Do you want to query both? How much are you willing to pay for that in other factors?

Put each graph in a separate dataset (one graph per dataset), /dbpedia and /wikidata.

The cost is you then can't make a single query across both at the same time (without using SERVICE) but as the sources are independent, I can't see how you can anyway. Instead ask one graph, get results, do whatever mapping is needed, ask other graph.

    Andy

PS In fact you can ALSO have a RDFDataset across both (different named graphs, tdb:dataset pointing to the "<#tdbDataset> rdf:type tdb:DatasetTDB" which is also direct referenced in fuseki:dataset.

Try on small scale data.

On 26/11/17 18:30, Laura Morales wrote:
Let's say you want a local (in your LAN) fuseki server with two graphs: dbpedia 
and wikidata. Then, when a new wikidata dump is available you want to update 
your local graph. The easier approach is to delete the old graph and add the 
new one. So, how do you do this? Do you s-delete and then s-put?
What I was trying to do is, have dbpedia and wikidata in 2 separate folders, so 
that I can easily delete one folder and replace it with the new updated graph, 
instead of transmitting the whole thing over HTTP. Makes sense?

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