CartograTree: Connecting Forest Tree Genomes, Phenotypes, and Environment

Today, forestry researchers spend a tremendous time gathering, formatting, filtering, and visualizing data collected from disparate sources.  Under the umbrella of forest tree biology, our newly developed tool, Cartogratree, seeks to leverage modern technologies to connect biotic and abiotic data in a manner that is easy for researchers to use. Our goal is to provide an integrated web-based workspace that connects environmental, genomic, and phenotypic data via geo-referenced coordinates from around the world. This application enables a variety of analysis including phylogenetics, population structure, and association studies.  To accomplish this goal, we implemented SSWAP (Simple Semantic Web Architecture and Protocol), developed at the iPlant Collaborative, to enable the primary genomics database, TreeGenes, to communicate with semantic web services. CartograTree implements GoogleMaps technology for visualization and implements user-friendly features, such as data filtering and spreadsheet functionality. This project has established collaboration with data providers such as AmeriFlux, WorldClim, TreeGenes, and TRY-DB. To date, Cartogratree stores data on 368 species including approximately 89,000 phenotypes, 470,000 sequences, and 10 million genotypes from the TreeGenes genomics database and TRY-DB trait repository.   Environmental data is provided by AmeriFlux and WorldClim, which represents 461 map points of abiotic data. The novelty of CartograTree lies in the interactive workspace that allows for geographic information systems (GIS) visualization and engagement of high performance computing (HPC) resources.  The application provides a unique tool set to facilitate research on the ecology, physiology, and evolution of forest tree species.  Access CartograTree at: http://dendrome.ucdavis.edu/cartogratree.