Synergy between science and informatics is required to develop a more robust understanding of the Earth as a system of systems. Interaction of Earth systems is recorded in both geological and biological data, yet the capability to integrate across disciplines is hampered by diverse social and technological approaches to research and communication. Ontology-based informatics provides the ability to share, access, and discover data across disciplines. This ability will lead to data integration and new models that enable evaluation of past, present, and future changes associated with Earth systems. Significant challenges that must be met in order to promote such an understanding encompass social and technical considerations, such as professional credit for data sharing, development of data registration services for ready access to heterogeneous and distributed data, and development of new approaches for evaluating trust and security in a web environment. Integration of data from different scientific disciplines will require development and management of new Earth system ontologies. If done properly, this development will not only enable but engage the next generation workforce.