AndreaBozzo/ceres-open-data-index huggingface dataset:
The Residential Population Generator (RPGen): A tool to parameterize residential, demographic, and physiological data to model intraindividual exposure, dose, and risk

This repository contains scripts, input files, and some example output files for the Residential Population Generator, an R-based tool to generate synthetic human residental populations to use in making estimates of near-field chemical exposures. This tool is most readily adapted for using in the workflow for CHEM, the Combined Human Exposure Model, avaialable in two other GitHub repositories in the HumanExposure project, including ProductUseScheduler and source2dose. CHEM is currently best suited to estimating exposure to product use. Outputs from RPGen are translated into ProductUseScheduler, which with subsequent outputs used in source2dose. 

Tags: computational-toxicology, exposure-and-dose-models, new-approach-methodologies, pbpk-models
Organization: U.S. Environmental Protection Agency
PISA 2009 Results: Students On Line Digital Technologies and Performance (Volume VI)

This sixth volume of PISA 2009 results explores students’ use of information technologies to learn. For PISA 2009, the framework for reading literacy has been developed to encompass reading electronic texts. This has led to an expansion of the description of text types to take account of the electronic environment, as well as a redefinition of the aspects of reading, to embrace, for example, the requirement for integration of information from multiple unrelated texts, as well as other features. The PISA 2009 reading framework and the assessment instrument together provide an operational definition and description of the distinctive structures and types of both text and task that constitute electronic reading, allowing an exploration of factors that contribute to difficulty. PISA 2009 therefore provides an opportunity to investigate electronic reading on a large scale. This book presents some initial findings.

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Organization: Department of State
Evaluation of quantitative structure property relationship algorithms for predicting plasma protein binding in humans-UW-QSPR-Supplementary data

Observed fup data obtained from the literature; SMILES structures obtained from Pubchem SDF files. 

This dataset is associated with the following publication:
Yun, Y.E., R. Tornero-Velez, T. Purucker, D. Chang, and A.N. Edginton. Evaluation of Quantitative Structure Property Relationship algorithms for predicting plasma protein binding in humans.   Computational Toxicology. Elsevier B.V., Amsterdam,  NETHERLANDS, 17: 100142, (2021).

Tags: cheminformatics, environmentally-relevant, plasma-protein-binding, pubchem, qspr
Organization: U.S. Environmental Protection Agency
Data contributed by EPA/ORD/CEMM/AESMD to the manuscript "Four decades of United States mobile source pollutants: spatial-temporal trends assessed by ground-based monitors, air quality models, and satellites"

Files containing daily average NO, NO2, CO, and EC concentrations simulated by WRF/CMAQ at 36 km resolution for the time period 1990 – 2010. These data were contributed by EPA/ORD/CEMM/AESMD researchers to the manuscript “Four decades of United States mobile source pollutants: spatial-temporal trends assessed by ground-based monitors, air quality models, and satellites”. Portions of this dataset are inaccessible because: Data files have now been uploaded. They can be accessed through the following means: Data files have now been uploaded. Format: Data files have now been uploaded. 

This dataset is associated with the following publication:
Henneman, L., H. Shen, C. Hogrefe, A. Russell, and C. Zigler. Four Decades of United States Mobile Source Pollutants: Spatial–Temporal Trends Assessed by Ground-Based Monitors, Air Quality Models, and Satellites.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 55(2): 882-892, (2021).

Tags: air-quality-trends, cmaq, remote-sensing, traffic-related-air-pollution
Organization: U.S. Environmental Protection Agency
The Tox21 10K Compound Library: Part 1 - Collaborative chemistry advancing toxicology

Table S1: Tox21 IDs mapped to NCGC IDs, PubChem IDs, and DSSTox IDs, and indicating NCATS, NTP and EPA partner library associations (date stamped February 24, 2020). Table S2: DSSTox TOX21SL list of substance IDs and structure formula, molecular weight, SMILES, InChI, and QSAR-ready SMILES (downloaded January 24, 2020). Table S3: DSSTox TOX21SL DTXSID overlaps with EPA CompTox Dashboard lists (downloaded January 24, 2020). Table S4: Predicted physicochemical properties and toxicities generated from OPERA, T.E.S.T, CORINA, and Derek Nexus models. Table S5: ToxPrint (V2.0_r711) fingerprint file for the TOX21SL chemical list. Table S6: Chemotype enrichment workflow results generated from binarized activity hit calls for ToxCast and Tox21 assay end points (aeids) obtained from EPA’s public ToxCast database, invitroDBv2. Table S7: Tox21 binarized assay hit call matrix for stereo and salt pairs, extracted from EPA’s public ToxCast database, invitroDBv3. 

This dataset is associated with the following publication:
Richard, A., R. Huang, S. Waidyanatha, P. Shinn, B.J. Collins, I. Thillainadarajah, C. Grulke, A. Williams, R. Lougee, R. Judson, K. Houck, M.A. Shobair, C. Yang, J.F. Rathman, A. Yasgar, S.C. Fitzpatrick, A. Simeonov, R. Thomas, K.M. Crofton, R.S. Paules, J.R. Bucher, C.P. Austin, R.J. Kavlock, and R.R. Tice. The Tox21 10K Compound Library: Collaborative Chemistry Advancing Toxicology.   CHEMICAL RESEARCH IN TOXICOLOGY. American Chemical Society, Washington, DC, USA, 34(2): 189-216, (2021).

Tags: 10k-library, chemical-diversity, chemical-safety-research, chemical-space, cheminformatics, chemotype-enrichment, curated-data, high-throughput-screening, models, pharmacokinetics, qhts, qsar, tox21, toxicology
Organization: U.S. Environmental Protection Agency
Improved estimation of trends in U.S. ozone concentrations adjusted for interannual variability in meteorological conditions

Two .Rdata files containing the data used for the statistical modeling and figures in the paper.  
daily_2000_2016.Rdata  = dataset with daily meteorology and ozone data for 2000 through 2016
ozone_sites_2000_2016.Rdata = dataset with information on the ozone monitoring sites (e.g., longitude, latitude). 

This dataset is associated with the following publication:
Wells, B., P. Dolwick, B. Eder, M. Evangelista, K. Foley, E. Mannshardt, C. Misenis, and A. Weshampel. Improved estimation of trends in U.S. ozone concentrations adjusted for interannual variability in meteorological conditions.   ATMOSPHERIC ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 248: 118234, (2021).

Tags: air-quality-modeling, cmaq, model-evaluation
Organization: U.S. Environmental Protection Agency
National Inventory of Phosphorus (v1, 8.30.19)

This is a project assessing the state of major input and outputs of reactive nitrogen (Nr) and phosphorus across the coterminous US at the HUC 8 scale for three snapshots of time (2002, 2007, and 2012). 

Tags: agriculture, fertilizer-p, nonpoint-source-pollution, phosphorus, point-source, stream-water-quality
Organization: U.S. Environmental Protection Agency
Data File 1: Metabolism of cyclic phenones in rainbow trout in vitro assays

Files contain summary reports of chemical and Mass Spectrometry raw and analyzed data  used as basis for plot generation and text discussions in the Cyclic phenone metabolism  manuscript. File dataset includes a Definition Xcel file listing the supporting files in set. Specifically, the dataset  includes individual chemical  slice exposure Xcel data summaries for the model cyclic phenones  DPK, CBP and CPK as well as well as hepatocyte cytosol exposure data to the same chemicals. Each  file contains data organized in labelled tabs that includes General Experimental information, Quantitative and qualitative methods used to process/analyze the raw data for parent and chemical metabolites, chemical mass balances and conclusions. Power point files with the summarized data were presented in the manuscript's Supplemental data. 

This dataset is associated with the following publication:
Serrano, J., M. Tapper, R. Kolanczyk, B. Sheedy, T. Lahren, D. Hammermeister, J. Denny, M. Hornung, A. Kubatova, P. Kosian, J. Voelker, and P. Schmieder. Metabolism of cyclic phenones in rainbow trout in vitro assays.   XENOBIOTICA. Taylor & Francis, Inc., Philadelphia, PA, USA, 50(2): 115-131, (2019).

Tags: cyclic-phenones, endocrine-disruption, estrogen-receptor, fish-liver-slices, gc-ms, in-vitro-assays, lc-ms-ms, lc-tof-ms, metabolism, vtg-gene-expression
Organization: U.S. Environmental Protection Agency
PISA 2009 Results: Learning to Learn Student Engagement, Strategies and Practices (Volume III)

Volume III of PISA 2009 results examines 15-year-olds’ motivation, their engagement with reading and their use of effective learning strategies. The book opens with an introduction to PISA and a reader's guide to help user's understand the findings.  Chapter 1 examines how engaging in reading activities and approaching  learning positively relates to reading proficiency. Chapter 2 examines how much students read for enjoyment, what they read, and how much they enjoy reading. Chapter 3 examines the extent to which reading and learning habits relate to performance differences between boys and girls. The final chapter discusses the policy implications of the findings. Annexes provide detailed statistical data and technical information.

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Organization: Department of State
SaferProducts API

On March 11, 2011, the U.S. Consumer Product Safety Commission launched SaferProducts.gov. This site hosts the agency's new Publicly Available Consumer Product Safety Information Database. On SaferProducts.gov, consumers can submit reports of harm or reports of potential harm. After a short amount of time for review by the agency and named manufacturer, these reports go live on SaferProducts.gov and are searchable by the public. The public also can export search results. The Application Protocol Interface (API), to open the published SaferProducts.gov data to developers and businesses so that the information in SaferProducts.gov can be accessed by an even greater number of consumers online and on mobile devices.

Tags: baby, child, child-safety, children, consumer, cpsc, hazard, hazardous, infant, products, recall, recalls, safety
Organization: US Consumer Product Safety Commission
Brumfield et al 20xx_Data Set

Log10 fecal score ratios for eligible microbial source tracking qPCR assays. 

This dataset is associated with the following publication:
Brumfield, K.D., J.A. Cotruvo, O. Shanks, M. Sivaganesan, J. Hey, N.A. Hasan, A. Huq, R.R. Colwell, and M.B. Leddy. Metagenomic Sequencing and Quantitative Real-Time PCR for Fecal Pollution Assessment in an Urban Watershed.   Frontiers in Water. Frontiers, Lausanne,  SWITZERLAND, 3: 626849, (2021).

Tags: fecal-indicator-bacteria, metagenomics, microbial-source-tracking, qpcr, stormwater
Organization: U.S. Environmental Protection Agency
NOAA Data

Data owner is Sachidananda Mishra (sachi.mishra@noaa.gov) and Richard Stumpf at NOAA. This dataset is not publicly accessible because: Data is property of NOAA. It can be accessed through the following means: Sachidananda Mishra (sachi.mishra@noaa.gov) and Richard Stumpf at NOAA. Format: Data is raster format and table format. 

This dataset is associated with the following publication:
Mishra, S., R. Stumpf, B. Schaeffer, J. Werdell, K. Loftin, and A. Meredith. Evaluation of a satellite-based cyanobacteria bloom detection algorithm using field-measured microcystin data.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 774: 145462, (2021).

Tags: cyanobacteria, harmful-algae, health, satellite, toxin, water-quality
Organization: U.S. Environmental Protection Agency
Data Mining Applied to Life Cycle Inventory Modeling for Cumene and Sodium Hydroxide Manufacturing, Version 1, 09/2018

This file contains the life cycle inventories (LCIs) developed for an associated journal article. Potential users of the data are referred to the journal article for a full description of the modeling methodology. LCIs were developed for cumene and sodium hydroxide manufacturing using data mining with metadata-based data preprocessing. The inventory data were collected from US EPA's 2012 Chemical Data Reporting database, 2011 National Emissions Inventory, 2011 Toxics Release Inventory, 2011 Electronic Greenhouse Gas Reporting Tool, 2011 Discharge Monitoring Report, and the 2011 Biennial Report generated from the RCRAinfo hazardous waste tracking system. 

The U.S. average cumene gate-to-gate inventories are provided without (baseline) and with process allocation applied using metadata-based filtering. In 2011, there were 8 facilities reporting public production volumes of cumene in the U.S., totaling to 2,609,309,687 kilograms of cumene produced that year.

The U.S. average sodium hydroxide gate-to-gate inventories are also provided without (baseline) and with process allocation applied using metadata-based filtering. In 2011, there were 24 facilities reporting public production volumes of sodium hydroxide in the U.S., totaling to 3,878,021,614 kilograms of sodium hydroxide produced that year. Process allocation was only conducted for the top 12 facilities producing sodium hydroxide, which represents 97% of the public production of sodium hydroxide.

The data have not been compiled in the formal Federal Commons LCI Template to avoid users interpreting the template to mean the data have been fully reviewed according to LCA standards and can be directly applied to all types of assessments and decision needs without additional review by industry and potential stakeholders. 

This dataset is associated with the following publication:
Meyer, D.E., S. Cashman, and A. Gaglione. Improving the reliability of chemical manufacturing life cycle inventory constructed using secondary data.   JOURNAL OF INDUSTRIAL ECOLOGY. Berkeley Electronic Press, Berkeley, CA, USA, 25(1): 20-35, (2021).

Tags: chemical-manufacturing, cumene, data-mining, life-cycle-assessment, life-cycle-inventory, metadata-filtering, sodium-hydroxide
Organization: U.S. Environmental Protection Agency
TREE BOX PERFORMANCE IN EXFILTRATING STORMWATER RUNOFF

This study determines the exfiltration rates in six tree boxes and analyzes their performance over time. The study site is in Louisville, KY, where we monitored the performance of six tree boxes and other stormwater control measures (SCMs).  Each tree box is 1.5 m wide, 1.5 m long, and 1.8 m deep.  Street and parking lot runoff enters tree boxes though a curb cut. A 46-cm diameter shaft was drilled at the bottom of each tree box to reach the underlying permeable soil layer.  A pressure transducer installed at the bottom of the shaft measured the water level depth and water temperature. From the water level data, the exfiltration rate of six tree boxes was calculated for 121 rain events.  For each rain event the exfiltration rate was calculated at different water levels inside the shaft. The effects of water level inside the shaft, temperature, and age on the exfiltration rate were analyzed. Exfiltration rate increased with water level and exfiltration rate in first year is significantly larger than second year. Overall in second year the decrease in geometric mean exfiltration rate was largest for moderate depth. The exfiltration rate of the tree boxes is significantly larger for warmer rain events and significantly smaller for cooler rain events. This paper highlights the use of continuous two years’ water level monitoring data to quantify the potential for local recharge via exfiltration, and the effect of different parameter on the exfiltration rate of six tree boxes. 

This dataset is associated with the following publication:
Ahmed, F., and M. Borst. TREE BOX PERFORMANCE IN EXFILTRATING STORMWATER RUNOFF.   WATER ENVIRONMENT RESEARCH. Water Environment Federation, Alexandria, VA, USA, 92(1): 106-114, (2020).

Tags: exfiltration, pressure-transducer, seasonal-effect, stormwater-control-measure
Organization: U.S. Environmental Protection Agency
The Alginate Immobilization of Metabolic Enzymes (AIME) Platform Retrofits an Estrogen Receptor Transactivation Assay with Metabolic Competence

The objective of this study was to develop an approach to retrofit existing HTS assays with hepatic metabolism. The Alginate Immobilization of Metabolic Enzymes (AIME) platform encapsulates hepatic S9 fractions in alginate microspheres attached to 96-well peg lids. Functional characterization across a panel of reference substrates for phase I cytochrome P450 enzymes revealed substrate depletion with expected metabolite accumulation. Performance of the AIME method in the VM7Luc estrogen receptor (ER) transactivation assay was evaluated across 15 reference chemicals and 48 test chemicals that yield metabolites previously identified as ER active or inactive. 

This dataset is associated with the following publication:
Deisenroth, C., D. DeGroot, T. Zurlinden, A. Eicher, J. McCord, M. Lee, P. Carmichael, and R. Thomas. The Alginate Immobilization of Metabolic Enzymes Platform Retrofits an Estrogen Receptor Transactivation Assay with Metabolic Competence.   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,  178(2): 281-301, (2020).

Tags: endocrine-toxicology, estrogen-receptor, high-throughput-screening, xenobiotic-metabolism
Organization: U.S. Environmental Protection Agency
Connecting Channels 2014 - 2015 Water Quality Data - 8/15/2018

These results include water chemistry data collected in the St. Marys River and Huron-Erie Corridor in 2014 - 2016. 

This dataset is associated with the following publication:
Wick, M., T. Angradi, M. Pawlowski, D. Bolgrien, J. Launspach, J. Kiddon, and M. Nord. A synoptic assessment of water quality in two Great Lakes connecting channels.   JOURNAL OF GREAT LAKES RESEARCH. International Association for Great Lakes Research, Ann Arbor, MI, USA, 45(5): 901-911, (2019).

Tags: ecosystem-assessment, huron-erie-corridor, laurentian-great-lakes, st-marys-river, water-quality
Organization: U.S. Environmental Protection Agency
NaHRSI Scored Results

Domains, Indicators and Metrics of NaHRSI and CRSI. 

This dataset is associated with the following publication:
Summers, K., L. Harwell, K. Buck, L. Smith, J. Harvey, D. Vivian, J. Bousquin, M. McLaughlin, and S. Hafner. Development of a Climate Resilience Screening Index (CRSI): An Assessment of Resilience to Acute Meteorological Events and Selected Natural Hazards. U.S. Environmental Protection Agency, Washington, DC, USA, 2017.

Tags: crsi, nahrsi, natural-hazards, recovery, resilience, vulnerability
Organization: U.S. Environmental Protection Agency
Augustine, S. (2018). Data for Boquerón Beach, PR immunoprevalence study [Data set]. U.S. EPA Office of Research and Development (ORD). https://doi.org/10.23719/1390125

Augustine, S. (2018). Data for Boquerón Beach, PR immunoprevalence study [Data set]. U.S. EPA Office of Research and Development (ORD). https://doi.org/10.23719/1390125. 

This dataset is associated with the following publications:
Augustine, S., K. Simmons, T. Eason, C. Curioso, S. Griffin, T. Wade, A. Dufour, S. Fout, A. Grimm, K. Oshima, E. Sams, M. See, and L. Wymer. Immunoprevalence to Six Waterborne Pathogens in Beachgoers at Boquerón Beach, Puerto Rico: Application of a Microsphere-Based Salivary Antibody Multiplex Immunoassay.   Frontiers in Public Health. Frontiers, Lausanne,  SWITZERLAND, 5(84): 1-11, (2017).
Augustine, S., T. Eason, K. Simmons, S. Griffin, C. Curioso, M. Ramudit, E. Sams, K. Oshima, A. Dufour, and T. Wade. Rapid Salivary IgG Antibody Screening for Hepatitis A.   JOURNAL OF CLINICAL MICROBIOLOGY. American Society for Microbiology, Washington, DC, USA, 58(10): e00358-20, (2020).

Tags: asymptomatic-infections, chemokines, coinfections, cytokines, environmental-exposures, immunoconversions, immunoprevalence, multiplex-immunoassay, public-health-surviellance, rapid-antibody-screening-tools, saliva, salivary-antibodies, waterborne-infection, waterborne-pathogens
Organization: U.S. Environmental Protection Agency
Augustine, S. (2019). Data for Boquerón Beach, Puerto Rico immunoconversion study [Data set]. U.S. EPA Office of Research and Development (ORD). https://doi.org/10.23719/1503882

Augustine, S. (2019). Data for Boquerón Beach, Puerto Rico immunoconversion study [Data set]. U.S. EPA Office of Research and Development (ORD). https://doi.org/10.23719/1503882

Augustine, S. (2018). Data for Boquerón Beach, PR immunoprevalence study [Data set]. U.S. EPA Office of Research and Development (ORD). https://doi.org/10.23719/1390125. 

This dataset is associated with the following publication:
Augustine, S., T. Eason, K. Simmons, S. Griffin, C. Curioso, M. Ramudit, E. Sams, K. Oshima, A. Dufour, and T. Wade. Rapid Salivary IgG Antibody Screening for Hepatitis A.   JOURNAL OF CLINICAL MICROBIOLOGY. American Society for Microbiology, Washington, DC, USA, 58(10): e00358-20, (2020).

Tags: asymptomatic-infections, chemokines, coinfections, cytokines, environmental-exposures, immunoconversions, immunoprevalence, multiplex-immunoassay, public-health-surviellance, rapid-antibody-screening-tools, saliva, salivary-antibodies, waterborne-infection, waterborne-pathogens
Organization: U.S. Environmental Protection Agency
PISA 2009 Results: Learning Trends Changes in Student Performance Since 2000 (Volume V)

This volume of PISA 2009 results looks at the progress countries have made in raising student performance and improving equity in the distribution of learning opportunities. Following an Introduction to PISA and a Reader's Guide helping users interpret the data, Chapter 1 summarises overall performance over time.   Chapter 2 looks at trends in reading.  Chapter 3 looks at trends in mathematics and science.  Chapter 4 examines trends in equity. Chapter 5 explores trends in attitudes and student-school relations.  The final chapter analyzes implications for policy. Annexes provide techical background and tables of results.

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Organization: Department of State