Architecture of the Atlas data warehouse. The data integrated in Atlas are first downloaded as data files from the public repositories shown in the Data Source panel. These data files are then parsed and loaded into the MySQL relational databases using the Atlas loaders. The Atlas Databases panel shows the databases grouped by biological theme. These groups are sequences (green), molecular interactions (yellow); genes and functional categorization (blue); and ontologies (orange). For each database the available data retrieval methods are marked as SQL (S), C++ Atlas API (C), Java Atlas API (J), and Perl Atlas API (P). The Retrieval panel shows the flexible, layered architecture of the interfaces to the databases. Data can be accessed directly using the MySQL client with SQL statements, through the APIs in C++, Java, and Perl, and through the end-user applications implemented in the Toolbox. The APIs can also be used to implement web-based tools, or standalone applications.