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Numbers of applications of GIS essentially are models for analyzing in different themes, and they are also examples of problem solving in AI. Therefore many theories and technologies from AI can be embedded in GIS to strengthen its ability of automatic analysis. Fortunately, mathematical programming is a kind of powerful tool to settle problems with a feature of optimization or satisfiability under some constraint conditions. And many applications of GIS happen to be in a category of optimization, for they can usually be approximated accurately by some mathematical models. Due to the establishment of any mathematical programming is highly knowledge-based or intelligence-required, so a knowledge-based subsystem should be included into our hybrid system for the sake of autonomously creating a mathematical programming for a GIS application. This problem has a typical characteristic of multiple domains crossing from perspective of knowledge engineering, so some novel knowledge-processing methods, like knowledge dependence, knowledge transition and knowledge reference, are studied. And a knowledge system represented by frames and a reference-based knowledge-using method are presented here. In this paper examples demonstrate all steps of creating a mathematical programming in detail, and one real application about how to lay a new metro line is presented.