Data From: TERRA-REF, An Open Reference Data Set From High Resolution Genomics, Phenomics, and Imaging Sensors

picture of TERRA REF field scanner, a large gantry system with multiple sensors in a box over a field of sorghum

The ARPA-E funded TERRA-REF project generated open-access reference datasets for the study of plant sensing, genomics, and phenomics. Sensor data were generated by a field scanner sensing platform that captures color, thermal, hyperspectral, and active fluorescence imagery as well as three dimensional structure and associated environmental measurements. This dataset is provided alongside data collected using traditional field methods in order to support calibration and validation of algorithms used to extract plot level phenotypes from these datasets.

Data were collected at the University of Arizona Maricopa Agricultural Center in Maricopa, Arizona.
This site hosts a large field scanner with fifteen sensors, many of which are capable of capturing mm-scale images and point clouds at daily to weekly intervals.

These data are intended to be reused and are accessible as a combination of files and databases linked by spatial, temporal, and genomic information. In addition to providing open access data, the entire computational pipeline is open source, and we enable users to access high-performance computing environments.

The study has evaluated a sorghum diversity panel, biparental cross populations, and elite lines and hybrids from structured sorghum breeding populations.
In addition, a durum wheat diversity panel was grown and evaluated over three winter seasons.
The initial release includes derived data from two seasons in which the sorghum diversity panel was evaluated.
Future releases will include data from additional seasons and locations.

The TERRA-REF reference dataset can be used to characterize phenotype-to-genotype associations, on a genomic scale, that will enable knowledge-driven breeding and the development of higher-yielding cultivars of sorghum and wheat.
The data is also being used to develop new algorithms for machine learning, image analysis, genomics, and optical sensor engineering.

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Link to dataset at Datadryad.orghtml
The ARPA-E funded TERRA-REF project is generating open-access reference...
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Field	Value
Tags	Field-based high-throughput phenotyping Genetics Genomics Breeding Sorghum bicolor phenotype EARTH SCIENCE > AGRICULTURE > AGRICULTURAL PLANT SCIENCE > PLANT BREEDING AND GENETICS TERRA-REF ARDN-dev
Modified	2022-09-08
Release Date	2022-09-08
Identifier	75934be5-e8c9-45f7-ae23-9699ec0895f1
Spatial / Geographical Coverage Area	POLYGON ((-111.9747967 33.0764953, -111.9747966 33.0745228, -111.9750963 33.074485715, -111.9750964 33.0764584, -111.9747967 33.0764953))
Publisher	Dryad
Spatial / Geographical Coverage Location	Agricultural research field under the field scanner at the University of Arizona Maricopa Agricultural Center in Maricopa, Arizona
Temporal Coverage	February 13, 2016 to October 1, 2019
License	Creative Commons CCZero
Contact Name	LeBauer, David
Contact Email	dlebauer@arizona.edu
Public Access Level	Public

Extended Metadata:

Field	Value
Authors	LeBauer, David S. (ORCID) Burnette, Maxwell A. (ORCID) Demieville, Jeffrey (ORCID) Fahlgren, Noah (ORCID) Flinn, Barry (ORCID) French, Andrew N. (ORCID) Garnett, Roman (ORCID) Kooper, Rob (ORCID) Li, Zongyang (ORCID) Maimaitijiang, Maitiniyazi (ORCID) Morris, Geoffrey P. (ORCID) Newcomb, Maria (ORCID) Ottman, Michael J. (ORCID) Ozersky, Philip (ORCID) Paheding, Sidike (ORCID) Pauli, Duke (ORCID) Pless, Robert (ORCID) Riemer, Kristina (ORCID) Rohde, Gareth S (ORCID) Rooney, William L. (ORCID) Sagan, Vasit (ORCID) Shakoor, Nadia (ORCID) Stylianou, Abby (ORCID) Thorp, Kelly (ORCID) Ward, Richard (ORCID) White, Jeffrey W. (ORCID) Willis, Craig (ORCID) Zender, Charles S. (ORCID)
Peer Reviewed	No
Intended Use	This data publication consists of data and metadata, as described below. Plot level phenotypes, experimental meta-data, and a catalog of large files are available on Dryad. The file catalog provides the location of larger sensor files that can be accessed using the Globus file transfer service. Because the dataset contains over 400TB of sensor data files, these large files are stored at the National Center for Supercomputing Applications and are made available using the Globus file transfer service. In addition to hosting an archival copy of data on Dryad, the documentation includes instructions for browsing and accessing these data through a variety of online portals. These portals provide access to web user interfaces as well as databases, apis, and R and Python clients. In some cases it will be easier to access data through these portals using web interfaces and software libraries. Except where clearly indicated for sensor data, the structure of directories that contain data and metadata refer to the contents of the Dryad archive. There are four directories: `data`, `metadata`, `code`, and `documentation`. The TERRA-REF documentation is hosted at https://docs.terraref.org. The section "How to Access Data" (https://docs.terraref.org/user-manual/how-to-access-data) provides an overview of methods that can be used to access data beyond what is provided in this repository. There is also a PDF copy of the documentation in the file `docs.terraref.org_2020_04_06.pdf` in the `metadata/` directory. Tutorials for getting started with TERRA-REF data are available at https://terraref.github.io/tutorials and on GitHub at https://github.com/terraref/tutorials. The TERRA-REF YouTube channel hosts 1) video walkthroughs of the tutorials https://www.youtube.com/channel/UComeQAqYR5aZrXN_3K5iFGw and 2) a playlist of videos related to the project https://www.youtube.com/playlist?list=PLNgRX4VLed8213stlJp60MvVx2p6VTv6N.
Use Limitations	All data are released to the public domain under the CC-0 license (https://creativecommons.org/share-your-work/public-domain/cc0/). All original software are licensed with the BSD 3-clause or MIT/BSD compatible license. All software used for data processing have been archived on Zenodo and are available on GitHub in the `terraref` organization: https://github.com/terraref.
Equipment or Software Used	TERRA-REF Computing Pipeline
Funding Sources	U.S. Department of Energy DE-AR0000598 National Science Foundation ACI-1548562
Primary Article	Burnette, M., Kooper, R., Maloney, J. D., Rohde, G. S., Terstriep, J. A., Willis, C., Fahlgren, N., Mockler, T., Newcomb, M., Sagan, V., Andrade-Sanchez, P., Shakoor, N., Sidike, P., Ward, R., & LeBauer, D. (2018). TERRA-REF Data Processing Infrastructure. In Proceedings of the Practice and Experience on Advanced Research Computing. ACM. https://doi.org/10.1145/3219104.3219152
Related Articles	Brenton, Z. W., Cooper, E. A., Myers, M. T., Boyles, R. E., Shakoor, N., Zielinski, K. J., Rauh, B. L., Bridges, W. C., Morris, G. P., & Kresovich, S. (2016). A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy. Genetics, 204(1), 21-33. https://doi.org/10.1534/genetics.115.183947 Burnette, M., Kooper, R., Maloney, J. D., Rohde, G. S., Terstriep, J. A., Willis, C., Fahlgren, N., Mockler, T., Newcomb, M., Sagan, V., Andrade-Sanchez, P., Shakoor, N., Sidike, P., Ward, R., & LeBauer, D. (2018). TERRA-REF Data Processing Infrastructure. In Proceedings of the Practice and Experience on Advanced Research Computing. ACM. https://doi.org/10.1145/3219104.3219152
Dataset DOI (digital object identifier)	10.5061/dryad.4b8gtht99
Product Type	Collection

Field	Value
ISO Topic(s)	environment farming geoscientificInformation imageryBaseMapsEarthCover
State or Territory	Arizona
National Agricultural Library Thesaurus Term	data collection genomics phenomics image analysis scanners algorithms phenotype databases plant breeding durum wheat winter cultivars artificial intelligence engineering Sorghum bicolor
Ag Data Commons Keywords	Agroecosystems & Environment Geography Remote sensing Agroecosystems & Environment Geography Agroecosystems & Environment Management Agroecosystems & Environment Maps & Multimedia Genomics & Genetics
Program	ARDN

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