title: Querying metabolism under different physiological constraints.
abstract: Metabolism is a representation of the biochemical principles that govern the production, consumption, degradation, and biosynthesis of metabolites in living cells. Organisms respond to changes in their physiological conditions or environmental perturbations (i.e. constraints) via cooperative implementation of such principles. Querying inner working principles of metabolism under different constraints provides invaluable insights for both researchers and educators. In this paper, we propose a metabolism query language (MQL) and discuss its query processing. MQL enables researchers to explore the behavior of the metabolism with a wide-range of predicates including dietary and physiological condition specifications. The query results of MQL are enriched with both textual and visual representations, and its query processing is completely tailored based on the underlying metabolic principles.
authors.affiliation: Department of Electrical Engineering & Computer Science, Case Western Reserve University, USA. cakmak@case.edu
authors.forename: Ali
authors.initials: A
authors.lastname: Cakmak
authors.forename: Gultekin
authors.initials: G
authors.lastname: Ozsoyoglu
authors.forename: Richard W
authors.initials: RW
authors.lastname: Hanson
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D003196:Computer Graphics; D016208:Databases, Factual; D006801:Humans; D016247:Information Storage and Retrieval; D008099:Liver / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D055432:Metabolomics / Q000706:statistics & numerical data*; D008954:Models, Biological; D012984:Software; D049490:Systems Biology