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However, Protege is a modeling tool not a database. So when you start getting into large amounts of data (e.g., 10K instances or more) you will need another tool, ideally a database. There are tools to do what's called Data Virtualization, where you can represent your data (what OWL users call the A-Box, i.e., the equivalent of instances in OOP or rows in a relational DB) in a relational database and map the data... Source: almost 2 years ago
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