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rsc-ontologies / rxno

Name Reaction Ontology
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Addition of trimerization, cyclotrimerization & protein trimerization to MOP #34

Closed hujo91 closed 2 years ago

hujo91 commented 2 years ago

Addition of 3 missing reactions:

  1. trimerization (MOP:0000715) Def.: The formation of a trimer from three molecular subunits. Parent class: molecular process (MOP:0000543)

  2. cyclotrimerization (MOP:0000716) Def.: The formation of a trimer by cycloaddition of three unsaturated compounds (e.g. alkynes, alkenes, nitriles or mixtures thereof). A metal catalyst is usually required for this type of reaction. Parent class: cycloaddition (MOP:0000562) & trimerization (MOP:0000715) Source: https://doi.org/10.1002/anie.200700802

  3. protein trimerization (GO:0070206) - Import from Gene Ontology Def.: The formation of a protein trimer, a macromolecular structure consisting of three noncovalently associated identical or nonidentical subunits. Parent class: trimerization (MOP:0000715) Source: http://purl.obolibrary.org/obo/GO_0070206

note:

batchelorc commented 2 years ago

I think it's best to go for the lowest unused MOP ID, which is MOP:0000825.

batchelorc commented 2 years ago

But here's a thing - is it a cyclisation according to the Gold Book definition? I'm not sure it is.

hujo91 commented 2 years ago

Definition of "cyclization" in the Goldbook: "Formation of a ring compound from a chain by formation of a new bond." According to this definition, I guess it is indeed the case that cyclotrimerization is not a cyclization (MOP:0000561), because it does not happen from a chain. Thanks for the hint! Anyway, I think that actually a definition of cyclotrimerization should also be included in the Goldbook in the future. Maybe I will suggest that. @batchelorc your opinion on this?

batchelorc commented 2 years ago

There is no harm in suggesting new terms for the Gold Book, but it might well take a while.

The other thing I am wondering is whether there are any trimerisations that aren't cyclic?

hujo91 commented 2 years ago

So, as I understand it, the essential feature of trimerization is the formation of a trimer from three molecular subunits. This can be done as cyclotrimerization by cycloaddition and thus formation of a cyclic trimer. However, this need not be necessarily the case. I am thinking, for example, of the metal-catalyzed trimerization of ethene to 1-hexene, as a trimerization without ring formation. That would be more in the sense of an oligomerization. All in all, I would say that cyclotrimerization is a (common) special case of trimerization.

StroemPhi commented 2 years ago

Do I understand you two right, that this means we also need to add to MOP a parent class called "trimerization" under which to subsume "cyclotrimerization" as well as probably GO's protein trimerization and the one from the above example?

If so, I assume the parent class of "trimerization" to be "molecular process (MOP:0000543), right?

hujo91 commented 2 years ago

@StroemPhi, yes I think that sums it up quite well. Parent class "trimerization" (metal-catalyzed trimerization of ethene to 1-hexene is an example for this) under "molecular process (MOP:0000543), with the subclass "cyclotrimerization" and maybe also "protein trimerization" from GO? @batchelorc your opinion on that?

StroemPhi commented 2 years ago

I think it was a bad idea to include GO's "protein trimerization" and propose to get it out of MOP again as it is not within the scope of MOP. If it was me introducing this error, than I'm really sorry. EDIT: I made a PR (#46) to do so.

StroemPhi commented 2 years ago

see also https://github.com/rsc-ontologies/rxno/issues/45