AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: A <i>Lacto</i><i>coccus lactis</i> starter culture reduces bloater defect in cucumber fermentations brined with low salt

<p dir="ltr">This is an excel spreadsheet and equivalent comma delimited file containing absorbance data of <i>Lactiplantibacillus pentosus</i>, <i>Lactococcus lactis</i>, <i>Enterobacteriaceae</i>, and <i>Leuconostocaceae</i> growth in cucumber juice medium prepared from size 3A cucumbers. Such data was collected from continues measurements of absorbance from 96-well plates filled with cucumber juice medium expressed from size 3A cucumbers that was inoculated with the bacteria identified above. Absorbance was measured at 630 nm using a BioTek ELx808 Microstation or plate reader. The Excel spreadsheet with raw absorbance data was used for calculating growth rate in Table 3 of the associated publication.</p>

Tags: absorbance-data-set, enterobacteriaceae-related, growth-rate-calculation, lactiplantibacillus-pentosus, lactococcus-lactis, leuconostocaceae
Organization: Department of Agriculture
Neodiprion lecontei Official Gene Set v1.1

<p>This dataset presents the <em>Neodiprion</em> Official Gene Set (OGS) v1.1. It was generated using Maker v2.31.8, followed by CrossMap re-mapping of coordinates to genome assembly Nlec1.1 (<a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_001263575.2/">https://www.ncbi.nlm.nih.gov/assembly/GCA_001263575.2/</a>).</p>
<p>This dataset is now obsolete - a new genome assembly, iyNeoleco1.1 (<a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_021901455.1">https://www.ncbi.nlm.nih.gov/assembly/GCF_021901455.1</a>) has been produced by the Ag100Pest project, with annotations from NCBI's RefSeq resource. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Neodiprion lecontei Official Gene Set v1.1.</p> <p>File Name: neolec_OGSv1.1.tar.gz</p><p>Resource Description: The files in this directory are derived from Neolec OGSv1.0 (not publicly released). The gff3 file was updated to assembly GCA_001263575.2 (<a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_001263575.2">https://www.ncbi.nlm.nih.gov/assembly/GCA_001263575.2</a>) using CrossMap v0.2.8 (<a href="http://crossmap.sourceforge.net/">http://crossmap.sourceforge.net/</a>).</p>
<p>neolec_OGSv1.1.gff3: Neolec OGSv1.0, updated to GCA_001263575.2
neolec_OGSv1.1_removed.tsv: Features from Neolec OGSv1.0 that were removed in the update
neolec_OGSv1.1_summary.tsv: The % of individual features from Neolec OGSv1.0 that were retained in the update
Nlec_v1_transcripts_renamed_alphabetized.fasta: Transcript sequences derived from Neolec OGSv1.0
Nlec_v1_proteins_renamed_alphabetized.fasta: Protein sequences derived from Neolec OGSv1.0
</p></li></ul><p></p>

Tags: ars, arthropods, data-gov, i5k, neodiprion-lecontei
Organization: Department of Agriculture
Grape Vine Shoot Length Data

<p dir="ltr">We collected grapevine shoot growth over a growing season of 2024 (April to June) in a vineyard of the horticultural unit 2 farm of the Ohio State University (40.73866822022149, -81.90273359323078). The measurements were made with a measuring tape.</p>

Tags: combination, error, imprecision, length, measurement, models, vector-data
Organization: Department of Agriculture
Data from: "Genome report -  chromosome-scale genome assembly of the Olive fly Bactrocera oleae (Diptera-Tephritidae)"

<p dir="ltr">The olive fruit fly, <i>Bactrocera oleae </i>(Rossi) (Diptera: Tephritidae), is a specialist of fruits of the genus <i>Olea</i> and is a major pest of commercial olives due to their adverse impacts to olive production. In support of genomic and physiological research of the olive fly, we sequenced, assembled, and annotated two independent genomes, one from a wild-collected male and one from a wild-collected female. The resulting genomes are highly contiguous, collinear, and complete, attesting to the accuracy and quality of both assemblies. In addition to the autosomes captured as single contigs, the X and Y chromosomes were also captured as evidenced by the X chromosome showing diploid coverage in the female assembly compared to haploid coverage in the male assembly and the Y chromosome being entirely absent from the female assembly. In addition, a complete genome assembly of a known obligate symbiont to the olive fly, <i>Candidatus Erwinia dacicola (</i><i>Ca. E. dacicola)</i>, was fully captured.</p><p dir="ltr">Dataset includes scripts used in the assembly of the <i>Bactrocera oleae </i>genomes and the obligate symbiont <i>Candidatus Erwinia dacicola</i> genome. It can be used to replicate the steps necessary to assemble the male and female genomes described in National Center for Biotechnology Information (NCBI) BioProject: PRJNA1089778 and PRJNA1275571, male and female, respectively. It can also be used to replicate the steps to assemble the symbiont genome described in National Center for Biotechnology Information (NCBI) BioProject: PRJNA1090968. The olive fruit fly genome assembly workflow was performed on the United States Department of Agriculture (USDA) - SCINet/Mississippi State University High Performance Computing Cluster (HPC) Atlas and installed via Conda. The <i>Ca. E. dacicola</i> genome assembly workflow was performed on the United States Department of Agriculture (USDA) – SCINet (HPC) Ceres and installed via Conda.</p>

Tags: chromosome, diptera, fruit-fly, genome-assembly, genomics, insect, pest, source-code, symbiosis, tephritidae
Organization: Department of Agriculture
EV Smith Study for Resilient Economic Agricultural Practices in Auburn, Alabama

<p>EV Smith Study for Resilient Economic Agricultural Practices in Auburn, Alabama
There is a potential in the southeastern US to harvest winter cover crops from cotton (Gossypium hirsutum L.) fields for biofuels or animal feed use, but this could impact yields and nitrogen (N) fertilizer response. An experiment was established to examine rye (Secale cereale L.) residue management (RM) and N rates on cotton productivity. Three RM treatments (no winter cover crop (NC), residue removed (REM) and residue retained (RET)) and four N rates for cotton were studied. Cotton population, leaf and plant N concentration, cotton biomass and N uptake at first square, and cotton biomass production between first square and cutout were higher for RET, followed by REM and NC. However, leaf N concentration at early bloom and N concentration in the cotton biomass between first square and cutout were higher for NC, followed by REM and RET. Seed cotton yield response to N interacted with year and RM, but yields were greater with RET followed by REM both years. These results indicate that a rye cover crop can be beneficial for cotton, especially during hot and dry years. Long-term studies would be required to completely understand the effect of rye residue harvest on cotton production under conservation tillage.</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Auburn, AL EV Smith (ALAUEVS) data.</p> <p>File Name: ALAUEVS_csv_data.zip</p><p>Resource Description: CSV format data on Experimental Units, Field Sites, Residue Management, Persons, Treatments, Weather Daily, Weather Station. 
</p></li></ul>

Tags: ars, data-gov, environment, farming, iso-metadata, np211, np212
Organization: Department of Agriculture
Data from: Evaluation of Mating Disruption for Suppression of Plodia interpunctella Populations in Retail Stores

<p dir="ltr">Mating disruption is a commercially available management tactic for pyralid moths that are pests of stored products. However, evaluations of efficacy have had limited replication which limits the ability to draw conclusions about effectiveness or impact of different variables on efficacy. We evaluated mating disruption of Plodia interpunctella in 33 retail pet supply stores, and the impact of factors such as insect density and application rate on efficacy. The objective of the project reported here was to evaluate how well mating disruption can suppress moth populations in retail pet stores, by assessing treatments under ‘real world’ conditions found in commercial operations. Data set included the characteristics of the stores including volume and geographic location, the mating disruption treatment types including the number and location of dispensers, and the captures of moths in pheromone baited traps over time before applying the mating disruption treatment and during the mating disruption treatment.</p>

Tags: indian-meal-moth, integrated-pest-management, mating-disruption, plodia-interpunctella, retail-stores, stored-products
Organization: Department of Agriculture
3DADE

<p>3DADE is a Fortran computer program for evaluating a series of analytical solutions of the 3-Dimensional Advection-Dispersion Equation. The analytical solutions pertain to three-dimensional solute transport during steady unidirectional water flow in porous media with uniform transport and flow properties. The transport equation contains terms accounting for solute movement by advection and dispersion, as well as for solute retardation, first-order decay, and zero-order production.  The3DADE code can be used to solve the direct problem, i.e., the concentration is calculated as a function of time and space for specified model parameters, and the indirect (inverse) problem in which the program estimates selected parameters by fitting one of the analytical solutions to specified experimental data. Transient analytical solutions are evaluated for five different transport scenarios (three boundary value problems and two initial value problems) in either a Cartesian or cylindrical coordinate system. Simple steady-state solutions are also provided for three initial value problems.</p>
<p>The program comes with a user manual giving detailed descriptions of the different transport problems, listing the main program variables, input file formats, sample input and output files, and providing a hard copy of the FORTRAN source code. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: 3DADE Download Page.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/research/software/download/?softwareid=93&modecode=20-36-15-00">https://www.ars.usda.gov/research/software/download/?softwareid=93&modecode=20-36-15-00</a> </p></li></ul><p></p>

Tags: 3-dimensional-advection-dispersion-equation, ars, data-gov, hydrologic-model, three-dimensional-solute-transport
Organization: Department of Agriculture
Data from: Assessment of Oklahoma phlox in the Gypsum Hills of northwestern Oklahoma and southern Kansas

<p>These data describe aspects of the abiotic environment for 1000 randomly selected points and 529 points where Oklahoma phlox was observed along the 2020 and 2021 survey route.</p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource Title: Random locations along 2020 and 2021 survey route
File Name: phlox_study_data-RandLoc.kml</p>
</li>
<li>
<p>Resource Title: Locations along 2020 and 2021 survey route where Oklahoma phlox was observed
File Name: phlox_study_data-PhloxLoc.kml</p>
</li>
<li>
<p>Resource Title: Survey route with cultivation adjacent the route noted
File Name: phlox_study_data-SurveyRoute.kml
Resource Description: The survey route used in 2020 and 2021 with information as to whether the land adjacent on each segment was cultivated or not and if so, which side was cultivated during the period.</p>
</li>
<li>
<p>File Title: Data Dictionary
File Name: DataDictionary.csv</p>
</li>
</ul><p></p>

Tags: ars, data-gov, np215, oklahoma-phlox, phlox-oklahomensis
Organization: Department of Agriculture
Data from: Haplotype-resolved genome assembly of ‘Manhattan’ perennial ryegrass (<i>Lolium </i><i>perenne</i> L.) and characterization of drought responsive late embryogenesis abundant genes

<p dir="ltr">Genome sequence and annotation files of Lpman haplotype 1 and haplotype 2 genome assembly reported in the manuscript "Haplotype-resolved genome assembly of ‘Manhattan’ perennial ryegrass (<i>Lolium </i><i>perenne</i> L.) and characterization of drought responsive late embryogenesis abundant genes". Also included is the transposable element (TE) annotation from EDTA and the organelles (chloroplast and mitochondria) genomes with annotation.</p>

Tags: deydrin, grass-synteny, late-embryogenesis-abundant-lea
Organization: Department of Agriculture
LTAR Walnut Gulch Experimental Watershed Lucky Hills Phenocam

<p>A stationary camera overlooking the Lucky Hills sub-watershed in the Walnut Gulch Experimental Watershed used to track vegetation phenology (RGB and IR imagery). Images are taken every 30 minutes between 4:00am and 10:30pm local standard time. 

A link to the Phenocam's network FAQ: https://phenocam.sr.unh.edu/webcam/faq</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/77d59ee9-6b19-4fe6-9599-ca784c2497a2" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/77d59ee9-6b19-4fe6-9599-ca784c2497a2</a> </p></li></ul>

Tags: ars, biota, cameras, data-gov, environment, farming, np211, phenocam, photographs, vegetation, watersheds
Organization: Department of Agriculture
Angus Sequence Dataset Collection

<p>Whole genome sequence data for Bovidae Bos taurus - beef Angus, 30 animals in total. The data is in "fastq" format. There are two versions of each file because we did paired end sequencing. There are two reads for each of the 210 data lines (a forward and a reverse read) summing to 420 total. A diagram of this is attached. In the diagram, the two reads would correspond to read 1 and read 3. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: CSU_136201_SampleSheet.csv - list of all Angus sequence files.</p> <p>File Name: CSU_136201_SampleSheet.csv</p><p>Resource Description: This spreadsheet lists all 210 data files associated with the sequencing of these 30 Angus animals</p>
<p></p></li><br><li><p>Resource Title: Sequence Reads Diagram.</p> <p>File Name: SequenceReads.png</p><p>Resource Description: There are two reads for each of the 210 data lines (a forward and a reverse read) summing to 420 total. In the diagram, the two reads would correspond to read 1 and read 3.</p></li></ul><p></p>

Tags: animals, ars, cryopreservation, data-gov, dna-sequence, genetic-diversity, germplasm, grin, np101
Organization: Department of Agriculture
Data from: Microbiota of maize kernels as influenced by Aspergillus flavus infection in susceptible and resistant inbreds

<p>This repository contains the code and data to reproduce the figures and analyses in the paper "Microbiota of maize kernels as influenced by Aspergillus flavus infection in susceptible and resistant inbreds" by Moore et al. The paper investigates how biocontrol application affects the diversity and composition of the bacterial and fungal communities associated with maize kernels, using 16S and ITS amplicon sequencing. Also available at <a href="https://github.com/kcamnairb/biocontrol_microbiome_analysis">https://github.com/kcamnairb/biocontrol_microbiome_analysis</a></p>

Tags: 16s-and-its-amplicon, ars, data-gov, microbiome-analysis, np108, reproducible-code
Organization: Department of Agriculture
Data from: Genome sequence resource of Streptomyces spp. from agricultural soil that inhibit Verticillium dahliae

<p>Annotation data of genome assemblies of <em>Streptomyces</em> spp. isolated from agricultural soil.  </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Annotation data for MCL20-2.</p> <p>File Name: MCL20-2_prokka.zip</p></li><br><li><p>Resource Title: Annotation data for SCL15-4.</p> <p>File Name: SCL15-4_prokka.zip</p></li><br><li><p>Resource Title: Annotation data for SCL15-6.</p> <p>File Name: SCL15-6_prokka.zip</p></li><br><li><p>Resource Title: Annotation data for SJL17-1.</p> <p>File Name: SJL17-1_prokka.zip</p></li><br><li><p>Resource Title: Annotation data for SJL17-4.</p> <p>File Name: SJL17-4_prokka.zip</p></li></ul><p></p>

Tags: ars, data-gov, genome, np303, np304, soil-microbiome, streptomyces-spp
Organization: Department of Agriculture
Northwest Weather Service - Palouse Conservation Field Station

<p>Northwest Weather Service, Palouse Conservation Field Station located at Palouse Conservation Field Station near Pullman, WA</p>
<p>DAILY DATA FOR A MONTH - daily maximum, minimum and average temperature (degrees F), average temperature departure from normal (degrees F), heating and cooling degree days (base 65), precipitation, snowfall and snow depth (inches) for all days of the selected month. Basic monthly summary statistics are also provided. </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/8f831fbe-15db-443b-bb77-054a68da672e">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/8f831fbe-15db-443b-bb77-054a68da672e</a> </p></li></ul><p></p>

Tags: ars, data-gov, earth-science-atmosphere-atmospheric-temperature-surface-temperature-air-temperature, earth-science-atmosphere-precipitation, earth-science-atmosphere-weather-events, environment, farming
Organization: Department of Agriculture
TDEI Sidewalk Dataset Hurrah City Edges

This is a single dataset from the <a href='https://tdei.cs.washington.edu/'>Transportation Data Exchange Initiative (TDEI) System</a>.

The WSP_Hurrah_City dataset is an OSW v0.2 compliant collection focused on sidewalks in Hurrah City, Yakima County as part of the ITS JPO ITS4US project. Collected by Gaussian Solutions and University of Washington on February 5, 2025, it captures mapped pedestrian infrastructure with validity through 2027. The dataset (version 1.1) integrates Hexagon HxGN imagery from July 5, 2023, and includes a TCAT quality report for verification. It defines a polygon feature boundary within Hurrah City, documenting tract 1613-9400.01. See attachments below for the raw .geojson file.

Crowd contributions are permitted, supporting ongoing improvements. Released with notes highlighting sidewalk mapping, the dataset advances accessible mobility insights and is structured for integration in spatial analysis, planning, and infrastructure quality assessment.

Tags: intelligent-transportation-systems-its, its-joint-program-office-jpo, its4us, occupancy-data, pedestrian-detection, pedestrian-in-crosswalk-warning, tdei-sidewalk-data, trajectories, work-zone-data-exchange
Organization: Department of Transportation
ITS4US UW Transportation Data Exchange Initiative TDEI

What is the <a href='https://tdei.cs.washington.edu/'>Transportation Data Exchange Initiative (TDEI)</a>? 

Cities, organizations, and individuals currently lack detailed, accurate, and standardized data on the locations of footpaths, cycle paths, sidewalks, and crossings. Moreover, there is inconsistent information about the attributes of these pathways that affect walking, rolling, and non-motorized travel, as well as a limited understanding of how these paths are connected or disconnected.

The OpenSidewalks project aims to address this data deficiency by proposing a) a robust data schema (OpenSideWalks or OSW) and b) a comprehensive data tools ecosystem that support collection and maintenance of sidewalk data (which we call the TDEI).

These resources are designed to give planners, policy makers, and community advocates the data they need to improve pedestrian infrastructure, particularly in historically underserved areas.

Current funding is provided by the USDOT/JPO ITS4US program under the University of Washington’s TDEI deployment project.
OpenSidewalks is led by the Taskar Center for Accessible Technology (TCAT) housed by the Paul G. Allen School for Computer Science and Engineering at the University of Washington.

Tags: bicycle, crosswalk, first-mile-last-mile, intelligent-transportation-systems-its, its-joint-program-office-jpo, multi-modal-trip-planning, pedestrian, sidewalk
Organization: Department of Transportation
TDEI Sidewalk Dataset Hurrah City Nodes

This is a single dataset from the <a href='https://tdei.cs.washington.edu/'>Transportation Data Exchange Initiative (TDEI) System</a>.

The WSP_Hurrah_City dataset is an OSW v0.2 compliant collection focused on sidewalks in Hurrah City, Yakima County as part of the ITS JPO ITS4US project. Collected by Gaussian Solutions and University of Washington on February 5, 2025, it captures mapped pedestrian infrastructure with validity through 2027. The dataset (version 1.1) integrates Hexagon HxGN imagery from July 5, 2023, and includes a TCAT quality report for verification. It defines a polygon feature boundary within Hurrah City, documenting tract 1613-9400.01. See attachments below for full raw geojson file.

Crowd contributions are permitted, supporting ongoing improvements. Released with notes highlighting sidewalk mapping, the dataset advances accessible mobility insights and is structured for integration in spatial analysis, planning, and infrastructure quality assessment.

Tags: intelligent-transportation-systems-its, its-joint-program-office-jpo, its4us, occupancy-data, pedestrian-detection, pedestrian-in-crosswalk-warning, tdei-sidewalk-data, trajectories, work-zone-data-exchange
Organization: Department of Transportation