The identification of candidate genes underlying agronomically important traits representsa key strategy for molecular breeding. Different transcriptional strategies can be addressed, depending on the species and its available molecular tools. In sunflower, the lack of a commercial oligonucleotide-based chip has limited transcriptional studies. The development of comprehensiveand well organized annotated unigene collections is a foundational step to generate a specific microarray and other tools. Cleaning and assembly of cultivated sunflower EST available in public repositories was performed to obtain a curated and trustable unigene collection comprising 41,013 putative transcripts.The collection allowed the generation of the first custom sunflower microarray under Agilent technology. This platform is currently being used to test sunflower gene expression under different stress conditions. In this work, we have approached the problem of building a database(DB) and web interface (web UI) to this data. The DB is based on GMOD Chado schema. The web UI was specifically developed considering threemain goals: to be a comprehensive tool accepting and combining data from popular formats, to provide easy ontology driven data exploration, plus collection management, and to allow data integration, working as an information repository and a tool to do fast data and result checks on experiments. The DB and web UI are already in use for the sunflower unigene collection. Regarding interoperability and result checking, some applications are functional, but more important, having an ontology driven database has opened a lot of new perspectives that we are starting to explore.