Managing and querying mammalian metabolic networks: a metabolism query language and its query processing

Ali Cakmak*, Gultekin Ozsoyoglu, Richard W. Hanson

Departmen of Electrical Eng. and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA. cakmak@case.edu

Proc LSS Comput Syst Bioinform Conf. August, 2009. Vol. 8, p. 189-191. Full-Text PDF

*To whom correspondence should be addressed.

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 in-depth metabolism queries, and its query processing heavily employs metabolic principles.