BacillOndex: an integrated data resource for systems and synthetic biology.

Goksel Misirli, Anil Wipat, Joseph Mullen, Katherine James, Matthew Pocock, Wendy Smith, Nick Allenby, Jennifer S. Hallinan

Research output: Contribution to journalArticleResearchpeer-review

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.

LanguageEnglish
Article number224
Pages1-14
Number of pages14
JournalJournal of integrative bioinformatics
Volume10
Issue number2
Publication statusPublished - 2013

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Synthetic Biology
Systems Biology
Bacillus subtilis
Information Systems
Single Nucleotide Polymorphism
Knowledge Bases
Information Storage and Retrieval
Gram-Positive Bacteria
Biotechnology
Systems Analysis
Genes
Phenotype

Cite this

Misirli, G., Wipat, A., Mullen, J., James, K., Pocock, M., Smith, W., ... Hallinan, J. S. (2013). BacillOndex: an integrated data resource for systems and synthetic biology. Journal of integrative bioinformatics, 10(2), 1-14. [224].
Misirli, Goksel ; Wipat, Anil ; Mullen, Joseph ; James, Katherine ; Pocock, Matthew ; Smith, Wendy ; Allenby, Nick ; Hallinan, Jennifer S. / BacillOndex : an integrated data resource for systems and synthetic biology. In: Journal of integrative bioinformatics. 2013 ; Vol. 10, No. 2. pp. 1-14.
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Misirli, G, Wipat, A, Mullen, J, James, K, Pocock, M, Smith, W, Allenby, N & Hallinan, JS 2013, 'BacillOndex: an integrated data resource for systems and synthetic biology.', Journal of integrative bioinformatics, vol. 10, no. 2, 224, pp. 1-14.

BacillOndex : an integrated data resource for systems and synthetic biology. / Misirli, Goksel; Wipat, Anil; Mullen, Joseph; James, Katherine; Pocock, Matthew; Smith, Wendy; Allenby, Nick; Hallinan, Jennifer S.

In: Journal of integrative bioinformatics, Vol. 10, No. 2, 224, 2013, p. 1-14.

Research output: Contribution to journalArticleResearchpeer-review

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Misirli G, Wipat A, Mullen J, James K, Pocock M, Smith W et al. BacillOndex: an integrated data resource for systems and synthetic biology. Journal of integrative bioinformatics. 2013;10(2):1-14. 224.