Injury from causes such as falls, traffic accidents, or violence is a major public health issue globally. Injury prevention research aims to identify vulnerable populations and places by analyzing the spatial patterns of demographic and socio-economic risk factors associated with elevated injury rates. The stakeholders in injury prevention and control are often distributed across government and public health institutions, non-profits, and even the private sector (e.g. insurance firms). While this situation calls for distributed, online research tools, their implementation may conflict with health data confidentiality and license limitations for socio-economic data. In this article, we present the Online Injury Atlas for Ontario, which was designed with the explicit goal of making use of, and contributing to, the Canadian Geospatial Data Infrastructure. We propose a service-based architecture that integrates publicly accessible map services with protected data layers. Thereby, we demonstrate the benefits of using spatial data infrastructures alongside private data at different levels of protection. In addition, we discuss the extensive data processing needs and specific cartographic design requirements of a Web atlas in the health and social sciences domain.