A semantic query over an RDF database is received with RDF database statistics and access methods for evaluating triple patterns in the query. The semantic query is expressed as a parse tree containing triple patterns and logical relationships among the triple patterns. The parse tree and access methods create a data flow graph containing a plurality of triple pattern and access method pair nodes connected by a plurality of edges, and an optimal flow tree through the data flow graph is determined such that costs are minimized and all triple patterns in the semantic query are contained in the optimal flow tree. A structure independent execution tree defining a sequence of evaluation through the optimal flow tree is created and is transformed into a database structure dependent query plan. This is used to create an SQL query that is used to evaluate the semantic query over the RDF database.