Inconstitencies in RXNO

[StroemPhi]

• there seem to be issues with regard to the subsumption hierarchy of some classes
• there are some classes that should be but are not being declared as disjoint (for why see here)
• there seem to be wrong equivalent to axioms

[hujo91]

Some main classes to be used according to the RXNO reaction assignment flowchart are not present in RXNO, because they were not imported directly from MOP (i.e. 'addition reaction', MOP:0000642 is not present, but 'elimination reaction', MOP:0000656 as counterpart is).

[hujo91]

'molecular skeleton joining reaction' (RXNO:0000000) should not be a subclass of 'carbon-carbon coupling reaction' (RXNO:0000002) (also based on the RXNO reaction assignment scheme, see decision at question 15) and should not have the property "Equivalen To: 'carbon-carbon coupling reaction'...". This leads to misclassifications, since not every reaction in 'molecular skeleton joining reaction' (RXNO:0000000) necessarily proceeds via a C-C bond linkage.

Example: In the 'thiol-ene reaction' (RXNO:0000300) the skeleton is extended by the linkage of a new C-S bond.

[hujo91]

'azacycle synthesis' (RXNO:0000347), 'oxacycle synthesis' (RXNO:0000346) & 'thiacycle synthesis' (RXNO:0000348) as subclasses of 'heterocycle synthesis' (RXNO:0000349) should not appear again as subclasses of 'molecular process' (MOP:0000543) on the same level as the parent class 'heterocycle synthesis'.

Note: many more such example can be found

[StroemPhi]

left RNXO with MOP directly imported right RXNO as it is atm

[StroemPhi]

Why are 'pyridine synthesis', 'pyrrole synthesis', 'quinoline synthesis' made eqivalent to molecular process, when they are actually planned processes?

[hujo91]

'Bingel reaction' (RXNO:0000646) should be classified as 'cycloaddition' (MOP:0000562).

Note: It might be useful to add a new subclass "cyclopropanation" to 'cycloaddition' (MOP:0000562) and then put the Bingel reaction under this subclass.

[hujo91]

Definition and "Equivalent To" statement of 'ring formation reaction step' (RXNO:0000005) should be revised as this class once appears on the same level as 'cyclization' (MOP:0000561), but at the same time is also a subclass of it.

The similar applies for 'fused-ring-system formation' (RXNO:0000052).

[StroemPhi]

The 'ring formation reaction step' (RXNO:0000005) is a good example to discuss the differences betwenn the textual definition "A planned reaction step where the product contains a ring that was not in any of the reactants." and the logical definition done via the "Equivalent To" statement 'molecular process' and ('has specified product' some 'cyclic compound'). Following the textual definition, it should rather be equivalent to: 'planned reaction step' and ('has specified product' some 'cyclic compound').