BACKGROUND: Metabolic reconstructions (MRs) are common denominators in systems biology and represent biochemical, genetic, and genomic (BiGG) knowledge--bases for target organisms by capturing currently available information in a consistent, structured manner. Salmonella enterica subspecies I serovar Typhimurium is a human pathogen, causes various diseases and its increasing antibiotic resistance poses a public health problem. RESULTS: Here, we describe a community--driven effort, in which more than 20 experts in S. Typhimurium biology and systems biology collaborated to reconcile and expand the S. Typhimurium BiGG knowledge--base. The consensus MR was obtained starting from two independently developed MRs for S. Typhimurium. Key results of this reconstruction jamboree include i) development and implementation of a community--based workflow for MR annotation and reconciliation; ii) incorporation of thermodynamic information; and iii) use of the consensus MR to identify potential multi--target drug therapy approaches. CONCLUSION: Taken together, with the growing number of parallel MRs a structured, community--driven approach will be necessary to maximize quality while increasing adoption of MRs in experimental design and interpretation.
Revised: March 2, 2011 |
Published: January 18, 2011
Citation
Thiele I., D.R. Hyduke, B. Steeb, G. Fankam, D.K. Allen, S. Bazzani, and P. Charusanti, et al. 2011.A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.BMC Systems Biology 5.PNNL-SA-77733.doi:10.1186/1752-0509-5-8