Published online 24 September 2011 Nucleic Acids Research, 2012, Vol. 40, Database issue D605–D609 doi:10.1093/nar/gkr796 BkG@Sbase—a microbial gene expression and comparative genomic database Adam A. Witney1,*, Denise E. Waldron 1 , Lucy A. Brooks1, Richard H. Tyler1, Michael Withers1, Neil G. Stoker2, Brendan W. Wren 3 , Philip D. Butcher1 and Jason Hinds1 1Bacterial Microarray Group, Centre for Infection & Immunity, Division of Clinical Sciences, St George’s, University of London, Cranmer Terrace, London, SW17 0RE, UK, 2Department of Pathology and Infectious Diseases, Royal Veterinary College, Royal College Street, London NW1 0TU, UK and 3Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK Received August 15, 2011; Revised and Accepted September 9, 2011 ABSTRACT The reducing cost of high-throughput functional genomic technologies is creating a deluge of high volume, complex data, placing the burden on bio- informatics resources and tool development. The Bacterial Microarray Group at St George’s (BkG@S) has been at the forefront of bacterial microarray design and analysis for over a decade and while serving as a hub of a global network of microbial research groups has developed BkG@Sbase, a mi- crobial gene expression and comparative genomic database. BkG@Sbase (http://bugs.sgul.ac.uk/ bugsbase/) is a web-browsable, expertly curated, MIAME-compliant database that stores comprehen- sive experimental annotation and multiple raw and analysed data formats. Consistent annotation is enabled through a structured set of web forms, which guide the user through the process following a set of best practices and controlled vocabulary. The database currently contains 86 expertly curated publicly available data sets (with a further 124 not yet published) and full annotation informa- tion for 59 bacterial microarray designs. The data can be browsed and queried using an explorer-like interface; integrating intuitive tree diagrams to pre- sent complex experimental details clearly and con- cisely. Furthermore the modular design of the database will provide a robust platform for integrat- ing other data types beyond microarrays into a more Systems analysis based future. INTRODUCTION Despite advances in health treatment, pathogenic bacteria represent one of the most important threats to human health worldwide. Attention has focused on a range of problems, including the alarming spread of antibiotic re- sistance, microbial contamination of food, the threat of bioterrorism, the global resurgence of tuberculosis, and other emerging and re-emerging infections triggered by lifestyle, political, economical and ecological changes. Research in bacteria has fundamentally changed in the last few years from a piecemeal approach of characterizing individual determinants to a global analysis of host– pathogen interactions. This status has been fuelled by high-throughput technologies, such as microarrays and more recently next generation sequencing. However, these vital efforts are producing unmanageable amounts of data and so it is imperative that resources are available to enable effective mining of not only the new data gene- rated but also the data that is already available. Following the successful example of the public sequence databases, the European Bioinformatics Institute (EBI) and the National Center for Biotechnology (NCBI) have both de- veloped large scale public repositories (ArrayExpress and GEO respectively) to manage these data; however these resources cannot provide focused support to every research community. Thus there is a need for domain speciﬁc data- base resources that can engage at a more personal level. Indeed, Parkhill et al. (1) have recommended a three-tier model for the organization of genomic information re- sources, in which the Tier 1 database is located in indi- vidual research laboratories, collecting and analysing locally generated data; the Tier 3 database is the large public repository; and between the two tiers, providing *To whom correspondence should be addressed. Tel: 02087250698; Fax: 02086720234; Email: awitney@sgul.ac.uk The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.