AndreaBozzo/ceres-open-data-index huggingface dataset:
Genetic Stocks Oryza (GSOR) Collection Website

<p>The GSOR website describes the GSOR germplasm collection; provides information on how to donate to the collection and how to request from the collection. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Web Page.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/southeast-area/stuttgart-ar/dale-bumpers-national-rice-research-center/docs/genetic-stocks-oryza-gsor-collection-home/">https://www.ars.usda.gov/southeast-area/stuttgart-ar/dale-bumpers-national-rice-research-center/docs/genetic-stocks-oryza-gsor-collection-home/</a> </p></li></ul><p></p>

Tags: ars, breeding, data-gov, genetic-stocks, germplasm, mapping-populations, mutants, rice, rice-production
Organization: Department of Agriculture
The Wheat and Barley Scab Initiative

<p>The goal of the U.S. Wheat and Barley Scab Initiative (USWBSI) is to develop effective control measures that minimize the threat of Fusarium head blight (scab), including the reduction of mycotoxins, to the producers, processors, and consumers of wheat and barley. Community activities are reported here. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Web Page.</p> <p>File Name: Web Page, url: <a href="https://scabusa.org">https://scabusa.org</a> </p></li></ul><p></p>

Tags: ars, data-gov, genetics-genomics-breeding
Organization: Department of Agriculture
Cooperative Oat Research Enterprise

<p>This is part of the CORE project efforts to further develop tools for oat research through the development of oat SNP panels and Identification of loci affecting key traits in North American germplasm. Project activities are reported here. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Web Page.</p> <p>File Name: Web Page, url: <a href="https://avena.pw.usda.gov/CORE">https://avena.pw.usda.gov/CORE</a> </p></li></ul><p></p>

Tags: ars, data-gov, genetics-genomics-breeding, germplasm, loci, oats, single-nucleotide-polymorphism
Organization: Department of Agriculture
USDA Potato Small RNA Database

<p>This is a public resource highlighting efforts at ARS in developing small RNA genome information for the potato genome. Updates and progress are reported here. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Web Page.</p> <p>File Name: Web Page, url: <a href="https://potato.pw.usda.gov">https://potato.pw.usda.gov</a> </p></li></ul><p></p>

Tags: ars, data-gov, genetics-genomics-breeding, online-database
Organization: Department of Agriculture
Quantification of TAGs by LC-MS

<p>This Microsoft Excel workbook contains spreadsheets for calculating response-factor normalized triacylglycerol (TAG) compositions from response factors derived from GC-FID of fatty acid methyl esters (FAME). This workbook (1.160 Mb) reads the output from a ThermoScientific XCalibur Quan Browser •Excel Short Report• (In XCalibur: File • Export data to Excel • Export Short Excel report), and requires input of the FA composition determined by GC-FID (manually entered or read from Excel spreadsheet [provided upon request]). </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: QuaQuantification of TAGs by LC-MS.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/research/software/download/?softwareid=457&modecode=80-40-05-05">https://www.ars.usda.gov/research/software/download/?softwareid=457&modecode=80-40-05-05</a> </p><p>download page</p></li></ul><p></p>

Tags: computer-software, fatty-acid-methyl-esters, gas-chromatography, models, triacylglycerols
Organization: Department of Agriculture
Palouse Conservation Field Station, Pullman, Washington Weather Observations

<p>OPERATION OF THE PALOUSE, WASHINGTON 9WA240 NAPD/NTN SITE </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Web Page.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/Services/docs.htm?docid=18718">https://www.ars.usda.gov/Services/docs.htm?docid=18718</a> </p></li></ul><p></p>

Tags: ars, data-gov, palouse, pullman, washington, weather
Organization: Department of Agriculture
Cryptocephalinae of the World

<p>The Cryptocephalinae of the World (<a href="http://camptosomata.myspecies.info/">http://camptosomata.myspecies.info/</a>) serves to maintain images, updated classification, and bibliography of cryptocephaline leaf beetles. Currently, focus is largely on <em>Stegnocephala</em>, New World <em>Cryptocephalus</em>, and Fulcidacini; however, with time and continued collaboration we hope to build upon this work. Images are based almost exclusively on type specimens, but authoritatively identified material is also included. The identity of most species herein is finally confirmed after almost 150 years since their original description. This dataset was funded by an Encyclopedia of Life Postdoctoral Fellowship awarded to the author. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Cryptocephalinae of the World.</p> <p>File Name: Web Page, url: <a href="http://camptosomata.myspecies.info/">http://camptosomata.myspecies.info/</a> </p><p>Link to the web site for Cryptocephalinae of the World.</p></li></ul><p></p>

Tags: ars, beetles, chrysomelidae, coleoptera, cryptocephalinae, cryptocephalus, data-gov, fulcidacini, leaf-beetles, stegnocephala, systematics, taxonomy
Organization: Department of Agriculture
Transformative Research for Large Genome Physical Maps

<p>The main goal of the project is to construct and utilize high-resolution genome-wide RH-based physical maps of the wheat D-genome chromosomes to facilitate the construction of sequence-ready physical maps. This research provides an unprecedented view into the evolution of cereal genomes. Importantly, the methodology is being developed to be applied to other large and complex genomes such as polyploid wheat. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Web Page.</p> <p>File Name: Web Page, url: <a href="https://wheat.pw.usda.gov/RHmapping/">https://wheat.pw.usda.gov/RHmapping/</a> </p></li></ul><p></p>

Tags: ars, data-gov, genetics-genomics-breeding
Organization: Department of Agriculture
Imperfect SSR Finder

<p>The Imperfect SSR Finder is an online tool to help geneticists find Simple Sequence Repeats (SSR), aka microsatellites or Short Tandem Repeats (STR), in uploaded FASTA sequences.</p>
<p>The Imperfect SSR Finder is an interactive website to help you find imperfect (and perfect) SSRs. You can test small snippets or upload large files, change the lengths and types of the SSRs your are looking for, and create output with SSRs in inverted case and/or color highlights. A tabular information file is also created in .CSV format, for easy import into any spreadsheet program. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Imperfect SSR Finder.</p> <p>File Name: Web Page, url: <a href="https://ssr.nwisrl.ars.usda.gov/">https://ssr.nwisrl.ars.usda.gov/</a> </p></li></ul><p></p>

Tags: biological-sciences, computer-software, microsatellite-repeats, nucleotides
Organization: Department of Agriculture
A Baseflow Filter for Hydrologic Models in R

<p>A Baseflow Filter for Hydrologic Models in R </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: A Baseflow Filter for Hydrologic Models in R.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/research/software/download/?softwareid=383&modecode=20-72-05-00">https://www.ars.usda.gov/research/software/download/?softwareid=383&modecode=20-72-05-00</a> </p><p>download page</p></li></ul><p></p>

Tags: base-flow, computer-software, hydrologic-models, models
Organization: Department of Agriculture
USDA Public Citrus Genome Database

<p>This is a public resource highlighting efforts at ARS in developing genome information for the Citrus Carrizo Genome. Updates and progress are reported here. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Web Page.</p> <p>File Name: Web Page, url: <a href="https://citrus.pw.usda.gov">https://citrus.pw.usda.gov</a> </p></li></ul><p></p>

Tags: ars, data-gov, genetics-genomics-breeding, online-database
Organization: Department of Agriculture
Brachypodium Resources

<p>The Brachypodium Resource site focuses on research efforts located at the ARS GGD research site toward developing the plant Brachypodium distachyon as a model system to study plant genes for cereals species. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Web Page.</p> <p>File Name: Web Page, url: <a href="https://brachypodium.pw.usda.gov/">https://brachypodium.pw.usda.gov/</a> </p></li></ul><p></p>

Tags: ars, data-gov, genetics-genomics-breeding
Organization: Department of Agriculture
GEOPACK

<p>Geopack is a comprehensive, user-friendly software package containing several computer programs for carrying out geostatistical analyses of spatially correlated data. The programs were written so that they can be used by scientists, engineers or regulators with little experience in geostatistical techniques and still satisfy the requirements of more advanced users. Using the programs, and spending a little time becoming familiar with geostatistics, the end-user should be able to include the geostatistical techniques in their work and research environment. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: GEOPACK download page.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/research/software/download/?softwareid=95&modecode=20-36-15-00">https://www.ars.usda.gov/research/software/download/?softwareid=95&modecode=20-36-15-00</a> </p></li></ul><p></p>

Tags: computer-software, geostatistics, models, natural-resources-earth-and-environmental-sciences
Organization: Department of Agriculture
USDA ARS Image Gallery

<p>This Image Gallery is provided as a complimentary source of high-quality digital photographs available from the Agricultural Research Service information staff. Photos, (over 2,000 .jpegs) in the Image Gallery are copyright-free, public domain images unless otherwise indicated.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: USDA ARS Image Gallery (Web page) .</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/oc/images/image-gallery/" target="_blank">https://www.ars.usda.gov/oc/images/image-gallery/</a> </p><p></p><p>Over 2000  copyright-free images from ARS staff.</p>
<p></p></li></ul>

Tags: ars, data-gov, digital-image, image-gallery, jpeg, np-990, photographs
Organization: Department of Agriculture
Agrilus planipennis community manual annotations

<p dir="ltr">Manual annotation at the i5k Workspace@NAL (<a href="https://i5k.nal.usda.gov/" target="_blank">https://i5k.nal.usda.gov</a>) is the review and improvement of gene models derived from computational gene prediction. Community curators compare an existing gene model to evidence such as RNA-Seq or protein alignments from the same or closely related species and modify the structure or function of the gene accordingly, typically following the i5k Workspace@NAL manual annotation guidelines (<a href="https://i5k.nal.usda.gov/content/rules-web-apollo-annotation-i5k-pilot-project" target="_blank">https://i5k.nal.usda.gov/content/rules-web-apollo-annotation-i5k-pilot-project</a>). If a gene model is missing, the annotator can also use this evidence to create a new gene model. Because manual annotation, by definition, improves or creates gene models where computational methods have failed, it can be a powerful tool to improve computational gene sets, which often serve as foundational datasets to facilitate research on a species.</p><p dir="ltr">Here, community curators used manual annotation at the i5k Workspace@NAL to improve computational gene predictions from the dataset <i>Agrilus planipennis</i> genome annotations v0.5.3. The i5k Workspace@NAL set up the Apollo v1 manual annotation software and multiple evidence tracks to facilitate manual annotation. From 2014-10-20 to 2018-07-12, five community curators updated 263 genes, including developmental genes; cytochrome P450s; cathepsin peptidases; cuticle proteins; glycoside hydrolases; and polysaccharide lyases. For this dataset, we used the program LiftOff v1.6.3 to map the manual annotations to the genome assembly GCF_000699045.2. We computed overlaps with annotations from the RefSeq database using gff3_merge from the GFF3toolkit software v2.1.0. FASTA sequences were generated using gff3_to_fasta from the same toolkit. These improvements should facilitate continued research on <i>Agrilus planipennis</i>, or emerald ash borer (EAB), which is an invasive insect pest.</p><p dir="ltr">While these manual annotations will not be integrated with other computational gene sets, they are available to view at the i5k Workspace@NAL (https://i5k.nal.usda.gov) to enhance future research on <i>Agrilus planipennis.</i></p>

Tags: agrilus-planipennis, coleoptera, emerald-ash-borer, genome-annotation, manual-annotation
Organization: Department of Agriculture
Pesticide Data Program

The USDA Pesticide Data Program (PDP) database provides national data on pesticide residues in food and water, with an emphasis on foods consumed by infants and children. PDP data are used primarily by EPA to prepare realistic pesticide dietary exposures for pesticide registration activities. Data for each calendar-year survey are stored in a separate dataset.

Tags: baby, chemical, child, children, diet, exposure, food, infant, residue, water
Organization: Department of Agriculture
ConvertCufflinksToExcel

<p>This program converts several Cufflinks output files into easily readable Microsoft Excel tables using Apache's POI library. Only the "cuffdiff" output format currently is supported, but future versions may include other output formats.</p>
<p>The source code and executable directory structure must be downloaded at the GitHub repository using the "Download ZIP" button on the right-hand side of the page: <a href="https://github.com/njdbickhart/ConvertCufflinksToExcel">https://github.com/njdbickhart/ConvertCufflinksToExcel</a>.</p>
<p>Installation and usage information can be found at <a href="https://github.com/njdbickhart/ConvertCufflinksToExcel/blob/master/README.md">https://github.com/njdbickhart/ConvertCufflinksToExcel/blob/master/README.md</a>. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: ConvertCufflinksToExcel.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/research/software/download/?softwareid=493&modecode=80-42-05-30">https://www.ars.usda.gov/research/software/download/?softwareid=493&modecode=80-42-05-30</a> </p><p>download page</p></li></ul><p></p>

Tags: ars, computer-software, data-gov, enzymes, genes, memory
Organization: Department of Agriculture
Mid-Century Modern Architecture Inventory

Mid-century modern architecture and buildings of the recent past are enjoying a resurgence of appreciation and interest nationwide, but here in Philadelphia, our eclectic collection of postwar buildings is often overlooked. To help identify and celebrate these emerging landmarks, the Preservation Alliance is compiling a list of notable structures built within the city between 1945 and 1980. The inclusion of a building in this inventory does not imply endorsement of it for designation or other purposes, nor does its absence imply a lack of significance. Rather, the list is meant to illustrate the breadth and depth of design from an era often overshadowed by earlier periods and styles.

Tags: architects, architecture, arts, buildings, culture, historic-preservation, history, land-records, real-estate
Organization: City of Philadelphia
Inventory of Historic Religious Properties

Founded as William Penn's "Holy Experiment," Philadelphia has a centuries-long history of fostering and constructing prominent houses of worship throughout the city. In recent decades, as congregations face declining membership and shifting neighborhood demographics, these historically- and architecturally-significant properties have often suffered from deferred maintenance, insensitive alterations, and partial or complete demolition.

Advocacy organizations like the Preservation Alliance for Greater Philadelphia and Partners for Sacred Places have focused on this issue for years, highlighting the threats to Philadelphia's neighborhoods and communities if these structures continue to be abandoned or lost. Over the summer of 2011, in order to more fully understand and address the issue, the Preservation Alliance partnered with Philadelphia Historical Commission and Partners for Sacred Places to develop a comprehensive index of historic churches covering the entire city. Compiling, verifying, and updating data from a number of different sources, University of Pennsylvania graduate student Molly Lester assembled a database which includes every purpose-built house of worship constructed in the city before 1960.

Data elements include:  current congregation, original congregation, address, year of construction, original architect and whether or not the build is on the Philadelphia or National Historic Registers.


Tags: architects, architecture, arts, churches, culture, historic-preservation, history, land-records, national-historic-register, real-estate
Organization: City of Philadelphia
Inventory of African American Historic Sites

An inventory compiled by the Preservation Alliance for Greater Philadelphia containing all the known African American historic sites in Philadelphia. Data fields for each site include Site Name, Address, Neighborhood, Significance, Site Type, Date Built, and Architect.   This inventory of 400+ structures includes churches, schools, businesses, homes, clubs, benevolent associations, and more.

Tags: african-american, architects, architecture, arts, churches, clubs, culture, historic-preservation, history, land-records, real-estate, schools
Organization: City of Philadelphia
Free Wi-Fi Locations

These dataset, dashboard and app tools identify what city-owned sites have free public Wi-Fi available. Between 2025 and 2026, all of    these sites are slated to receive fiber install and Meraki Wi-Fi routers that greatly increase the speed and quality of available Wi-Fi. The dataset and dashboard notes what sites have had this install completed, among other amenities available at each site.

Tags: department-of-health-and-human-services, digital-divide, digital-equity, health, human-services, wi-fi
Organization: City of Philadelphia
Childcare Map

Childcare Map helps Philadelphians make decisions about childcare.

Collection Process: TRF culled childcare data for the City of Philadelphia from various sources, and incorporated data from the Census related to demographics, income, poverty, and transportation. TRF also gathered overlays of various city boundaries from OpenDataPhilly and other local sources. More information on sources is available at http://www.policymap.com/files/ChildcareMapDataDirectory.pdf.

Data Purpose:  TRF collected the data to provide as clear a picture as possible of the supply of and demand for childcare in the city, and to better understand where the gaps are so that stakeholders can work to address them.
Intended Audience:  Childcare providers, investors, policy makers, and parents.
Why Collected:  High-quality childcare supports positive child development and prepares children for success in school and beyond.  As such, accessing high-quality care is important for the well-being of neighborhoods and families.  By identifying areas where shortages of high-quality childcare exist, policymakers and investors can work towards increasing access for all.

Tags: child-care, health, human-services
Organization: City of Philadelphia
Predicting lake chlorophyll from stream phosphorus concentrations (2024): Data and Scripts

Monitoring data from Minnesota and from national surveys of lakes and streams that were used in the analysis for the paper: Predicting lake chlorophyll from stream phosphorus concentrations. 

mod.mn.R.txt: R script for fitting TP-Chl model using Minnesota data
mod.nat.R.txt: R script for fitting TP-Chl model using national data
dat.nat.1.csv: National stream TP data
dat.nat.2.csv: National lake Chl data
dat.mn.1.csv: Minnesota lake Chl data
dat.mn.2.csv: Minnesota stream TP data. Citation information for this dataset can be found in Data.gov's References section.

Tags: chlorophyll, total-phosphorus
Organization: U.S. Environmental Protection Agency
San Juan Watershed Lead Isotope Data

The U.S. Environmental Protection Agency characterized sediments and seeps/springs in the San Juan watershed located in southwestern Colorado and the four corners region of Colorado, New Mexico, Arizona, and Utah (western United States). The Datasets contain field and laboratory data that resulted from that sampling. Samples for this project were collected from 2018 to 2021. Results of new Pb isotope ratio measurements are provided for sediments (n = 96) collected from across the watershed and seeps/springs (n = 73) from the mineralized headwaters region of the watershed. The Microsoft Excel spreadsheets contain sample data and Quality Control data, including results of primary standards, second source standards, and sample duplicate analyses.

Tags: animas-river, lead, lead-isotopes, san-juan-watershed, source-attribution
Organization: U.S. Environmental Protection Agency
EnviroAtlas - 2015 EPA Discharge Monitoring Report Watershed Statistics by 12-digit HUC for the Conterminous United States

This EnviroAtlas dataset includes a number of Discharge Monitoring Report (DMR) metrics summarized by watershed for a given year (https://echo.epa.gov/help/loading-tool/watershed-statistics-help). These metrics include the number of facilities and wastewater discharges located within watersheds according to the Integrated Compliance Information System National Pollutant Discharge Elimination System (ICIS-NPDES), to track the permit compliance and enforcement status of facilities regulated by the NPDES under the Clean Water Act (https://echo.epa.gov/tools/data-downloads/icis-npdes-download-summary). This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

Tags: 12-digit hucs, alabama, arizona, arkansas, california, colorado, connecticut, delaware, ecosystem, ecosystem services, enviroatlas, environment, environmental atlas, florida, georgia, idaho, illinois, impact, indiana, iowa, kansas, kentucky, louisiana, maine, maryland, massachusetts, michigan, minnesota, mississippi, missouri, montana, nebraska, nevada, new hampshire, new jersey, new mexico, new york, north carolina, north dakota, ohio, oklahoma, oregon, pennsylvania, quality, regulatory, rhode island, south carolina, south dakota, surface water, tennessee, texas, united states, utah, vermont, virginia, washington, washington dc, west virginia, wisconsin, wyoming
Organization: U.S. Environmental Protection Agency