Computational Solutions in Forest Tree Biology: Connecting Genomic, Ecological, and Physiological Repositories through Web Services and Ontologies

iPlant is a community of researchers, educators, and students working to enrich all plant sciences through the development of cyberinfrastructure: the physical computing resources, collaborative environment, virtual machine resources, and interoperable analysis software and data services that are essential components of modern plant biology. The Tree Biology working group is one of four funded seed projects with a goal of increasing communication between traditionally isolated fields (genomics, ecology, and physiology) under the umbrella of tree biology. This goal will be achieved through a combination of semantic ontologies and web services to provide a mechanism for exchange between independent data repositories.  iPlant's Simple Semantic Web Architecture and Protocol (SSWAP) can be integrated for communication on common terms, rather then site-specific database structures.  Implementation of this protocol allows for rapid exchange of data by the semantic reasoner component which enables automatic transformation and integration with other services using the same protocol. SSWAP is being implemented initially on the TreeGenes database to enable researchers to locate ecological and physiological datasets associated with specific geo-referenced individuals in independent databases.  For example, a specific genotyped or sequenced individual can be connected to environmental data (e.g. CO₂ concentration or soil temperature) from Ameriflux and physiological measurements such as leaf area or nitrogen content from TRY-DB.  The resulting tree biology cyberinfrastructure will allow researchers to take advantage of complex, independent datasets through simple queries.