AndreaBozzo/ceres-open-data-index huggingface dataset:
Iowa Households with Adults 65 Years and Over by Household Type (ACS 5-Year Estimates)

This dataset contains Iowa households with and without adults 65 years and over by household type for State of Iowa, individual Iowa counties, Iowa places and census tracts within Iowa.  Data is from the American Community Survey, Five Year Estimates, Table B11007.

Household type includes All Households Types, 1 Person Household, 2 or More Person Households, 2 or More Person Family Households, and 2 or More Person Nonfamily Households.

A family household is a household maintained by a householder who is in a family.  A family group is defined as any two or more people residing together, and related by birth, marriage, or adoption.

Tags: acs-5-year-estimates, american-community-survey, census-tract, county, household-type, households, place
Organization: State of Iowa
Iowa Median Household Income in the Past 12 Months (ACS 5-Year Estimates)

This dataset contains estimate for median household income in past 12 months for State of Iowa, individual Iowa counties, Iowa places and census tracts within Iowa.  Median household income is inflation adjusted based on last year in data collection period.  Data is from the American Community Survey, Five Year Estimates, Table B19013.

Tags: acs-5-year-estimates, american-community-survey, census-tract, county, median-household-income, place
Organization: State of Iowa
Data From: Habitat type and host grazing regimen influence the soil microbial diversity and communities within potential biting midge larval habitats

<p><em>Culicoides</em> biting midges are important vectors of diverse microbes such as viruses, protozoa, and nematodes that cause diseases in wild and domestic animals. However, little is known about the role of microbial communities in midge larval habitat utilization in the wild. In this study, we characterized microbial communities (bacterial, protistan, fungal and metazoan) in soils from disturbed (bison and cattle grazed) and undisturbed (non-grazed) pond and spring potential midge larval habitats. We evaluated the influence of habitat and grazing disturbance and their interaction on microbial communities, diversity, presence of midges, and soil properties. These data can be used to better understand environmental microbial communities in tallgrass prairie ecosystems associated with grazed versus ungrazed pond and spring habitats and to draw inferences on the interactions of these communities and soil properties with the presence of biting midge larvae. These data should not be used to make inferences for ecosystems other than tallgrass prairie, for animal management methods other than open cow-calf or bison grazing (such as feedlots, dairies, or stockyards), or for other grazing mammals (such as sheep or goats). These data were collected between the months of September and December and therefore are not representative of microbial communities present from January through August. Abbreviations used include Total Carbon (TC), Total Nitrogen (TN), Organic Matter (OM), Konza Prairie Biological Station (KPBS), Operational Taxonomic Unit (OTU), Principal Coordinates Analysis (PCoA), ribosomal RNA (rRNA), and vesicular stomatitis virus (VSV).</p>
<p>The raw Illumina MiSeq sequence data for this project can be found here: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA862140">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA862140</a></p>
<p>Resources in this dataset:</p>
<ul>
<li>Resource Title: Metadata for Midge Larval Habitat Soil Microbiome
File Name: Metadata for NCBI Accession PRJNA862140.xlsx
Resource Description: This spreadsheet links the raw sequence reads on NCBI with data on the presence/absence of Culicoides midges and soil chemistry data (% total soil nitrogen, % total soil carbon, and % organic matter).</li>
</ul>

Tags: ars, bison, cattle, culicoides, data-gov, np104, soil-microbiome
Organization: Department of Agriculture
Data from: The Pacific Biosciences de novo assembled genome dataset from a parthenogenetic New Zealand wild population of the longhorned tick, Haemaphysalis longicornis Neumann, 1901

<p>The longhorned tick, <em>Haemaphysalis longicornis</em>, feeds upon a wide range of bird and mammalian hosts. Mammalian hosts include cattle, deer, sheep, goats, humans, and horses. This tick is known to transmit a number of pathogens causing tick-borne diseases, and was the vector of a recent serious outbreak of oriental theileriosis in New Zealand. A New Zealand-USA consortium was established to sequence, assemble, and annotate the genome of this tick, using ticks obtained from New Zealand's North Island. In New Zealand, the tick is considered exclusively parthenogenetic and this trait was deemed useful for genome assembly. Very high molecular weight genomic DNA was sequenced on the Illumina HiSeq4000 and the long-read Pac Bio Sequel platforms. Twenty-eight SMRT cells produced a total of 21.3 million reads which were assembled with Canu on a reserved supercomputer node with access to 12 TB of RAM, running continuously for over 24 days. The final assembly dataset consisted of 34,211 contigs with an average contig length of 215,205 bp. The quality of the annotated genome was assessed by BUSCO analysis, an approach that provides quantitative measures for the quality of an assembled genome. Over 95% of the BUSCO gene set was found in the assembled genome. Only 48 of the 1066 BUSCO genes were missing and only 9 were present in a fragmented condition. The raw sequencing reads and the assembled contigs/scaffolds are archived at the National Center for Biotechnology Information. </p>
<p>Funded by USDA-ARS Knipling-Bushland US Livestock Insects Research Laboratory CRIS project 3094-32000-036-00 </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: The Pacific Biosciences de novo assembled genome dataset from a parthenogenetic New Zealand wild population of the longhorned tick, Haemaphysalis longicornis Neumann, 1901.</p> <p>File Name: Web Page, url: <a href="https://doi.org/10.1016/j.dib.2019.104602">https://doi.org/10.1016/j.dib.2019.104602</a> </p><p>NCBI data referenced in the article can be found in the related content links of this record
</p></li></ul><p></p>

Tags: ars, cattle-tick, data-gov, genome-annotation, np104, pac-bio-de-novo-assembly, tick-genome
Organization: Department of Agriculture
MTA Subway Entrances and Exits: 2024

This is a dataset containing the entrances and exits at New York City Subway and Staten Island Railway stations. Information is provided on the entrance or exit, including their coordinates, the borough they are in, whether it allows entries and exits, and the type of entrance (more information below). The dataset also includes the name of the station complex, the complex ID number, the name of the specific station in the complex the entrance is for (constituent station), the station ID number, the GTFS Stop ID, the daytime routes that stop at the station complex, and the line and division the constituent station is on.

Tags: coordinates, entrances, exits, new-york-city-transit, nyct, stations, subway, subway-stations
Organization: State of New York
SWAT - Soil and Water Assessment Tool

<p>The <a href="https://swat.tamu.edu/">Soil and Water Assessment Tool (SWAT)</a> is a public domain model jointly developed by USDA Agricultural Research Service (USDA-ARS) and Texas A&M AgriLife Research, part of The Texas A&M University System. SWAT is a small watershed to river basin-scale model to simulate the quality and quantity of surface and ground water and predict the environmental impact of land use, land management practices, and climate change. SWAT is widely used in assessing soil erosion prevention and control, non-point source pollution control and regional management in watersheds.  </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Website Pointer to SWAT - Soil and Water Assessment Tool .</p> <p>File Name: Web Page, url: <a href="https://swat.tamu.edu/">https://swat.tamu.edu/</a> </p><p>Soil and Water Assessment Tool (SWAT) website, including software tools, documentation, events, publications, and developer resources.</p></li></ul><p></p>

Tags: ars, climate-change, data-gov, environmental-impact, ground-water, land-management, model, np211, np212, np215, pollution, river-basin, soil, soil-and-water-assessment-tool, soil-erosion, surface-water, swat, water, watershed
Organization: Department of Agriculture
Data from: Data on xylem sap proteins from Mn- and Fe-deficient tomato plants obtained using shotgun proteomics

<p>This article contains consolidated proteomic data obtained from xylem sap collected from tomato plants grown in Fe- and Mn-sufficient control, as well as Fe-deficient and Mn-deficient conditions. Data presented here cover proteins identified and quantified by shotgun proteomics and Progenesis LC-MS analyses: proteins identified with at least two peptides and showing changes statistically significant (ANOVA; p ≤ 0.05) and above a biologically relevant selected threshold (fold ≥ 2) between treatments are listed. The comparison between Fe-deficient, Mn-deficient and control xylem sap samples using a multivariate statistical data analysis (Principal Component Analysis, PCA) is also included. Data included in this article are discussed in depth in "Effects of Fe and Mn deficiencies on the protein profiles of tomato (<em>Solanum lycopersicum</em>) xylem sap as revealed by shotgun analyses", Ceballos-Laita et al., <em>J. Proteomics</em>, 2018. This dataset is made available to support the cited study as well to extend analyses at a later stage. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: ProteomeExchange submission PXD007517. Xylem sap shotgun proteomics from Fe- and Mn-deficient and Mn-toxic tomato plants. .</p> <p>File Name: Web Page, url: <a href="http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD007517">http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD007517</a> </p><p>The MS proteomics data have been deposited to the ProteomeXchange Consortium via the Pride partner repository with the data set identifier PXD007517. Also includes FTP location.</p>
<p>Files available at <a href="https://www.ebi.ac.uk/pride/archive/projects/PXD007517">https://www.ebi.ac.uk/pride/archive/projects/PXD007517</a> via HTML, FTP, or Fast (Aspera) download : 1 SEARCH.xml file, 1 Peak file, 24 RAW files, 1 Mascot information.xlsx file.</p>
<p>Supplementary data associated with this article can be found in the online version at <a href="http://dx.doi.org/10.1016/j.dib.2018.01.034">http://dx.doi.org/10.1016/j.dib.2018.01.034</a></p></li></ul><p></p>

Tags: ars, data-gov, shotgun-proteomics, xylem-sap-proteins
Organization: Department of Agriculture
Data from: Effects of conifer treatments on soil nutrient availability and plant composition in sagebrush steppe

<p>Conifer control in sagebrush steppe of the western United States causes various levels of site disturbance influencing vegetation recovery and resource availability. The data set presented in this article include growing season availability of soil micronutrients and levels of total soil carbon, organic matter, and N spanning a six year period following western juniper (<em>Juniperus occidentalis</em> spp. <em>occidentalis</em>) reduction by mechanical cutting and prescribed fire of western juniper woodlands in southeast Oregon. These data can be useful to further evaluate the impacts of conifer woodland reduction to soil resources in sagebrush steppe plant communities. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Bates, J. D., & Davies, K. W. (2017). Data set on the effects of conifer control and slash burning on soil carbon, total N, organic matter and extractable micro-nutrients. Data in Brief 14:515-523.</p> <p>File Name: Web Page, url: <a href="https://www.sciencedirect.com/science/article/pii/S2352340917303815">https://www.sciencedirect.com/science/article/pii/S2352340917303815</a> </p><p>The data shows micronutrient availability, 2007–2012, for two big sagebrush-bunchgrass communities following western juniper control. Soil carbon, SOM, and TSN are presented for the BLUEBUNCH and FESCUE sites. All graphical data are in means and standard errors.</p></li></ul><p></p>

Tags: ars, cheatgrass, data-gov, fuel-reduction, resin-probes, tree-control-measures
Organization: Department of Agriculture
Data from: Defensive aphid symbiont Hamiltonella defensa effects on Aphelinus glycinis and Aphelinus atriplicis

<p>Endosymbiont interactions with hosts have important effects on fitness, including the fitness of many pest and beneficial species. Among these interactions, facultative endosymbiotic bacteria can protect aphids from parasitoids. <em>Aphis craccivora</em> and <em>Acyrthosiphon pisum</em> can harbor the symbiotic bacteria <em>Hamiltonella defensa</em> and its bacteriophage APSE. Infection by <em>H. defensa</em> defends these aphids against some but not all parasitoid species in the hymenopteran family Braconidae. Here, we report results on the effect of <em>H. defensa</em> on parasitism of these aphids by species in the other major lineage of aphid parasitoids, <em>Aphelinus</em> species in the family Aphelinidae. Parasitism of aphids infected with <em>H. defensa</em> /APSE by two <em>Aphelinus</em> species did not differ from that of uninfected aphids. While <em>Aphelinus atriplicis</em> showed no difference in fitness components between infected and uninfected aphids, <em>Aphelinus glycinis</em> actually produced more adult progeny and larger female progeny on infected than on uninfected aphids. <em>Aphelinus glycinis</em> may increase host quality for itself by changing the titer of nutritional versus protective bacteria in such a way that aphids infected with <em>H. defensa</em> can be made more suitable for parasitoid development than uninfected aphids. Our results and reasoning suggest that these Aphelinus species may be less prone to harm by <em>H. defensa</em> /APSE that affect eggs because they have anhydropic, heavily chorionated eggs, which may not absorb toxins during embryogenesis. </p>
<p>See the included methods-DefensiveAphidSymbiont.txt file for more information on the methods and design structure of this study.</p>

Tags: acyrthosiphon-pisum, aphelinus-atriplicis, aphelinus-glycinis, aphid-endosymbionts, aphis-craccivora, apse, ars, beneficial-insects, biological-control, china, data-gov, hamiltonella-defensa, introduced-species, np304, republic-of-georgia
Organization: Department of Agriculture
Data from: Host specificity of Aphelinus species considered for introduction to control Diuraphis noxia

<p>Diuraphis noxia, the Russian wheat aphid, has become a major pest of wheat and barley since first being detected in the western USA in 1986. However, it is rarely a pest in Eurasia, its area of origin, and research has shown that natural enemies can limit its abundance there. Among the most important of natural enemies of D. noxia in Eurasia are parasitoids in the genus Aphelinus. These data are results of laboratory experiments on host specificity of ten populations of seven species from two species complexes in the genus Aphelinus. Host specificity was not related to host plant species or the phylogenetic relatedness of the aphids or the parasitoids. While some species had very broad host ranges and others had intermediate host ranges, Aphelinus hordei had a very narrow host range, being restricted primarily to species in the genus Diuraphis, and especially D. noxia. We also report the results of experiments on the mechanisms of this host specificity. Most of the host specificity of A. hordei can be explained by differences in the behavior of females when they encountered different aphid species. Females of A. hordei rarely approach, sting, oviposit or host feed on aphids outside the genus Diuraphis, and they oviposit most frequently in D. noxia. From these results, we conclude that A. hordei is an excellent candidate for introduction into the USA to control D. noxia. </p>

Tags: aphelinus-asychis-complex, aphelinus-hordei, aphelinus-varipes-complex, ars, biological-control, data-gov, np304, russian-wheat-aphid
Organization: Department of Agriculture
Growth and Yield Data for the Bushland, Texas, Cotton Datasets

<p>This dataset consists of growth and yield data for each season when upland cotton [<em>Gossympium hirsutum</em> (L.)] was grown for lint and seed at the USDA-ARS Conservation and Production Research Laboratory (CPRL), Soil and Water Management Research Unit (SWMRU), Bushland, Texas (Lat. 35.186714°, Long. -102.094189°, elevation 1170 m above MSL). In the 2000 through 2004, 2008, 2010, 2012, and 2020  seasons, cotton was grown on from one to four large, precision weighing lysimeters, each in the center of a 4.44 ha square field also planted to cotton. The square fields were themselves arranged in a larger square with four fields in four adjacent quadrants of the larger square. Fields and lysimeters within each field were thus designated northeast (NE), southeast (SE), northwest (NW), and southwest (SW). Cotton was grown on different combinations of fields in different years. When irrigated, irrigation was by linear move sprinkler system years before 2014, and by both sprinkler and subsurface drip irrigation in 2020. Irrigation protocols described as full were managed to replenish soil water used by the crop on a weekly or more frequent basis as determined by soil profile water content readings made with a neutron probe to 2.4-m depth in the field. Irrigation protocols described as deficit typically involved irrigation at rates established as percentages of full irrigation ranging from 33% to 75% depending on the year.</p>
<p>The growth and yield data typically include plant population density, height, plant row width, leaf area index, growth stage, total above-ground biomass, leaf and stem biomass, boll mass (when present), lint mass, seed mass, final yield, and lint quality. Data are from replicate samples in the field and non-destructive (except for final harvest) measurements on the weighing lysimeters. In most cases yield data are available from only manual sampling on replicate plots in each field and lysimeters.</p>
<p>These datasets originate from research aimed at determining crop water use (ET), crop coefficients for use in ET-based irrigation scheduling based on a reference ET, crop growth, yield, harvest index, and crop water productivity as affected by irrigation method, timing, amount (full or some degree of deficit), agronomic practices, cultivar, and weather. Prior publications have focused on cotton ET, crop coefficients, crop water productivity, and simulation modeling of crop water use, growth, and yield. Crop coefficients have been used by ET networks. The data have utility for testing simulation models of crop ET, growth, and yield and have been used for testing, and calibrating models of ET that use satellite and/or weather data.</p>
<p>See the README for descriptions of each data file.</p>

Tags: ars, cotton, cotton-fiber, cotton-seed, data-gov, evapotranspiration, fiber-quality, growth-and-yield, np211
Organization: Department of Agriculture
UNSODA 2.0: Unsaturated Soil Hydraulic Database. Database and program for indirect methods of estimating unsaturated hydraulic properties

<p>This database contains measured soil water retention, hydraulic conductivity, and water diffusivity data, as well as pedological information of some 790 soil samples from around the world.</p>
<p>Quantifying water flow and chemical transport in the vadose zone typically requires knowledge of the unsaturated soil hydraulic properties. The UNsaturated SOil hydraulic DAtabase (UNSODA) was developed to provide a source of unsaturated hydraulic data and some other soil properties for practitioners and researchers. A first MS-DOS version of the database was released in 1996. It has been applied in numerous studies. In this paper, we describe the second version (UNSODA V2.0) for use with Microsoft Access-97®1. The format and structure of the new database have been modified to provide additional and more convenient options for data searches, to provide compatibility with other programs for easy loading and downloading of data, and to allow users to customise the contents and look of graphical output. This paper reviews the structure and contents of the database as well as the operations that can be performed on the different data types in UNSODA V2.0. The use and application of the new database are illustrated with two examples. The retrieval of data is briefly illustrated, followed by a more detailed example regarding the interpolation of soil particle-size distribution data obtained according to different national definitions of particle-size classes. The interpolation procedure, which is based on finding similar particle-size distribution curves from a large European data set, also performed well for soils that originate from other geographical areas.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: UNSODA 2.0 README.</p> <p>File Name: UNSODA 2.0 README.pdf</p></li><br><li><p>Resource Title: UNSODA 2.0 zip package.</p> <p>File Name: unsoda.ZIP</p><p>Resource Description: Contains a README file and Microsoft Access database. Files added to original record on June 8, 2020.</p></li></ul>

Tags: ars, data-gov, earth-science-agriculture-soils-soil-moisture-water-content, hydraulic-conductivity, np211, water-diffusivity-data
Organization: Department of Agriculture
Leptinotarsa decemlineata Official Gene set v1.2

<p>The <em>Leptinotarsa decemlineata</em> genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The <em>L. decemlineata</em> research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.2. OGSv1.1 is an integration of automatic gene predictions from Maker (performed by Dan Hughes at Baylor College of Medicine) with manual annotations by the research community (done via the Apollo manual annotation software). The coordinates of OGSv1.1 were converted to the latest genome assembly, <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000500325.1">GCF_000500325.1</a>, using <a href="https://github.com/NAL-i5K/coordinates_conversion">coordinates_conversion</a> and <a href="https://github.com/NAL-i5K/remap-gff3">remap-gff3</a>, to generate OGSv1.2.</p>
<p>If you wish to use this dataset, please follow the Baylor College of Medicine's conditions for data use: <a href="https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use">https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use</a></p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Leptinotarsa decemlineata Official Gene Set OGSv1.2.</p> <p>File Name: lepdec_OGSv1-2.tar.gz</p><p>Resource Description: The attached tar.gz archive (lepdec_OGSv1-2.tar.gz) contains the following files:

* lepdec_OGSv1.2_GCF_000500325.1_cds.fa - CDS sequences for OGSv1.2  
* lepdec_OGSv1.2_GCF_000500325.1_pep.fa - protein sequences for OGSv1.2
* lepdec_OGSv1.2_GCF_000500325.1_trans.fa - transcript sequences for OGSv1.2
* lepdec_OGSv1.2_GCF_000500325.1.gff3 - GFF3 file for OGSv1.2
* lepdec_OGSv1.2_GCF_000500325.1_removed-features.tsv - a list of features removed between OGSv1.1 and OGSv1.2. The list includes feature type, ID, Name, and owner.
* lepdec_OGSv1.2_GCF_000500325.1_update-summary.tsv - summary statistics of the features removed between OGSv1.1 and OGSv1.2 
</p></li></ul>

Tags: colorado-potato-beetle, i5k, insects, leptinotarsa-decemlineata, organism-project
Organization: Department of Agriculture