Querying metabolism under different physiological constraints

Ali Cakmak*, Gultekin Ozsoyoglu, Richard W. Hanson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)247-293
Number of pages47
JournalJournal of Bioinformatics and Computational Biology
Issue number2
Publication statusPublished - Apr 2010
Externally publishedYes


∗This work is supported by the National Science DBI-0743705, CRI-0551603, and CCF-0820217.

FundersFunder number
National Science FoundationCRI-0551603, DBI-0743705, CCF-0820217, 0849956


    • Biochemical networks
    • Metabolic pathways
    • Metabolic perturbations
    • Metabolic simulation
    • Metabolism
    • Metabolite changes
    • Metabolomics
    • Physiological states
    • Query language


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