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BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology

Lookup NU author(s): Dr Goksel Misirli, Professor Anil Wipat, Joseph Mullen, Dr Katherine JamesORCiD, Dr Matthew Pocock, Dr Wendy Smith, Dr Jennifer Hallinan

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Abstract

BacillOndex is an extension of the Ondex data integration system, providing a semantically annotated, integrated knowledge base for the model Gram-positive bacterium Bacillus subtilis. This application allows a user to mine a variety of B. subtilis data sources, and analyse the resulting integrated dataset, which contains data about genes, gene products and their interactions. The data can be analysed either manually, by browsing using Ondex, or computationally via a Web services interface. We describe the process of creating a BacillOndex instance, and describe the use of the system for the analysis of single nucleotide polymorphisms in B. subtilis Marburg. The Marburg strain is the progenitor of the widely-used laboratory strain B. subtilis 168. We identified 27 SNPs with predictable phenotypic effects, including genetic traits for known phenotypes. We conclude that BacillOndex is a valuable tool for the systems-level investigation of, and hypothesis generation about, this important biotechnology workhorse. Such understanding contributes to our ability to construct synthetic genetic circuits in this organism.

Publication metadata

Author(s): Misirli G, Wipat A, Mullen J, James K, Pocock M, Smith W, Allenby N, Hallinan J

Publication type: Article

Publication status: Published

Journal: Journal of Integrative Bioinformatics

Year: 2013

Volume: 10

Issue: 2

ISSN (electronic): 1613-4516

Publisher: Bielefeld University

URL: http://dx.doi.org/10.2390/biecoll-jib-2013-224

DOI: 10.2390/biecoll-jib-2013-224

PubMed id: 23571273

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