Data generated during the course of research activities carried out by the International Centers of Excellence for Malaria Research (ICEMR) is heterogeneous, large, and multi-scaled. The complexity of federated and global data operations and the diverse uses planned for the data pose tremendous challenges and opportunities for collaborative research. In this article, we present the foundational principles for data management across the ICEMR Program, the logistics associated with multiple aspects of the data life cycle, and describe a pilot centralized web information system created in PlasmoDB to query a subset of this data. The paradigm proposed as a solution for the data operations in the ICEMR Program is widely applicable to large, multifaceted research projects, and could be reproduced in other contexts that require sophisticated data management.