AndreaBozzo/ceres-open-data-index huggingface dataset:
T3 Wheat

<p><a href="https://wheat.triticeaetoolbox.org">The Triticeae Toolbox Wheat</a> (T3 Wheat) is a repository for public wheat data generated by the Wheat Coordinated Agricultural Project (Wheat CAP). Funding is provided by the National Institute for Food and Agriculture (NIFA) and the United States Department of Agriculture (USDA). The current project is funded through NIFA's International Wheat Yield Partnership (IWYP) and part of the Agriculture and Food Research Initiative (AFRI). </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: T3 Wheat.</p> <p>File Name: Web Page, url: <a href="https://wheat.triticeaetoolbox.org">https://wheat.triticeaetoolbox.org</a> </p><p>T3 Wheat holds data generated for Triticum spp. It is being enhanced in database performance, community curation and user tools. T3 contains germplasm line information, pedigree, genotype and phenotypic data from breeding programs participating in the CAP and core germplasm collections maintained by the USDA National Small Grains Collection.</p></li></ul><p></p>

Tags: ars, data-gov, np301, online-database, phenotype, plants-crops, triticum-aestivum, wheat
Organization: Department of Agriculture
Cotton Irrigation Tool

<p>Dropping Ogallala aquifer levels and changing commodity prices and energy costs make irrigation management an important but uncertain issue to west Texas cotton producers. For example, is deficit or full irrigation more profitable under the current lint price and pumping cost conditions? Also, what is the best way to divide production into dryland and irrigated acreage with limited well capacity? To help producers answer these questions this web application estimates the effects of irrigation on the profitability of center pivot cotton production on the Southern High Plains. It's main purpose is to show the impact of irrigation on yield and the related effects on both profits per acre and profits over a center pivot area with combined dryland and irrigated production. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Cotton Irrigation Tool.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/research/software/download/?softwareid=486&modecode=30-96-05-00">https://www.ars.usda.gov/research/software/download/?softwareid=486&modecode=30-96-05-00</a> </p><p>download page</p></li></ul><p></p>

Tags: ars, cotton, data-gov, irrigation, online-database, texas
Organization: Department of Agriculture
PhenoCam images from JERGRASSLAND2 site, Jornada Experimental Range, New Mexico, USA since 2022

<p>This data set consists of repeat digital imagery from the tower-mounted digital cameras (hereafter, PhenoCams) at the Jornada Experimental Range. JER is a member of the PhenoCam network, which has as its mission to serve as a long-term, continental-scale, phenological observatory. Imagery is uploaded to the PhenoCam server every 30 minutes. The archived images provide a permanent record that can be visually-inspected to determine the phenological state of the vegetation at any point in time. Vegetation greenness metrics (e.g., GCC) derived from the ratio of the green color band to sum of red, green, and blue color bands serve as proxies for vegetation greenness.  Greenness metrics can be extracted from the images using simple image processing methods in 1-day or 3-day increments.</p>
<p>This dataset is available to the public and may be freely downloaded. Please keep the designated Contact person informed of any plans to use the dataset. Consultation or collaboration with the original investigators is strongly encouraged. Publications and data products that make use of the dataset must include proper acknowledgement.</p>
<p>The development of PhenoCam has been supported by multiple entities. Those include the Northeastern States Research Cooperative, NSF’s Macrosystems Biology program (award EF-1065029), DOE’s Regional and Global Climate Modeling program (award DE-SC0016011), the US National Park Service Inventory and Monitoring Program, the USA National Phenology Network (grant number G10AP00129 from the United States Geological Survey), and is currently supported by the Department of Agriculture (USDA) Agricultural Research Service.</p>
<p>This research is a contribution from the Long-Term Agroecosystem Research (LTAR) network. LTAR and the Jornada Experimental Range are supported by the United States Department of Agriculture (USDA) Agricultural Research Service.</p>

Tags: ars, data-gov, digital-image, long-term-monitoring-sites, ltar, new-mexico, np216, phenocam, phenology, primary-productivity
Organization: Department of Agriculture
Data from: An in vitro analysis of how lactose modifies the gut microbiota structure and function of adults in a donor-independent manner

<p>The impact of lactose on the gut microbiota of healthy adults was examined, using a short-term, in vitro strategy where fecal samples harvested from 18 donors were cultured anaerobically with and without lactose. Donors represented 3 adult age groups. Data collected include: amplicon sequencing of the V1-V2 regions of the 16S rRNA gene (available in the NCBI Sequence Read Archive associated with BioProject PRJNA883645: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA883645">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA883645</a>), RT-qPCR of Bifidobacterium 16S rRNA genes, and short-chain fatty acid concentrations. </p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource Title: lactose sample attributes
File Name: lactose_sample_metadata.csv</p>
</li>
<li>
<p>Resource Title: lactose SCFA, pH, and gas production data
File Name: lactose_SCFA_data.csv</p>
</li>
<li>
<p>Resource Title: Total bacterial and Bifidobacterium genus qPCR
File Name: lactose_qPCR_all_bacteria_and_bifido.csv</p>
</li>
</ul>

Tags: 16s-rrna-sequence-data, ars, data-gov, lactose, np306, short-chain-fatty-acids
Organization: Department of Agriculture
Data from: Bacteria in the genus Streptomyces are effective biological control agents for management of fungal plant pathogens - a meta-analysis

<p>These data represent a meta-analysis testing if Streptomyces biological control agents reduce disease caused by fungal plant pathogens and identify factors that alter biological control efficacy of these bacteria. Meta-data and control and treatment data were compiled from 160 studies representing 44 publications that tested the effect of Streptomyces on diseases caused by fungal plant pathogens of agronomic and horticultural crops. Effect sizes and variances were calculated based on the log-response ratio. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Meta-data and effect size calculations used in meta-analysis.</p> <p>File Name: AgDataCommonsEffectSizes.txt</p><p>Resource Description: Descriptor of column headers are listed below. </p>
<p>Reference:  Original publication reporting data from a given study
Disease pressure:   Level of disease pressure when biological control agent was tested
Plant:  Species of plant
Pathogen:   Species of pathogen
Disease:    Type of disease
Inoculation method: Method used to apply bacteria for biological control
Environment:    Environment that experiments were conducted under
LRR:    Log response ratio effect size estimated from individual studies
VarianceL   Variance estimate associated with effect size calculation</p></li></ul><p></p>

Tags: ars, biological-control, data-gov, meta-analysis, np303, streptomyces-sp
Organization: Department of Agriculture
Tennessee Valley Study for Resilient Economic Agricultural Practices in Auburn, Alabama

<p>Tennessee Valley Study for Resilient Economic Agricultural Practices in Auburn, Alabama
Maize ( Zea mays L.) produced in narrow rows can increase yields and accelerate canopy closure. Costly equipment modifications make narrow rows impractical, but a twin-row configuration may boost pro­ duction with fewer equipment modifications. Four field experiments were conducted to measure weed biomass, leaf area index (LAI), and yield for a conventional (CN) and a glyphosate-resistant (GR) hybrid across three plant densities (low 4.0–4.4 plants m - 2 ; medium 5.9–6.4 plants m - 2 ; and high 7.9–8.4 plants m - 2 ) and two row configurations (single vs. twin) in a conservation tillage system during the 2005 grow­ ing season. The experimental design was a split–split plot with a RCB arrangement of whole plots where hybrids were assigned to main plots, row configurations to subplots, and plant density to sub-subplots with four replications. Row configuration had little effect on weed biomass compared to plant density and hybrid. Leaf area index increased with higher plant density at all locations. In general, LAI increased with the twin-row configuration, but LAI also varied with hybrid based on interactions between hybrid and plant density or row configuration. Row configuration had little impact on maize yields, while plant density had the most effect on yields. Plant density also interacted with hybrid or row configuration at multiple locations, although maize yields did not always increase with higher plant density. Conventional hybrids may also provide an alternative to GR hybrids, particularly at lower plant densities. Maize yield increases with twin rows were minimal and may not justify twin row conversion under dryland condi­ tions, but growers that already utilize twin-row equipment will not suffer yield decreases by planting twin rows.</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Auburn, AL Tennessee Valley Study (ALAUTVS) CSV data.</p> <p>File Name: ALAUTVS_csv_data.zip</p><p>Resource Description: CSV format data on Experimental Units, Field Sites, Residue Management, Persons, Treatments, Weather Daily, Weather Station. </p></li></ul>

Tags: ars, data-gov, environment, farming, iso-metadata, np211, np212
Organization: Department of Agriculture
PhenoCam images from ARSLTARMDCRRESW site, Caroline County, Maryland, USA since 2019

<p>This data set consists of repeat digital imagery from a tower-mounted digital camera (hereafter, PhenoCam) maintained by the USDA-ARS Hydrology Remote Sensing Laboratory (HRSL) in the Lower Chesapeake Bay (LCB) watershed. HRSL is a member of the PhenoCam network, which has as its mission to serve as a long-term, continental-scale, phenological observatory. Imagery is uploaded to the PhenoCam server every 30 minutes. The archived images provide a permanent record that can be visually-inspected to determine the phenological state of the vegetation at any point in time. Vegetation greenness metrics (e.g., GCC) derived from the ratio of the green color band to sum of red, green, and blue color bands serve as proxies for vegetation greenness. Greenness metrics can be extracted from the images using simple image processing methods in 1-day or 3-day increments.</p>
<p>This dataset is available to the public and may be freely downloaded. Please keep the designated Contact person informed of any plans to use the dataset. Consultation or collaboration with the original investigators is strongly encouraged. Publications and data products that make use of the dataset must include proper acknowledgement.</p>
<p>The development of PhenoCam has been supported by multiple entities. Those include the Northeastern States Research Cooperative, NSF’s Macrosystems Biology program (award EF-1065029), DOE’s Regional and Global Climate Modeling program (award DE-SC0016011), the US National Park Service Inventory and Monitoring Program, the USA National Phenology Network (grant number G10AP00129 from the United States Geological Survey), and is currently supported by the Department of Agriculture (USDA) Agricultural Research Service.</p>
<p>This research was a contribution from the Long-Term Agroecosystem Research (LTAR) network. LTAR is supported by the United States Department of Agriculture (USDA) Agricultural Research Service.</p>

Tags: ars, choptank-river, data-gov, long-term-monitoring-sites, ltar, np211, np212, phenocam, phenology, primary-productivity, wetlands
Organization: Department of Agriculture
PhenoCam images from ARSLTARMDCRNATW site, Caroline County, Maryland, USA since 2019

<p>This data set consists of repeat digital imagery from a tower-mounted digital camera (hereafter, PhenoCam) maintained by the USDA-ARS Hydrology Remote Sensing Laboratory (HRSL) in the Lower Chesapeake Bay (LCB) watershed. HRSL is a member of the PhenoCam network, which has as its mission to serve as a long-term, continental-scale, phenological observatory. Imagery is uploaded to the PhenoCam server every 30 minutes. The archived images provide a permanent record that can be visually-inspected to determine the phenological state of the vegetation at any point in time. Vegetation greenness metrics (e.g., GCC) derived from the ratio of the green color band to sum of red, green, and blue color bands serve as proxies for vegetation greenness. Greenness metrics can be extracted from the images using simple image processing methods in 1-day or 3-day increments.</p>
<p>This dataset is available to the public and may be freely downloaded. Please keep the designated Contact person informed of any plans to use the dataset. Consultation or collaboration with the original investigators is strongly encouraged. Publications and data products that make use of the dataset must include proper acknowledgement.</p>
<p>The development of PhenoCam has been supported by multiple entities. Those include the Northeastern States Research Cooperative, NSF’s Macrosystems Biology program (award EF-1065029), DOE’s Regional and Global Climate Modeling program (award DE-SC0016011), the US National Park Service Inventory and Monitoring Program, the USA National Phenology Network (grant number G10AP00129 from the United States Geological Survey), and is currently supported by the Department of Agriculture (USDA) Agricultural Research Service.</p>
<p>This research was a contribution from the Long-Term Agroecosystem Research (LTAR) network. LTAR is supported by the United States Department of Agriculture (USDA) Agricultural Research Service.</p>

Tags: ars, choptank-river, data-gov, long-term-monitoring-sites, ltar, np211, np212, phenocam, phenology, primary-productivity, wetlands
Organization: Department of Agriculture
Data from: Earthworms increase the potential for enzymatic bio-activation of biochars made from co-pyrolyzing animal manures and plastic wastes

<p>This is digital research data corresponding to a published manuscript in "Earthworms increase the potential for enzymatic bio-activation of biochars made from co-pyrolyzing animal manures and plastic wastes" J. Hazardous Materials 2021, Vol. 408, 124405. Dataset may be assessed via the included link at the Dryad data repository.
We assessed the enzymatic activation of four different biochars produced from pyrolyzing swine manure and poultry litter, and by co-pyrolyzing these livestock residues with agricultural spent mulch plastic film wastes (plastichars). Enzymatic activation consisted of incubating biochars in soil inoculated with earthworms (<em>Lumbricus terrestris</em>), which acted as biological vectors to facilitate retention of extracellular enzymes onto biochar surface. The activity of carboxylesterase ‒a pesticide-detoxifying enzyme‒ was measured in non-bioturbed soils (reference), linings of the burrows created by earthworms, casts (feces) and biochar particles recovered from the soil.
Methods are described in the manuscript <a href="https://doi.org/10.1016/j.jhazmat.2020.124405">https://doi.org/10.1016/j.jhazmat.2020.124405</a>. Descriptions corresponding to each figure and table in the manuscript are placed on separate tabs to clarify abbreviations and summarize the data headings and units.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Earthworms increase the potential for enzymatic bio-activation of biochars made from co-pyrolyzing animal manures and plastic wastes - Dryad Dataset.</p> <p>File Name: Web Page, url: <a href="https://doi.org/10.5061/dryad.kprr4xh6q" target="_blank">https://doi.org/10.5061/dryad.kprr4xh6q</a> </p><p>The data file, Fig2-5.xslx is an Excel spreadsheet consisting of multiple sub-tabs which are associated with Figures 2, 3, 4, and 5.
Tab “Fig 2A and 2B” - raw data for earthworm mortality and weight for Fig. 2A and 2B along with descriptive statistics such as mean, standard deviation, etc.
Tab “Fig 3” - raw data for carboxylesterase activity in biochar-amended soils after 30 days of incubation.  All replicate sample data for different regions of soil are included for Figure 3.
Tab “Fig 4” - all replicate raw data for carboxylesterase activity of biochar particles recovered after incubation for Figure 4.
Tab “Fig 5” -  all replicate raw data for enzyme activities in fresh and bioturbed soil and the means and standard deviations for Figure 5.
</p></li></ul>

Tags: ars, biochar, co-pyrolysis, data-gov, earthworms, manure, np212, plastic-waste, plastic-wastes, plastichar
Organization: Department of Agriculture
Data from: Persistence of the Probiotic Lacticaseibacillus rhamnosus Strain GG (LGG) in an In Vitro Model of the Gut Microbiome

<p>Using the SHIME (an in vitro simulator of the human gut microbiome) we tracked the fate of the probiotic Lacticaseibacillus rhamnosus GG (LGG) over time and across colonic regions. Using fecal inoculum from three healthy human donors, reactors were established representing three colonic regions and both the luminal and mucosal microbiome in those regions. Community composition before, during, and after inoculation of the reactors with LGG as well as short chain fatty acid concentrations representing microbiome metabolic outputs. This dataset includes short-chain fatty acid concentrations and qPCR-based cell concentrations. Raw 16S rRNA amplicon sequencing of the V1-V2 regions can be found in the NCBI Sequence Read Archive associated with BioProject PRJNA893635: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA893635">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA893635</a>.</p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource Title: Short Chain Fatty Acid concentrations
File Name: LGG_SCFA_data.csv</p>
</li>
<li>
<p>Resource Title: LGG qPCR concentrations
File Name: LGG_qPCR_data.csv</p>
</li>
<li>
<p>Resource Title: Sample metadata
File Name: LGG_16S_metadata.csv</p>
</li>
</ul>

Tags: 16s-rrna-sequence-data, ars, data-gov, np306, probiotics, short-chain-fatty-acids
Organization: Department of Agriculture
PhenoCam images from JERSHRUBLAND2 site, Jornada Experimental Range, New Mexico, USA since 2022

<p>This data set consists of repeat digital imagery from the tower-mounted digital cameras (hereafter, PhenoCams) at the Jornada Experimental Range. JER is a member of the PhenoCam network, which has as its mission to serve as a long-term, continental-scale, phenological observatory. Imagery is uploaded to the PhenoCam server every 30 minutes. The archived images provide a permanent record that can be visually-inspected to determine the phenological state of the vegetation at any point in time. Vegetation greenness metrics (e.g., GCC) derived from the ratio of the green color band to sum of red, green, and blue color bands serve as proxies for vegetation greenness.  Greenness metrics can be extracted from the images using simple image processing methods in 1-day or 3-day increments.</p>
<p>This dataset is available to the public and may be freely downloaded. Please keep the designated Contact person informed of any plans to use the dataset. Consultation or collaboration with the original investigators is strongly encouraged. Publications and data products that make use of the dataset must include proper acknowledgement.</p>
<p>The development of PhenoCam has been supported by multiple entities. Those include the Northeastern States Research Cooperative, NSF’s Macrosystems Biology program (award EF-1065029), DOE’s Regional and Global Climate Modeling program (award DE-SC0016011), the US National Park Service Inventory and Monitoring Program, the USA National Phenology Network (grant number G10AP00129 from the United States Geological Survey), and is currently supported by the Department of Agriculture (USDA) Agricultural Research Service.</p>
<p>This research is a contribution from the Long-Term Agroecosystem Research (LTAR) network. LTAR and the Jornada Experimental Range are supported by the United States Department of Agriculture (USDA) Agricultural Research Service.</p>

Tags: ars, data-gov, digital-image, long-term-monitoring-sites, ltar, new-mexico, np216, phenocam, phenology, primary-productivity
Organization: Department of Agriculture
REAP (Resilient Economic Agricultural Practices)

<p>REAP (Resilient Economic Agricultural Practices), formerly known as the Renewable Energy Assessment Project, was initially organized to quantitatively assess the impacts of crop residue (e.g., corn stover) on soil properties. The project's current vision is to revitalize soil health and resiliency, thereby enabling soil resources to meet expanding societal demands while safe-guarding planetary health. Goals include 1)  Identifying physical, chemical, or biological parameters and index tools that quantify management effects on carbon sequestration and soil health; 2)  Conducting coordinated, quantitative multi-location comparisons of business as usual vs. improved management practices designed to enhance nutrient use efficiency and soil health; 3) Identification of critical indicators and index tools to quantify site-specific soil health and water quality effects; 4) Developing, expanding, and coordinating among ARS teams providing data and databases needed to sustainably supply cellulosic-based bioenergy feedstock and other national natural resource and agricultural challenges. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: REAP Data Search.</p> <p>File Name: Web Page, url: <a href="https://agcros-usdaars.opendata.arcgis.com/datasets?group_ids=01c66889194d40e18e7c0bc3e3a9754f">https://agcros-usdaars.opendata.arcgis.com/datasets?group_ids=01c66889194d40e18e7c0bc3e3a9754f</a> </p></li></ul><p></p>

Tags: agricultural-research-service, ars, corn-stover, crop-residue, data-gov, national-program-211, national-program-212, natural-resource-and-genomics, np211, np212, nutrient-use-efficiency, online-database, reap, resilient-economic-agricultural-practices, soil-health-and-resiliency, soil-properties, supply-cellulosic-based-bioenergy-feedstock
Organization: Department of Agriculture
Southern Plains - Micronet

<p>Temporal (5 minute or daily) data from the Little Washita and Ft. Cobb watersheds.  Includes precipitation and net radiation (discontinued) along with soil temperature and volumetric water content at 3 depths, 5, 25, and 45 centimeters.</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: GeoData Catalog record.</p> <p>File Name: Web Page, url: <a href="https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/f7ce55b6-84bd-4410-b21a-fe43ce40a06c" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/f7ce55b6-84bd-4410-b21a-fe43ce40a06c</a> </p></li></ul>

Tags: ars, biota, data-gov, earth-science-agriculture-soils-soil-moisture-water-content, earth-science-agriculture-soils-soil-temperature, earth-science-atmosphere-precipitation, environment, farming, precipitation, radiation, soil-temperature, soil-volumetric-water-content, watersheds
Organization: Department of Agriculture