The use of SMILES as a string representation of chemical structure makes possible much of what has been discussed in earlier chapters of this book. A chemical reaction could be represented as a collection of SMILES, some identified as reactants and some as products. It is possible to define a table to do this, or perhaps use some arrays of character data types, but a syntax extension of standard SMILES allows reaction to be expressed easily. SMIRKS is an extension of SMILES and SMARTS. It is used to represent chemical transformations. SMIRKS can also be used in a transformation function to combine SMILES reactants to produce SMILES products.

This chapter describes some of the aspects of SMIRKS and shows how it can be integrated into a relational database using new SQL functions. It discusses ways in which chemical transformations and reactions can be used to improve the robustness and usefulness of a chemical relational database.