Health data autonomously collected by users are presently considered as largely beneficial for wellness, prevention, disease management, as well as clinical research, especially when longitudinal, chronic, home-based monitoring is needed. However, data quality and reliability are the main barriers to overcome, in order to exploit such potential. To this end, we designed, implemented, and tested a system to integrate patient-generated personally collected health data into the clinical research data workflow, using a standards-based architecture that ensures the fulfillment of the major requirements for digital data in clinical studies. The system was tested in a clinical investigation for the optimization of deep brain stimulation (DBS) therapy in patients with Parkinson's disease that required both the collection of patient-generated data and of clinical and neurophysiological data. The validation showed that the implemented system was able to provide a reliable solution for including the patient as direct digital data source, ensuring reliability, integrity, security, attributability, and auditability of data. These results suggest that personally collected health data can be used as a reliable data source in longitudinal clinical research, thus improving holistic patient's personal assessment and monitoring.