community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

• Published in: BMC systems biology Vol. 5; no. 8; p. 8
• Main Authors: Thiele, Ines, Hyduke, Daniel R, Steeb, Benjamin, Fankam, Guy, Allen, Douglas K, Bazzani, Susanna, Charusanti, Pep, Chen, Feng-Chi, Fleming, Ronan M.T, Hsiung, Chao A, Keersmaecker, Sigrid C.J. de, Liao, Yu-Chieh, Marchal, Kathleen, Mo, Monica L, Özdemir, Emre, Raghunathan, Anu
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 18-01-2011; BioMed Central
• Subjects: 60 APPLIED LIFE SCIENCES; animal pathogenic bacteria; annotation; Anti-Bacterial Agents - metabolism; Anti-Bacterial Agents - pharmacology; ANTIBIOTICS; biochemical, genetic and genomic knowledge bases; biochemistry; BIOLOGY; Community development; Cooperative Behavior; Databases, Factual; DESIGN; DISEASES; Drug resistance; Escherichia-coli; Genes, Bacterial - genetics; Genetic aspects; genomes; genomics; Humans; IMPLEMENTATION; KNOWLEDGE BASE; MATHEMATICAL MODELS; Metabolic Networks and Pathways; metabolic reconstructions; metabolism; microbial genetics; microbial physiology; Models, Biological; networks; Pathogenic microorganisms; PATHOGENS; protein; PUBLIC HEALTH; reconstruction; SALMONELLA; Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium; SALMONELLA TYPHIMURIUM; Salmonella typhimurium - drug effects; Salmonella typhimurium - genetics; Salmonella typhimurium - metabolism; Systems Biology; TARGETS; THERAPY; THERMODYNAMICS; United States
• ISSN: 1752-0509; 1752-0509
• DOI: 10.1186/1752-0509-5-8

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.