Knowledge bases (KBs) are increasingly used in diverse knowledge-processing tasks. Widely used RDF-style KBs represent knowledge as subject – predicate – object triples, whereas many external sources are described in non-RDF formats. Therefore, applications often need to integrate KBs with such external sources. In our previous work, we proposed an integrated query environment named Knowledge Mediator (KM), in which external sources are accessed via SPARQL magic properties, letting users query them as if they were parts of the KB. KM performs entity linking (EL) to find corresponding KB entities for external objects. However, EL may yield multiple plausible entities, and the results may involve uncertainty. In this study, we propose a model that represents data integration while allowing for the expression of uncertainty in query results caused by EL. Furthermore, we propose an efficient query processing method that retrieves only those results whose likelihoods exceed a user-specified threshold.