Use-Case: Addition "ligand exchange reaction" Chemotion ELN

[hujo91]

This issue is for documenting the workflow of the above mentioned use case of a Chemotion ELN user who would like to have the entry "ligand exchange reaction" added to the reaction tag selection. The associated issue branch is 15-Use-Case-Addition-ligand-exchange-reaction-Chemotion-ELN.
For more details regarding the workflow see here.

[hujo91]

• 1. check if the requested entry already exists in an ontology -> no suitable entry available (checked with OLS)
• 2. find suitable ontology for the new entry to be added -> MOP seems to be probably the most suitable candidate due to its scope
• 3. find suitable location (i.e. parent class) in the chosen ontology for the new entry to be added -> the new reaction could be inserted under "coordination" (MOP:0000797); since a ligand exchange in the broadest sense is also a substitution, an entry under "substitution reaction" (MOP:0000790) would also be conceivable, although the definition of the parent class might not be entirely appropriate here; @StroemPhi please give feedback to this point
• 4. search for a suitable source (preferably the IUPAC Gold Book or similar) for the definition of the new entry -> currently, the Gold Book does not provide a definition for "ligand exchange reaction", only "isostructural reaction" is defined as a special case (Comment 22.10.: request to add the term "ligand excahnge reaction" to Gold Book sent to Stuart)
• 5. import/creation or linking of the substance classes necessary for the description of the new added entry ->the class "ligand" does not yet exist in MOP itself, therefore import under the MOP class "polyatomic entity" (CHEBI:36357) from CHEBI (CHEBI:52214) seems to be most suited (Comment: import from SIO (SIO:010432) may also a possible option, but CHEBI is preferred
• 6. submitting the proposal for the ontology update -> i.e. submit updated MOP .owl & .obo files via pull request
• 7. updated ontology must be retrieved and used by the Chemotion ELN for reaction classification -> ask Chemotion to use updated MOP (see Include also MOP ontology into ELN as ontology to describe reactions ComPlat/chemotion_ELN#567)

[hujo91]

Sorry mistakenly closed

[hujo91]

#16 as PR into our master
due to ambiguities regarding the classification, the new entry "ligand exchange reaction" (MOP:0000714) was initially classified under the general parent class "molecular process" (MOP:0000543)
-> PR withdrawn to our master and instead requested direct PR to upstream repo

[hujo91]

Proposal for addition to MOP accepted by PR on 03.11.21.