D606 Nucleic Acids Research, 2012, Vol. 40, Database issue bidirectional data ﬂow and aggregating domain speciﬁc knowledge and tools, are the mid-level Tier 2 database resources. This structured model should allow Tier 2 re- sources to provide added value to information ﬂowing to Tier 3 and present more domain speciﬁc tools to the users of Tier 1. The biological context of any experiment is essential if the data is to be of further use outside its originating la- boratory. In order to communicate this context, standards have been developed to provide a checklist of information that needs to be provided with any data set when pub- lished or submitted to a public repository. The Minimum Information about a Microarray Experiment (MIAME) (2) standard has become the requirement for most journals publishing microarray data; this has been followed by other standards, all now described under the umbrella of the Minimum Information for Biological and Biomedical Investigations (MIBBI) project (3). The bacterial microarray group at St George’s (BmG@S), funded by the Wellcome Trust for the last dec- ade, is a community-wide functional genomics resource, that has been designing and producing whole genome microarrays for 16 important bacterial pathogens. In parallel to designing, producing and testing over 30 000 microarrays the BmG@S group was tasked to develop a system to provide domain speciﬁc database and analysis tools to the worldwide microbial community that it serves (4). BmG@Sbase is a web-browsable, expertly curated, MIAME-compliant database that acts as a microbial domain speciﬁc resource ﬁlling the space between the bench research scientist and ArrayExpress/GEO. It enables bench scientists to deposit directly all information relating to experimental design and data output and provides public searchable access to published data. IMPLEMENTATION BmG@Sbase has been implemented using all free, open source software. The database backend uses PostgreSQL (http://www.postgresql.org) and the web interface is designed using a combination of PHP (http://www.php .net), Perl (http://www.perl.org), the Javascript libraries jQuery (http://jquery.com) and Overlib (http://www .bosrup.com/web/overlib/), and is served using the Apache web server (http://httpd.apache.org). All systems are hosted using the Linux operating system. DATABASE DESIGN The database design of BmG@Sbase was inﬂuenced by the Microarray and Gene Expression Object Model (MAGE- OM) (http://www.mged.org/Workgroups/MAGE/mage- om.html) and so is able to capture all aspects of the experimental process, including experimental design, sample treatments, data analysis/transformation and protocol information. A recursive approach to sample/ treatment and data/transformation object associations allows the capture of either simple or highly complex experimental procedures. The advantage of this approach is that the exact biological context of the experiment can be captured and displayed, such that the reader can clearly identify all the steps performed if trying to reproduce the experiment and/or analysis. Each process step is also associated with protocol descriptions and par- ameters, further providing descriptive power to the database content; indeed the database is essentially used as an electronic lab book. Additionally all objects in the database are annotated using a microbial subset of the MGED Ontology (MO) (5), ensuring data is consistently described within the database and can be compared to external data resources that are also using MO. The database has a mature and extensively tested security model that allows individual research groups to complete ﬁne-grained control over the privacy and sharing of their own data. Read/write permission to any data object can be granted to any user or group, thus allowing users to share data with collaborators before publication. Published data, however, is publicly available and searchable. Protocols are used throughout the database to annotate all procedural steps; they can be associated with any number of parameters or hardware/software. Protocols can be created on a per lab basis with a set of parameter ﬁelds (designated as required or not), which can be popul- ated when the protocol is added to an experimental process. DATABASE CONTENT The database currently (September 2011) contains data from 210 experimental investigations of 16 different bac- terial pathogens (including the genera: Campylobacter, Clostridium, Francisella, Haemophilus, Helicobacter, Listeria, Mycobacterium, Neisseria, Staphylococcus, Streptococcus, Yersinia); 86 of these are published and therefore publicly available (Table 1). The data has been generated by microbial research groups worldwide with a range of interests (the BmG@S project forms the hub of a collaborative network of over 80 research groups and 250 individual scientists). The research scientists individu- ally enter the data into BmG@Sbase with assistance from the BmG@S curators ensuring uniformity and high quality experimental data curation to internationally recognized standards. Data entry is provided through a set of web-enabled forms, which guide the user through the process of providing MIAME-compliant data. The forms also allow for efﬁcient annotation of data using microbial speciﬁc MO terms. Several convenience tools have also been de- veloped to assist the user in this process; sample Table 1. BmG@Sbase data statistics (September 2011) Number of Experiments (Public) Number of Experiments (Total) Number of hybridizations (Public) Number of hybridizations (Total) Number of Species with data Number of Bacterial Array designs 86 210 2474 4452 35 58 (Note that in BmG@Sbase, an experiment is equivalent to the datasets contained within a publication).