Managing and Querying Mammalian Metabolic Networks: a Metabolism Query Language and Its Query Processing

A metabolic network describes how different cellular processes (i.e., pathways) are connected and work together as part of a metabolism. The complexity of metabolisms and their working principles increase dramatically in higher order organisms (e.g., mammalians) in comparison to relatively lower level organisms (e.g., prokaryotes). As the complexity increases, managing, querying, and visualizing metabolic network data computationally in a manner that is faithful to the underlying biochemistry becomes more and more challenging. In this paper, we present a metabolism query language (MQL). MQL allows the formulation of a wide variety of indepth metabolism queries, and its query processing heavily employs metabolic principles.