CartograTree: connecting tree genomes, phenotypes and environment

• Published in: Molecular ecology resources Vol. 13; no. 3; pp. 528 - 537
• Main Authors: Vasquez-Gross, Hans A., Yu, John J., Figueroa, Ben, Gessler, Damian D. G., Neale, David B., Wegrzyn, Jill L.
• Format: Journal Article
• Language: English
• Published: Oxford Blackwell Publishing Ltd 01.05.2013; Blackwell; Wiley Subscription Services, Inc
• Subjects: Animal and plant ecology; Animal, plant and microbial ecology; association study; Biological and medical sciences; Classical genetics, quantitative genetics, hybrids; Environment; forest trees; Fundamental and applied biological sciences. Psychology; General aspects; Genetics of eukaryotes. Biological and molecular evolution; Genome, Plant - genetics; Genomics - methods; genotype; Geography; Internet; landscape genomics; Phenotype; Population genetics, reproduction patterns; Semantics; Software; Synecology; Trees - genetics; web services; forest trees; landscape genomics; Phenotype; Landscape; web services; Genomics; association study; Forest tree; Environment; Genotype; Genome
• ISSN: 1755-098X; 1755-0998
• DOI: 10.1111/1755-0998.12067

Today, researchers spend a tremendous amount of time gathering, formatting, filtering and visualizing data collected from disparate sources. Under the umbrella of forest tree biology, we seek to provide a platform and leverage modern technologies to connect biotic and abiotic data. Our goal is to provide an integrated web‐based workspace that connects environmental, genomic and phenotypic data via geo‐referenced coordinates. Here, we connect the genomic query web‐based workspace, DiversiTree and a novel geographical interface called CartograTree to data housed on the TreeGenes database. To accomplish this goal, we implemented Simple Semantic Web Architecture and Protocol to enable the primary genomics database, TreeGenes, to communicate with semantic web services regardless of platform or back‐end technologies. The novelty of CartograTree lies in the interactive workspace that allows for geographical 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. CartograTree can be accessed at: http://dendrome.ucdavis.edu/cartogratree.