Figure 11.

The use of communication standards allows for a high degree of flexibility in delivery of information. Data stored in files can be either imported or linked into the content repositories, and then annotated. RMI interfaces expose the basic read/write functionality. This information can be searched using structured querying (sql or xpath based), as well as using free text (inverse index based) searching. To ensure accessibility to the data and flexibility of use we provide a REST API which provides additional integration points. For the data analysis pipelines (or toolsets in GenePattern) standardized modules are provided which use the REST API directly to search for files, as well as read/write information into the content repositories. Application programming language integration is provided through the REST API returning JSON objects, so that while the integration is stateless it supports any language that can access URIs and parse JSON (e.g. Matlab, R, Java, C#, Perl). The system can also be used to integrate with the semantic web, as RDF graphs which directly represent information within the repository can also be returned. Dynamic Web Content is generated and managed using Spring, with controllers being used to service AJAX requests. We use AJAX/JSON calls to populate pages and visualizations in a variety of web frameworks (including portlets and JSF). Desktop integration is essential to the usage of the repositories, and the REST access layer can be used to return information in a number of protocols: URI access can be used to allow direct access; WebDAV can be used to integrate with common desktop tools and allow for browsing; and the REST API can be used to return directory (tree) based structures.