Electronic health record (EHR) automates the clinician workflow, allowing evidence-based decision support and quality management. We aimed to start a framework for domain standardization of cardiovascular risk stratification into the EHR, including risk indices whose calculation involves ECG signal processing. We propose the use of biomedical ontologies completely based on the conceptual model of SNOMED-CT, which allows us to implement our domain in the EHR. In this setting, the present study focused on the heart rate turbulence (HRT) domain, according to its concise guidelines and clear procedures for parameter calculations. We used 289 concepts from SNOMED-CT, and generated 19 local extensions (new concepts) for the HRT specific concepts not present in the current version of SNOMED-CT. New concepts included averaged and individual ventricular premature complex tachograms, initial sinus acceleration for turbulence onset, or sinusal oscillation for turbulence slope. Two representative use studies were implemented: first, a prototype was inserted in the hospital information system for supporting HRT recordings and their simple follow up by medical societies; second, an advanced support for a prospective scientific research, involving standard and emergent signal processing algorithms in the HRT indices, was generated and then tested in an example database of 27 Holter patients. Concepts of the proposed HRT ontology are publicly available through a terminology server, hence their use in any information system will be straightforward due to the interoperability provided by SNOMED-CT.