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Study region: We do not target particular region, but we implement the workshop experiments towards the researcher groups in the laboratories. Study focus: When we discuss hydrology in the context of water–energy–food nexus, the discussion will inevitably include interdisciplinary contents. For example, in the impact assessment of groundwater use we need understanding whole mechanisms composed of all kinds of causal linkages from the groundwater concept or the groundwater issues. In this article we focus on ontology engineering, which is one of the base technologies in Semantic Web technology, as a method providing common terms, concepts, and semantics. New hydrological insights: We discuss the effectiveness of ontology engineering approach in the process of collaborative research, and propose the way of ontology use contributing to interdisciplinary research through the experimental workshops of research development. The introduction of ontology engineering approach will enable us to share a common language and a common theoretical basis. But the development of the new method based on ontology engineering is necessary. For example, knowledge structuring according to each perspective of researchers and simple figure accompanied with a reasoned argument in the background are the directions of tool development.