AndreaBozzo/ceres-open-data-index huggingface dataset:
USDA Agricultural Research Service- Available Biological Materials

<p>The biological materials in this section are unpatented, proprietary intellectual property, available for licensing under a Biological Materials License Agreement: Hybridoma Cell Lines; Microbial Isolates; Cloned Genetic Material; Cell Lines; Viruses; Plasmids. Updated June 2018. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Biological Materials Data Dictionary.</p> <p>File Name: biological-materials-data-dictionary.csv</p><p>Resource Description: Defines fields, data type, allowed values etc. in biological materials tables.</p></li><br><li><p>Resource Title: Available Biological Materials - June 2018.</p> <p>File Name: biological-materials-2018-06.csv</p><p>Resource Description: Listing of available biological materials including Hybridoma Cell Lines, Microbial Isolates, Cloned Genetic Material, Cell Lines, Viruses, and Plasmids. This CSV file provides the title, technology type, docket number, contact, description, and category for each item. Machine-readable content extracted from corresponding slides accompanying this dataset.</p></li><br><li><p>Resource Title: Biological Materials - Available Technologies, June 2018.</p> <p>File Name: Biological Materials.pdf</p><p>Resource Description: Slides presenting title, contact, docket number(s), description, image, description, and applications of each new technology.</p></li></ul><p></p>

Tags: ars, cell-lines, cloned-genetic-material, data-gov, hybridoma-cell-lines, microbial-isolates, plasmids, viruses
Organization: Department of Agriculture
Data from: A fast method for the detection of <i>Salmonella</i> Typhimurium cells in egg biofilms on three different surfaces

<p><em>Salmonella</em> is a pathogenic microorganism linked to foodborne outbreaks associated with egg and egg products. This microorganism can resist sanitation of the egg processing equipment and form biofilms. The main challenge is detecting <em>Salmonella</em> cells in the early stages of biofilm formation to use effective interventions to control and remove the <em>Salmonella</em> biofilms. This work aimed to study the biofilm formation of <em>S.</em> Typhimurium in liquid whole egg (LWE) on three common food-contact surfaces, stainless steel, silicone, and nylon, during the first five hours of incubation at 37°C and compare traditional microbiological methods to innovative and fast detection techniques. The results showed that using general plate counts, <em>Salmonella</em> cells were detected after three h of incubation with less than 1 – log of growth, silicone was the material with most cells attached, followed by stainless steel. Long-read whole genome sequencing detected <em>Salmonella</em> on stainless steel, silicone, and nylon after only one h of incubation. The results of this study suggest that long-read sequencing could be very useful for detecting <em>Salmonella</em> at low concentrations in the processing environment.</p>
<p><br></p>
<p>This research used the resources provided by SCINet project and the AI Center of Excellence of the USDA Agricultural Research Service, ARS project number 0500-00093-001-00-D.</p>

Tags: biofilms, bioinformatics, egg, food-pathogens, long-read-whole-genome-sequencing, salmonella
Organization: Department of Agriculture
ARS Collection of Entomopathogenic Fungal Cultures (ARSEF)

<p>NOTE: Due to security issues, the ARSEF database search function is not currently available and we are transitioning to a site on the ARS-AZURE cloud. Please contact the curator (Kathryn.Bushley@usda.gov) if you need information about specific groups or a custom search of the database that can be sent via e-mail. Printed PDF catalogues of all isolates and other information about the collection are available on the ARSEF website at <a href="https://www.ars.usda.gov/northeast-area/ithaca-ny/robert-w-holley-center-for-agriculture-health/emerging-pests-and-pathogens-research/docs/mycology/">https://www.ars.usda.gov/northeast-area/ithaca-ny/robert-w-holley-center-for-agriculture-health/emerging-pests-and-pathogens-research/docs/mycology/</a></p>
<p>The Agricultural Research Service Collection of Entomopathogenic Fungal Cultures is the world's largest, most kaleidoscopic, and most comprehensive collection of living cultures of fungi that are pathogenic to or associated with insects, spiders, mites, ticks, and other invertebrates. Some isolates in the collection are not themselves invertebrate pathogens but are critically important for the improvements of taxonomies and systematics for the many diverse groups of fungi represented here. As of July 2016, ARSEF maintains more than 13000 isolates of more than 700 taxa of fungi isolated from 1300 hosts collected at more than 2400 locations on every continent.</p>
<p>The database is searchable by Fungi, Hosts, Locations, Provenance, or Accessions. Results are provided in PDF format.</p>
<p>Catalog files are in the Adobe Acrobat (PDF) format and are readable with the Adobe Acrobat Reader.</p>
<p>All catalogs and live searches of isolate data incorporate the most current supportable taxonomies for ARSEF fungi. Significant changes in the nomenclatural rules for many fungi have a large and ongoing impact on the entomopathogens in the order Hypocreales. These changes are discussed the introductory material in the catalogs.</p>
<p>If you are unsure about the most current identifications for isolates, online searches of ARSEF accessions return taxonomic information in the collection database at the moment of the search.</p>

Tags: ars, cultures, data-gov, entomopathogenic-fungi, fungi, insects, invertebrates, mites, online-database, organisms, spiders, taxonomy, ticks
Organization: Department of Agriculture
iSnobal

<p>iSnobal is a physically-based distributed snowmelt model. Snowmelt is the principal source for soil moisture, ground-water re-charge, and stream-flow in mountainous regions of the western US, Canada, and other similar regions of the world. Information on the timing, magnitude, and contributing area of melt under variable or changing climate conditions is required for successful water and resource management. A coupled energy and mass-balance model iSnobal is used to simulate the development and melting of the seasonal snowcover in several mountain basins in California, Idaho, and Utah. Simulations are done over basins varying from 1 to 2500 km2 , with simulation periods varying from a few days for the smallest basin, Emerald Lake watershed in California, to multiple snow seasons for the Park City area in Utah. The model is driven by topographically corrected estimates of radiation, temperature, humidity, wind, and precipitation. Simulation results in all basins closely match independently measured snow water equivalent, snow depth, or runoff during both the development and depletion of the snowcover. Spatially distributed estimates of snow deposition and melt allow us to better understand the interaction between topographic structure, climate, and moisture availability in mountain basins of the western US. Application of topographically distributed models such as this will lead to improved water resource and watershed management.  </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Image Processing Workbench (IPW).</p> <p>File Name: Web Page, url: <a href="https://gitlab.com/ars-snow/ipw">https://gitlab.com/ars-snow/ipw</a> </p><p>GitHub repository where the model can be accessed and downloaded.</p></li></ul><p></p>

Tags: ars, data-gov, np211
Organization: Department of Agriculture
Terrestrial Condition Assessment (TCA) Alaska Wildfire Potential (Map Service)

<span style='font-family:&quot;Avenir Next W01&quot;, &quot;Avenir Next W00&quot;, &quot;Avenir Next&quot;, Avenir, &quot;Helvetica Neue&quot;, sans-serif; font-size:16px;'>The percent area of a landscape analysis unit where the Wildland Fire Hazard 2020 class is High.</span>

Tags: gtac, open-data, tca, usfs, wildfire
Organization: Department of Agriculture
USDA Nematode Collection Database

<p>The USDA Nematode Collection is one of the largest and most valuable nematode collections in existence. It contains over 49,000 permanent slides and vials, with a total repository of nematode specimens reaching several million, including Cobb-Steiner, Thorne, and other valuable collections. Nematodes contained in this collection originate from world-wide sources.</p>
<p>The USDA Nematode Collection Database contains over 38,000 species entries. A broad range of data is stored for each specimen, including species, host, origin, collector, date collected and date received. All records are searchable and available to the public through the online database.</p>
<p>The physical collection is housed at the USDA Nematology Laboratory in Beltsville, MD. Specimens are available for loan to scientists who cannot personally visit the collection. Please see the <a href="https://www.ars.usda.gov/ARSUserFiles/2279/Loan Policy.pdf">Policy for Loaning USDANC Specimens</a> for more information on this process. </p>
<p>Scientists and other workers are always welcomed and encouraged to deposit material into the collection. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: USDA Nematode Collection Database.</p> <p>File Name: Web Page, url: <a href="https://nt.ars-grin.gov/nematodes/search.cfm">https://nt.ars-grin.gov/nematodes/search.cfm</a> </p><p>The database portal for this collection</p></li></ul><p></p>

Tags: ars, data-gov, nematode, online-database, organisms, specimens
Organization: Department of Agriculture
Animal Germplasm Resources Information Network (A-GRIN)

<p>Animal genetic resources underpin the livestock sector's production and profitability. As a result livestock industries contribute billions of dollars to national economies. The Animal Germplasm Resources Information Network (A-GRIN) mission is to acquire, evaluate and preserve these strategic resources so that industry and the research community can have access to a broad array of genetic variability for: national security, introduction of genetic variation, corrective breeding, and various research initiatives. There are three major technical components:</p>
<ul>
<li><strong>Information Systems</strong> to better understand genetic diversity in the collection of germplasm and live populations.</li>
<li><strong>Genetic Evaluation</strong> - understanding genetic diversity for the collection of germplasm and live populations.</li>
<li><strong>Cryobiology</strong>, the discipline that enables the program to store gametes and various tissues at ultra-low temperatures (about -196°C).</li>
</ul>
<p>In addition this program interacts with a wide range of livestock producers, researchers, and various industry representatives. Users can drill down to explore the germplasm collection by species, breed, line, and individual; compare taxonomies; find animals that meet their criteria to make a germplasm request.  </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: National Animal Germplasm Program Website.</p> <p>File Name: Web Page, url: <a href="https://agrin.ars.usda.gov/main_webpage_dev/ars?language=EN&record_source=US">https://agrin.ars.usda.gov/main_webpage_dev/ars?language=EN&record_source=US</a> </p><p>The Agricultural Research Service’s National Animal Germplasm Program operates a gene bank for livestock, aquatic, poultry and insect genetic resources. Exploring these pages you will find information concerning the genetic resources collection and other issues related to genetic resources and how the program operates.
</p></li></ul><p></p>

Tags: animals, ars, cryopreservation, data-gov, genetic-diversity, germplasm, grin, np101, online-database
Organization: Department of Agriculture
Data from: Genomic Sequence of Campylobacter jejuni subsp. jejuni HS:19 Penner Serotype Reference Strain RM3420

<p><em>Campylobacter jejuni</em> subsp. <em>jejuni</em> infections are a leading cause of foodborne gastroenteritis and the most prevalent antecedent to Guillain-Barré syndrome (GBS). Penner serotype HS:19 is among several capsular types shown to be markers for GBS. This study describes the genome of <em>C. jejuni</em> subsp. <em>jejuni</em> HS:19 Penner reference strain RM3420. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: GenBank Accession No. CP017456 - Campylobacter jejuni subsp. jejuni str. RM3420, complete genome.</p> <p>File Name: Web Page, url: <a href="https://www.ncbi.nlm.nih.gov/nuccore/CP017456">https://www.ncbi.nlm.nih.gov/nuccore/CP017456</a> </p></li></ul><p></p>

Tags: ars, data-gov, np108, penner-serotype-reference-strain-rm3420
Organization: Department of Agriculture
Data from: Genome-wide Association and Genomic Prediction Identifies Soybean Cyst Nematode Resistance in Common Bean Including a Syntenic Region to Soybean Rhg1 Locus

<p>A panel of single nucleotide polymorphisms (SNPs) for 363 common bean accessions was generated. A genome-wide association study (GWAS) was applied to detect SNPs significantly associated with resistance to Heterodera glycines (HG) also known as the soybean cyst nematode (SCN) in the core collection of common bean, Phaseolus vulgaris. There were 84,416 SNPs identified in 363 common bean accessions.   </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: SNP Location on Chromosomes.</p> <p>File Name: SNP locations chr and position.csv</p></li><br><li><p>Resource Title: Bean lines and genotypes.</p> <p>File Name: Bean lines and genotype.csv</p></li></ul><p></p>

Tags: ars, data-gov, np303
Organization: Department of Agriculture
LCA Domain Metadata Schema Inventory

<p>This excel workbook is a compilation of the major metadata schemas for life cycle assessment. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title:  LCADomain_MetadataSchema_Inventory_v1_0_2.</p> <p>File Name: LCADomain_MetadataSchema_Inventory_v1_0_2.xlsm</p></li></ul><p></p>

Tags: ars, data-dictionary, data-gov, ecospold, ilcd, international-reference-life-cycle-data-system, iso-14048, lca-commons, metadata, nal-ksd
Organization: Department of Agriculture
AMS Market News Historical Annual  Summaries

The primary function of the AMS Market News Program is to compile and disseminate information that will aid producers, consumers, and distributors in the sale and purchase of agricultural related products nationally and internationally.

Tags: beans, beef, by-products, calves, cattle, chicken, duck, eggs, feeder-pigs, feedstuff, fowl, goats, grain, grain-basis, hay, hogs, lamb, lentils, offal, peas, pork, rabbits, retail, sheep, turkey
Organization: Department of Agriculture
Recording District

<div style="text-align:Left;"><div><div><p>This feature class includes States, Counties or Boroughs, Congressional Districts, Alaska Recording Districts, County Subdivisions, and Places boundaries that are derived from the latest official Census Bureau and Alaska Department of Natural Resources datasets. Features within Forest Service Administrative Forest boundaries may have been modified by the Forest Service for improved accuracy and spatial coincidence(vertical integration).</p></div></div></div>

Tags: alp-geopolitical-dataset, boundaries, land-status, usda-forest-service
Organization: Department of Agriculture
Copy (3) Southwest Watershed Research Center Online Data Access

<p>Hydrologic data, primarily precipitation and runoff, have been collected on experimental watersheds operated by the U.S. Department of Agriculture Agricultural Research Service (USDA-ARS) and on other lands in southeastern Arizona since the 1950s. These data are of national and international importance and make up one of the most comprehensive semiarid watershed data sets in the world. The USDA-ARS Southwest Watershed Research Center has recently developed an electronic data processing system that includes an online interface (<a href="https://tucson.ars.ag.gov/dap">https://tucson.ars.ag.gov/dap</a>) to provide public access to the data. The goal of the system is to promote analyses and interpretations of historic and current data by improving data access. The publicly accessible part of the system consists of an interactive Web site, which provides an interface to the data, and a relational database, which is used to process, store, and manage data. In addition, DAP was expanded to put sediment, meteorological, soil moisture and temperature, vegetation, CO2 and water flux, geographic information system (GIS) and aircraft and satellite spectral imagery data on line and to publish metadata for all WGEW long-term measurements. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Web Page.</p> <p>File Name: WGEWsoils.xls, url: <a href="https://www.tucson.ars.ag.gov/dap/Files/WGEWsoils.xls">https://www.tucson.ars.ag.gov/dap/Files/WGEWsoils.xls</a> </p></li></ul><p></p>

Tags: aircraft-spectral-imagery, ars, co2-flux, data-gov, erosion, geographic-information-system, gis, hydrology, meteorology, precipitation, runoff, santa-rita-experimental-range, satellite-spectral-imagery, sediment, semi-arid, soil, soil-moisture, soil-temperature, upper-san-pedro-partnership, upper-san-pedro-river, vegetation, walnut-gulch-experimental-watershed, water-flux
Organization: Department of Agriculture
Mixed Linear Model Approaches for Quantitative Gen

<p><strong>Purpose</strong></p>
<p>Computer software for estimating variance and covariance components, correlations, and predicting genetic effects.</p>
<p><strong>Software Description</strong></p>
<p>We describe a suite of genetic software that employs mixed linear model approaches.  The various components relate to three categories, viz, genetic models for diallel crosses, seed traits, and developmental traits.  It can also be used to analyze regional agronomic trials.</p>
<p>This software has several features:</p>
<ol>
<li>Handles complicated genetic models for agronomic traits, seed traits, and developmental traits</li>
<li>Analyzes unbalanced data</li>
<li>Utilizes jackknifing techniques to test the significance of each genetic parameter</li>
<li>Provides some important references containing results</li>
<li>
<p>Fast computation</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Mixed Linear Model Approaches for Quantitative Gen.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/research/software/download/?softwareid=199&modecode=60-64-05-10" target="_blank">https://www.ars.usda.gov/research/software/download/?softwareid=199&modecode=60-64-05-10</a> </p><p>download page</p></li></ul>
</li>
</ol>

Tags: agronomic-traits, computer-software, covariance, diallel-analysis, genetic-models, linear-models, models, prediction, variance
Organization: Department of Agriculture
SolarCalc 1.0

<p>Solar Calc: Estimating Hourly Incoming Solar Radiation from Limited Meteorological Data</p>
<p>Two major properties which determine weed seed germination are soil temperature and moisture content. Incident radiation is the primary variable controlling energy input to the soil system and thereby influences both moisture and temperature profiles. However, a majority of agricultural field sites lack proper instrumentation to measure solar radiation directly. To overcome this shortcoming, an empirical model was developed to estimate total incident solar radiation (beam and diffuse) with hourly time steps.</p>
<p>Input parameters for the model are latitude, longitude, and elevation of the field site, along with daily precipitation (mm) with daily minimum and maximum air temperatures (degrees C). The file format for this weather data file is a comma spaced value file (CSV) with the following format:</p>
<p>DOY, MIN, MAX, PREC</p>
<p>Where DOY is day of year, MIN is the minimum air temperature, MAX is the maximum air temperature, and PREC is the total daily rainfall. Each day has a separate line in the file. Field validation of this model was conducted at a total of 18 sites, where sufficient meteorological data were available for validation, allowing a total of 42 individual yearly comparisons.</p>
<p>The model performed well, with an average Pearson correlation of 0.92, d-index of 0.95, modeling efficiency of 0.80, root mean square error of 111 W m-2, and a mean absolute error of 56 W m-2. These results compare favorably to other developed empirical solar radiation models, but with the advantage of predicting hourly solar radiation for the entire year based on limited climatic data and no site-specific calibration requirement. This solar radiation prediction tool can be integrated into dormancy, germination and growth models to improve microclimate-based simulation of development of weeds and other plants.</p>
<p>Disclaimer: The USDA-ARS makes no warranties as to the merchantability or fitness of SolarCalc 1.0 for any particular purpose, or any other warranties expressed or implied. Since some portions of SolarCalc 1.0 have been validated with only limited data sets, it should not be used to make operational management decisions. The USDA-ARS is not liable for any damages resulting from the use or misuse of SolarCalc 1.0, its output and its accompanying documentation. </p>
<p>SolarCalc 1.0 was written in Java, and therefore can run on multiple platforms (e.g. Windows, Mac, Unix). </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: SolarCalc 1.0.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/research/software/download/?softwareid=62&modecode=50-60-05-00">https://www.ars.usda.gov/research/software/download/?softwareid=62&modecode=50-60-05-00</a> </p><p>download page</p></li></ul><p></p>

Tags: ars, data-gov, np305
Organization: Department of Agriculture
Data from: Enzymatic Modification of Menhaden Oil to Incorporate Caprylic and/or Stearic Acid

<p>Menhaden oil was enzymatically modified with caprylic (C8:0) and/or stearic acid (C18:0) to produce structured lipids (SL) with high amount of polyunsaturated fatty acids (PUFA) and melting point of 25-35 degrees centigrade. Linear interpolation was used to determine substrate molar ratios for the reaction. Thermal behavior was determined with DSC and volatile oxidation products by solid phase microextraction (SPME) fiber.</p>
<p>The data files are provided in their original .xlsx format, as well as in .csv. The folders are broken down into the following categories: linear interpolation initial experiments (10g, various molar ratios (1:1,1:3, 1:5), and validation under optimal conditions (both 10g and 500g), and finally large-scale reactions (1kg). There is also a folder (“Data”) containing the initial 10g reactions for the caprylic/stearic acid blends (A,B,C).</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Enzymatic Modification of Menhaden Oil to Incorporate Caprylic and/or Stearic Acid.</p> <p>File Name: Martini_dataset_NIFA.zip</p><p>Resource Description: The .zip file includes the original .xlsx versions and files same files converted to .csv that demonstrating the various reaction models, as well as a README file that describes the dataset and provides a data dictionary and description of file naming structure.</p></li><br><li><p>Resource Title: Dataset README file.</p> <p>File Name: README-menhaden-oil-dataset.txt</p><p>Resource Description: Provides a description of the arrangement of folders, contents of the data files, acronyms, codes, abbreviations, parameters/variables, and special software required to use the data.</p></li></ul>

Tags: ars, caprylic-acid, data-gov, enzymatic-modification, menhaden-oil, stearic-acid
Organization: Department of Agriculture