The objective of this study is to describe a target water–energy–food (WEF) nexus domain world including causal linkages and trade-off relationships between WEF resources and their stakeholders, and to develop a WEF nexus system map as an interdisciplinary tool used for understanding the subsequent complexity of WEF nexus systems. An ontology engineering method, which is a qualitative method, was applied for the replicability of the WEF nexus domain ontology and the map, because ontology engineering is a method of semantic web development for enhancing the compatibility of qualitative descriptions logically or objectively. The WEF nexus system map has three underlying concepts: (1) systems thinking, (2) holistic thinking, and (3) an integrated approach at an operational level, according to the hypothesis that the chains of changes in linkages between water, energy, and food resources holistically and systemically affect the WEF nexus system, including natural and social systems, both temporally and spatially. This study is significant because it allows us to (1) develop the WEF nexus domain ontology database, including defining the concepts and sub-concepts of trade-offs relating to WEF for the replicability of this study; (2) integrate the qualitative ontology method and quantitative network analysis method to identify key concepts serving as linkage hubs in the WEF nexus domain ontology; and (3) visualize human–nature interactions such as linkages between water, energy, and food resources and their stakeholders in social and natural systems. This paper also discusses future challenges in the application of the map for a science–policy–society interface.
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