Abstract The volume and complexity of knowledge produced by medical research calls for the development of technology for automated management and analysis of such knowledge. In this paper, we identify scenarios where a researcher or a clinician may wish to use automated systems for analysing knowledge from clinical trials. For this, we propose a language for encoding, capturing and synthesising knowledge from clinical trials and a framework that allows the construction of arguments from such knowledge. We develop this framework and demonstrate its use on a case study regarding chemotherapy regimens for ovarian cancer.