Acquisition of biomedical data is, nowadays, widespread, originating a deluge of data that may contain relevant and interesting information for healthcare professionals, biosignal researchers, and the individuals themselves. This creates the need to organize the information in a structured way, facilitating collaboration and research efforts. Therefore, for that purpose, this paper investigates database systems and file formats, dis- cussing current technologies, requirements and possible implementations. These implementations were put through a benchmarking package to analyze their insertion, query and update performance. A final approach combining the use of HDF5, a hierarchical file format for numerical data, and MongoDB, a NoSQL database, is proposed, as it showed the best combination of properties from the tested solutions.