AndreaBozzo/ceres-open-data-index huggingface dataset:
Upper Chesapake Bay LTAR Dataset: NFARM, Inorganic N, & C Production, 2016-2018

<p>In situ denitrification rates in intact soil cores from the Upper Chesapeake Bay (UCB) LTAR site in PA quantified by directly measuring dinitrogen (N2) and nitrous oxide (N2O) production via the Nitrogen-Free Air Recirculation Method (N-FARM) from 2016-2018. 10-day laboratory incubations provided estimates of ancillary soil data, including microbial respiration and potential net N mineralization and nitrification. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Upper Chesapeake Bay Data Dictionary.</p> <p>File Name: Upper Chesapeake Bay Data Dictionary.csv</p><p>Resource Description: Data Dictionary for UCB dataset.</p></li><br><li><p>Resource Title: Upper Chesapeake Bay Metadata.</p> <p>File Name: Upper Chesapeake Bay Metadata.csv</p><p>Resource Description: Metadata for UCB dataset.</p></li><br><li><p>Resource Title: Upper Chesapeake Bay Dataset.</p> <p>File Name: Upper Chesapeake Bay Dataset.csv</p><p>Resource Description: UCB dataset.</p></li></ul><p></p>

Tags: ammonium, ars, carbon-dioxide, data-gov, denitrification, dinitrogen, hot-moment, hot-spot, laboratory-incubation, ltar, mineralization, nitrate, nitrification, nitrogen, nitrous-oxide-flux, respiration, soil, surface-soil, upper-chesapeake-bay-ltar, usda-long-term-agricultural-research-ltar-network
Organization: Department of Agriculture
T3 Oat

<p><a href="https://oat.triticeaetoolbox.org">The Triticeae Toolbox Oat</a> (T3 Oat) is the repository of oat phenotype and genotype data for the Global Oat Genetics Database.</p>
<p>The Triticeae Toolbox (T3) is the web portal for data generated by the <a href="http://triticeaecap.org/">Triticeae Coordinated Agricultural Project</a> (T-CAP), funded by the National Institute for Food and Agriculture (NIFA) of the United States Department of Agriculture (USDA). It also contains data from US Uniform Regional Nurseries, supported by the <a href="http://scabusa.org/">US Wheat and Barley Scab Initiative</a>. The database was initially developed as The Hordeum Toolbox (THT) to hold barley data generated by the Barley CAP project (2006-2010). T3 Barley hods data generated for Hordeum vulgare L. T3 Wheat holds data generated for Triticum spp. T3 Oat holds data generated for Avena. All are 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 <a href="http://www.ars.usda.gov/Main/docs.htm?docid=21891">USDA National Small Grains Collection</a>. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: T3 Oat.</p> <p>File Name: Web Page, url: <a href="https://oat.triticeaetoolbox.org">https://oat.triticeaetoolbox.org</a> </p><p>T3/Oat is the repository of oat phenotype and genotype data for the Global Oat Genetics Database, a project initiated in January 2014 by</p>
<ul>
<li>Gabe Gusmini (PepsiCo)</li>
<li>Joe Lutz (General Mills)</li>
<li>Bruce Roskens (Grain Millers)</li>
<li>Nicholas Tinker (AAFC)</li>
<li>Kay Simmons, Jack Okamuro, Jose Costa, Jean-Luc Jannink, and Gerard Lazo (USDA-ARS)</li>
</ul>
<p></p></li></ul><p></p>

Tags: ars, avena, data-gov, np301, oat, online-database, phenotype, plants-crops
Organization: Department of Agriculture
USDA National Nutrient Database for Standard Reference, Legacy Release

<p>[Note: Integrated as part of FoodData Central, April 2019.]
The USDA National Nutrient Database for Standard Reference (SR) is the major source of food composition data in the United States and provides the foundation for most food composition databases in the public and private sectors.  This is the last release of the database in its current format.  SR-Legacy will continue its preeminent role as a stand-alone food composition resource and will be available in the new modernized system currently under development. SR-Legacy contains data on 7,793 food items and up to 150 food components that were reported in SR28 (2015), with selected corrections and updates. This release supersedes all previous releases.   </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: USDA National Nutrient Database for Standard Reference, Legacy Release.</p> <p>File Name: SR-Leg_DB.zip</p><p>Resource Description: Locally stored copy - The USDA National Nutrient Database for Standard Reference as a relational database using Acess</p></li><br><li><p>Resource Title: USDA National Nutrient Database for Standard Reference, Legacy Release.</p> <p>File Name: SR-Leg_ASC.zip</p><p>Resource Description: ASCII files containing the data of the USDA National Nutrient Database for Standard Reference, Legacy Release.</p></li><br><li><p>Resource Title: USDA National Nutrient Database for Standard Reference, Legacy Release.</p> <p>File Name: SR-Leg_ASC.zip</p><p>Resource Description: Locally stored copy - ASCII files containing the data of the USDA National Nutrient Database for Standard Reference, Legacy Release.</p></li></ul><p></p>

Tags: ars, data-gov, food, food-composition, np107, nutrition, online-database
Organization: Department of Agriculture
Data and analysis scripts for: Prolonged soybean absence in the field selects for rhizobia that accumulate more polyhydroxybutyrate during symbiosis

<p dir="ltr">During symbiosis, C that rhizobia respire to power N fixation can be stored as polyhydroxybutyrate (PHB), shown to support rhizobia survival under laboratory starvation. We collected soil in 2015 from four replicate plots per treatment in two long-term experiments at Waseca, Minnesota. Treatments differed in the intervals between soybean (<i>Glycine max</i> (L.) Merr.) hosts. We measured PHB accumulation in eight nodules per plant from four soybean (cv. ‘MN0095’) trap plants per soil sample. Trap plants were arranged in a greenhouse, common-garden experiment, and PHB accumulation was measured using flow cytometry. Treatments sampled after long intervals without soybean (greater than two years) showed a greater relative abundance of high-PHB strains. Treatments sampled after the first year of soybean following five years of a non-host crop showed a decreased relative abundance of high-PHB strains, compared to treatments sampled after long intervals without soybean. The latter result is consistent with the hypothesis (not tested directly here) that some high-PHB strains were “sanctioned” by plants as less-beneficial. Our results suggest that rhizobia strains with the tendency to allocate more C to N fixation at the expense of PHB accumulation may be less likely to persist where soybean is grown infrequently or where soil conditions make PHB particularly valuable. However, with typical two-year rotations in Minnesota, differences in PHB storage are unlikely to have a major effect on the relative survival of strains.</p><p dir="ltr">See README.md for a detailed description of data files and scripts. </p>

Tags: long-term-agroecosystem-research-network, polyhydroxybutyrate-phb, soybean-glycine-max-l-merr, symbiotic-nitrogen-fixation-snf
Organization: Department of Agriculture
Data from: Galls formed by Aceria genistae (Acari: Eriophyidae) alter resource allocation of the invasive weed Scotch broom (Cytisus scoparius) v2

<p>[ 2023-07-10 - Supersedes version 1, <a href="https://doi.org/10.15482/USDA.ADC/1528679">https://doi.org/10.15482/USDA.ADC/1528679</a> ]</p>
<p>The Scotch broom gall mite, Aceria genistae, attacks Cytisus scoparius (Scotch broom), an invasive shrub in California, USA. Feeding causes galls (localized tissue distortion) but the effect of A. genistae on overall host vigor and reproduction has not been assessed. We collected data on plant parts between two plants partitioned between two groups, heavily or lightly galled plants, at three northern California sites. Plant parts were measured in the field (plant height, plant width) and others were recorded after harvesting plants (stem, leaf, gall, seed pod, seeds, etc.) and drying them in an oven to a constant weight. Data were natural log transformed. Columns represent (in order): observation number (obs), plant identifier (plantID), Site, treatment (heavy or light galling), Diameter at soil (lnDAS), height, leaf weight (lnLeaf), stem weight (lnStem), fruit weight (lnFruit), gall weight (lnGalls), number of pods (lnpods), seed weight (lnseeds), number of seeds per plant (lnseedsplant), canopy volume (lnVol), canopy diameter at its widest point (lnWidest), canopy area (lnCanopyArea), total biomass of all plant fractions combined (lnTotal), number of stem branches (lnResource). </p>
<p>Resources in this dataset:</p>
<ul>
<li>Resource Title: Scotch broom biomass dataset
File Name: Scotch broom gall mite.csv
Description: Dataset is comma deliminated</li>
</ul>

Tags: aceria-genistae, allometry, ars, data-gov, np304, scotch-broom, weed
Organization: Department of Agriculture
Long Term Agroecosystem Research Network (LTAR) Meteorological Station Data on the Central Plains Experimental Range (CPER)

<p>Provisional 15- minute Meteorological data collected on the Central Plains Experimental Range according to concept of operations created for the LTAR Network, NP215</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/1ff14e72-313b-4fcc-83d5-3141d5ca9610" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/1ff14e72-313b-4fcc-83d5-3141d5ca9610</a> </p></li></ul>

Tags: ars, data-collection, data-gov, earth-science, earth-science-services, in-situ-laboratory-instruments-pressure-height-meters, in-situ-laboratory-instruments-radiation-sensors, in-situ-laboratory-instruments-recorders-loggers, in-situ-laboratory-instruments-temperature-humidity-sensors, meteorological-data, np215, rangeland
Organization: Department of Agriculture
NGPRL Meteorological Towers

<p>This dataset is part of the common observation in the centralized repository for public access, also known as the Common Observatory Repository (CORe), of the USDA ARS Long-Term Agro-ecosystem Research (LTAR) network. This is part of the National Program 216 (NP#216): Agricultural System and Competitiveness and Sustainability. Also The National Wind Erosion Research Network was established in 2014 as a collaborative effort led by the US Department of Agriculture (USDA) Long Term Agro-Ecosystem Research (LTAR) network and the Bureau of Land Management (BLM). The research domain incorporates the diverse soils and vegetation communities in the rangelands and croplands of the western United States, with sites located in New Mexico, Texas, Oklahoma, Arizona, California, Colorado, North Dakota, Utah, Idaho and Washington. We have a tower that collects data for the North Dakota Agricultural Weather Network. Our site is part of the NEON project with a tower that is designed to collect and provide open data that characterize and quantify complex, rapidly changing ecological processes across the US. We have a National Center for Environmental Information (NOAA) tower that collects daily summaries of weather data. A Natural Resource Conservation (NRCS) National Water and Climate tower that collects snow and water data.</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/51f15ad7-206a-4884-83ad-0cfe87f2ff55" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/51f15ad7-206a-4884-83ad-0cfe87f2ff55</a> </p></li></ul>

Tags: ambient-relative-humidity, ars, biota, data-gov, elevation, environment, farming, incoming-short-and-long-wave-radiation, np211, photosynthetically-active-radiation, rainfall, wind-direction, wind-speed
Organization: Department of Agriculture
Data from: Exploring soil ecology gradient concepts: Sensitivity of ecosystem properties to symbiotic fungi in semiarid prairie

<p dir="ltr">Dataset that accompanies a research paper entitled, "Exploring soil ecology gradient concepts: Sensitivity of ecosystem properties to symbiotic fungi in semiarid prairie" to be submitted to a peer-reviewed journal. Journal information will be updated when paper is published. Files include a readme file, datasets, and the respective R script for analyzing the individual data files.</p><p dir="ltr">Results are relevant to arid and semiarid mixed-grass prairie ecosystems with calcareous and alkaline subsoils, especially sites with soils of Eapa loam soil series, frigid Aridic Argiustolls or Mollisols. The focal system was of northern mixed-grass prairie vegetation near Miles City, Montana which is in eastern Montana, USA (46.304583, -105.978050, elevation 849 m).</p><p dir="ltr">The study consisted of a five year field experiment and two complementary pot bioassays. The experiments were designed to improve understanding effects of mycorrhizal fungi on plant properties, soil structure, and soil hydrologic functioning. We performed experiments and evaluated evidence of AMF (arbuscular mycorrhizal fungi) effects on plants, plant-plant interactions, plant nutrient limitation, and nutrient acquisition strategy. First, we tested how AMF suppression affected plant biomass and composition; indicators of plant nutrient limitation (i.e. shoot nitrogen-to-phosphorus ratio, N:P) and P acquisition (i.e. shoot manganese concentration, [Mn]); and structure and function of soil with a five-year field experiment. This informed pot bioassays. Pot bioassays tested how dominant grass coexistence was affected by three pairs of soil treatments 1) field soil inoculant (FSI) versus FSI with AMF suppression, 2) FSI versus sterilized FSI, and 3) AMF inoculant versus sterilized AMF inoculant.</p>

Tags: calcareous-grassland, mixed-grass-prairie, mycorrhizal-fungi, northern-mixed-grass-prairie, phosphorus-acquisition-strategy, plant-soil-biota-interactions, soil-aggregate-stability, soil-water-transport
Organization: Department of Agriculture
Data and code from: Electron beam irradiation for management of in-shell pecan weevil larvae (Coleoptera: Curculionidae)

<p dir="ltr">This dataset contains all the data and code needed to reproduce the model fitting, model predictions, and data visualizations from the manuscript:</p><p dir="ltr">Cottrell, T.E., Read, Q.D. & Starns, C. (2025). Electron beam irradiation for management of in-shell pecan weevil larvae (Coleoptera: Curculionidae). <i>J. Econ. Entomol.</i> <a href="https://doi.org/10.1093/jee/toaf300" rel="noreferrer" target="_blank">https://doi.org/10.1093/jee/toaf300</a></p><p dir="ltr">Pecan weevils are an economically important pest of pecans. Irradiation treatment has been suggested as a means of managing this pest and satisfying quarantine restrictions. Here, we present a survival analysis of pecan weevils that were exposed to e-beam radiation under different conditions. This dataset includes the raw observations of mortality in CSV format and an RMarkdown notebook that goes through the steps of importing, processing, and visualizing the data, fitting a Bayesian binomial generalized linear mixed model with complementary log-log link function (equivalent to a proportional hazards survival model in this case), and producing model predictions in table and figure form. We also include the rendered HTML output of the notebook, as well as a pre-fit model object (.rds format) if it is desired to reproduce the model predictions without having to refit the model.</p><ul><li><b>pecan weevil radiation.csv</b>: raw observations of mortality, with the following columns</li><li><ul><li><i>Date</i>: M/D/YYYY format</li><li><i>e-beam strength</i>: radiation intensity treatment (Gy)</li><li><i>Rep</i>: experimental replicate</li><li><i>#</i>: ID of individual insect</li><li><i>Exposure to e-beam</i>: exposure treatment (Tube, Nut, Bare PW)</li><li><i>Live/Dead</i>: 1 denotes live and 0 denotes dead</li></ul></li><li><b>pecan_weevil_ebeam_survival_analysis.Rmd</b>: RMarkdown notebook with all code and text interpretation</li><li><b>pecan_weevil_ebeam_survival_analysis.Rmd</b>: HTML rendered output of notebook</li><li><b>binomcloglog_noattr_beamlevel_gammaprior.rds</b>: pre-fit model object (created by R package <b>brms</b>)</li></ul><p dir="ltr"><br></p>

Tags: carya-illinoinensis, curculionidae, e-beam, irradiation, pasteurization, pecan, quarantine, weevil
Organization: Department of Agriculture
Data from: Two new species of Plasmopara affecting wild grapes in the United States

<p>Sequence alignments for cox2 and nc LSU rDNA datasets, as well as a reduced cox2 dataset used to determine the variable molecular characters that help to distinguish between the two new <em>Plasmopara</em> species described. The earliest specimen studied was collected in 1884, the most recent in 2021. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Cox2 dataset, aligned.</p> <p>File Name: Salgado_Salazar_COX2_dataset_Plasmoparaspnov.fasta</p></li><br><li><p>Resource Title: Cox2 dataset for barcoding, alignment.</p> <p>File Name: Salgado-Salazar_COX2_Plasmoparaspnov_barcodes.fasta</p></li><br><li><p>Resource Title: rDNA LSU dataset, alignment.</p> <p>File Name: Salgado-Salazar_LSU_dataset_Plasmoparaspnov.fasta</p></li></ul><p></p>

Tags: ars, data-gov, downy-mildew, new-species, np303, peronosporaceae, plasmopara, vitaceae
Organization: Department of Agriculture
Data from: A Whole Genome Assembly of the Horn Fly, Haematobia irritans, and Prediction of Genes with Roles in Metabolism and Sex Determination

<p>To provide a foundation for identification of genomic loci for insecticide resistance and for discovery of new control technology, we report the sequencing, assembly, and annotation of the horn fly genome. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: A Whole Genome Assembly of the Horn Fly, Haematobia irritans, and Prediction of Genes with Roles in Metabolism and Sex Determination.</p> <p>File Name: Web Page, url: <a href="https://doi.org/10.1534/g3.118.200154">https://doi.org/10.1534/g3.118.200154</a> </p><p>Listed data resources also linked in this record's related content.</p></li></ul><p></p>

Tags: ars, data-gov, haematobia-irritans, metabolic-resistance, np104, pesticide-resistance
Organization: Department of Agriculture
LTAR - Meteorological Stations - Walnut Gulch Experimental Watershed

<p>The Southwest Watershed Research Center (SWRC) operates the Walnut Gulch Experimental Watershed (WGEW) in southeastern Arizona as an outdoor laboratory for studying semiarid rangeland hydrologic, ecosystem, climate, and erosion processes.  </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/2f6d09cc-4097-494a-b57a-19bc9ecfba66">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/2f6d09cc-4097-494a-b57a-19bc9ecfba66</a> </p></li></ul><p></p>

Tags: air-pressure, air-temperature, ars, climate, data-gov, longwave-radiation, meteorological-data, np211, shortwave-radiation, weather, wind-speed
Organization: Department of Agriculture
USDA's Expanded Flavonoid Database for the Assessment of Dietary Intakes, Release 1.1 - December 2015

<p>This database was developed with support from the Office of Dietary Supplements, National Institutes of Health for flavonoid intake studies.  The database is a useful tool  for flavonoid intake and health outcome studies for any population globally.  It contains data for 29 individual flavonoid compounds in six subclasses of flavonoids for every food in a subset of 2,926 food items which provide the basis for the Food and Nutrient Database for Dietary Studies (FNDDS 4.1).  Proanthocyanidins data are not included at the present time. For flavonoid intake data for the U.S. population based on NHANES 2007-08, please refer to the Food Surveys Research Group<a href="https://www.ars.usda.gov/northeast-area/beltsville-md/beltsville-human-nutrition-research-center/food-surveys-research-group/"> website</a>.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: READ ME - USDA’s Expanded Flavonoid Database for the Assessment of Dietary Intakes Documentation and User Guide.</p> <p>File Name: FDB-EXP.pdf</p><p>Resource Description: Information regarding documentation, development of the database, limitations, format, and references.</p><p>Resource Software Recommended: Adobe Acrobat Reader,url: <a href="http://www.adobe.com/prodindex/acrobat/readstep.html" target="_blank">http://www.adobe.com/prodindex/acrobat/readstep.html</a> </p></li><br><li><p>Resource Title: Data Dictionary.</p> <p>File Name: FDB_EXP_DD.pdf</p></li><br><li><p>Resource Title: FDB-EXP_R01-1.accdb.</p> <p>File Name: FDB-EXP_R01-1.accdb_.zip</p><p>Resource Description: This file contains USDA's Expanded Flavonoid Database for the Assessment of Dietary Intakes imported into a MS Access database version 2007 or later. The file structure is the same as that of the USDA National Nutrient Database for Standard Reference.
</p></li></ul>

Tags: ars, data-gov, flavonoids, isofavones, np107, proanthocyanidin
Organization: Department of Agriculture
A ‘Chambourcin’ x <i>Vitis vinifera</i> ‘Cabernet Sauvignon’ mapping population to genetically map powdery mildew resistance and other traits

<p dir="ltr">This Vitis mapping population consisted of F1 hybrids derived from a cross between female parent ‘Chambourcin’ with a pollen donor ‘Cabernet Sauvignon’. These hybrids were planted at the Missouri State Fruit Experiment Station (MSFES), Mountain Grove, MO 65711 (latitude 37°09'14.8"N; longitude 92°14'46.8" W). An initial planting in 2014 contained 100 progeny, followed by 26 progeny in 2015 and 180 progeny in 2016. The data set includes microsatellite (SSR) and core genome rhAmpSeq haplotype marker data that was used to develop genetic map and phenotype data generated from Blackbird microscopy robot analysis of grapevine powdery mildew (<i>Erysiphe necator</i>) severity.</p>

Tags: disease-susceptibility-loci, genetic-map, grapevine, leaf-disc-assay, powdery-mildew
Organization: Department of Agriculture
Data from: An Interactive R-Based Custom Quantification Program for Quantitative Analysis of Triacylglycerols in Bovine Milk

<p dir="ltr">[Note: Title updated 2024-04-23]</p><p dir="ltr">Liquid chromatography-mass spectrometry (LC-MS) experiment data files for bovine milk lipid extracts, standards, and blanks, in mzML format. For use with "An Open-Source R-Based Workflow for Qualitative and Quantitative Lipidomics of Bovine Milk". Chromatography used a fast (10 minute) non-aqueous reversed-phase UHPLC separation. MS analysis was performed on a ThermoScientific QExactive Orbitrap high-resolution, accurate-mass mass spectrometer operated in electrospray ionization (ESI) mode.</p><p dir="ltr">Resources in this dataset:</p><ul><li>Resource Title: Bovine Milk Data acquired 06/10/21 File Name: ByrdwellData_Milk_061021.zip Resource Description: Sequence of runs containing 10 Blanks, 30 Standards (6 Levels x 5 replicates), and 48 Bovine Milk extracts, as follows: 2 Cows, 3 feeding periods, 2 days (samples) per feeding period, 4 replicates for 24 samples per cow x 2 cows. 88 runs (separate data files) altogether. All files originally in proprietary .RAW format converted to .mzML. Data obtained on ThermoScientific QExactive orbitrap high-resolution, accurate-mass mass spectrometer.</li></ul><p></p>

Tags: ars, bovine-milk, data-gov, esi-ms, lc-ms, lipidomics, lipids, np107, orbitrap, triacylglycerols, uhplc
Organization: Department of Agriculture