To yet, the research process for producing, evaluating, and applying information has gotten less attention from informatics than the operational processes for performing clinical trials. The study protocol, which is an abstract description of a clinical study’s scientific design, is at the heart of these scientific procedures - the science of clinical research. The Ontology of Clinical Trials is an OWL 2 model of the relationships between entities of study design protocols intended to aid in the design and analysis of human studies computationally. The modelling done by OCRe is not dependent on any particular study design or therapeutic domain. It features a study design typology as well as an ERGO Annotation dedicated module for expressing the significance of eligibility criteria. In this work, we outline the major informatics use cases at each phase of a study’s scientific lifecycle, introduce OCRe and the ideas that underpin its modelling, and discuss how OCRe and related technologies can be applied to a variety of clinical research use cases. OCRe encapsulates the central semantics that underpins clinical research scientific procedures and can be used as an informatics foundation to support the whole spectrum of knowledge activities that make up clinical research science.