AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: BBGD: an online database for blueberry genomic data

<p>This dataset is supplemental to the article "BBGD: an online database for blueberry genomic data," (2007); it is titled "list of genes printed on microarray slides."</p>
<p>The article, "BBGD: an online database for blueberry genomic data," (2007) involving  blueberry cold hardiness experiments has a list of all the genes that were printed on microarray slides. This dataset, supplemental to the article, is called: "list of genes printed on microarray slides." 1471-2229-7-5-s1.xls 663k.
By using the BBGD database, researchers developed EST-based markers for mapping, and have identified a number of "candidate" cold tolerance genes that are highly expressed in blueberry flower buds after exposure to low temperatures. 

BBGD (<a href="http://bioinformatics.towson.edu/BBGD/">http://bioinformatics.towson.edu/BBGD/</a>) is a public online database, and was developed for blueberry genomics. BBGD is both a sequence and gene expression database: it stores both EST and microarray data, and allows scientists to correlate expression profiles with gene function. Presently, the main focus of the database is the identification of genes in blueberry that are significantly induced or suppressed after low temperature exposure.</p>
<p>Data was collected sometime between 2000 and 2007 - exact dates are unknown. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: List of genes printed on microarray slides, 1471-2229-7-5-s1.xls.</p> <p>File Name: 1471-2229-7-5-s1.xls</p></li><br><li><p>Resource Title: Data dictionary.</p> <p>File Name: BBGD-data-dictionary.csv</p><p>Resource Description: Defines fields for list of genes.</p></li></ul><p></p>

Tags: ars, bbgd, blueberry, data-gov, genomics, np301, online-database
Organization: Department of Agriculture
AnthWest, occurrence records for wool carder bees of the genus Anthidium (Hymenoptera: Megachilidae, Anthidiini) in the Western Hemisphere

<p>AnthWest is  a large dataset, one of the outcomes of a comprehensive, broadly comparative study on the diversity, biology, biogeography, and evolution of <em>Anthidium</em> Fabricius in the Western Hemisphere. In this dataset a total of 22,648 adult occurrence records comprising 9,657 unique events are documented for 92 species of <em>Anthidium</em>, including the invasive range of two introduced species from Eurasia, <em>A. oblongatum</em> (Illiger) and <em>A. manicatum</em> (Linnaeus). The geospatial coverage of the dataset extends from northern Canada and Alaska to southern Argentina, and from below sea level in Death Valley, California, USA, to 4,700 m a.s.l. in Tucumán, Argentina. The majority of the records in the dataset correspond to information recorded from individual specimens examined by the authors during this project, and deposited into 60 biodiversity collections located in Africa, Europe, North and South America.
A fraction (4.8%) of the occurrence records were taken from the literature, largely California records from a taxonomic treatment with some additional records for the two introduced species. The temporal scale of the dataset represents collection events recorded between 1886 and 2012.</p>
<p>The data underpinning the analysis reported in this paper are deposited at GBIF, the Global Biodiversity Information Facility, <a href="http://ipt.pensoft.net/ipt/resource.do?r=anthidium">http://ipt.pensoft.net/ipt/resource.do?r=anthidium</a>.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: AnthWest, Occurrence Records for Wool Carder Bees of the Genus Anthidium (Hymenoptera: Megachilidae, Anthidiini) in the Western Hemisphere (Data Dictionary).</p> <p>File Name: meta.xml</p><p>Resource Description: The data dictionary for the Darwin Core Archive of AnthWest. </p></li><br><li><p>Resource Title: Darwin Core Archive.</p> <p>File Name: dwca-anthidium-v7.0.zip</p><p>Resource Description: Zip file includes database field name definitions (meta.xml); also includes the data paper (eml.xml), and occurrence data (occurrence.txt, tab-separated ). Find web download at http://ipt.pensoft.net/ipt/archive.do?r=anthidium</p></li></ul><p></p>

Tags: anthidiini, anthidium, anthophila, apoidea, ars, bees, biodiversity, data-gov, floral-hosts, invasive-species, pollinators, wool-carder-bees
Organization: Department of Agriculture
Ewe and lamb body condition, breeding and production data from the Montana Agricultural Experiment station, Montana State University, Bozeman, MT from 1960 - 2012

<p>Red Bluff Research Ranch is a 13,750-acre ranch is part of the Montana Agricultural Experiment station, and associated with Montana State University in Bozeman, MT. The ranch occupies most of the once thriving late 19th- to early 20th-century gold mining community in the Hot Springs Mining District, which was second only in gold production to Alder Gulch. The ranch nearly surrounds the town of Norris. Historically about 900 head of sheep were maintained year-round at the research ranch. The livestock, as well as the rangeland, are used for both teaching and research. Sheep nutrition studies included nutrition levels, management practices and sheep behavior. Animal scientists look at breeding as a major way to improve livestock production. Hybridization was studied in sheep to help predict staple length, open faces, smoothness and body conformation related to better and more meat. These data include ewe and lamb body condition, breeding and production data from 1960-2012.</p>
<p>Supported/funded by Montana State University College of Agriculture, Montana Agricultural Research Service, Montana Wool Lab., and the USDA Agricultural Research Service.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: MSU_EWES_1960-2012.</p> <p>File Name: MSU_EWES_1960-2012.csv</p></li><br><li><p>Resource Title: MSU_LAMBS_1960-2012.</p> <p>File Name: MSU_LAMBS_1960-2012.csv</p></li><br><li><p>Resource Title: Data dictionary for Montana State University ewe data 1960-2012.</p> <p>File Name: MSU_Ewe_DataDictionary.csv</p></li><br><li><p>Resource Title: Data dictionary for Montana State University lamb data 1960-2012.</p> <p>File Name: MSU_Lamb_DataDictionary.csv</p></li></ul>

Tags: ars, data-gov, grazing, livestock, rangeland, sheep
Organization: Department of Agriculture
Data from: Datasets for transcriptomic analyses of maize leaves in response to Asian corn borer feeding and/or jasmonic acid

<p>Corn (<em>Zea mays</em>) is one of the most widely grown crops throughout the world. However, many corn fields develop pest problems such as corn borers every year that seriously affect its yield and quality. Corn's response to initial insect damage involves a variety of changes to the levels of defensive enzymes, toxins, and communicative volatiles. Such a dramatic change secondary metabolism necessitates the regulation of gene expression at the transcript level. This <em>Data In Brief</em> paper summarizes the datasets of the transcriptome of corn plants in response to corn stalk borers (<em>Ostrinia furnacalis</em>) and/or methyl jasmonate (MeJA). Altogether, 39, 636 genes were found to be differentially expressed. The sequencing data are available in the NCBI SRA database under accession number SRS965087. This dataset will provide more scientific and valuable information for future work such as the study of the functions of important genes or proteins and develop new insect-resistant maize varieties. Includes supplementary tables and data in fasta and GTF format.  </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Datasets for transcriptomic analyses of maize leaves in response to Asian corn borer feeding and/or jasmonic acid.</p> <p>File Name: Web Page, url: <a href="https://www.sciencedirect.com/science/article/pii/S2352340916301792">https://www.sciencedirect.com/science/article/pii/S2352340916301792</a> </p><p>Data in Brief Article including supplemental data in fasta and GTF format.</p></li></ul><p></p>

Tags: acb-damage, ars, data-gov, exogenous-meja, illumina-hiseq-2500-sequencing-platform, insect-herbivory, plant-defense, raw-reads-in-fastq-format, volatile-responses
Organization: Department of Agriculture
SGP97 Surface: NCDC Summary of the Day COOP Precipitation Data

<p>The Southern Great Plains 1997 (SGP97) Hydrology Experiment originated from an interdisciplinary investigation, "Soil Moisture Mapping at Satellite Temporal and Spatial Scales" (PI: Thomas J. Jackson, USDA Agricultural Research Service, Beltsville, MD) selected under the NASA Research Announcement 95-MTPE-03. The region selected for investigation is the best instrumented site for surface soil moisture, hydrology and meteorology in the world. This includes the USDA/ARS Little Washita Watershed, the USDA/ARS facility at El Reno, Oklahoma, the ARM/CART central facility, as well as the Oklahoma Mesonet. The National Climatic Data Center (NCDC) Summary of the Day Co-operative Precipitation Dataset is one of several surface precipitation datasets provided in the Global Energy and Water Cycle Experiment (GEWEX) Continental-Scale International Project (GCIP) by UCAR/JOSS. The primary thrust of the cooperative observing program is the recording of 24-hour precipitation amounts. The observations are for the 24-hour period ending at the time of observation. Observer convenience or special program needs mean that observing times vary from station to station.  However, the vast majority of observations are taken near either 7:00 AM or 7:00 PM local time. The National Weather Service (NWS) Cooperative Observer Daily Precipitation dataset was formed by extracting the daily incremental precipitation values provided in the National Climatic Data Center (NCDC) TD 3200 dataset. The Daily Precipitation data set contains six metadata parameters and four data parameters. The metadata parameters describe the station location and time at which the data were collected. The four data parameters repeat once for each day in the monthly record. Every record has 31 days reported, regardless of the actual number of days in the month. For months with less than 31 days, the extra days are reported as missing (i.e., '-999.99 7 M'). Each 24 hour precipitation value has an associated observation hour. The observation hour is the ending UTC hour for the 24 hour period for which the precipitation value is valid.</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/SGP97COOPprecipitation_jjm_2015-05-04_0933" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/SGP97COOPprecipitation_jjm_2015-05-04_0933</a> </p></li></ul>

Tags: ars, data-gov, environment, farming, hydrology, land-cover, land-use, rain, snow, soil, watersheds
Organization: Department of Agriculture
Data from: Are historical trends in weather consistent with model predictions in the Central United States?

<p dir="ltr">This dataset includes the monthly and daily data used for the analysis of historical and future trends in precipitation and temperature at five Long-Term Agroecosystem Research (LTAR) sites: Kellogg Biological Station (KBS) in Michigan, Upper Mississippi River Basin (UMRB) in Iowa, Central Mississippi River Basin (CMRB) in Missouri, Southern Plains (SP) in Oklahoma, and Lower Mississippi River Basin (LMRB) in Mississippi. Historical data include the longest available record of daily precipitation, minimum temperature, and maximum temperature at weather stations from KBS, UMRB, CMRB, and LMRB, and the monthly 1895-2020 data from the National Ocean and Atmospheric Administration for the climate divisions that represent the five LTAR sites. Future data include 2020-2100 monthly predictions for the five sites from 26 Earth System Models and two Shared Socio-economic Pathways (SSP): the middle of the road SSP245 (a continuation of current emission rates and geo-political conditions), and the fossil fueled development scenario SSP 585 (intensification of fossil fuel energy sources and corresponding emissions). In addition, the data includes the trends calculated from historical and future data, snippets of R code used to calculate these trends, and README files that detail the content of each file.</p><p dir="ltr">Trends in records of 50 years or more showed that temperatures have changed from 1900-2020, more for minimum (0.1 - 0.3 ℃ decade<sup>-1</sup>) than maximum (-0.1 - 0.2 ℃<sup> </sup>decade<sup>-1</sup>), more for winter (-0.1 - 0.3 ℃<sup> </sup>decade<sup>-1</sup>) than summer (-0.1 - 0.1 ℃ decade<sup>-1</sup>), and more often in the north than in the south. Except in Mississippi, annual precipitation has increased at rates of 25 mm decade<sup>-1</sup> or greater over 1950-2020, but monthly trends were inconsistent. Projected trends suggest continued temperature increases, highlighting the need for research on management systems that are resilient to such increases.</p>

Tags: cmip-6-dataset, ltar, precipitation, source-code, temperature, trend-analysis-background-data
Organization: Department of Agriculture
SGP97 Surface: DOE ARM Energy Balance Bowen Ratio (EBBR) Data

<p>The Southern Great Plains 1997 (SGP97) Hydrology Experiment originated from an interdisciplinary investigation, "Soil Moisture Mapping at Satellite Temporal and Spatial Scales" (PI: Thomas J. Jackson, USDA Agricultural Research Service, Beltsville, MD) selected under the NASA Research Announcement 95-MTPE-03. The temporal coverage for this dataset is as follows: Begin datetime: 1997-06-01 00:00:00, End datetime: 1997-07-31 23:59:59. The Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) program operates a network of 12 Energy Balance Bowen Ration (EBBR) stations at its Southern Great Plains site. EBBR provides 30-min observations of latent and sensible heat flux along with net radiation, atmospheric pressure, bowen ratio, wind speed and direction, and the following parameters at five locations surrounding the sites: soil moisture, soil temperature, soil heat flow, soil heat capacity and soil heat flow at the surface. The Energy Balance Bowen Ratio (EBBR) system is a ground-based system using in situ sensors to estimate the vertical fluxes of sensible and latent heat at the local surface. EBBR systems will be installed at up to 15 grassland locations within the SGP CART Site. Flux estimates are made from observations of net radiation, soil heat flow, and the vertical gradients of temperature and relative humidity; these data are used in the Bowen ratio energy balance technique.</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/SGP97armEBBR_JJM_2015-04-24_1531" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/SGP97armEBBR_JJM_2015-04-24_1531</a> </p></li></ul>

Tags: ars, atmospheric-pressure, data-gov, environment, farming, heat-flux, hydrology, land-heat-capacity, net-radiation, radar, soil, soil-heat-budget, soil-temperature, watersheds, wind-direction, wind-speed
Organization: Department of Agriculture
SGP97 GCIP/EOP Surface: Precipitation NCEP/EMC 4KM Gridded Data (GRIB) Gage-Only 24h accumulated RFC -2001

<p>The Southern Great Plains 1997 (SGP97) Hydrology Experiment originated from an interdisciplinary investigation, "Soil Moisture Mapping at Satellite Temporal and Spatial Scales" (PI: Thomas J. Jackson, USDA Agricultural Research Service, Beltsville, MD) selected under the NASA Research Announcement 95-MTPE-03. The Global Energy and Water Cycle Experiment (GEWEX) Continental-scale International Project (GCIP) Enhanced Observing Period (EOP) takes place in the Mississippi River basin during 1995-2000. The Mississippi River basin provides a number of watershed areas that are potentially useful for hydrologic focused studies. During this period, there will be a number of Enhanced Seasonal Observing Periods (ESOPs) in various smaller scale areas. The temporal coverage for this dataset is as follows: Begin date: 1995-10-01 00:00:00, End date: 2000-10-01 23:59:59. This dataset contains the National Centers for Environmental Prediction (NCEP) Environmental Modeling Center (EMC) 4 KM GRIB gage-only analysis using 24h accumulated ("RFC") dataset. A prototype, real-time, hourly, multi-sensor National Preciptation Analysis (NPA) has been developed at NCEP in cooperation with the Office of Hydrology (OH). This analysis merges two data sources that are currently being collected in real-time by OH and NCEP. Hourly digital precipitation (HDP) radar estimates are created by the WSR-88D Radar Product Generator on a 131 X 131 4-km grid centered over each radar site. Data analysis routines, including a bias correction of the radar estimates using rain gage data, have been adapted by NCEP on a national 4-km grid from algorithms developed by OH and executed regionally at NWS River Forecast Centers (RFC). The format of the files is GRIB. The files are compressed using the UNIX "compress" command and "uncompress" must be used before decoding.</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/SGP974KM_JJM_2015-04-23_1504" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/SGP974KM_JJM_2015-04-23_1504</a> </p></li></ul>

Tags: ars, data-gov, earth-science-agriculture-soils-soil-moisture-water-content, environment, farming, radar, rain, rain-gauge
Organization: Department of Agriculture
Poultry Litter Study for Agricultural Antibiotic Resistance in Bowling Green, Kentucky

<p>Poultry litter (PL) is a by-product of broiler production. Most PL is land applied. Land-applied PL is a valuable nutrient source for crop production but can also be a route of environmental contamination with manure-borne bacteria. The objective of this study was to characterize the fate of pathogens, fecal indicator bacteria (FIB), and bacteria containing antibiotic resistance genes (ARGs) after application of PL to soils under conventional till or no-till management. This 2-yr study was conducted in accordance with normal agricultural practices, and microbial populations were quantified using a combination of culture and quantitative, real-time polymerase chain reaction analysis. Initial concentrations of Campylobacter jejuni in PL were 5.4 ± 3.2 × 106 cells g-1 PL; Salmonella sp. was not detected in the PL but was enriched periodically from PL-amended soils. Escherichia coli was detected in PL (1.5 ± 1.3 × 102 culturable or 1.5 ± 0.3 × 107 genes g-1) but was rarely detected in field soils, whereas enterococci (1.5 ± 0.5 × 108 cells g-1 PL) were detected throughout the study. These results suggest that enterococci may be better FIB for field-applied PL. Concentrations of ARGs for sulfonamide, streptomycin, and tetracycline resistance increased up to 3.0 orders of magnitude after PL application and remained above background for up to 148 d. These data provide new knowledge about important microbial FIB, pathogens, and ARGs associated with PL application under realistic field-based conditions. </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/07bc5fb2-462e-40bc-bee6-d24e735ea9b1">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/07bc5fb2-462e-40bc-bee6-d24e735ea9b1</a> </p></li></ul><p></p>

Tags: ars, data-gov, environment, farming, iso-metadata, np211, np212
Organization: Department of Agriculture
SGP97 GCIP/NESOB-97 Sub-Surface: NOAA/Atmospheric Turbulence and Diffusion Division (ATDD) Little Washita 30 Minute Soil Moisture

<p>The Southern Great Plains 1997 (SGP97) Hydrology Experiment originated from an interdisciplinary investigation, "Soil Moisture Mapping at Satellite Temporal and Spatial Scales" (PI: Thomas J. Jackson, USDA Agricultural Research Service, Beltsville, MD) selected under the NASA Research Announcement 95-MTPE-03. The National Oceanic and Atmospheric Administration (NOAA)/Atmospheric Turbulence and Diffusion Division (ATDD) Soil Moisture Dataset is one of several sub-surface datasets provided for the Global Energy and Water Cycle Experiment (GEWEX) Continental-Scale International Project (GCIP) Near Surface Observation Data Set (NESOB) 1997 project. This dataset contains data from one station, the Little Washita Watershed Long Term Flux Site (near Chickasha, Oklahoma) within the NESOB 1997 domain (100.5W to 94.5W longitude and 34N to 39N latitude) and time period (01 April 1997 through 31 March 1998). The NOAA/ATDD Soil Moisture Dataset contains eight metadata parameters and one data parameter and flag. The metadata parameters describe the date, time, network, station and location at which the data were collected. Data values are valid for the 30 minutes preceding the time of observation, and all times are UTC. The data parameter consists of soil volumetric water content at 10 centimeter zone.</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/SGP97NESOB_NOAAsoilmoisture_jjm_2015-05-04_1228" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/SGP97NESOB_NOAAsoilmoisture_jjm_2015-05-04_1228</a> </p></li></ul>

Tags: ars, data-gov, environment, farming, soil, soil-moisture, water
Organization: Department of Agriculture
Data from: Raw Pacific Biosciences and Illumina sequencing reads and assembled genome data for cattle ticks Rhipicephalus microplus and Rhipicephalus annulatus

<p>This study produced reference quality genomes of two cattle ticks <em>Rhipicephalus microplus</em> and <em>Rhipicephalus annulatus</em>, which can be used to identify drug targets with acaricidal activity and refine anti-tick vaccine approaches. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Raw pacific biosciences and illumina sequencing reads and assembled genome data for the cattle ticks Rhipicephalus microplus and Rhipicephalus annulatus.</p> <p>File Name: Web Page, url: <a href="https://doi.org/10.1016/j.dib.2021.106852">https://doi.org/10.1016/j.dib.2021.106852</a> </p><p>Files referenced in the article may be found in the related content section of this record.</p></li></ul><p></p>

Tags: ars, canu-assembler, cattle-tick, data-gov, large-genome-assembly, np104, pacbio-genome-sequencing, rhipicephalus-annulatus, rhipicephalus-microplus
Organization: Department of Agriculture