Nancy Cartwright introduced an interesting distinction with regard to modeling of physical phenomena. According to Cartwright, a mathematical theory is not applied directly to such phenomena. Rather, one first builds a basic mathematical model of the phenomenon in question, in a step Cartwright refers to as phenomenological model-building (I think she uses "phenomenological" in the sense of "empirical" but I may be wrong). Only then does one exploit a full-fledged mathematical theory, applied not to the original phenomenon but rather to the basic mathematical model. Since I am not familiar with the relevant literature, I am wondering if this distinction has been explored further in recent work.
The relevant papers are the following:
Cartwright, Nancy; Shomar, Towfic; Su'arez, Mauricio. The tool box of science. Tools for the building of models with a superconductivity example. Poznan Studies in the Philosophy of the Sciences and the Humanities 44 (1995), 137--149.
Su'arez, Mauricio; Cartwright, Nancy. Theories: Tools versus models. Studies in History and Philosophy of Science Part B: Studies in History and Philosophy of Modern Physics, Vol. 39, Issue 1 (2008), 62--81. https://doi.org/10.1016/j.shpsb.2007.05.004.