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Introduction

The original concept of CartograTree was envisioned by a group of forest tree biology researchers that represented traditionally separate research areas including physiology, ecology, genomics, and systematics. Guided by the NSF-funded iPlant Cyberinfrastructure, the focus was to enable interdisciplinary forest tree biology research through geo-referenced data with an application that could be easily deployed, expanded, and used by members of all disciplines. CartograTree is a web-based application that allows researchers to identify, filter, compare, and visualize geo-referenced biotic and abiotic data. Its goal is to support numerous multi-disciplinary research endeavors including: phylogenetics, population structure, and association studies.

TreeGenes Database

The TreeGenes database provides custom informatics tools to manage the flood of information resulting from high-throughput genomics projects in forest trees from sample collection to downstream analysis. This resource is enhanced with systems that are well connected with federated databases, automated data flows, machine learning analysis, standardized annotations and quality control processes. The database itself contains several curated modules that support the storage of data and provide the foundation for web-based searches and visualization tools.

Development and Advisory Team

Member Institution Position
Abdullah Almsaeed University of Tennessee TreeSnap Developer
Nic Herndon University of Connecticut Programmer
Emily Grau University of Connecticut TreeGenes Lead Database Administrator
Taylor Falk University of Connecticut Bioinformatics Developer
Damian Gessler Semantic Options, LLC Advisory member
Risharde Ramnath Dove Technologies TreeGenes Developer
Ronald Santos University of Connecticut Programmer
Margaret Staton University of Tennessee Principal Investigator
Jill Wegrzyn University of Connecticut Principal Investigator

TreeSnap

TreeSnap is a forest tree map utility that allows users to locate and take pictures of trees around the nation. TreeSnap was developed as a collaboration between Scientists at the University of Kentucky and the University of Tennessee. CartograTree makes use of the tree data collected by TreeSnap

Citing

Falk, T., Herndon, N., Grau, E., Buehler, S., Richter, P., Zaman, S., Baker, E. M., Ramnath, R., Ficklin, S., Staton, M., Feltus, F. A., Jung, S., Main, D., & Wegrzyn, J. L (2018) Growing and cultivating the forest genomics database, TreeGenes Database, Volume 2018

Herndon, N., Grau, E. S., Batra, I., Demurjian Jr., S. A., Vasquez-Gross, H. A., Staton, M. E., and Wegrzyn, J. L. (2016) CartograTree: Enabling Landscape Genomics for Forest Trees. In Proceedings of the Open Source Geospatial Research & Education Symposium (OGRS 2016), Perugia, Italy.

Vasquez-Gross H.A., Yu J.J., Figueroa B., Gessler D.D.G., Neale D.B., and Wegrzyn J.L. (2013) CartograTree: connecting tree genomes, phenotypes, and environment Molecular Ecology Resources, 13(3), 528-537

In collaboration with: