We present a research methodology developed for the theory of scientific knowledge which use conceptual mapping, cognitive science theory, theory of didactic transposition and algorithmic language. This tool should help the identification of the constituent elements of a scientific theory, its epistemological construction, the current paradigm and the teaching methodology employed. It is suggested that in particular cases, as in the study of the theory of scientific knowledge, that conceptual mapping should be constructed under well-defined rules. Due to certain particularities of how Physical theories are constructed and expressed in terms of Physical laws we will have to generalize the tool "conceptual maps" to describe how the Physical theories are elaborated. This generalization will be called "Mapping of Scientific Knowledge Structures". We will apply this to the study of potentially significant teaching units.