We present Collaborative Open Plant Omics (COPO), a brokering service between plant scientists and public repositories which enables aggregation and publication of research outputs, as well as providing easy access to services comprising disparate sources of information via web interfaces and Application Programming Interfaces (APIs). Users will be able to deposit their data and view/aggregate open access data from a variety of sources, as well as seamlessly pulling these data into suitable analysis environments such as Galaxy or iPlant and subsequently tracking the outputs and their metadata in COPO. COPO streamlines the process of data deposition to public repositories by hiding much of the complexity of metadata capture and data management from the end-user. The ISA infrastructure is leveraged to provide the interoperability between metadata formats required for seamless deposition to public repositories and to facilitate links to data analysis platforms. Aggregated metadata are stored as Research Objects , with logical groupings of Research Objects relating to a body of work being represented in a common standard, and are publicly queryable. COPO therefore generates and facilitates access to a large network of ontologically related metadata, which will develop over time to allow for intelligent inference over open access Linked Data fragments, providing user-customised suggestions for future avenues of investigation and potential analyses.