The Generation Challenge Programme (GCP; http://www.generationcp. org) is a globally-distributed crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. To achieve interoperability and integration within the GCP across diverse data types published by project-distributed data sources and consumed by end-user data analysis tools, the GCP adopted the development paradigm of a \model-driven architecture". At the core of the GCP architecture is a scienti c domain model, heavily parameterized with GCP-indexed ontology. The GCP scienti c domain model is an object model that encapsulates key crop science concepts and is documented using Uni ed Modeling Language. The GCP-indexed ontology reuses established international standards where available, converts other publicly-available controlled vocabulary into formallymanaged ontology, and develops novel ontology if no public vocabularies yet exist. The GCP architecture is being translated into various open source objectoriented software libraries and into data types for various public semantic web protocols. The GCP model-driven architecture is speci ed as a common semantic framework for the implementation of interoperability and integration of diverse crop data sets and analysis tools. The architecture and associated open source software are accessible at http://pantheon.generationcp.org