AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: Amino acid, sugar, phenolic, and terpenoid profiles are capable of distinguishing Citrus tristeza virus infection status in grapefruit, lemon, mandarin, and sweet orange leaves

<p>Amino acid, sugar, phenolic, and terpenoid compound level data collected from different citrus species that were healthy or infected with different CTV strains, with CTV titer and symptoms provided. This data was analyzed in a peer-reviewed manuscript, and provided for transparency or to use to evaluate variables not discussed within the manuscript (e.g. individual CTV strain effects on chemistry versus group effects). </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Healthy and CTV-Infection Effects on Amino Acid, Sugar, Phenolic, and Terpenoid Levels and Titer/Disease Data.</p> <p>File Name: Citrus CTV Chemistry.xlsx</p><p>Resource Description: Data utilized in the associated manuscript, including titer/disease measurements, amino acid levels, sugar levels, phenolic levels, and terpenoid levels.</p></li></ul><p></p>

Tags: amino-acids, ars, citrus-sinensis, citrus-tristeza-virus-ctv, data-gov, host-plant-interactions, np303, phenolics, sugars, terpenoids
Organization: Department of Agriculture
Data from: Automated Detection of On-Farm Irrigation Reservoirs: A Necessary Precursor for Conjunctive Water Management in Two Critical Groundwater Regions of Arkansas

<ol><li>The Inventory from Model (White)</li><li>Model Reservoirs (Red)</li><li>Mary and Co's reservoirs (Blue)</li><li>NHD water (Orange)</li><li>CDL water (Yellow)<br><br>The Inventory from Model map (1) represents all the water found within the three areas identified the 2023 project; (2) is where the model indicates a reservoir based on the elevation difference based on the Yeager et al. (2017) reservoirs; (3) is based on the Yeager et al. (2017) reservoir boundaries which were plugged into the fifth step of the model (the water identification steps were skipped). Then the model was used to evaluate and classify them into elevation classes. NHD Water map (4) is every waterbody polygon from the National Hydrography Dataset that falls within the three study area areas. The CDL Water map (5) is every open water and aquaculture polygon vectorized from the Cropland Data Layer raster within the three study areas.</li></ol><p dir="ltr">This Data is a zipped, ArcGIS Pro (V3.1.2) project. The project geodatabase contains the model. In this project there are five maps representing different datasets.</p><p dir="ltr">NOTE (2024-05-13): ISO xml metadata files added to the root of the zipped folder, describing specific items in the project, saved in ArcGIS Pro V.3.2.2.</p>

Tags: elevation, irrigation-reservoir, reservoir-detection
Organization: Department of Agriculture
SGP97 GCIP/NESOB Surface: Skin Temperature Composite

<p>This 30 minute Skin Temperature Composite is one of several surface-layer data sets provided in the Atmospheric Radiation Measurement (ARM)/Global Energy and Water Cycle Experiment (GEWEX) Continental-Scale International Project (GCIP) Near Surface Observation Data Set - 1997 (NESOB-97). This Skin Temperature composite was formed from three data sources: the 10m and 25m ARM/Clouds and Radiation Testbed (CART) Multi-Filter Radiometer (MFR) 20 second data, and 30 minute data from the GCIP National Oceanic and Atmospheric Administration (NOAA)/Atmospheric Turbulence and Diffusion Division (ATDD) Little Washita, Oklahoma long term flux monitoring site. This composite was developed by the merging of the 30-minute averaged values of skin temperature as provided by NOAA/ATDD for its Little Washita station and the 30-minute averaged values of skin temperature as derived by University Corporation for Atmospheric Research/Joint Office for Science Support (UCAR/JOSS) from the 20-second values provided by ARM for its 10m and 25m MFR stations. UCAR/JOSS computed standard deviations for the ARM 10m and 25m MFR data when at least 15 observations were available within the 30-minute averaging interval. The ARM/GCIP NESOB-97 Skin Temperature Composite contains 8 metadata parameters and 3 data parameters. The metadata parameters describe the date/time, network, station, and location at which the data were collected. The 3 data parameters repeat once for each 30 minute period from UTC 0000 through UTC 2330. Data reported for a designated 30 minute time represents data collected during the previous 30 minute period. All times are reported in UTC, and skin temperature values are reported in degrees Celsius. Each data value is followed by a Quality Control flag, but UCAR/JOSS does not Quality Control the data at the present time. The Quality Control flag is set to "U" for "Unchecked", unless the datum is missing, in which case the flag is set to "M". Missing values are -999.99. The standard deviation was calculated for the ARM 10m and 25m MFR Skin Temperature values when there were at least 15 measurements in the 30 minute averaging interval. No standard deviations were calculated for the Little Washita data, since it originated in 30 minute frequency.</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/f45c0d23-6589-4259-b198-28cbda6b360f" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/f45c0d23-6589-4259-b198-28cbda6b360f</a> </p></li></ul>

Tags: ars, data-gov, hydrologic-cycle, hydrology, soil, temperature, turbulent-flow, water
Organization: Department of Agriculture
Southern Great Plains 1997 (SGP97) Hydrology: Co-operative Agency Reservoir Data

<p>The Co-operative Agency Reservoir dataset is one of various hydrological datasets provided for the Southern Great Plains 1997 (SGP97) Project. This dataset contains reservoir data from 26 Co-operative Agency stations within the Enhanced Observing Period (EOP) domain and time period. No additional quality control was performed by the University Corporation for Atmospheric Research/Joint Office for Science Support (UCAR/JOSS). The Co-operative Agency reservoir dataset is provided "as is" in the original format. The Co-operative Agency data is in a non-consistent, ASCII format.</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/9a0ba33e-9475-4d72-962e-edbb77400e90" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/9a0ba33e-9475-4d72-962e-edbb77400e90</a> </p></li></ul>

Tags: agriculture, ars, data-gov, hydrology, rain, terrestrial-hydrosphere-indicators, water-quality, watersheds
Organization: Department of Agriculture
Bioenergy Cropping Systems Study for Resilient Economic Agricultural Practices in Mandan, North Dakota

<p>Bioenergy Cropping Systems Study for Resilient Economic Agricultural Practices in Mandan, North Dakota</p>
<p>Rigorous economic analyses are crucial for the successful launch of lignocellulosic bioenergy facilities in 2014 and beyond. Our objectives are to (1) introduce readers to a query tool developed to use data downloaded from the Agricultural Research Service (ARS) REAPnet for constructing enterprise budgets and (2) demonstrate the use of the query tool with REAPnet data from two field research sites (Ames, IA, and Mandan, ND) for evaluating short-term economic performance of various biofuel feedstock production strategies. Our results for both sites showed that short-term (<3 years) impacts on grain profitability were lower at lower average annual crop residue removal rates. However, it will be important to monitor longer term changes to see if grain profitability declines over time and if biomass harvest degrades soil resources. Analyses for Iowa showed short-term breakeven field-edge biomass prices of $26–$42 Mg−1 among the most efficient strategies, while results for North Dakota showed breakeven prices of $54–$73 Mg−1. We suggest that development of the data query tool is important because it helps illustrate several different soil and crop management strategies that could be used to provide sustainable feedstock supplies. </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/704e95b7-54ea-46af-8373-9f510da4e30c">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/704e95b7-54ea-46af-8373-9f510da4e30c</a> </p></li></ul><p></p>

Tags: ars, data-gov, environment, farming, iso-metadata, np211, np212
Organization: Department of Agriculture
Southern Great Plains 1997 (SGP97) Hydrology: United States Geological Survey (USGS) Daily Reservoir Data

<p>The United States Geological Survey (USGS) Reservoir dataset is one of various hydrological datasets provided for the Southern Great Plains 1997 (SGP97) project. This dataset contains reservoir data from stations in SGP97 domain. The data collected at USGS gaging stations consist of records of stage and measurements of discharge of streams or canals, and stage, surface area, and contents of lakes or reservoirs. This dataset contains only the USGS reservoir data. For a lake or reservoir, capacity tables giving the contents for any stage are prepared from stage-area relation curves defined by surveys. The application of the stage to the capacity table gives the contents, from which the daily, monthly, or yearly change in contents is computed. If the stage-capacity curve is subject to changes because of deposition of sediment in the reservoir, periodic resurveys of the reservoir are necessary to define new stage-capacity curves.  During the period between reservoir surveys, the computed contents may be increasingly in error due to the gradual accumulation of sediments. For some gaging stations there are periods when no gage-height record is obtained or the recorded gage height is so faulty that it cannot be used to compute daily discharge or contents. This happens when the recorder stops or otherwise fails to operate properly, intakes are plugged, the float is frozen in the well, or for various other reasons. For such periods, the daily contents may be estimated on the basis of operator's log, prior and subsequent records, inflow-outflow studies, and other information. The USGS reservoir data are provided in a single file and are provided "as is" in their original card image format. There are six different types of "cards images" which appear in the USGS reservoir dataset. Each card has a unique format, but the first character of a card image always indicates the card type. Depending upon the card type, the card image may contain metadata and/or data. No additional quality control was performed by the University Corporation for Atmospheric Research/Joint Office for Science Support (UCAR/JOSS).</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/04dfde8e-77ca-47c4-bd48-5fe7a1c3f12b" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/04dfde8e-77ca-47c4-bd48-5fe7a1c3f12b</a> </p></li></ul>

Tags: agriculture, ars, data-gov, discharge, flow, hydrology, lakes, rain, sediment-transport, soil, terrestrial-hydrosphere-indicators, water-quality, watersheds
Organization: Department of Agriculture
Food and Nutrient Database for Dietary Studies (FNDDS)

<p>[Note: Integrated as part of FoodData Central, April 2019.]
USDA's Food and Nutrient Database for Dietary Studies (FNDDS) is a database that is used to convert food and beverages consumed in What We Eat In America (WWEIA), National Health and Nutrition Examination Survey (NHANES) into gram amounts and to determine their nutrient values.  Because FNDDS is used to generate the nutrient intake data files for WWEIA, NHANES, it is not required to estimate nutrient intakes from the survey. FNDDS is made available for  researchers using WWEIA, NHANES to review the nutrient profiles for specific foods and beverages as well as their associated portions and recipes. Such detailed information makes it possible for researchers to conduct enhanced analysis of dietary intakes. FNDDS can also be used in other dietary studies to code foods/beverages and amounts eaten and to calculate the amounts of nutrients/food components in those items.    </p>
<p>FNDDS is released every two-years in conjunction with the WWEIA, NHANES dietary data release. The FNDDS is available for free download from the FSRG website.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Website Pointer to Food and Nutrient Database for Dietary Studies.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/northeast-area/beltsville-md-bhnrc/beltsville-human-nutrition-research-center/food-surveys-research-group/docs/fndds/" target="_blank">https://www.ars.usda.gov/northeast-area/beltsville-md-bhnrc/beltsville-human-nutrition-research-center/food-surveys-research-group/docs/fndds/</a> </p><p>USDA's Food and Nutrient Database for Dietary Studies (FNDDS) is a database that is used to convert food and beverages consumed in What We Eat In America (WWEIA), National Health and Nutrition Examination Survey (NHANES) into gram amounts and to determine their nutrient values.</p></li></ul>

Tags: analysis, ars, data-gov, dietary-intake, np107, nutrients, online-database, wweia
Organization: Department of Agriculture
Manuresheds: Redesigning crop-livestock agriculture for sustainable intensification

<p>Nutrient recycling is fundamental to sustainable agricultural systems, but few mechanisms exist to ensure that surplus manure nutrients from animal feeding operations are transported for use on nutrient-deficient croplands. As a result, manure nutrients concentrate in locations where they can threaten environmental health and devalue manure as a fertilizer resource. This data set is from a study advances the concept of the “manureshed” – the lands surrounding animal feeding operations onto which manure nutrients can be redistributed to meet environmental, production, and economic goals. Manuresheds can be managed at multiple scales, for example, on farms with both animals and crops, among animal farms and crop farms within a county, or even among animal farms and crop farms in distant counties. With a focus on redistribution among counties, we classified the 3109 counties of the contiguous United States by their capacity to either supply manure phosphorus (P) and nitrogen (N) from confined livestock production (“sources”) or to assimilate and remove excess P and N via crops (“sinks”) [see data for N tonnes, P tonnes, N kg/ha, P kg/ha]. Manure nutrient source counties were identified in 40 of the 48 states, with a substantial concentration in the southern US. Source counties for manure P greatly outnumbered source counties for manure N (390 vs. 100), and 99 of the 100 manure N source counties were also source counties for manure P. Conversely, sink counties for manure N outnumbered sink counties for manure P (2766 vs. 2317). We used the P balances of the source and sink counties to delineate four manuresheds dominated by various combinations of confined hog, poultry, dairy, and beef industries [see data for Manuresheds (tonnes)]. The four manuresheds differed in the transport distances needed to assimilate excess manure P from their respective source areas (from 147 ± 51 km for a beef dominated manureshed to 368 ± 140 km for a poultry dominated manureshed), highlighting the need for systems-level strategies to promote manure nutrient recycling that operate across local, county, regional, and national scales. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Agricultural Collaborative Research Outcomes System (AgCROS) and  Manureshed link.</p> <p>File Name: manureshed.zip</p><p>Resource Description: <strong>AgCROS</strong>: <a href="https://agcros-usdaars.opendata.arcgis.com/">https://agcros-usdaars.opendata.arcgis.com/</a></p>
<p><strong>Manureshed</strong>:  <a href="https://usdaars.maps.arcgis.com/apps/MapSeries/index.html?appid=881305934d62494bbbeeb5f36b735eb9">https://usdaars.maps.arcgis.com/apps/MapSeries/index.html?appid=881305934d62494bbbeeb5f36b735eb9</a> </p></li></ul><p></p>

Tags: agriculture, ars, beef, dairy, data-gov, hogs, jornada-experimental-range, long-term-agroecosystem-research, ltar, manure, manuresheds, nitrogen, nutrients, phosphorus, poultry, source-sink
Organization: Department of Agriculture
AmeriFlux ecosystem observation datasets - University of Nebraska, Lincoln, Agricultural Research Service rainfed maize-soybean rotation site

<p>The study site is one of three fields (all located within 1.6 km of each other) at the University of Nebraska Agricultural Research and Development Center near Mead, Nebraska. While the other two sites are equipped with irrigation systems, this site relies on rainfall. A tillage operation (disking) was done just prior to the 2001 planting to homogenize the top 0.1 m of soil, incorporate P and K fertilizers, as well as previously accumulated surface residues. Since initiation of the study in 2001, this site has been under no-till management.</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/UniversityOfNebraska_eaa_2015_March_17_1231" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/UniversityOfNebraska_eaa_2015_March_17_1231</a> </p></li></ul>

Tags: affiliation-id-74, agriflux, ars, ceptometer, croplands, data-gov, daylight, daymet, earth-science-agriculture-agricultural-plant-science-cropping-systems, earth-science-agriculture-soils-soil-temperature, earth-science-atmosphere-atmospheric-radiation, earth-science-atmosphere-atmospheric-radiation-incoming-solar-radiation, earth-science-atmosphere-atmospheric-temperature-air-temperature, earth-science-atmosphere-atmospheric-water-vapor, earth-science-atmosphere-atmospheric-water-vapor-humidity, earth-science-atmosphere-atmospheric-winds-surface-winds-wind-speed-wind-direction, earth-science-atmosphere-precipitation, earth-science-land-surface-land-use-land-cover-land-cover, earth-science-land-surface-soils-soil-temperature, eddy-covariance-flux, environment, farming, incident-shortwave-radiation-flux-density, maize, net-radiometers, open-path-co2-h2o-gas-analyzer, portable-photosynthesis-system, precipitation-gauge, pyranometers, pyrgeometers, site-953, snow-water, sonic-anemometer, soybeans, stream-gauges, temperature-humidity-probe, trace-gas-analyzer, us-ne3, water-vapor-pressure
Organization: Department of Agriculture
Breedbase

<p>Breedbase is a web-based, comprehensive breeding management and analysis software. It can be used to design field layouts, collect phenotypic information using tablets, support the collection of genotyping samples in a field, store large amounts of high density genotypic information, and provide Genomic Selection related analyses and predictions. Breedbase supports the Breeding Application Programming Interface (BrAPI) standard which defines data objects and methods for exchanging breeding data. The Breedbase system has evolved from the Sol Genomics Network (SGN) and Cassavabase and related sites (see <a href="https://RTBbase.org">RTBbase.org</a>). There are a number of instances running for diverse crops, including Cassava <a href="(https://cassavabase.org)">(https://cassavabase.org</a>, sweet potato (<a href="https://sweetpotatobase.org">https://sweetpotatobase.org</a>), banana (<a href="https://musabase.org">https://musabase.org</a>), rice (<a href="https://ricebase.org">https://ricebase.org</a>), tomato and other Solanaceae (<a href="https://solgenomics.net/">https://solgenomics.net/</a>) and many others. The Breedbase manual provides detailed information about available features. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Website Pointer for Breedbase.</p> <p>File Name: Web Page, url: <a href="https://breedbase.org/">https://breedbase.org/</a> </p><p>Search utilities: Wizard; Accessions and Plots; Organisms; Progenies and Crosses; Field Trials; Genotyping Plates; Genotyping Data Projects; Genotyping Protocols; Traits; Images; People; FAQ.</p>
<p>Manage utilities: User Roles; Breeding Programs; Locations; Accessions; Seed Lots; Crosses; Field Trials; Genotyping Trials; Field Book App; Phenotyping; Barcodes; Label Designer; Download; Upload; ODK Data Collection.</p>
<p>Analyze utilities:
Breeder Tools -- Selection Index; Genomic Selection; Population Structure; Accession Usage; Compare Trials; Graphical Filtering
Sequence Analysis -- BLAST; VIGS Tool; HapMap Jbrowse
Other -- Ontology Browser; Compose a New Trait.</p>
<p></p></li></ul><p></p>

Tags: ars, breedbase, data-gov, np301, online-database
Organization: Department of Agriculture
Data from: Toll-like receptor ligands enhance vaccine efficacy against virulent Newcastle disease virus challenge in chickens

<p>To enhance the efficacy of the current Newcastle disease vaccine, we have tested two potential adjuvants (Imiquimod and ODN-1826) in chickens. Birds were treated with PBS, Imiquimod or ODN-1826 (50 µg/bird) or vaccinated intranasally with live LaSota strain with or without Imiquimod or ODN-1826 (50 µg/bird). Two weeks after vaccination, birds were challenged with virulent New-castle disease virus (chicken/CA/212676/2002). The experimental setting was a laboratory with animal care as approved by the institutional animal care and use committee as appropriate for the species and age of bird. Data are the serum antibody titers to the vaccine or challenge virus as determined by hemagglutination inhibition assay. Virus shedding titers by the oral and cloacal route for individual birds exposed to virulent Newcastle disease virus were determined by quantitative real-time RT-PCR. Expression of antiviral genes from tissues collected at 1 and 3 days after treating 2 week old SPF chickens with adjuvant and/or vaccines were determined by quantitative PCR.</p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Hemagglutination inhibition (HI) antibody titers 14 days after vaccinating 2-week-old SPF chickens with LaSota vaccine with or without adjuvant (ODN-1826 or Imiquimod)
File Name: Lee et al., Serology Data I from Adjuvanted live NDV vaccine study.csv</p>
</li>
<li>
<p>Hemagglutination inhibition antibody titers 14 days after infecting 4 week old SPF chickens with virulent Newcastle disease virus (California/212676/2002)
File Name: Lee et al., Serology Data II from Adjuvanted live NDV vaccine study.csv</p>
</li>
<li>
<p>Cycle threshold (Ct) value of viral RNA from swabs collected at 2 and 4 days after infecting 4-week-old SPF chickens with virulent Newcastle disease virus (California/212676/2002)
File Name: Lee et al.,Virus Shedding Data from Adjuvanted live NDV vaccine study.csv</p>
</li>
<li>
<p>Cycle threshold (Ct) value of target specific mRNA collected at 1 and 3 days after treating 2-week-old SPF chickens with adjuvant and/or vaccines
File Name: Lee et al.,Transcription Data from Adjuvanted live NDV vaccine study.csv</p>
</li>
</ul>

Tags: antibody-response, antiviral-response, ars, data-gov, newcastle-disease, np103, vaccine
Organization: Department of Agriculture