Case Study: Enabling Forest Tree Genomics through Association Studies with the use of SSWAP

CartograTree is a web-based application that serves genomic, phenotypic, and environmental data for over 10,000 forest trees.  TreeGenes, a forest tree genomics database, supplies over 10 million genotypes.  TRY-DB, Ameriflux, and Worldclim provide metrics for over 90,000 phenotypes and a multitude of environmental variables.  Current development on CartograTree is focused on enabling users to perform association studies in order to identify relationships between genes/alleles and traits of interest.  The Simple Semantic Web Architecture and Protocol (SSWAP) developed at the iPlant Collaborative enables communication with other semantic web services by implementing data ontologies with self describing documents, facilitating data marshaling, and performing semantic matching.  This allows researchers to select data through CartograTree or TreeGenes and submit it to SSWAP where existing or custom pipelines can be initiated.  SSWAP can recognize the data type (raw sequence, tree identifiers, phenotypes, etc), and will present services available for it.  The key feature is the integration of iPlant’s SSWAP with the High Performance Computing (HPC) resources available through iPlant.  Currently, this allows users to push their selected data to applications such as Tassel, Muscle, and FastTree. Explore Cartogratree at: http://dendrome.ucdavis.edu/cartogratree.