This research proposes a Web-based system for constructing knowledge structures and suggesting study materials links. Within Web-based learning, it is still difficult for learners to identify and choose study materials that match their current and desired abilities. In addition, learners may fail to recognize missing prerequisite learning, and may fail to identify the knowledge they seek. Most e-learning systems do not provide the information needed to assist learners and avoid these difficulties. We propose pedagogically-informed knowledge structures and associated applications, including a tool for designing and building such structures, a tool for navigating the structures for particular purposes (e.g., identifying knowledge missing from learners' existing knowledge), and a tool for recommending appropriate materials. In this research the knowledge structures are derived from the subject matter within a targeted knowledge domain using task analysis. In this paper, a method of constructing a knowledge structure is proposed. An experimental study investigated users' design and use of a knowledge structure. Learners will be expected to gain significantly higher levels of achievement by using the knowledge structures and associated tools proposed in this research, and educational communities will be able to share the knowledge structures and use the tools to support learners.