The Semantic Web allows knowledge discovery on graph-based data sets and facilitates answering complex queries that are extremely difficult to achieve using traditional database approaches. Intuitively, the Semantic Web query language (SPARQL) has a ‘property path’ feature that enables knowledge discovery in a knowledgebase using its reasoning engine. In this article, we utilise the property path of SPARQL and the other Semantic Web technologies to answer sophisticated queries posed over a disease data set. To this aim, we transform data from a disease web portal to a graph-based data set by designing an ontology, present a template to define the queries and provide a set of conjunctive queries on the data set. We illustrate how the reasoning engine of ‘property path’ feature of SPARQL can retrieve the results from the designed knowledgebase. The results of this study were verified by two domain experts as well as authors’ manual exploration on the disease web portal.