Introduction The secondary use of Electronic Healthcare Records (EHRs) often requires the identification of patient cohorts. In this context, an important problem is the heterogeneity of clinical data sources, which can be overcome with the combined use of standardized information models, Virtual Health Records, and semantic technologies, since each of them contributes to solving aspects related to the semantic interoperability of EHR data. Our main objective is to develop methods allowing for a direct use of EHR data for the identification of patient cohorts leveraging current EHR standards and semantic web technologies. Materials and Methods We propose to take advantage of the best features of working with EHR standards and ontologies. Our proposal is based on our previous results and experience working with both technological infrastructures. Our main principle is to perform each activity at the abstraction level with the most appropriate technology available. This means that part of the processing will be performed using archetypes (i.e., data level) and the rest using ontologies (i.e., knowledge level). Our approach will start working with EHR data in proprietary format, which will be first normalized and elaborated using EHR standards and then transformed into a semantic representation, which will be exploited by automated reasoning. Results We have applied our approach to protocols for colorectal cancer screening. The results comprise the archetypes, ontologies and datasets developed for the standardization and semantic analysis of EHR data. Anonymized real data has been used and the patients have been successfully classified by the risk of developing colorectal cancer. Conclusion This work provides new insights in how archetypes and ontologies can be effectively combined for EHR-driven phenotyping. The methodological approach can be applied to other problems provided that suitable archetypes, ontologies and classification rules can be designed. ; Ministerio de Economia y Competitividad ; FEDER TIN2010-21388-C01 TIN2010-21388-C02 ; Fundacion Seneca 15555/FPI/2010 ; Fernández-Breis JT; Maldonado Segura, JA.; Marcos M; Legaz-García MD; Moner Cano, D.; Torres-Sospedra J; Esteban-Gil A. (2013). Leveraging electronic healthcare record standards and semantic web technologies for the identification of patient cohorts. Journal of the American Medical Informatics Association. 20(E2):288-296. doi:10.1136/amiajnl-2013-001923. ; Senia ; 288 ; 296 ; 20 ; E2