A method and system for providing data integration of multiple data stores with diverse formats. The data integration engine accepts queries using a standard query language such as XML-QL, executes those queries against the multiple data stores, and returns the results. The data stores may include relational databases, hierarchical databases, file systems, application data available via APIs, and so on. A query may reference data that resides in different data stores. The data integration engine allows operations such as joins across multiple data stores.