hujo91
commented
3 years ago - [x] 1. check if the requested entry already exists in an ontology -> no suitable entry available (checked with OLS)
- [x] 2. find suitable ontology for the new entry to be added -> MOP seems to be probably the most suitable candidate due to its scope
- [x] 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
- [x] 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)
- [x] 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
- [x] 6. submitting the proposal for the ontology update -> i.e. submit updated MOP .owl & .obo files via pull request
- [x] 7. updated ontology must be retrieved and used by the Chemotion ELN for reaction classification -> ask Chemotion to use updated MOP (see https://github.com/ComPlat/chemotion_ELN/issues/567)
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.