AndreaBozzo/ceres-open-data-index huggingface dataset:
Genome Sequence Data Set01

The fasta files (Genome_Set01.zip) contain the reference-assisted de novo assemblies (as contigs) of three Escherichia coli  isolates. The table contains rows as isolates (yellow) and columns as attributes (green) for each individual genome. 

This dataset is associated with the following publication:
Gomez-Alvarez, V., and J. Hoelle-Schwalbach. Draft Genome Sequences of Antibiotic-Resistant Escherichia coli Isolates from U.S. Wastewater Treatment Plants.   Microbiology Resource Announcements. American Society for Microbiology, Washington, DC, USA, 8(23): e00351-19, (2019).

Tags: assembly, carbapenem-resistant-e-coli, carbapenemase-and-extended-spectrum-beta-lactamase-genes, draft-genome, isolates, phylotyping, wastewater-treatment
Organization: U.S. Environmental Protection Agency
Data tables, and data used in figures presented in the manuscript "High-Throughput Screening and Chemotype-Enrichment Analysis of ToxCast Phase II Chemicals Evaluated for Human Sodium-Iodide Symporter (NIS) Inhibition"

All tables, plus the data for generating figures presented in the manuscript "High-Throughput Screening and Chemotype-Enrichment Analysis of ToxCast Phase II Chemicals Evaluated for Human Sodium-Iodide Symporter (NIS) Inhibition". 

This dataset is associated with the following publication:
Wang, J., D. Hallinger, A. Murr, A. Buckalew, R. Lougee, A. Richard, S. Laws, and T. Stoker. High-Throughput Screening and Chemotype-Enrichment Analysis of ToxCast Phase II Chemicals Evaluated for Human Sodium-Iodide Symporter (NIS) Inhibition.   ENVIRONMENT INTERNATIONAL. Elsevier B.V., Amsterdam,  NETHERLANDS,  377-386, (2019).

Tags: chemotype, endocrine-disruptor, high-throughput-in-vitro-screening-assay, sodium-iodide-symporter, thyroid, toxprint
Organization: U.S. Environmental Protection Agency
Scientific Reports - O'Shaughnessy et al. A transient window of hypothyroidism alters neural progenitor cells and results in abnormal brain development

This dataset includes information on rat dam and pup bodyweights, thyroid hormone concentrations in serum, gene expression in brain, cell counts for cell proliferation in brain. 

This dataset is associated with the following publication:
OShaughnessy, K., S. Thomas, S. Spring, J. Ford, R. Ford, and M. Gilbert. A transient window of hypothyroidism alters neural progenitor cells and results in abnormal brain development.   Scientific Reports. Nature Publishing Group, London,  UK,  1-14, (2019).

Tags: childrens-health, developmental-hypothyroidism, thyroid-hormone-insufficiency
Organization: U.S. Environmental Protection Agency
Data resides with a Swiss Federal Institute

NA. 

This dataset is associated with the following publication:
Volk, M., S. Bassin, M. Lehmann, M.G. Johnson, and C.P. Andersen. 13C isotopic signature and C concentration of soil density fractions illustrate reduced C allocation to subalpine grassland soil under high atmospheric N deposition.   SOIL BIOLOGY AND BIOCHEMISTRY. Elsevier Science Ltd, New York, NY, USA, 125: 178-184, (2018).

Tags: c-sequestration, co2, density-fractions, nitrogen-deposition, seasonal-dynamics, soil-respiration, stable-c-isotopes
Organization: U.S. Environmental Protection Agency
Integrating data gap filling techniques: A case study predicting TEFs for neurotoxicity TEQs to facilitate the hazard assessment of polychlorinated biphenyls

The experimental data were taken from Simon et al., who compiled potency data for effects related to neurotoxicity from four experimental datasets, Stenberg et al. [18] and Wigestrand et al. The measures of potency were EC50 (µM) or IC50 values for all the effects except Stenberg data, which were expressed as a percentage of the control uptake for different concentrations measured. 

This dataset is associated with the following publication:
Pradeep, P., L. Carlson, R. Judson, G. Lehmann, and G. Patlewicz. Integrating data gap filling techniques: A case study predicting TEFs for neurotoxicity TEQs to facilitate the hazard assessment of polychlorinated biphenyls.   REGULATORY TOXICOLOGY AND PHARMACOLOGY. Elsevier Science Ltd, New York, NY, USA, 101: 12-23, (2019).

Tags: dsstox, neurotoxic-equivalent-factor-nef, neurotoxicity, pcb-congeners, qsar, toxic-equivalency-factors-tefs
Organization: U.S. Environmental Protection Agency
Use of Threshold of Toxicological Concern (TTC) with High Throughput Exposure Predictions (HTE) as a Risk-Based Screening Approach to Prioritize More Than Seven Thousand Chemicals

The dataset that was evaluated in this approach was taken from Wambaugh et al [29] who filtered the Tox21 library to reflect substances with similar uses to those in NHANES.

The zip file contains the supplementary information being provided for the re-analysis performed in this dataset. 
There was no specific code as such developed for the analysis aside from using KNIME to help combine different outputs from different tools including Leadscope in order to arrive at the counts reflected in Table 2 of the manuscript. 
Instead of this very laborious approach, we re-did the analysis using Toxtree alone and streamlined the processing of the outcomes with R. This is documented in the supplementary information file. 

List of files:

SMARTS Toxtree schemes use to identify carbamates, OPs and steroids
Carbamates.tml
OPs.tml
Steroids.tml

R code used to manipulate the various outputs derived from processing the associated sdf through the Kroes, specific Toxtree schemes and Cramer scheme within Toxtree
TTC_HTTK.R

R data file
HTTK_TTC_070218.RData

sdf file used in the analysis
HTTK_7K_mod_kekule.sdf. 

This dataset is associated with the following publication:
Patlewicz, G., J. Wambaugh, S. Felter, T. Simon, and R. Becker. Utilizing Threshold of Toxicological Concern (TTC) with High Throughput Exposure Predictions (HTE) as a Risk-Based Prioritization Approach for thousands of chemicals.   Computational Toxicology. Elsevier B.V., Amsterdam,  NETHERLANDS, 7: 58-67, (2018).

Tags: dsstox, high-throughput-exposure-hte, risk-based-prioritization, threshold-of-toxicological-concern-ttc
Organization: U.S. Environmental Protection Agency
ApplyingEnvironmentalReleaseInventories_Data

Physicochemical and environmental data on compounds found in thermochemical and biochemical routes for producing biofuels. 

This dataset is associated with the following publication:
Smith, R., E. Tan, and G. RuizMercado. Applying Environmental Release Inventories and Indicators to the Evaluation of Chemical Manufacturing Processes in Early Stage Development.   ACS Sustainable Chemistry & Engineering. American Chemical Society, Washington, DC, USA, 7(12): 10937-10950, (2019).

Tags: biofuels, greenscope, indicators, life-cycle-assessment, life-cycle-inventory, releases, sustainability
Organization: U.S. Environmental Protection Agency
Full-Scale qPCR FSI in the Tillamook Bay Watershed_April 2019

Fecal source identification qPCR, land use, and weather data used in the manuscript entitled, "Large-Scale Implementation of Standardized Quantitative Real-Time PCR Fecal Source Identification Procedures in the Tillamook Bay Watershed". 

This dataset is associated with the following publication:
Li, X., M. Sivaganesan, C. Kelty, A. Zimmer-Faust, P. Clinton, J. Reichman, Y. Johnson, W. Matthews, S. Bailey, and O. Shanks. Large-scale implementation of standardized quantitative real-time PCR fecal source identification procedures in the Tillamook Bay Watershed.   PLoS ONE. Public Library of Science, San Francisco, CA, USA, 14(6): e0216827, (2019).

Tags: fecal-pollution, microbial-source-tracking, qpcr
Organization: U.S. Environmental Protection Agency
SPECIATE Emission Source Profile Ranking Results

Shows the points assigned to each prominent emission source profile for each NOAA climate region and then ranks the profile by the highest regional average. Analysis based on emission mass and reactivty assigned by the 2014 emissions modeling platform (https://www.epa.gov/air-emissions-modeling/emissions-modeling-tools; https://www.epa.gov/air-emissions-modeling/2014-2016-version-7-air-emissions-modeling-platforms). 

This dataset is associated with the following publication:
Bray, C., M. Strum, H. Simon, L. Riddick, M. Kosusko, M. Menetrez, M. Hays, and V. Rao. An assessment of important SPECIATE profiles in the EPA emissions modeling platform and current data gaps.   ATMOSPHERIC ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 207: 93-104, (2019).

Tags: emissions, pm-2-5, speciate, voc
Organization: U.S. Environmental Protection Agency
In Vitro Ozone Responsiveness Data

Data collected during the comparison of ozone responsiveness in primary bronchial epithelial cells from a range of distinct donors. 

This dataset is associated with the following publication:
Bowers, E., S. McCullough, D. Morgan, L. Dailey, and D. Diaz-Sanchez. ERK1/2 and p38 regulate inter-individual variability in ozone-mediated IL-8 gene expression in primary human bronchial epithelial cells.   Scientific Reports. Nature Publishing Group, London,  UK, 8(1): 9398, (2018).

Tags: air-pollution, epigenetics, inflammation, inter-indivudal-variability, signaling-pathways
Organization: U.S. Environmental Protection Agency
Metadata for biofilm samples and their DNA concentrations

The excel spreadsheet includes sample IDs and labeling information for DNA sequencing raw data. In addition, DNA concentrations for all the biofilm samples analyzed are presented. 

This dataset is associated with the following publication:
Li, L., Y. Jeon, S. Lee, H. Ryu, J. Santodomingo, and Y. Seo. Dynamics of the Physiochemical and Community Structures of Biofilms under the Influence of Algal Organic Matter and Humic Substances.   WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 158: 136-145, (2019).

Tags: algal-organic-matter, biofilm-development, drinking-water, humic-substance, physical-and-community-structure
Organization: U.S. Environmental Protection Agency
Inactivation rates of enteroviruses by UVC-LEDs

There are three types of dataset.
1. Main results (file name is 'UV-LED_Enteroviruses'): this file contains raw data and figures used for the manuscript.
2. Statistical analyses (three files. file names begin with Enteroviruses-): these files contain the results of statistical analyses used for this study.
3. UV-dose calculation (three files. file names begin with numbers such as 260 280, 260 and 280): these files include the entire calculation procedures for estimating UV doses. 

This dataset is associated with the following publication:
Woo, H., S. Beck, L. Boczek, K. Carlson, N. Brinkman, K. Linden, O. Lawal, S. Hayes, and H. Ryu. Efficacy of Inactivation of Human Enteroviruses by Dual-Wavelength germicidal ultraviolet (UV-C) light emitting diodes (LEDs).   WATER. MDPI AG, Basel,  SWITZERLAND, 11(6): 1131, (2019).

Tags: dual-wavelength, human-enteroviruses, synergy, ultraviolet-disinfection, uv-c-leds, viral-inactivation-efficacy
Organization: U.S. Environmental Protection Agency
Metadata for FIA P3 data on lichen

This data describe the abundance of individual lichen species across the U.S. as recorded in the Forest Health and Monitoring dataset of the Forest Inventory and Analysis program (i.e. Phase 3 plots). This dataset is not publicly accessible because: These data are already housed on the USFS Forest Inventory and Analysis site (see below). It can be accessed through the following means: The lichen data for this product are from the USDA Forest Services (USFS) Forest Inventory and Analysis (FIA) Phase 3 (P3) dataset - Forest Health and Monitoring. The metadata and database description for the FIA-P3 is here (https://www.fia.fs.fed.us/library/database-documentation/). The data itself is located at the USFS Data Mart here (https://apps.fs.usda.gov/fia/datamart/CSV/datamart_csv.html) in two files: “LICHEN_PLOT_SUMMARY.zip,” and “LICHEN_VISIT.zip.”

Point of contact: Linda Geiser, lgeiser@fs.fed.us. Format: The data are in .csv format.

Tags: annual-naaqs, atmospheric-deposition, biodiversity, critical-loads, lichen, nitrogen-deposition, sulfur-deposition
Organization: U.S. Environmental Protection Agency
Sustainable Chemistry Expert Framework Source Code

Link to Github repository containing the source code that can be used to build the Sustainable Chemistry Expert Framework tool. 

This dataset is associated with the following publication:
Barrett, W., S. Takkellapati, K. Tadele, T. Martin, and M. Gonzalez. Linking Molecular Structure via Functional Group to Chemical Literature for Establishing a Reaction Lineage for Application to Alternatives Assessment.   ACS Sustainable Chemistry & Engineering. American Chemical Society, Washington, DC, USA, 7(8): 7630-7641, (2019).

Tags: cheminformatics, functional-group, life-cycle-inventory, sustainable-chemistry
Organization: U.S. Environmental Protection Agency
Data Set

The data set contains information on the relative abundance of Cu species present for each geographical location and sampling location within the mesocosm. 

This dataset is associated with the following publication:
Shah, V., T.P. Luxton, V.K. Walker, T. Brumfield, J. Yost, S. Shah, J.E. Wilkinson, and M. Kambhampati. Fate and Impact of Zero-Valent Copper Nanoparticles on Geographically-Distinct Soils.  D.Barcelo Culleres, and Jay Gan  SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 573: 661-670, (2016).

Tags: copper-nanoparticles, environmental-impact, nanomaterials, speciation, transport
Organization: U.S. Environmental Protection Agency
statistical models of fecal coliform levels

fecal coliform data from the Oregon Dept. of Agriculture from 01/2006-12/2015 collected in Tillamook Bay, OR. This dataset is not publicly accessible because: This data is Oregon Dept. of Agriculture data and not EPA-generated data. It can be accessed through the following means: independent variables used in the model are available on public websites - summarized in table 1 of the paper and associated text. Format: This is Oregon Department of Agriculture data. It is not available to provide a link or file. 

This dataset is associated with the following publication:
Zimmer-Faust, A., C. Brown, and A. Manderson. Statistical models of fecal coliform levels in Pacific Northwest estuaries for improved shellfish harvest area closure decision making.   MARINE POLLUTION BULLETIN. Elsevier Science Ltd, New York, NY, USA, 137: 360-369, (2018).

Tags: eutrophication, macroalgae, nutrient-pollution-index, nutrients, seagrass, temperature, wasting-disease, zostera-japonica, zostera-marina
Organization: U.S. Environmental Protection Agency
LaneCharles_A-g1kf_Dataset_05092018

Data used in assessing the location and accuracy of the vegetative analysis. 

This dataset is associated with the following publication:
Berhane, T., H. Costa, C. Lane, O. Anenkhonov, V. Chepinoga, and B. Autrey. The Influence of Region of Interest Heterogeneity on Classification Accuracy in Wetland Systems.   Remote Sensing. MDPI AG, Basel,  SWITZERLAND, 11(5): 551, (2019).

Tags: methodology, remote-sensing
Organization: U.S. Environmental Protection Agency
Corteselli et al. JoVE Science Hub Data

Data corresponding to the figures in this article. 

This dataset is associated with the following publication:
Corteselli, E., J. Samet, and E. Gibbs-Flournoy. IMAGING APPROACHES TO ASSESSMENTS OF TOXICOLOGICAL OXIDATIVE STRESS USING GENETICALLY ENCODED FLUOROGENIC SENSORS.   Journal of Visualized Experiments. JoVE, Somerville, MA, USA, 132: 56945, (2018).

Tags: confocal-microscopy, live-cell-imaging, lung-cells, methods, oxidant-stress
Organization: U.S. Environmental Protection Agency
Associations between environmental quality and adult asthma prevalence in medical claims data

The MarketScan health claims database is a compilation of nearly 110 million patient records with information from more than 100 private insurance carriers and large self-insuring companies. Public forms
of insurance (i.e., Medicare and Medicaid) are not included, nor are small (< 100 employees) or medium (< 1000 employees) self-insuring companies. For this cross-sectional study, approved claims for the years
2003–2013, which includes 17.5–45.2 million persons annually, are linked across years and geocoded at the county level. The dataset includes both inpatient and outpatient claims, medical procedures and
prescription medications. In addition to diagnostic and pharmacy claims, records include patient's age (in years), county of residence, and sex. This dataset defines the population in which we are estimating
associations, specifically, U.S. adults aged 18–65 with private health insurance, primarily from large employers (those with>1000 employees). We excluded the relatively few (n=6735) individuals over
65 years of age because Medicare is the primary insurance of U.S. adults over 65.

The EQI was constructed for 2000-2005 for all US counties and is composed of five domains (air, water, built, land, and sociodemographic), each composed of variables to represent the environmental quality of that domain. Domain-specific EQIs were developed using principal components analysis (PCA) to reduce these variables within each domain while the overall EQI was constructed from a second PCA from these individual domains (L. C. Messer et al., 2014). To account for differences in environment across rural and urban counties, the overall and domain-specific EQIs were stratified by rural urban continuum codes (RUCCs) (U.S. Department of Agriculture, 2015). This dataset is not publicly accessible because: EPA cannot release personally identifiable information regarding living individuals, according to the Privacy Act and the Freedom of Information Act (FOIA). This dataset contains information about human research subjects. Because there is potential to identify individual participants and disclose personal information, either alone or in combination with other datasets, individual level data are not appropriate to post for public access. Restricted access may be granted to authorized persons by contacting the party listed. It can be accessed through the following means: Human health data are not available publicly. EQI data are available at: https://edg.epa.gov/data/Public/ORD/NHEERL/EQI. Format: Data are stored as csv files. 

This dataset is associated with the following publication:
Gray, C., D. Lobdell, K. Rappazzo, Y. Jian, J. Jagai, L. Messer, A. Patel, S. Deflorio-Barker, C. Lyttle, J. Solway, and A. Rzhetsky. Associations between environmental quality and adult asthma prevalence in medical claims data.   ENVIRONMENTAL RESEARCH. Elsevier B.V., Amsterdam,  NETHERLANDS, 166: 529-536, (2018).

Tags: air-quality, built-environment, environmental-quality, land-quality, sociodemographic-quality, water-quality
Organization: U.S. Environmental Protection Agency
Associations between environmental quality and infant mortality in the United States, 2000-2005

Infant mortality was defined as death before completion of first year of life [1]. We obtained linked birth and infant death data from the U.S. Centers for Disease Control and Prevention for the years 2000–2005, corresponding to the time frame covered by the EQI.

The EQI was constructed for 2000-2005 for all US counties and is composed of five domains (air, water, built, land, and sociodemographic), each composed of variables to represent the environmental quality of that domain. Domain-specific EQIs were developed using principal components analysis (PCA) to reduce these variables within each domain while the overall EQI was constructed from a second PCA from these individual domains (L. C. Messer et al., 2014). To account for differences in environment across rural and urban counties, the overall and domain-specific EQIs were stratified by rural urban continuum codes (RUCCs) (U.S. Department of Agriculture, 2015). This dataset is not publicly accessible because: EPA cannot release personally identifiable information regarding living individuals, according to the Privacy Act and the Freedom of Information Act (FOIA). This dataset contains information about human research subjects. Because there is potential to identify individual participants and disclose personal information, either alone or in combination with other datasets, individual level data are not appropriate to post for public access. Restricted access may be granted to authorized persons by contacting the party listed. It can be accessed through the following means: Human health data are not available publicly. EQI data are available at: https://edg.epa.gov/data/Public/ORD/NHEERL/EQI. Format: Data are stored as csv files. 

This dataset is associated with the following publication:
Patel, A., J. Jagai, L. Messer, C. Gray, K. Rappazzo, S. DeflorioBarker, and D. Lobdell. Associations between environmental quality and infant mortality in the United States, 2000-2005.   Archives of Public Health. BioMed Central Ltd, London,  UK, 76(60): 1, (2018).

Tags: air-quality, built-environment, environmental-quality, land-quality, sociodemographic-quality, water-quality
Organization: U.S. Environmental Protection Agency
Shepherd Creek Data for LRFD application demonstration

This data is stream flow and nutrient data (dissolved inorganic nitrogen and total phosphorus) for 6 sites in the Shepherd Creek watershed, Cincinnati, OH. The data could be useful to others with interest in studying nutrient loading in small streams draining suburban hillslopes. 

This dataset is associated with the following publication:
Riasi, S., A. Teklitz, W. Shuster, C. Nietch, and L. Yeghiazarian. Reliability-Based Water Quality Assessment with Load Resistance Factor Design: Application to TMDL.   Journal of Hydrologic Engineering. American Society of Civil Engineers  (ASCE), Reston, VA, USA, 23(12): 1943-5584, (2018).

Tags: load-resistance-factor-design, margin-of-safety, tmdl, water-quality-assessment, watershed
Organization: U.S. Environmental Protection Agency
HTTK R Package v1.0

httk: High-Throughput Toxicokinetics

Functions and data tables for simulation and statistical analysis of chemical toxicokinetics ("TK") using data obtained from relatively high throughput, in vitro studies. Both physiologically-based ("PBTK") and empirical (e.g., one compartment) "TK" models can be parameterized for several hundred chemicals and multiple species. These models are solved efficiently, often using compiled (C-based) code. A Monte Carlo sampler is included for simulating biological variability and measurement limitations. Functions are also provided for exporting "PBTK" models to "SBML" and "JARNAC" for use with other simulation software. These functions and data provide a set of tools for in vitro-in vivo extrapolation ("IVIVE") of high throughput screening data (e.g., ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK"). 

This dataset is associated with the following publication:
Pearce , R., C. Strope , W. Setzer , N. Sipes , and J. Wambaugh. (Journal of Statistical Software) HTTK: R Package for High-Throughput Toxicokinetics.   Journal of Statistical Software. American Statistical Association, Alexandria, VA, USA, 79(4): 1-26, (2017).

Tags: expocast, exposure, pbpk, pbpk-reverse-dosimetry, physiologically-based-pharmacokinetic-model, r-package, toxcast, toxicokinetics
Organization: U.S. Environmental Protection Agency
Data used in manuscript

The data was used to construct figures used in the manuscript. 

This dataset is associated with the following publication:
Chen, A., L. Wang, D. Lytle, and T. Sorg. Arsenic/Iron Removal from Groundwater with Elevated Ammonia and Natural Organic Matter.   JOURNAL OF THE AMERICAN WATER WORKS ASSOCIATION. American Water Works Association, Denver, CO, USA, 110(3): E2-E17, (2018).

Tags: ammonia, arsenic, ground-water, iron-removal, natural-organic-matter
Organization: U.S. Environmental Protection Agency