AndreaBozzo/ceres-open-data-index huggingface dataset:
PRISM Scaled Dataset

Data for 2015 US Census Tracts includes multi-hazard exposure estimates for 12 natural hazards. There are also estimates of loss, vulnerability, and risk for land area, population, and property within each tract. 

This dataset is associated with the following publication:
Buck, K., and K. Summers. Application of a multi-hazard risk assessment for local planning.   Geomatics, Natural Hazards and Risk. Taylor & Francis Group, London,  UK, 11(1): 2058-2078, (2020).

Tags: exposure, index, local, loss, multi-hazard, policy, risk
Organization: U.S. Environmental Protection Agency
DataSet_Bathroom_Community

1. 16S rRNA sequences, generated using Illumina sequencer, and 2. water parameters, included temperature and chlorine residual concentrations. 

This dataset is associated with the following publication:
Zhang, C., K. Qin, I. Struewing, H.Y. Buse, J. SantoDomingo, D. Lytle, and J. Lu. The Bacterial Community Diversity of Bathroom Hot Tap Water Was Significantly Lower Than That of Cold Tap and Shower Water.   Frontiers in Microbiology. Frontiers, Lausanne,  SWITZERLAND, 12: 625324, (2021).

Tags: bacterial-community-structure, cold-tap-water, hot-tap-water, premise-plumbing-systems, shower-water
Organization: U.S. Environmental Protection Agency
Dataset for the analysis of the cost-effectiveness of Nutrient Management on Nitrate-N

Midwest and nitrate-N loss data for nutrient management. 

This dataset is associated with the following publication:
Liu, W., Y. Yuan, and L. Koropeckyj-Cox. Effectiveness of Nutrient Management on Water Quality Improvement: A Synthesis on Nitrate-Nitrogen Loss from Subsurface Drainage.   Transactions of the ASABE. AMERICAN SOCIETY OF AGRICULTURAL AND BIOLOGICAL ENGINEERS, ST. JOSEPH, MI, USA, 64(2): 675-689, (2021).

Tags: conservation-practice, corn-yields, cost-effectiveness, nitrate-n-loss, nutrient-management, subsurface-drainage
Organization: U.S. Environmental Protection Agency
Considerations when using nutrient inventories to prioritize water quality restoration/improvement efforts across the US

The corresponding database integrates multiple streams of information to provide estimates of fluxes and surpluses across urban and agricultural domains as well as highlight areas where N and P are being managed inefficiently. This database gives decision makers a succinct platform to identify likely areas of water quality degradation. With this quantitative information to prioritize watersheds for restoration, decision makers can then engage with stakeholders to develop meaningful and effectual watershed restoration strategies. 

This dataset is associated with the following publication:
Sabo, R., C. Clark, and J. Compton. Considerations when using nutrient inventories to prioritize water quality improvement efforts across the US.   Environmental Research Communications. IOP Publishing, PHILADELPHIA, PA, USA, 3: 045005, (2021).

Tags: inventory, nitrogen, total-phosphorus, water-quality, watershed
Organization: U.S. Environmental Protection Agency
Vapor uptake inhalation data for chloroform in F344 rats

This dataset describes disappearance of chloroform from a vapor uptake chamber with time due to metabolism. The research concentrates on optimization for estimation of metabolic constants using a novel technique. 

This dataset is associated with the following publication:
Evans, M., C. Eklund, D. williams, Y. Sey, and J. Simmons. Global Optimization of the Michaelis-Menten parameters using physiologically-based pharmacokinetic (PBPK) modeling and chloroform vapor uptake data in F344 rats.   INHALATION TOXICOLOGY. Taylor & Francis, Inc., Philadelphia, PA, USA, 32(3): 97-109, (2020).

Tags: chloroform, pbpk-model, vapor-uptake-inhalation
Organization: U.S. Environmental Protection Agency
Bioaccumulation of bis-(2-ethylhexyl)-3,4,5,6-tetrabromophthalate and mono-(2-ethylhexyl)-3,4,5,6-tetrabromophthalate by Lumbriculus variegatus

- Concentration of TBPH and TBMEHP in sediment
- Weigh and lipid contents of Lumbriculus variegatus over time
- Concentrations in Lumbriculus variegatus of TBPH and TBMEPH, and L. variegatus lipid contents
- Chemical Concentrations in Method Blanks. 

This dataset is associated with the following publication:
Burkhard, L., T. Lahren, T. Highland, R. Hockett, D. Mount, and T. Norberg-King. Bioaccumulation of bis-(2-ethylhexyl)-3,4,5,6-tetrabromophthalate and mono-(2-ethylhexyl)-3,4,5,6-tetrabromophthalate by Lumbriculus variegatus.   ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY. Springer, New York, NY, USA, 80: 579–586, (2021).

Tags: bioaccumulation, bioavailability, chemical-uptake, fish-dietary-studies, sediment, sediment-testing
Organization: U.S. Environmental Protection Agency
PFLA extracellular enzyme activity

USDA Data. This dataset is not publicly accessible because: USDA hasn't published a link yet - will modify ScienceHub when link is available. It can be accessed through the following means: USDA owns data will have a link eventually. Format: Excel files. 

This dataset is associated with the following publication:
Trippe, K.M., V.A. Manning, C.L. Reardon, A.M. Klein, C. Weidman, T.F.  Ducey, J.M. Novak, D.W. Watts, H.  Rushmiller, K.A. Spokas, J.A. Ippolito, and M.G. Johnson. Phytostabilization of acidic mine tailings with biochar, biosolids, lime, and locally-sourced microbial inoculum: Do amendment mixtures influence plant growth, tailing chemistry, and microbial composition?.   Applied Soil Ecology. Elsevier Science Ltd, New York, NY, USA, 165: 103962, (2021).

Tags: biochar, plants, remediation, soil
Organization: U.S. Environmental Protection Agency
Assessing Toxicokinetic Uncertainty and Variability in Risk Prioritization

The supplemental information for this paper includes chemical-specific analytical methods, raw instrument data for chemical concentration analysis, processed data for experiments on intrinsic hepatic clearance (CLint -- metabolism) and chemical fraction unbound in the presence of human plasma protein (fup). Figures showing the curve fits for determining CLint are provided. Finally, all data were released publicly as HTTK R Package v1.10.1. 

This dataset is associated with the following publication:
Wambaugh, J., B. Wetmore, C. Ring, C. Nicolas, R. Pearce, G. Honda, R. Dinallo, D. Angus, J. Gilbert, T. Sierra, A. Badrinarayanan, B. Snodgrass, A. Brockman, C. Strock, R. Setzer, and R. Thomas. Assessing Toxicokinetic Uncertainty and Variability in Risk Prioritization.   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,  172(2): 235-251, (2019).

Tags: expocast, exposure
Organization: U.S. Environmental Protection Agency
MagnusonMatthew_A-rxx4_dataset_20180604

The dataset contains the raw data for the graphs in the paper. 

This dataset is associated with the following publication:
Phillips, R., R. James, and M. Magnuson. Functional categories of microbial toxicity resulting from three advanced oxidation process treatments during management and disposal of contaminated water.   CHEMOSPHERE. Elsevier Science Ltd, New York, NY, USA, 238: 124550, (2020).

Tags: advanced-oxidation, treatment, wastewater, water-security
Organization: U.S. Environmental Protection Agency
Independent roles of beta-adrenergic and glucocorticoid receptors in systemic and pulmonary effects of ozone

A manuscript describing the independent roles of beta adrenergic and glucocorticoid receptors in mediating ozone-induced pulmonary and systemic effects. 

This dataset is associated with the following publication:
Henriquez, A., S. Snow, M.C. Schladweiler, C. Miller, and U. Kodavanti. Independent roles of beta-adrenergic and glucocorticoid receptors in systemic and pulmonary effects of ozone.   INHALATION TOXICOLOGY. Taylor & Francis, Inc., Philadelphia, PA, USA, 32(4): 155-169, (2020).

Tags: adrenergic-receptors, glucocorticoid-receptor, glucocorticoid-receptors, lung-injury, lung-injury-and-inflammation, metabolic-response, ozone, stress-response, systemic-metabolic-effects
Organization: U.S. Environmental Protection Agency
Predictive Models for In Vitro Toxicokinetic Parameters to Inform High-throughput Risk-assessment_Prachi

The data used in this analysis was obtained from published literature and available through the high-throughput toxicokinetic (HTTK) R package. The dataset consists of 1486 chemicals that span a variety of use classes including pharmaceuticals, food-use chemicals, pesticides and industrial chemicals of which 1139 chemicals had experimental human in vitro fraction unbound data and 642 chemicals that had experimental human in vitro intrinsic clearance data. Structures were curated and obtained from the DSSTox database. The distribution of experimental values for fraction unbound and intrinsic clearance is shown in Supplementary Figure S1. Since the data were non-normally distributed they were appropriately transformed before any analysis was conducted. The details of the transformation and the transformed data distribution are presented in the results section and Supplementary Figures S2 and S3. A complete list of chemicals with CAS registry numbers (CASRN), DSSTox generic substance IDs (DTXSIDs), structure and experimental data for both parameters are included as supplemental data (1.ChemicalListData.csv and 1.ChemicalList-QSARready.sdf). 

This dataset is associated with the following publication:
Pradeep, P., G. Patlewicz, R. Pearce, J. Wambaugh, B. Wetmore, and R. Judson. Using Chemical Structure Information to Develop Predictive Models for In Vitro Toxicokinetic Parameters to Inform High-throughput Risk-assessment.   Computational Toxicology. Elsevier B.V., Amsterdam,  NETHERLANDS, 16: 100136, (2020).

Tags: actor, in-silico, in-vitro-toxicity-data, ivive, predictive-models, qsar, toxicokinetic-tk-parameters
Organization: U.S. Environmental Protection Agency
NERACOOS Gulf of Maine Ocean Array: Realtime Buoy Observations: F01 Penobscot Bay: F01 AANDERAA Penobscot Bay

Ocean observation data from the Northeastern Regional Association of Coastal &amp; Ocean Observing Systems (NERACOOS). The NERACOOS region includes the northeast United States and Canadian Maritime provinces, as part of the United States Integrated Ocean Observing System (IOOS).  These data are served by Unidata's Thematic Realtime Environmental Distributed Data Services (THREDDS) Data Server (TDS) in a variety of interoperable data services and output formats.

Tags: chlorophyll, conductivity, current_direction data_quality, current_speed data_quality, current_u data_quality, current_v data_quality, density, depth, direction_of_sea_water_velocity, eastward_sea_water_velocity, latitude, longitude, neracoos, northeastern regional association of coastal and ocean observing systems (neracoos), northward_sea_water_velocity, ocean chemistry, ocean circulation, ocean currents, ocean optics, ocean pressure, ocean temperature, ocean waves, ocean winds, oceans, oxygen, salinity, salinity/density, sea level pressure, sea_water_temperature, sea_water_velocity, significant wave height, station_name, surface winds, temperature data_quality, time, turbidity, water temperature, wave period
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Dataset for ORD-029419: Identification of p53 Activators in a Human Microarray Compendium

The dataset contains chemicals that were predicted to activate p53 using the biomarker or using a high throughput assay for p53. 

This dataset is associated with the following publication:
Corton, J., K. Witt, and C. Yauk. Identification of p53 Activators in a Human Microarray Compendium.   CHEMICAL RESEARCH IN TOXICOLOGY. American Chemical Society, Washington, DC, USA, 32(9): 1748-1759, (2019).

Tags: biomarker, dna-damage, genotoxicity, p53
Organization: U.S. Environmental Protection Agency
Integrative computational approaches to inform relative bioaccumulation potential of per- and polyfluoroalkyl substances (PFAS) across species

Datasets included in the entry are Results from the US Environmental Protection Agency Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool and from the molecular modeling workflow that includes molecular docking and molecular dynamic simulations. All data that are represented in the figures, tables, and supplemental materials associated with this manuscript are included in this dataset entry. 

This dataset is associated with the following publication:
Cheng, W., J. Doering, C. LaLone, and C. Ng. Integrative computational approaches to inform relative bioaccumulation potential of per- and polyfluoroalkyl substances (PFAS) across species.   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,  180(2): 212-223, (2021).

Tags: adverse-outcome-pathway, bioaccumulation, cross-species-extrapolation, ecotoxicology, honey-bee, liver-fatty-acid-binding-protein, molecular-modeling, networks, per-and-poly-fluoroalkyl-substances, screening-and-prioritization, seqapass
Organization: U.S. Environmental Protection Agency
Analysis of transcriptomic data from duodena of mice exposed to hexavalent chromium in drinking water: Supplemental data supporting a research report.

These secondary data have been produced from the gene expression data generated from duodena of mice exposed to hexavalent chromium in drinking water and deposited in the GEO repository under accession number GSE87259. They include (i) inferred upstream regulators responsible for the observed changes in gene expression, (ii) genes significantly differentially expressed between duodena of exposed and control mice, and (iii) list of CFTR gene variants associated with cancers in COSMIC tumor repository.

Tags: carcinogenesis, cftr, chromium, cystic-fibrosis
Organization: U.S. Environmental Protection Agency
Phenotypic Profiling of Reference Chemicals across Biologically Diverse Cell Types Using the Cell Painting Assay

Cell Painting is a high-throughput, phenotypic profiling assay that uses fluorescent cytochemistry o visualize a variety of organelles and high-content imaging to derive a large number of morphological features at the single cell level. Here, we used the Cell Painting assay to characterize the phenotypic effects of sixteen phenotypic reference chemicals in concentration- response screening mode across six biologically diverse human-derived cell lines (U-2 OS, MCF7, HepG2, A549, HTB-9, ARPE-19). All cell lines were labeled using the same cytochemistry protocol and the same set of phenotypic features were calculated. We found it necessary to optimize image acquisition settings and cell segmentation parameters for each cell type but did not adjust the cytochemistry protocol. For some reference chemicals, similar subsets of phenotypic features corresponding to a particular organelle were associated with the highest effect magnitudes in each affected cell type. Overall, for certain chemicals the Cell Painting assay yielded qualitatively similar biological activity profiles across a group of diverse, morphologically distinct human-derived cell lines without the requirement for cell-type specific optimization of cytochemistry protocols. 

This dataset is associated with the following publication:
Willis, C., J. Nyffeler, and J. Harrill. Phenotypic Profiling of Reference Chemicals Across Biologically Diverse Cell Types Using the Cell Painting Assay.   SLAS Discovery. SAGE Publications, THOUSAND OAKS, CA, USA, 25(7): 755-769, (2020).

Tags: bioactivity-screening, cell-painting, computational-toxicology, concentration-response, high-content-screening, high-throughput-phenotypic-profiling, image-analysis, microscopy, toxicology
Organization: U.S. Environmental Protection Agency
Bioactivity screening of environmental chemicals using imaging-based high-throughput phenotypic profiling

In the present study, we adapted an existing phenotypic profiling assay (“Cell Painting”, (Bray et al., 2016)) to be compatible with in-house microfluidics capabilities for 384-well culture format, chemical exposures and fluorescent cytochemistry in order to facilitate concentration-response screening of several hundred environmental chemicals. In this assay, human-derived cells were labeled with multiple fluorescent probes to visualize various subcellular organelles and structural features. High content image analysis workflows were used to measure hundreds of morphological features at the level of the individual cell (i.e. shape of the cells, intensity, texture and distribution of fluorescent labels, etc.). The resultant data were then used to calculate well-level summary values, perform high-throughput concentration-response modeling and generate phenotypic response profiles. First, we identified and screened a set of candidate phenotypic reference chemicals for use as plate-based controls for evaluating HTPP assay performance during large-scale screening studies and identified an optimal exposure duration for HTPP screening. Second, we screened a set of 462 environmental chemicals in the U-2 OS cell model and derived in vitro potency estimates for bioactivity of all active chemicals. In addition, we demonstrated the technical reproducibility of the HTPP assay in concentration-response screening mode using the previously identified phenotypic reference chemicals. Next, we used reverse dosimetry to calculate administered equivalent doses (AEDs) corresponding to the thresholds for chemical bioactivity and compared those values to in vivo effect values from mammalian toxicity studies. 

This dataset is associated with the following publication:
Nyffeler, J., C. Willis, R. Lougee, A. Richard, K. Friedman, and J. Harrill. Bioactivity screening of environmental chemicals using imaging-based high-throughput phenotypic profiling.   TOXICOLOGY AND APPLIED PHARMACOLOGY. Academic Press Incorporated, Orlando, FL, USA, 389: 114876, (2020).

Tags: cell-painting, computational-toxicology, concentration-response, high-content-imaging, high-throughput-phenotypic-profiling, toxcast
Organization: U.S. Environmental Protection Agency
Selecting a Minimal set of Androgen Receptor Assays for Screening Chemicals

Screening certain environmental chemicals for their ability to interact with endocrine targets, including the androgen receptor (AR), is an important global concern. We previously developed a model using a battery of eleven in vitro AR assays to predict in vivo AR activity. Here we describe a revised mathematical modelling approach that also incorporates data from newly available assays and demonstrate that subsets of assays can provide close to the same level of predictivity. These subset models are evaluated against the full model using 1820 chemicals, as well as in vitro and in vivo reference chemicals from the literature. 

This dataset is associated with the following publication:
Judson, R., K. Houck, K. Friedman, J. Brown, P. Browne, P. Johnston, D. Close, K. Mansouri, and N. Kleinstreuer. Selecting a Minimal set of Androgen Receptor Assays for Screening Chemicals.   REGULATORY TOXICOLOGY AND PHARMACOLOGY. Elsevier Science Ltd, New York, NY, USA, 117(November 2020): 104764, (2020).

Tags: alternative-testing-methods, androgen-receptor, endocrine-disruption, high-throughput-screening, high-throughput-toxicology, in-vitro, toxcast
Organization: U.S. Environmental Protection Agency
Clean Air Status and Trends Network (CASTNET) Hourly Ozone Concentrations

Ground-level ozone is measured at CASTNET sites following the guidelines in 40 Code of Federal Regulations (CFR) Parts 50 and 58. Continuous measurements are averaged to hourly concentrations. Data are reported to AirNow and EPA's Air Quality System (AQS) database routinely. There are more than 80 CASTNET sites reporting hourly ozone concentrations throughout the United States. Site location information is included with this dataset. The QAPP and associated SOPs can be found on the CASTNET website: www.epa.gov/castnet/documents-reports. Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: air-quality, clean-air-status-and-trends-network-castnet, national-ambient-air-quality-standards, ozone-concentrations
Organization: U.S. Environmental Protection Agency
Database of pharmacokinetic time-series data and parameters for 144 environmental chemicals

This is a new, open, and transparent database of toxicokinetic data supporting EPA decision making. The database has already become the basis of research efforts within EPA to improve HTTK modeling using generic TK models and has facilitated the creation and validation of models for new exposure routes. Publishing the database supports open, transparent science and this database (the largest public database for this domain) will spur improvement and development of TK models by external experts in the field. Future efforts to improving the accessibility of this database (with a graphical user interface) and encouraging crowdsourcing to expand the size and scope of the database will lead to larger validation sets for our modeling efforts and likely lower uncertainties when estimating TK. 

This dataset is associated with the following publication:
Sayre, R., J. Wambaugh, and C. Grulke. Database of pharmacokinetic time-series data and parameters for 144 environmental chemicals.   Scientific Data. Springer Nature Group, New York, NY,  7: 122, (2020).

Tags: databases, environmental-sciences, expocast, exposure, pharmacokinetics, time-series, toxicology
Organization: U.S. Environmental Protection Agency
Nelms_Evaluating potential refinements to existing Thresholds of Toxicological Concern (TTC) values for environmentally-relevant compounds

The Toxic Substances Control Act (TSCA) mandates the US EPA perform risk-based prioritisation of chemicals in commerce and then, for high-priority substances, develop risk evaluations that integrate toxicity data with exposure information. One approach being considered for chemicals with limited chemical-specific toxicity data is a Threshold of Toxicological Concern (TTC)-to-Exposure ratio.  Here, TTC values derived using oral (sub)chronic No Observable (Adverse) Effect Level (NO(A)EL) data from the EPA’s Toxicity Values database (ToxValDB) were compared with published TTC values from Munro et al. (1996). 4554 chemicals with structures present in ToxValDB were assigned into their respective TTC categories using the Toxtree software tool.  Chemicals were assigned into the five TTC classes (Cramer structural class I, II, III, containing alerts for genotoxicity and acetylcholinesterase inhibitors). 114 (2.5%) chemicals were determined to be not appropriate for TTC. The TTC values derived from the ToxValDB were similar, but not identical to the Munro TTC values: Cramer I (37.3 compared to 30 ug/kg-day), Cramer II (34.6 compared to 9 ug/kg-day) and Cramer III (3.9 compared to 1.5 ug/kg-day). The 5th percentile values of Cramer classes I and II for the ToxValDB and Munro datasets were not statistically different whereas the class III 5th percentile values were different. Chemical features of the two class III datasets were evaluated to account for the differences in TTC values. The revised Kroes workflow was then applied to a large set of chemicals (~45,000). TTC values derived from this expanded dataset of toxicity values substantiated the original TTC values derived by Munro et al. (1996), reaffirming the utility of TTC as a promising tool in a risk-based prioritisation approach. 

This dataset is associated with the following publication:
Nelms, M., P. Pradeep, and G. Patlewicz. Evaluating potential refinements to existing Thresholds of Toxicological Concern (TTC) values for environmentally-relevant compounds.   REGULATORY TOXICOLOGY AND PHARMACOLOGY. Elsevier Science Ltd, New York, NY, USA, 109: 104505, (2019).

Tags: cramer-classes, dsstox, high-throughput-exposure-hte, risk-based-prioritisation, threshold-of-toxicological-concern-ttc, toxicity-values-database, toxtree, toxvaldb
Organization: U.S. Environmental Protection Agency