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Ag Data Commons migration begins October 18, 2023

The Ag Data Commons is migrating to a new platform – an institutional portal on Figshare. Starting October 18 the current system will be available for search and download only. Submissions will resume after the launch of our portal on Figshare in November. Stay tuned for details!

IMAP: Image Mapping & Analytics for Phenotyping

    A set of PYTHON programs to implement image processing of ground and aerial images by offering via graphical user interface (GUI) 1) plot-level metrics extraction through a series of algorithms for image conversion, band math, radiometric/geometric calibrations, segmentation, masking, adaptive region of interest (ROI), gridding, heatmap, and batch process, 2) GIS interface for GeoTIFF pixels to Lat/Lon, UTM conversion, read/write shapefile, Lat/Lon to ROI, grid to polygon, and 3) utility GUI functions for zooming, panning, rotation, images to video, file I/O, and histogram.

    Data from: Estimation of pool construction and technical error

      Animals were incorporated into pools in different proportions to estimate error and evaluate factors influencing error. Animals were incorporated into 2 types of pools, sub-pools and super pools. Within phenotype, liver abscess or normal, 16 animals were combined into 4 sub-pools, 4 animals per sub-pool in parts of 1:2:3:4. Sub-pools were constructed based on crushed frozen liver tissue mass. Within phenotype, 4 sub-pools were incorporated into 2 super pools in parts of 1:2:3:4 for super pool 1 and 3:4:1:2 for super pool 2. Super pools were made based on DNA quantity. Errors in DNA quantification would create error in forming super pools from sub-pools and variation in cell content or DNA content of liver tissue would result in error in combining sub-pools from animals.

      The Bronson Files, Dataset 2, Field 17, 2013

        Active optical proximal cotton canopy sensing spatial data and including additional related metrics canopy thermal and height are presented. Agronomic nitrogen and irrigation management related field operations are listed. Unique research experimentation intermediate analysis table is made available, along with raw data. The raw data recordings, and annotated table outputs with calculated VIs are made available. Plot polygon coordinate designations allow a re-intersection spatial analysis. Data was collected in the 2013 season at Maricopa Agricultural Center, Arizona, USA. High throughput proximal plant phenotyping via electronic sampling and data processing method approach is exampled. Acquired data using USDA Maricopa first mobile platforms, such as the Proximal Sensing Cart Mark 1. SAS and GIS compute processing output tables, including Excel formatted examples are presented, where data tabulation and analysis is available. The weekly proximal sensing data collected include canopy reflectance at six wavelengths, ultrasonic distance sensing of canopy height, and infrared thermometry. Lint and seed yields, first open boll biomass, and nitrogen uptake were also determined. Soil profile nitrate to 1.8 m depth was determined in 30-cm increments, before planting and after harvest. Nitrous oxide emissions were determined 20 or more weeks in the season with 1-L vented chambers (samples taken at 0, 12, and 24 minutes). Nitrous oxide was determined by gas chromatography (electron detection detector).

        TERRA-REF Season 6 phenotypes and agronomic metadata in BrAPI format

          This data represents a small subset of the TERRA-REF release available on Dryad (LeBauer et al 2020), including harvested biomass for each cultivar, plot location, planting date, harvest date, fertilizer application, genotype / accession names and metadata, and additional agronomic management metadata for a population of Sorghum bicolor evaluated over two growing seasons. The data can be accessed through a BrAPI-compliant endpoint at terraref.org/brapi. This dataset is a snapshot of the TERRA-REF BrAPI endpoint contents, representing the minimum data and metadata required to run a crop model.

          The Bronson Files, Dataset 1, Field 17, 2012

            Active optical proximal cotton canopy sensing spatial data and including additional related metrics such as thermal are presented. Agronomic nitrogen and irrigation management related field operations are listed. Unique research experimentation intermediate analysis table is made available, along with raw data. The raw data recordings, and annotated table outputs with calculated VIs are made available. Plot polygon coordinate designations allow a re-intersection spatial analysis. Data was collected in the 2012 season at Maricopa Agricultural Center, Arizona, USA. High throughput proximal plant phenotyping via electronic sampling and data processing method approach is exampled. Acquired data using USDA Maricopa first mobile platforms, such as the Proximal Sensing Cart Mark 1, and via people. SAS and GIS compute processing output tables, including Excel formatted examples are presented, where data tabulation and analysis is available. The weekly proximal sensing data collected include canopy reflectance at six wavelengths, ultrasonic distance sensing of canopy height, and infrared thermometry. Lint and seed yields, first open boll biomass, and nitrogen uptake were also determined. Soil profile nitrate to 1.8 m depth was determined in 30-cm increments, before planting and after harvest. Nitrous oxide emissions were determined 20 or more weeks in the season with 1-L vented chambers (samples taken at 0, 12, and 24 minutes). Nitrous oxide was determined by gas chromatography (electron detection detector).

            2014 Swine CAFO Study SE for Agricultural Antibiotic Resistance in Mississippi State, Mississippi

              The purpose of this study was to measure the microbial constituents of swine-sow, -nursery, and -finisher farm manure lagoon wastewater and determine the changes induced by farm management. A total of 37 farms were visited in the Mid-South USA and analyzed for the genes 16S rRNA, spaQ (Salmonella spp.), Camp-16S (Campylobacter spp.), tetA, tetB, ermF, ermA, mecA, and intI using quantitative PCR. Additionally, 16S rRNA sequence libraries were created.

              Data from: Phenotypic and nodule microbial diversity among crimson clover (Trifolium incarnatum L.) accessions

                Phenotypic evaluation of 37 crimson clover (Trifolium incarnatum L.) accessions from the US National Plant Germplasm System. Focus of the trial was on traits important for cover crop performance, including fall emergence, winter survival, flowering time, biomass, nitrogen (N) content in aboveground biomass, and proportion of plant N from biological nitrogen fixation (BNF). Experiments were conducted at the Beltsville Agricultural Research Center (Maryland, USA) across three growing seasons (2012-2013, 2013-2014, 2014-2015).

                Nebraska Prairie Study for Agricultural Antibiotic Resistance in Lincoln, Nebraska

                  The inherent spatial heterogeneity and complexity of antibiotic resistant bacteria and antibiotic resistance (AR) genes in manureaffected soils makes it difficult to sort out resistance that can be attributed to human antibiotic use from resistance that occurs naturally in the soil. This study characterizes native Nebraska prairie soils that have not been affected by human or food-animal waste products to provide data on background levels of resistance in southeastern Nebraskan soils.