In this paper, from the viewpoint that learners explore and construct knowledge actively, we proposed a method of note-taking by arranging concepts and a course for teaching the method through collaboration. We also carried out a practice-session of teaching the method. Through the method of note-taking used in this research, learners extract important concepts from learning materials and structure them as a concept map. The process consists of three phases; cutting, judgment, and relating. These activities, however, are too difficult for cognitively poor learners. So we set up an individual session and a collaborative session. In the individual session, a learner individually carries out cutting, judgment, and relating, and makes a concept map with paper cars and sheets. The purpose of this session is to make the learner think about the learning materials and prepare for the collaborative session. In the collaborative session, learners form small groups, examine their concept maps, and collaboratively make the group's concept map with the software "Undo-Kun". Another purpose of this session is to make the learners mutually learn from their differences and share their methods for arranging concepts. We carried out a teaching practice of "Workings of Current and Magnet" in junior high school, in which 120 students participated. As a result of the evaluation of the practice, the note-taking method and the teaching method proved to be effective.