cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.23719/1503738
title: Grulke_EPA’s DSSTox Chemical Structure Database

description: The US Environmental Protection Agency’s (EPA) Distributed Structure-Searchable Toxicity (DSSTox) database, launched publicly in 2004, currently exceeds 875 K substances spanning hundreds of lists of interest to EPA and environmental researchers. From its inception, DSSTox has focused curation eﬀorts on resolving chemical identiﬁer errors and conﬂicts in the public domain towards the goal of assigning accurate chemical structures to data and lists of importance to the environmental research and regulatory community. In 2014, the legacy, manually curated DSSTox_V1 content was migrated to a MySQL data model, with modern cheminformatics tools supporting both manual and automated curation processes to increase eﬃciencies. Currently, DSSTox serves as the core foundation of EPA’s CompTox Chemicals Dashboard [https://comptox.epa.gov/dashboard], which provides public access to DSSTox content in support of a broad range of modeling and research activities within EPA and, increasingly, across the ﬁeld of computational toxicology.
DOI: 10.23719/1503699
title: TZurlinden_pluripotent human (H9) embryonic stem cell 

description: The data presented here support the application of the Stemina devTOXqP platform for predictive toxicology and further demonstrate its value in ToxCast as a novel resource that can generate testable hypotheses aimed at characterizing potential pathways for teratogenicity and HTS prioritization of environmental chemicals for an exposure-based assessment of developmental hazard.

The dataset from the Stemina (STM) assay is annotated in the ToxCast portfolio as STM. Major findings from the analysis of ToxCast_STM dataset include (1) 19% of 1065 chemicals yielded a prediction of developmental toxicity, (2) assay performance reached 79%-82% accuracy with high specificity (> 84%) but modest sensitivity (< 67%) when compared with in vivo animal models of human prenatal developmental toxicity, (3) sensitivity improved as more stringent weights of evidence requirements were applied to the animal studies, and (4) statistical analysis of the most potent chemical hits on specific biochemical targets in ToxCast revealed positive and negative associations with the STM response, providing insights into the mechanistic underpinnings of the targeted endpoint and its biological domain. The results of this study will be useful to improving our ability to predict in vivo developmental toxicants based on in vitro data and in silico models.
DOI: 10.23719/1503823
title: KPF_Examining the Utility of In Vitro Bioactivity as a Protective Point of Departure: A Case Study_APCRA

description: The files and .R scripts here are provided to aid in understanding and reproduction of the analyses in the submitted paper, "Examining the Utility of In Vitro Bioactivity as a Protective Point of Departure: A Case Study."
The scripts in the .R folder reference source files in the other folders.
DOI: 10.23719/1520439
title: sensitivity analysis result

description: A regular adjoint model simulation result.
DOI: 10.23719/1504437
title: Transitioning the generalised read-across approach (GenRA) to quantitative predictions: A case study using acute oral toxicity data

description: This repository contains code, input and output files associated with the GenRA acute toxicity case study that was published by Helman et al (2019) in Computational Toxicology.
DOI: 10.23719/1518547
title: Community Water System and Contributing Area Characteristics

description: Operational, financial, and land use data to estimate drinking water treatment cost functions for 2006 calendar year.  Data are organized for surface water and groundwater systems.
DOI: 10.23719/1520520
title: Sister Study / EnviroAtlas Community Sample

description: Sister Study is a prospective cohort of 50,884 U.S. women aged 35 to 74 years old conducted by the NIEHS. Eligible participants are women without a history of breast cancer but with at least one sister diagnosed with breast cancer at enrollment during 2003 - 2009. Datasets used in this research effort include health outcomes, lifestyle factors, socioeconomic factors, medication history, and built and natural environment factors.
DOI: 10.23719/1504229
title: National Water Quality Data

description: Water quality data.
DOI: 10.23719/1519176
title: Results from Non-Targeted Analysis of Aqueous Film Forming Foams 

description: Screening library of detectable PFAS ions, results from identified PFAS from suspect screening of AFFF materials on the market.
DOI: 10.23719/1518922
title: Microbial Source Tracking Marker Concentrations in the Chattahoochee River National Recreation Area Watershed in 2015-2017, Georgia, USA

description: The dataset contains Esherichia coli and quantitative polymerase chain reaction data for microbial source tracking markers in the Chattahoochee River and streams within the Chattahoochee River National Recreation area from samples collected in the winter and summer of the federal fiscal years 2016 and 2017. Six water samples were collected from three sites on the Chattahoochee River each season. Eleven stream sites and one additional site on the Chattahoochee River were sampled once each season, with the exception of two sites, which were not sampled in winter FY16
DOI: 10.23719/1520144
title: Grab vs Composite metadata

description: Data described concentrations of human adenovirus, crAssphage and Pepper Mild Mottle virus in 1 hour composite wastewater samples and 24 h composite wastewater samples.
DOI: 10.2909/6b995798-e1bf-4f01-ac97-185cf52ec8dc
title: National Emission reductions Commitments (NEC) Directive emission inventory data, 1990-2021

description: Data on emissions of air pollutants (ammonia (NH3), non-methane volatile organic compounds (NMVOC), nitrogen oxides (NOx), particulate matter 2.5 (PM2.5) and sulphur dioxide (SO2)) reported annually by Member States to the European Commission (with copies to EEA) under Directive 2016/2284 of the European Parliament and of the Council on the reduction of national emissions of certain atmospheric pollutants.
DOI: 10.23719/1504101
title: Methane and carbon dioxide emission rates from reservoirs in Ohio, Kentucky, and Indiana

description: This dataset contains methane and carbon dioxide emission rates measured in 32 reservoirs distributed across Ohio, Kentucky, and Indiana.  Ancillary environmental data including reservoir morphology, watershed characteristics, and water chemistry are also included.
DOI: 10.23719/1520634
title: Global hunger and climate change adaptation through international trade - data file links

description: All the data used to generate estimates and figures are included on the publication's website, organized by graphic.
DOI: 10.23719/1519347
title: An evaluation of the performance of selected (Q)SARs/expert systems for predicting acute oral toxicity

description: Acute rat oral toxicity lethality data files, processed prediction files from 2 expert systems
DOI: 10.48366/r604602
title: Exploring Large Language Models augmented Knowledge Graph Completion Methods

description: Knowledge Graph Completion (KGC) infers missing facts in a given knowledge graph. Integration of large language models enables Knowledge Graph Completion methods to generate facts or encode the text for improving the performance. This comparison compares different LLM-augmented Knowledge Graph Completion methods.
DOI: 10.23719/1503855
title: Structural alerts for protein binding

description: The JRC dataset (doi: 10.1016/j.tiv.2016.07.014) includes reported outcomes in chemico, in vitro and in vivo tests for skin sensitisation.  The Tox21 dataset was downloaded from the EPA CompTox Chemicals Dashboard (available at: https://comptox.epa.gov/dashboard/chemical_lists/TOX21SL) and was filtered to retain substances that were discrete organics with normalized structures, i.e. only substances that had an associated QSAR-ready SMILES record.
DOI: 10.23719/1518600
title: Algal softening followed by ozonation: the fate of persistent micropollutants and natural organic matter in groundwater

description: 1. Physocochemical parameters: optical density (OD680), pH, hardness, alkalinity, DOC, AOC, UV254, SUVA, excitation-emission-matrix (EEM) fluorescence spectra, CBZ and DCF during the algal treatment 

2. Microscopy: Energy-dispersive X-ray (EDX) spectra and field emission scanning electron microscopy (FE-SEM) images of bio-solids
DOI: 10.23719/1504178
title: Nelms_Evaluating potential refinements to existing Thresholds of Toxicological Concern (TTC) values for environmentally-relevant compounds

description: 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.
DOI: 10.23719/1504532
title: Database of pharmacokinetic time-series data and parameters for 144 environmental chemicals 

description: 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.
DOI: 10.23719/1503835
title: K_Saili_Molecular characterization of a toxicological tipping point during human stem cell differentiation

description: We differentiated human induced pluripotent stem cells (hiPSCs) to embryonic endoderm and sought to identify a tipping point at which the developing system did not recover from perturbations caused by exposure to a known teratogen, all-trans retinoic acid (ATRA). Differentiating iPSC-derived endoderm was exposed to five concentrations of ATRA between 0.001 and 10 µM at 6h, 96h, or 192h and assessed for forkhead box A2 (FOXA2) protein expression and global gene transcript expression measured by RNA-sequencing. A tipping point of 17±11 nM was identified where patterns of differentially expressed genes supported a shift in the developmental trajectory away from embryonic endoderm in favor of mesoderm and extraembryonic endoderm.
Five concentrations of all-trans retinoic acid (ATRA) between 0.001 and 10 µM were compared to time-matched 0.1% DMSO controls at three timepoints (6h, 96h, and 192h) in differentiating endoderm. Two biological replicates were used. Undifferentiated controls (not in DMSO) were also included in duplicate as internal controls for 6h, 96h, and 144h.
DOI: 10.23719/1518717
title: Waterborne Disease Outbreak Data Set

description: CDC data on waterborne disease outbreak response
DOI: 10.23719/1518670
title: Variability and Sampling of Lead (Pb) in Drinking Water: Assessing Exposure Risk Depends on the Sampling Protocol

description: This is a literature review paper that did not generate any new data.
DOI: 10.23719/1519317
title: Fluorine measurements for target PFAS and PFAS mixtures

description: Fluorine measurements for target PFAS and PFAS mixtures, fluorine mass balance calculations, non-targeted compound abundances
DOI: 10.23719/1517657
title: Literature data for Assessing Human Exposure to Chemicals in Materials, Products and Articles

description: It is literature data.
DOI: 10.23719/1518776
title: The role of HONO in O3 formation and insight into its formation mechanism during the KORUS-AQ campaign

description: Data collected for this research provides information on mixing layer heights and in-situ formaldehyde concentrations at Olympic Park during the KORUS-AQ field campaign.
DOI: 10.23719/1520621
title: Datasets for manuscript "A data engineering approach for chemical flow analysis and circular economy"

description: As described in the README.md file, the GitHub repository EoL4Chem are Python scripts written to track chemical waste flows and identify recycling, energy recovery, treatment & disposal facilities (RETDFs) located across the United States of America, using publicly-available databases. EoL4Chem uses the U.S. Environmental Protection Agency (EPA)'s Chemical Data Reporting (CDR) to gather information about potential post-recycling scenarios for recycled chemicals (e.g., fuel or fuel agent). EoL4Chem integrates the PAU4Chem repository, which transforms data for performing chemical flow analysis for pollution abatement units (PAUs) or on-site end-of-life (EoL) operations (e.g., distillation). Also, EoL4Chem incorporates the physical properties (e.g., boiling point) from another repository that retrieves the properties using web scraping and automatization. These properties support chemical flow analysis performance.
Also, it describes the Python libraries required for running the code, how to use it, the obtained outputs files after running the Python script (all manuscript figures, e.g., file name Sankey_1.pdf	is the Sankey diagram shown in Figure 4A), and the corresponding Disclaimer.
DOI: 10.23719/1519319
title: Bioavailability, Bioaccessibility and speciation data.

description: Bioavailability, Bioaccessibility and speciation data.
DOI: 10.23719/1504126
title: NRSA Data 2008,2009, 2013, 2014

description: Rivers and Streams data for the National Aquatic Resource Surveys
DOI: 10.23719/1518420
title: Datasets for manuscript: Valuing Economic Impact Reductions of Nutrient Pollution from Livestock Waste

description: https://github.com/zavalab/JuliaBox/tree/master/HiddenImpacts 
This folder provides supporting codes for the paper "Valuing Economic Impact Reductions of Nutrient Pollution from Livestock Waste".
* The folder "sensitivity_analysis" contains the code and data files for different values of the economic impact/value of service (vos).
* The folder "GIS_data" contains the code and data files used to generate the maps of the Upper Yahara watershed region presented in the paper. 
* In each case, we have three Julia scripts: "market_model.jl", "market_Run.jl", and "market_print.jl". One should run "market_Run.jl" first, this script will automatically read the "market_model.jl" script, establish the model, and solve the model. Then, the "market_print.jl" should be run in order to print out all the result files.
* If a sensitivity analysis on the VOS needs to be conducted (similar to the paper), one can change the lambda value in line 26 in "market_model.jl".
* We recommend use Julia 0.6.4 and Gurobi 8.1 to run all code files for sensitivity analysis.
DOI: 10.23719/1518725
title: High-throughput Toxicogenomic Screening of Chemicals in the Environment Using Metabolically Competent, Human-derived Hepatic Cell Cultures 

description: Gene expression data from the Fluidigm qRT-PCR arrays was analyzed in R (v3.6.1; R Foundation for Statistical Computing, 2019). Prior to processing through the tcpl package, each qRT-PCR primer set was annotated as an individual assay endpoint (aeid) for analyses. For each plate, well types were designated for test compound wells (t), positive controls (c), (that is phenobarbital) and neutral controls (n, DMSO). Fold-change in the number of amplification cycles needed to pass the background threshold (Ct) for 96 transcripts to (ftp://newftp.epa.gov/COMPTOX/CCTE_Publication_Data/CCED_Publication_Data/Wambaugh/ToxCast_LTEA, file LTEA_Level2_20191119.zip) were normalized to the geometric mean of three housekeeping genes (ACTB, GAPDH, POLR2A) to generate ΔCt values (cval). Prior to calculating the response values (rval), or ΔΔCt, for each transcript (n = 96) per well, the baseline value (bval), the plate-wise median of the neutral control wells, was generated for each plate (the normalization process is described in detail in supplemental file SupFile4-DeltaCTCalculation.docx). The bval was subtracted from the cval to yield the rval or log2 Fold Change per transcript. 

Gene expression data from the Fluidigm qRT-PCR arrays was analyzed in R (v3.6.1; R Foundation for Statistical Computing, 2019). Prior to processing through the tcpl package, each qRT-PCR primer set was annotated as an individual assay endpoint (aeid) for analyses. For each plate, well types were designated for test compound wells (t), positive controls (c), (that is phenobarbital) and neutral controls (n, DMSO). Fold-change in the number of amplification cycles needed to pass the background threshold (Ct) for 96 transcripts to (ftp://newftp.epa.gov/COMPTOX/CCTE_Publication_Data/CCED_Publication_Data/Wambaugh/ToxCast_LTEA, file LTEA_Level5_20191119.zip) were normalized to the geometric mean of three housekeeping genes (ACTB, GAPDH, POLR2A) to generate ΔCt values (cval). Prior to calculating the response values (rval), or ΔΔCt, for each transcript (n = 96) per well, the baseline value (bval), the plate-wise median of the neutral control wells, was generated for each plate (the normalization process is described in detail in supplemental file SupFile4-DeltaCTCalculation.docx). The bval was subtracted from the cval to yield the rval or log2 Fold Change per transcript.

Supplemental File LTEA_Inucyte_Images.zip is comprised of 20,493 images totaling more than 15 gigabytes. Cell morphology images were acquired for each well/plate with an Essen IncuCyte™ FLR automated phase-contrast microscope located inside a tissue culture incubator. Six 96-well culture plates were loaded into the instrument and imaged for an elapsed time (~24 minutes). The IncuCyte™ software was used for image capturing and export of images in JPEG format.
DOI: 10.23719/1518475
title: Associations between cumulative environmental quality and ten selected birth defects in Texas

description: The Texas Birth Defects Registry (TBDR) of the Texas Department of State Health Services (TDSHS) is an active surveillance system that maintains information on infants with structural and chromosomal birth defects born to mothers residing in Texas at the time of birth (Texas Department of State Health Services, 2019). TBDR staff review medical records to identify and abstract relevant case information, which then undergoes extensive quality checks (Texas Department of State Health Services, 2019). All diagnoses are made prenatally or within one year after delivery (Texas Department of State Health Services, 2019). Data on cases was obtained from the TBDR. Information on live births for the denominators and on covariates for cases and denominators was obtained from the Texas Department of State Health Services Center for Health Statistics. This research was approved by the Texas Department of State Health Services Institutional Review Board and US EPA Human Subjects Review.

The Environmental Quality Index (EQI) estimates overall county-level environmental quality for the entire US for 2006-2010. The construction of the EQI is described elsewhere (United States Environmental Protection Agency, 2020). Briefly, the national data was compiled to represent simultaneous, cumulative environmental quality across each of the five domains: air (43 variables) representing criteria and hazardous air pollutants; water (51 variables), representing overall water quality, general water contamination, recreational water quality, drinking water quality, atmospheric deposition, drought, and chemical contamination; land (18 variables), representing agriculture, pesticides, contaminants, facilities, and radon; built (15 variables), representing roads, highway/road safety, public transit behavior, business environment, and subsidized housing environment; and sociodemographic (12 variables), representing socioeconomics and crime. The variables in each domain specific index were reduced using principal component analysis (PCA), with the first component retained as that domain’s index value. The domain specific indices were valence corrected to ensure that the directionality of the variables was consistent with higher values suggesting poorer environmental quality. The domain specific indices were then processed through a second PCA and the first index retained as the overall EQI. The overall and domain specific EQI indices are publicly available through the US EPA (United States Environmental Protection Agency: https://edg.epa.gov/data/Public/ORD/NHEERL/EQI).
DOI: 10.25345/c5pn8xr5r
title: MassIVE MSV000092656 - GNPS dataset five salvia species massive
title: This project is for five Salvia species for metabolomics studies
DOI: 10.23719/1520792
title: Clean Air Status and Trends Network (CASTNET) Hourly Ozone Concentrations

description: 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.
DOI: 10.23719/1518903
title: The Alginate Immobilization of Metabolic Enzymes (AIME) Platform Retrofits an Estrogen Receptor Transactivation Assay with Metabolic Competence

description: 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.
DOI: 10.23719/1520873
title: Web-based Tool of The Non-potable Environmental and Economic Water Reuse Calculator (NEWR) 

description: The methods and resource of the dataset
DOI: 10.23719/1519418
title: NOAA Data

description: Data owner is Sachidananda Mishra (sachi.mishra@noaa.gov) and Richard Stumpf at NOAA