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The move_base node uses an action interface for managing its goals which is built on top of ROS topics one of which is, in this case, move_base/cancel. You can send a message-based cancel request, but I'd recommend using an action client to interact with move_base. Documentation that will probably be useful includes, actionlib documentation (http://www.ros.org/wiki/actionlib), and a tutorial on sending goals to the navigation stack using actionlib (http://www.ros.org/wiki/navigation/Tutorials/SendingSimpleGoals).
Hope this helps.