The role of data on ships is transitioning from “recorder” to “decision-maker”. The idea of data-centric ship operation and management is vital in the next generation of ships. Therefore a data set that characterizes ship navigation safety status needs to be set up, and hopefully standardized. This paper carried out systematic analysis for constructing a data set characterizing ships’ navigation safety status. The concerns from three types of major stakeholders, i.e. ship owners, the crew, and regulatory authorities were analyzed, resulted in a list of core indicators. A reference data set framework was then proposed, which can be used in e.g. a machine readable navigation safety model. This is beneficial for ships with a higher degree of human-system collaboration, or eventually an autonomous ship, enabling a new, data-centric, paradigm, for the next-generation ship navigation system design.