In this paper, a ontology-based keyword structuring method is proposed to represent the knowledge structure of scholarly documents and to make inferences from the semantic relationships holding among them. The characteristics of thesaurus as a knowledge organization system(KOS) for subject heading is critically reviewed from the information retrieval point of view. The domain concepts are identified and classified by analysis of the information activities occurring in a general research process based on scholarly sensemaking model. The ontological structure of keyword set is defined in terms of the semantic relationship of the canonical concepts which constitute scholarly documents such as journal articles. As a result, each ontologically structured keyword set of a document represents the knowledge structure of the corresponding document as semantic index. By means of the axioms and inference rules defined for information needs, users can efficiently explore the scholarly communication network built on the semantic relationship among documents in an analytic way based on the scholarly sensemaking model in oder to efficiently retrieve the relevant information for problem solving.