Making explicit the mappings between real-world concepts and program elements that implement them is an essential step in understanding, using or evaluating the public interface of programs, libraries and other collections of classes that model core domain concepts. Unfortunately, due to the big abstraction gap between the modeled domain and today?s programming languages, the mapping is most of the times ambiguous as concepts and relations from the real world are distorted and diffused in the code. In this paper we present a comprehensive formal framework for describing the many-to-many mappings between domain concepts and the program elements, real-world relations and program relations and the real-world concept names and program identifiers. This framework allows us to describe and discuss typical classes of diffusion of the domain knowledge in code. Based on our formal framework we describe an algorithm to recover the mappings between entities from an ontology and program elements. We illustrate the framework by using examples from the Java standard library.