title: BacillOndex: an integrated data resource for systems and synthetic biology.
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.
authors.affiliation: School of Computing Science, Newcastle University, Newcastle upon Tyne, UK, NE1 7RU.
authors.forename: Goksel
authors.initials: G
authors.lastname: Misirli
authors.forename: Anil
authors.initials: A
authors.lastname: Wipat
authors.forename: Joseph
authors.initials: J
authors.lastname: Mullen
authors.forename: Katherine
authors.initials: K
authors.lastname: James
authors.forename: Matthew
authors.initials: M
authors.lastname: Pocock
authors.forename: Wendy
authors.initials: W
authors.lastname: Smith
authors.forename: Nick
authors.initials: N
authors.lastname: Allenby
authors.forename: Jennifer S
authors.initials: JS
authors.lastname: Hallinan
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics*; D030541:Databases, Genetic; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012984:Software; D058615:Synthetic Biology; D049490:Systems Biology