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BioMed Central, BMC Systems Biology, 1(5), 2011

DOI: 10.1186/1752-0509-5-8

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

Journal article published in 2011 by Daniel R. Hyduke, Benjamin Steeb, Guy Fankam, Douglas K. Allen ORCID, Susanna Bazzani, Pep Charusanti, Feng-Chi Chen, Ronan Mt T. Fleming, Chao A. Hsiung, Sigrid Cj J. De Keersmaecker, Yu-Chieh Liao ORCID, Kathleen Marchal, I;Hyduke DR;Steeb B;Fankam G;Allen DK;Bazzani S;Charusanti P;Chen FC;Fleming RMT;Hsiung CA;De Keersmaecker SCJ;Liao YC;Marchal K;Mo ML;Ozdemir E;Raghunathan A;Reed JL;Shin SI;Sigurbjornsdottir S;Steinmann J;Sudarsan S;Swainston N;Thijs IM;Zengler K;Palsson Thiele ORCID, Monica L. Mo, Emre Özdemir ORCID and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Abstract 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.