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Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data‐mining application that facilitates the reconstruction of molecular networks based on automated text‐mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the …