maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination

Abstract

Background: maxdLoad2 is a relational database schema and Java application for microarray experimental annotation and storage. It is compliant with all standards for microarray meta-data capture; including the specification of what data should be recorded, extensive use of standard ontologies and support for data exchange formats. The output from maxdLoad2 is of a form acceptable for submission to the ArrayExpress microarray repository at the European Bioinformatics Institute. maxdBrowse is a PHP web-application that makes contents of maxdLoad2 databases accessible via web-browser, the command-line and web-service environments. It thus acts as both a dissemination and data-mining tool.

Results: maxdLoad2 presents an easy-to-use interface to an underlying relational database and provides a full complement of facilities for browsing, searching and editing. There is a tree-based visualization of data connectivity and the ability to explore the links between any pair of data elements, irrespective of how many intermediate links lie between them. Its principle novel features are: the flexibility of the meta-data that can be captured, the tools provided for importing data from spreadsheets and other tabular representations, the tools provided for the automatic creation of structured documents, the ability to browse and access the data via web and web-services interfaces. Within maxdLoad2 it is very straightforward to customise the meta-data that is being captured or change the definitions of the meta-data. These meta-data definitions are stored within the database itself allowing client software to connect properly to a modified database without having to be specially configured. The meta-data definitions (configuration file) can also be centralized allowing changes made in response to revisions of standards or terminologies to be propagated to clients without user intervention.maxdBrowse is hosted on a web-server and presents multiple interfaces to the contents of maxd databases. maxdBrowse emulates many of the browse and search features available in the maxdLoad2 application via a web-browser. This allows users who are not familiar with maxdLoad2 to browse and export microarray data from the database for their own analysis. The same browse and search features are also available via command-line and SOAP server interfaces. This both enables scripting of data export for use embedded in data repositories and analysis environments, and allows access to the maxd databases via web-service architectures.

Conclusion: maxdLoad2 http://www.bioinf.man.ac.uk/microarray/maxd/ and maxdBrowse http://dbk.ch.umist.ac.uk/maxdBrowse are portable and compatible with all common operating systems and major database servers. They provide a powerful, flexible package for annotation of microarray experiments and a convenient dissemination environment. They are available for download and open sourced under the Artistic License.

Figure 1

The maxdLoad2 interface. Clockwise from the top-left, this figure shows (1) the main schema interface window (2) an example of a create mode manual entry form, (3) Browse Mode example, for viewing instances in the database, (4) the Load Mode interface for populating tables from spreadsheets.

Figure 2

Column specification Syntax for data loading. The column specification syntax controls the destination attribute field that a column of data should be entered into in the database. The data can be pre-processed before they are loaded into the fields including data enumerations to convert values, combinations to allow multiple fields to be recomposed into an attribute and regular expressions to perform complex operations such as separating values from units, or removing punctuation, amongst other procedures.

Figure 3

The maxdBrowse interface. This shows maxdBrowse linking an entry on the 'Measurement' table to entries in the 'LabelledExtract' and 'Source' tables. At the very top are site navigation tabs and a banner indicating that the database page is being accessed. Underneath this are tabs to switch between navigation modes, with link highlighted as the current mode. Underneath this is a selection form, where entries can be selected for linking to other tables, additional formatting options are available by clicking the (+) link on top of the 'go' button. Below this is the data presentation form showing the results of the query, in this case the 'Measurement' DrugX-(4 h) (Cy3) vs gDNA (Cy5) has been linked down to entries in LabelledExtract and Source. On the right is the TableNavigatorTree, highlighting the tables that are being linked. Help links (?) pop-up help about maxdBrowse features, and information links (i) pop-up help about maxdLoad2 schema elements displayed on the page.

Figure 4

The maxdBrowse query syntax. This shows maxdBrowse in basket-mode, retrieving one of several queries previously performed and saved to basket. The query shown is an advanced search of the Reporter table, where the Type. Physical ontology field is being searched for 'unknown_sequence' and the 'Name' free-text field is being searched for 'SCO001'. Also shown are examples of the command-line and XML query syntax that can be used to generate the same result

Figure 5

Entity relationship diagram. This shows the relationships between the tables in the maxd database schema.

Figure 6

Attribute Definition Mechanism. Clockwise from the top-left, this figure shows (1) a portion of the standard attribute definition file, (2) the section of the user interface that is generated from this definition, (3) customising the attribute definition by adding a new item "Growth Medium" and (4) how the user interface changes in response to the change.

Figure 7

A Use-case Diagram for maxdLoad2 and maxdBrowse. The 'system administrator' is the individual in charge of maintaining the lab's database and web server. The 'lab scientist (data provider)' is typically someone who does a lot of microarray experiments and manages his experiments using maxdLoad2. The 'lab scientist (data consumer)' is typically someone who may not perform as many microarray experiments, and may not even work in a microarray facility, but is interested in the data and could use maxdBrowse or maxdLoad2 for its access. The statistician would be interested in retrieving data and meta-data for analysis, and may prefer to access the data programmatically either with scripts using maxdBrowse on the command-line or via its SOAP interface. The 'bioinformatician (stand-in)' may be involved at any level with any of these activities.