bcnQL: A Query Language for Biochemical Network

This paper proposes a graph data model that can represent the Biochemical Network. In the data model, the Node class and extended Node subclasses are used to represent the Biochemical Entities and Interactions, and the Edge class is used to describe the relationships between nodes. Furthermore, the Path and Hyper-Path classes are proposed to represent various processes and pathways. The study presented in this paper also proposes a Query Language bcnQL that empowers users to query entities, interactions, processes and pathways with arbitrary conditions. In addition, new graphs can be composed with hyper-paths using supported graph functions. The language employs node formula, edge formula, path formula, hyper-path formula and graph formula to construct a collection of node objects, edge objects, path objects, hyper-path objects and graph objects respectively. Some query examples are presented to demonstrate the applicability of the language for this specific domain. Finally, we provide a prototype implementation for the query language.