In this paper, two formats of XML description in Genomic Object Net (GON) and System Biology Markup Language Level 2 (SBML Level 2) are compared. First, we discuss about the difference in representations of biological pathways with these two methods. Second, we compare these two formats step-by-step from small models to large models in the following order: (1) initial stage, (2) arrange one continuous place, (3) control variables, (4) arrange one continuous transition, (5) add arc from place to transition, and (6) several connections between elements. Based on these comparisons, we considered about problems which will be arise in performing conversion between these two formats, and discuss the method to improve these problems.