One of the problems in smart home systems today is the lack of interoperability on different levels. While applying closed, non-standard, and complex protocols can cause the problem on a lower level, the architecture and design of a common building control system can cause it on a higher level. We present a solution for enabling the interoperability on the higher level in building automation systems with XML based rules and a Web API. To ensure the interoperability, we define requirements for Web services based building automation control systems. A standard building automation guideline, oBIX, is used to provide interoperability on the low level, and adopted for the rule management and description on the high level. The resulting rule engine architecture and implementation are evaluated against the requirements. The solution provides interoperability using standard Web technologies and supports employing several control systems simultaneously.