The detection of treatment conflicts between multiple treatment protocols that are co-incident is a difficult and open problem that is particularly exacerbated regarding the treatment of multiple medical conditions co-occurring in aged patients. For example, a clinical protocol for prostate cancer treatment requires the administration of androgen-suppressing medication, which may negatively interact with another, co-incident protocol if the same patient were being treated for renal disease via haemodialysis, where androgen-enhancers are frequently administered. These treatment conflicts are subtle and difficult to detect using automated means. Traditional approaches to clinical decision support would require significant clinical knowledge. In this paper, the authors present an alternative approach that relies on encoding treatment protocols via process models (in BPMN) and annotating these models with semantic effect descriptions, which automatically detects conflicts. This paper describes an implemented tool (ProcessSEER) used for semantic effect annotation of a set of 12 cancer trial protocols and depicts the machinery required to detect treatment conflicts. The authors also argue whether the semantic effect annotations of treatment protocols can be leveraged for other tasks.