The advantage of RDF is that you can exchange with the linked data community. But indeed, many things are way easier to express directly in Prolog. For data storage I’d first consider library(persistency). This does mean you need to load all data into Prolog at startup. This leads to longer startup times and more memory usage. Upto a couple of millions of clauses it still works on your Raspberry Pi though and up to some 100 million should work fine on affordable server hardware. Query is simple, flexible and fast.
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