Understanding the interaction patterns among biological entities in a pathway can potentially reveal the role of the entities in biological systems. Although considerable effort has been contributed to this direction, querying biological pathways remained relatively unexplored. Querying is principally different in which we retrieve pathways satisfying a given property in terms of its topology, or constituents. One such property is subnetwork matching using various constituent parameters. In this paper, we introduce a logic based framework for querying biological pathways using a novel and generic subgraph isomorphism computation technique. We develop a graphical interface called IsoKEGG to facilitate flexible querying of KEGG pathways based on isomorphic pathway topologies as well as matching any combination of node names, types, and edges. It allows editing KGML represented query pathways and returns all isomorphic patterns in KEGG pathways satisfying a given query condition for further analysis.