About Us

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. These goals are supported and enabled through SSWAP (Simple Semantic Web Architecture and Protocol) which leverages high performance computing and data storage.


Please note: in order to use external tools such as TASSEL and MUSCLE through SSWAP, you must log in into an iPlant account. You can register for a free account here.


Development Team
Member Institution Position
Emily GrauUniversity of California, DavisProgrammer
Damian GesslerUniversity of Arizona & Semantic OptionsProgrammer
Hans Vasquez-GrossUniversity of California, DavisProgrammer
Jacob ZieveUniversity of California, DavisProgrammer
Jill WegrzynUniversity of ConnecticutPrincipal Investigator
Forest Tree Biology Advisory Panel
Member Institution
David NealeUniversity of California, Davis
Missy HolbrookHarvard University
Daniel KliebensteinUniversity of California, Davis
Michael DietzeUniversity of Illinois
Ram OrenDuke University
Ross WhettenNorth Carolina State University
Sally AitkenUniversity of British Columbia
Sarah MathewsHarvard University
Credits

Data Sources

TreeGenes provisions a public repository for forest tree genetic data recorded from high-throughput genomics projects that has served the community for over 15 years. Currently, TreeGenes holds next-generation sequencing data as well as valuable legacy Sanger data. The database provides a foundation for sequence data including genotypes, annotations, sequence assemblies, and genetic maps. TreeGenes currently houses information for 1,265 forest tree species represented by 901,113 sequences, 24,142,786 genotypes, and 19,441 phenotypes. Barcode identifiers assigned during sample collection and maintained in the database, identify an individual tree sample through DNA extraction, sequencing, genotyping, and phenotyping. Location information is also recorded for each sample, when available.

Ameriflux collects 85 meteorological and 76 biological measurements at regular time intervals for approximately 81 active remote sensing sites across North and South America. The organization is a member of the FLUX network, a collaboration that spans the globe to include Europe, Asia, and Africa. Measurements from an Ameriflux site are processed to generate hourly, daily, weekly, and monthly text files. The values collected include meteorological measurements such as air temperature, global radiation, soil temperature, as well as biological measurements such as: ecosystem respiration, gross primary production, and tree foliage biomass. There are currently 4,981 records available in CartograTree representing the active Ameriflux sites.

TRY-DB is an extensive international collaboration of public and private repositories for plant trait data covering a large range of biomes and geographic areas. The database currently holds approximately three million trait records for over 69,000 plant species. A subset of these trait records have geo-referenced locations associated and have been loaded for appropriate forest tree species within the application. The public release of CartograTree displays 80,366 geo-referenced phenotypic records represented by 368 forest tree species. Measured values can be accessed for traits such as: photosynthetic rate, seed morphology, cellulose content, wood density, and root nitrogen content. These phenotypic data are individual-based in situ or physiological measurements and different from TreeGenes data which includes these types with the addition of provenance and progeny based trials. In order to obtain specific measurements, users must complete an application at TRY-DB which is linked from CartograTree. This will entail the user to perform additional searches from within TRY -DB to find the measurements of interest.

Requesting TRY-DB Data: On TRY-DB map markers on CartograTree, trait terms are listed with no measurements. For researchers to gain access to these values, a formal proposal form must be completed directly through TRY-DB's website. Sorry, as of now, there is no way to simplify this process.

WorldClim is an environmental dataset spanning 50 years and compiled primarily from five climate databases representing the globe. A combination of dense recordings, accurate interpolation methods, and quality control processes are used to provide a comprehensive dataset for current conditions. CartograTree utilizes a subset of WorldClim's data which is composed of 380 pre-computed data points around the world. Calculated values are available for metrics such as: annual temperature, annual precipitation, topsoil composition, and subsoil composition.


Contributing Data

To contribute data to the project, we encourage users to submit directly to the source database.

TreeGenes accepts forest tree genetic, phenotypic, environmental, and genetic map information. Data can be submitted through their submission page.

Try-DB accepts phenotypic data types which can be submitted through their submission page.

AmeriFlux accepts environmental data types which can be submitted through their submission page.


Data Curation

Data within the application is updated at regular intervals depending on the source. AmeriFlux, Try-DB, and WorldClim data is updated every other month. TreeGenes updates are pushed to CartograTree each month. TreeGenes' annotation databases, including NCBI BLAST results and Gene Ontology are also updated monthly.


Reference CartograTree


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