Metadata Discovery Problem - We defined and expressed graph-based relationships of pieces of knowledge to allow cross-reference navigation of the knowledge as an ontology. We present a methodology for constructing an ontology-based knowledge navigation model to allow cross-reference navigation between pieces of knowledge, related concepts and datasets. We defined the structure of the dataset as metadata, the field names of the actual values, and the actual values. We defined the relationship between datasets as 3-layer such as metadata layer, field names layer, and data value layer. The relationships in the metadata layer was defined as the correspondence between metadata values. We standardized the field names in dataset to discover the relationships between field names. We designed a method to discover the relationship between data values based on common knowledge for each domain. To confirm the validity of the presented methodology, we applied our methodology to implement an ontology-based knowledge navigation model for actual disaster-related processes in operation. We built a knowledge navigation model based on spatial common knowledge to confirm that the configuration of the knowledge navigation model was correct.