The health information system PlunketPlus is a clinical initiative of Plunket (the Royal New Zealand Plunket Society) with a goal of further improving the health outcomes for children in New Zealand. The success of PlunketPlus depends heavily on how data is represented within the system. The purpose of the study described in this paper was to use PlunketPlus as a case study to inform the development of guidance on evaluating options for representing clinical data within health information systems, with a particular focus on automating existing informational processes. It has been possible to take some of the lessons learned to inform the development of initial more generic guidance that might be applicable across a range of domains. This paper concludes with a description of how Plunket applied the guidance as part of the development of PlunketPlus.