Autonomous and unmanned shipping is revolutionizing the maritime industry by introducing a paradigm shift on how to design the vessels and supporting land-side infrastructure. Currently, there is a lack of formalisms on how to plan for such operations, determining the varying degrees of autonomy and human responsibility, whilst ensuring safety and security. This paper describes fundamental concepts of autonomy in the context of ships. These are then applied in a methodology used to create systematic and structured descriptions for the operation of autonomous ship systems. The examples we use are based on ongoing efforts related to a planned autonomous inland waterway (IWW) barge operation. Finally, we show how the descriptions can be used in conjunction with existing safety and security analysis techniques. Our experience with this methodology is that it allows for a smooth transition from the autonomous ship system design phase to the assessment of the same system using UML notations. We believe that the same methodology can be easily applied to the other use cases and similar systems elsewhere.