This paper focuses on a collection of methods that can be used to analyze the water-energy-food (WEF) nexus. We classify these methods as qualitative or quantitative for interdisciplinary and transdisciplinary research approaches. The methods for interdisciplinary research approaches can be used to unify a collection of related variables, visualize the research problem, evaluate the issue, and simulate the system of interest. Qualitative methods are generally used to describe the nexus in the region of interest, and include primary research methods such as Questionnaire Surveys, as well as secondary research methods such as Ontology Engineering and Integrated Maps. Quantitative methods for examining the nexus include Physical Models, Benefit-Cost Analysis (BCA), OPEN ACCESSWater 2015, 7 5807Integrated Indices, and Optimization Management Models. The authors discuss each of these methods in the following sections, along with accompanying case studies from research sites in Japan and the Philippines. Although the case studies are specific to two regions, these methods could be applicable to other areas, with appropriate calibration.

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In sustainability science (SS), it is difficult to identify what needs to be solved, and it is also not clear how to solve the problems that are identified. There has been no consensus on the underlying question of ''What is structuring knowledge in SS?'' This paper focuses on knowledge structuring accompanied by supporting of thinking. It addresses the key challenges associated with knowledge structuring in SS, identifies the requirements for the structuring of knowledge, proposes a reference model, and develops an ontology-based mapping tool as a solution to one layer of the reference model. First, we identify the important requirements for SS knowledge structuring.Second, we develop a reference model composed of five layers based on three of the requirements. Third, we develop an ontology-based mapping tool at Layer 2 of the reference model for meeting the two major challenges for SS, namely, identifying what problems should be addressed in SS itself and proposing solutions for those problems. The tool is designed to store and retrieve information regarding SS, to provide access to a prototype ontology for SS, and to create multiple maps of conceptual chains depending on a user's interests and perspectives. Finally, we assess whether the developed tool successfully realizes the targeted part of the reference model for SS by examining the tool's conformity to the reference model, as well as its usability, effectiveness, and constraints. Although several issues were identified in the prototype ontology and the mapping tool, the study concluded that the mapping tool is useful enough to facilitate the function of Layer 2. In particular, the mapping tool can support thinking about SS from the viewpoint of: (a) finding new potentials and risks of technological countermeasures studied in SS; (b) helping users to get a more comprehensive picture of problems and their potential solutions; and (c) providing an effective opportunity to come up with new ideas that might not be thought of without such a tool.