To address the requirement of enabling a comprehensive perspective of life-sciences data, Semantic Web technologies have been adopted for standardized representations of data and linkages between data. This has resulted in data warehouses such as UniProt, Bio2RDF, and Chem2Bio2RDF, that integrate different kinds of biological and chemical data using ontologies. Unfortunately, the ability to process queries over ontologically-integrated collections remains a challenge, particularly when data is large. The reason is that besides the traditional challenges of processing graph-structured data, complete query answering requires inferencing to explicate implicitly represented facts. Since traditional inferencing techniques like forward chaining are difficult to scale up, and need to be repeated each time data is updated, recent focus has been on inferencing that can be supported using database technologies via query rewriting. However, due to the richness of most biomedical ontologies relative to other domain ontologies, the queries resulting from the query rewriting technique are often more complex than existing query optimization techniques can cope with. This is particularly so when using the emerging class of cloud data processing platforms for big data processing due to some additional overhead which they introduce. In this paper, we present an approach for dealing such complex queries on big data using MapReduce, along with an evaluation on existing real-world datasets and benchmark queries.