Scientific papers are essential manifestations of evolving scientific knowledge, and arguments are an important avenue to communicate research results. This study aims to understand how the argumentation process is represented in scientific papers, which is important for knowledge representation, discovery, and retrieval. First, based on fundamental argument theory and scientific discourse ontologies, a coding schema, including 17 categories was constructed. Thereafter, annotation experiments were conducted with 40 scientific articles randomly selected from two different research areas (library and information science and biomedical sciences). Statistical analysis and the sequential pattern mining method were then employed; the ratio of different argumentation units and evidence types were calculated, the argumentation semantics of figures and tables analyzed, and the argumentation structures extracted. A correlation analysis between argumentation and rhetorical structures was also performed to further reveal how argumentation was represented within scientific discourses. The results indicated a difference in the proportion of the argumentation units in the two types of scientific papers, as well as a similar linear construction with differences in the specific argument structures of each knowledge domain and a clear correlation between argumentation and rhetorical structure.Scientific papers are the most essential manifestations of evolving scientific knowledge, and argumentation is an important avenue through which research results are communicated (Walton & Zhang, 2013). Scientific discovery challenges existing theoretical analyses and empirical studies in a process of continuous argumentation; thus, argumentation forms the foundation of scientific papers, and articles demonstrating a rigorous argumentation process are essential for scientific development. Meanwhile, the "argumentation units" (along with the argumentation structure within a scientific paper) are a special implicit knowledge entity that represents the attribute of knowledge.Argumentation plays a critical role in identifying relevant arguments based on their content; thus, it seems reasonable to focus on identifying characteristic patterns of argumentation and the ways in which they are typically developed (Song et al., 2014). Revealing, extracting, and analyzing the argumentation structure of scientific papers plays an important role in interpreting the general rules of their content composition and benefits knowledge discovery, representation, retrieval, and ultimately access. Therefore, it is necessary to understand how argumentation is represented within scientific papers and to identify argument structures when they are extended to whole text segments (Walton, 2013;Walton et al., 2008).Recent research has placed particular emphasis on the definition, description, and representation of scientific content from the semantic and pragmatic perspectives. Several ontologies, such as the document element