2.1.3 is already correctly an xref on this term: id: GO:0004467 name: long-chain fatty acid-CoA ligase activity def: "Catalysis of the reaction: ATP + a long-chain fatty acid + CoA = AMP + diphosphate + an acyl-CoA; a long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [RHEA:15421] xref: EC:6.2.1.3

deustp01 commented 2 years ago

I'm not sure if there's agreement on what the cut-offs are for short/medium/long/very long fatty acids

Here's a common one - not sure that there is consensus on exact lengths and whether there is overlap between length classes, i.e., can any one enzyme act only on members of a single class or does it also have some smaller amount of activity on other classes -

Pharmaceutical nanotechnology: Brief perspective on lipid drug delivery and its current scenario Karthik Siram, ... R. Hariprasad, in Biomedical Applications of Nanoparticles, 2019

Based on the number of carbon atoms in the alkyl chain length, fatty acids can be classified into short-chain (2–4 carbon atoms), medium-chain (6–10 carbon atoms), and long-chain fatty acids (12–26 carbon atoms) (Shete and Patravale, 2013; Trevaskis et al., 2008).

hdrabkin commented 2 years ago

Well, I guess EC:6.2.1.3 shouldn't be with : GO:0031955; I'm on the fence with id: GO:0031957

sjm41 commented 2 years ago

I'm on the fence with id: GO:0031957 If we want to keep EC:6.2.1.3 associated with that, then it should be promoted to an xref rather than just in the definition...

But given EC:6.2.1.3 is already an accurate (1:1) xref on GO:0004467, I'd say it shouldn't appear in the xref/def of any other term.

hdrabkin commented 2 years ago

Done