AndreaBozzo/ceres-open-data-index huggingface dataset:
Extracting and benchmarking emerging adverse outcome pathway knowledge

A collection of R scripts useful for extracting and analyzing adverse outcome pathway network data from the adverse outcome pathway wiki (aopwiki.org). 

This dataset is associated with the following publication:
Pollesch, N., D. Villeneuve, and J. O'Brien. Extracting and benchmarking emerging adverse outcome pathway knowledge.   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,  168(2): 349-364, (2019).

Tags: adverse-outcome-pathway, adverse-outcome-pathway-network, aquatic-ecosystems, ecotoxicology, emergent-knowledge, endocrine-disruption, screening-and-prioritization
Organization: U.S. Environmental Protection Agency
Assessing bioactivity-exposure profiles of fruit and vegetable extracts in the BioMAP profiling system

The ToxCast program has generated in vitro screening data on over a thousand chemicals to assess potential disruption of important biological processes and assist in hazard identification and chemical testing prioritization. Few results have been reported for complex mixtures. To extend these ToxCast efforts to mixtures, we tested extracts from 30 organically grown fruits and vegetables in concentration-response in the BioMAP® assays. BioMAP systems use human primary cells primed with endogenous pathway activators to identify phenotypic perturbations related to proliferation, inflammation, immunomodulation, and tissue remodeling. 

This dataset is associated with the following publication:
Wetmore, B., R. Clewell, B. Cholewa, B. Parks, S. Pendse, M. Black, K. Mansouri, S. Haider, E. Berg, R. Judson, K. Houck, M. Martin, H. Clewell III, M. Andersen, R. Thomas, and P. McMullen. Assessing Bioactivity-Exposure Profiles of Fruits and Vegetables in the BioMAP Profiling System.   TOXICOLOGY IN VITRO. Elsevier Science Ltd, New York, NY, USA, 54: 41-57, (2019).

Tags: bioactivity, expocast, exposure, high-throughput, natural-products, toxcast
Organization: U.S. Environmental Protection Agency
A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics

The U.S. Tox21 Federal collaboration, which currently quantifies the biological effects of nearly 10,000 chemicals via quantitative high-throughput screening(qHTS) in in vitro model systems, is now making an effort to incorporate gene expression profiling into the existing battery of assays. Whole transcriptome analyses performed on large numbers of samples using microarrays or RNA-Seq is currently cost-prohibitive. Accordingly, the Tox21 Program is pursuing a high-throughput transcriptomics (HTT) method that focuses on the targeted detection of gene expression for a carefully selected subset of the transcriptome that potentially can reduce the cost by a factor of 10-fold, allowing for the analysis of larger numbers of samples. To identify the optimal transcriptome subset, genes were sought that are (1) representative of the highly diverse biological space, (2) capable of serving as a proxy for expression changes in unmeasured genes, and (3) sufficient to provide coverage of well described biological pathways. A hybrid method for gene selection is presented herein that combines data-driven and knowledge-driven concepts into one cohesive method. 

This dataset is associated with the following publication:
Mav, D., R.R. Shah, B.E. Howard, S.S. Auerbach, P.R. Bushel, J.B. Collins, D.L. Gerhold, R. Judson, A.L. Karmaus, E.A. Maull, D.L. Mendrick, B.A. Merrick, N.S. Sipes, D. Svoboda, and R.S. Paules. A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics.   PLoS ONE. Public Library of Science, San Francisco, CA, USA, 13(2): 1-17, (2018).

Tags: expocast, exposure, extrapolation, gene-expression, microarray, predictive-toxicology, toxicology, transcriptome-analysis
Organization: U.S. Environmental Protection Agency
Predictive Structure-Based Toxicology Approaches To Assess the Androgenic Potential of Chemicals

Chemical structures, RMSD values, docking scores, additional tables and figures, and methodological details (PDF)
Additional information concerning the starting data set, EPA-ARDB.csv (CSV)
Additional information concerning V1, V1_SI.csv (CSV)
Additional information concerning V2, V2_SI.csv (CSV)
Additional information concerning V3, V3_SI.csv (CSV). 

This dataset is associated with the following publication:
Trisciuzzi, D., D. Alberga, K. Mansouri, R. Judson, E. Novellino, G.F. Mangiatordi, and O. Nicolotti. Predictive structure-based toxicology approaches to assess the androgenic potential of chemicals.   Journal of Chemical Information and Modeling. American Chemical Society, Washington, DC, USA, 57(11): 2874-2884, (2017).

Tags: androgen-receptor, compara, expocast, exposure, in-silico
Organization: U.S. Environmental Protection Agency
Chronic Toxicity of Major Ion Salts and Their Mixtures to Ceriodaphnia dubia

This effort involved intensive chronic toxicity testing of major ion salts (comprised of Na, K, Ca, Mg, Cl, SO4, HCO3/CO3) with the cladoceran, Ceriodaphnia dubia, a species known to be relatively sensitive to ion enrichment.  This is the fourth in a series of manuscripts discussing the sensitivity of this species to major ions, with a specific focus of determining whether the principles governing acute response of this species to major ions also predict chronic responses.  Results show this to be true, with acute-chronic ratios that are fairly consistent across different major ions, and responses to binary mixtures that show the same types of joint toxicity profiles as was observed previously for acute toxicity of major ions to this species.  Mathematical models describing the response of these organisms were developed to predict the toxicity of major ion mixtures based on either chemical activity or chemical concentrations of ions in the mixture.  These models showed good agreement with independent literature data on the chronic toxicity of major ion salts or ion mixtures to C. dubia.  The datasets associated with this effort provide effect concentrations (EC20 and EC50) for 60 chronic toxicity tests conducted as part of this research, along with literature data extracted for comparison with model predictions.  Data generated in this effort will inform efforts by OW, Regions, States, and Tribes to develop water quality standards/criteria for specific major ions (e.g., Cl, SO4).  Perhaps more importantly, it provides part of the necessary scientific underpinning for developing standards/criteria that are sensitive to the specific composition of different sources of ion enrichment (e.g., produced water, mine drainage, irrigation return, industrial/municipal effluents) and can therefore support development of robust, integrated assessment tools. 

This dataset is associated with the following publication:
Mount, D., R. Erickson, B. Forsman, T. Highland, R. Hockett, D. Hoff, C. Jenson, and T. Norberg-King. Chronic toxicity of major ion salts and their mixtures to Ceriodaphnia dubia.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 38(4): 769-783, (2019).

Tags: freshwater, major-ion-toxicity
Organization: U.S. Environmental Protection Agency
In Silico Prediction of Physicochemical Properties of Environmental Chemicals Using Molecular Fingerprints and Machine Learning

QSAR Model Reporting Formats. Examples of R code: feature selection and regression analysis. Figure S1: Data distribution of logBCF, BP, MP and logVP. Figures S2–S5: Relationship between model complexity and prediction errors as well as the plots of estimated values versus experimental data for logBCF, BP, MP, and logVP, respectively. Figure S6: Plots of leverage versus standardized residuals for logBCF, BP, MP, and logVP models. Table S1: Chemical product classes for training and test sets. Tables S2–S5: Regression statistics for logBCF, BP, MP, and logVP, respectively. Table S6: Applicability domains for logBCF, BP, MP, and logVP. Tables S7–S12: Chemicals with large prediction residuals for the six properties (PDF)

Chemical names, CAS registry number and SMILES as well as experimentally measured and estimated property values of the training and test sets (XLSX). 

This dataset is associated with the following publication:
Zang, Q., K. Mansouri, A. Williams, R. Judson, D. Allen, W.M. Casey, and N.C. Kleinstreuer. (Journal of Chemical Information and Modeling) In Silico Prediction of Physicochemical Properties of Environmental Chemicals Using Molecular Fingerprints and Machine Learning.   Journal of Chemical Information and Modeling. American Chemical Society, Washington, DC, USA, 57(1): 36-49, (2017).

Tags: environmental-chemicals, expocast, exposure, in-silico, machine-learning, physicochemical-properties
Organization: U.S. Environmental Protection Agency
phase 2/3 oil agent ecotox sci hub data files

The data set consists of ecotoxicity values for crude oils and spill response agents. 

This dataset is associated with the following publications:
Conmy, R., M. Barron, D. Sundaravadivelu, R. Groser, R. Venkatapathy, A. Burkes, and E. Holder. SCREENING OF POTENTIAL REFERENCE OILS FOR THE NATIONAL CONTINGENCY PLAN PRODUCT SCHEUDLE. U.S. Environmental Protection Agency, Washington, DC, USA, 2019.
Barron, M., A. Bejarano, R. Conmy, D. Sundaravadivelu, and P. Meyer. Toxicity of oil spill response agents and crude oils to five aquatic test species.   MARINE POLLUTION BULLETIN. Elsevier Science Ltd, New York, NY, USA, 153(110954): 110954, (2020).

Tags: acute-toxicity
Organization: U.S. Environmental Protection Agency
The CompTox Chemistry Dashboard: a community data resource for environmental chemistry

The contents of the chemistry database, presently containing ~ 760,000 substances, are available as public domain data for download. The chemistry content underpinning the Dashboard has been aggregated over the past 15 years by both manual and auto-curation techniques within EPA’s DSSTox project.These data include physicochemical, environmental fate and transport, exposure, usage, in vivo toxicity, and in vitro bioassay data, surfaced through an integration hub with link-outs to additional EPA data and public domain online resources. 

This dataset is associated with the following publication:
Williams, A., C. Grulke, J. Edwards, A. McEachran, K. Mansouri, N. Baker, G. Patlewicz, I. Shah, J. Wambaugh, R. Judson, and A. Richard. (Journal of Cheminformatics) The CompTox Chemistry Dashboard - A Community Data Resource for Environmental Chemistry.   Journal of Cheminformatics. Springer, New York, NY, USA, 9(61): 1-27, (2017).

Tags: computational-toxicology, edsp21, environmental-chemistry, expocast, exposure, non-targeted-analysis, toxcast, toxicity-data, toxrefdb
Organization: U.S. Environmental Protection Agency
Fruit and Vegetable Data

Pyrethroid metabolite concentration data for fruits and vegetables. 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: Contact PI. Format: List of pyrethroids and pyrethroid degradation. 

This dataset is associated with the following publication:
Li, W., M. Morgan, S. Graham, and J. Starr. Measurement of pyrethroids and their environmental degradation products in fresh fruits and vegetables using a modification of the quick easy cheap effective rugged safe (QuEChERS) method.   TALANTA. Elsevier Science Ltd, New York, NY, USA, 151: 42-50, (2016).

Tags: environmental-degradates, lc-ms-ms, mdls-mqls, pyrethroids, quechers-method, solid-phase-extraction
Organization: U.S. Environmental Protection Agency
Li et al 20xx_Data set

Data available in Science Hub includes measurements used to generate Figures 1, 2, S3, and S4.  All other data is reported in the manuscript text. 

This dataset is associated with the following publication:
Li, X., L. Peed, M. Sivaganesan, C. Kelty, C. Nietch, and O. Shanks. Evidence of Genetic Fecal Marker Interactions between Water Column and Periphyton in Artificial Streams.   ACS Omega. American Chemical Society, Washington, DC, USA, 3(8): 10107-10113, (2018).

Tags: fecal-pollution, microbial-source-tracking, periphyton, qpcr
Organization: U.S. Environmental Protection Agency
Method 200.8: Plus 2 paper

Method 200.8: Plus 2 paper. 

This dataset is associated with the following publication:
Smith, S., N. Hanks, P. Creed, K. Kovalcik, R. Wilson, K. Kubachka, J. Brisbin, J. Landero Figueroa, and J. Creed. Analytical considerations associated with implementing M2+ correction factors to address false positives on As and Se within U.S. EPA method 200.8.   JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY. Royal Society of Chemistry, Cambridge,  UK, 34(10): 2094-2104, (2019).

Tags: false-positives, icp-ms, m2, method-200-8, polyatomic, rare-earth-elements
Organization: U.S. Environmental Protection Agency
HTTK: R Package for High-Throughput Toxicokinetics

Functions and data tables for simulation and statistical analysis of chemical toxicokinetics ("TK") as in Pearce et al. (2017) <doi:10.18637/jss.v079.i04>. Chemical-specific in vitro data have been obtained from relatively high throughput experiments. 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. 

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, high-throughput, httk, pharmacokinetics, toxcast
Organization: U.S. Environmental Protection Agency
Ship Power Model Summary Data

The dataset is contained in a .zip file containing the two .csv files with data, and a data dictionary file. 
summedEmissionsSpeeds contains emissions estimates summed over several different modeling parameters, DwtSubtypes gives the mapping of shipType, and subtypes, to deadweight tonnage ranges as used in the linked publication. Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: marine-emissions
Organization: U.S. Environmental Protection Agency
Projecting Changes in Expected Annual Damages From Riverine Flooding in the United States

Summary of datasets for flooding analysis reported in Wobus et al. (2019)
1)	Wobus_Flood_Damages_huc10.xlsx – contains total flood damages for floods of each specified recurrence interval, organized by HUC10, for watersheds with RiskMAP data from 3 or 5 recurrence intervals. Also includes lookup table to crosswalk from HUC10 to NCA region, and from HUC10 to the ReachID associated with the modeled flow data.
2)	CONUS_model_dT.xlsx – contains the year that each of the 29 models evaluated meets the specified temperature threshold relative to 2001-2020 baseline, on a CONUS average basis. Sheet “Summary” in that workbook is the main result from that analysis. 
3)	annmaxs_all85.zip – Contains annual maximum timeseries from all nodes in the geospatial fabric as modeled by NCAR/USBR in the VIC downscaled hydrologic dataset. These are the raw data used to generate extreme value statistics for baseline (2001-2020) and future time periods (see below). Variables are “reaches” (57116x1) with reachIDs; “modelnames85” (1x29) with model IDs; “years” (150x1) with years from 1950-2100; and “annmaxs_rcp85” (57116x150x29) with annual maximum flow values by reachID, year and model. Note the step function in annual maximum flows as reported by Wobus et al. (2017) in the year 2000 – do NOT compare pre-2000 vs post-2000 data. Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: climate-change, flood-risk, hydrology
Organization: U.S. Environmental Protection Agency
IHS Sea-web Ship Details and Technical Specifications

This data is a CSV file containeing ship technical details from IHS Sea-web. This dataset is not publicly accessible because: EPA cannot release CBI, or data protected by copyright, patent, or otherwise subject to trade secret restrictions. Request for access to CBI data may be directed to the dataset owner by an authorized person by contacting the party listed. It can be accessed through the following means: The vessel details in this dataset can be accessed via a subscription to IHS Sea-web:
https://maritime.ihs.com/EntitlementPortal/Home/Index. Format: This data set was compiled as a CSV file. Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: commercial-marine-vessels
Organization: U.S. Environmental Protection Agency
2017 NAIS Work Order 7060851

This data is in the form of a CSV file provided by the U.S. Coast Guard from their NAIS dataset.
the request period was: 01/01/2017-06/30/2017
the upper right bound of the data set is: 38.242°N,  −116.796°W
the lower left bound of the data set is 32.6703°N, −128.296°W
The data was delivered in 5 minute intervals
The fields contained in the data set are:
MSG_TYPE,MMSI,NAME,PERIOD,LAT_AVG,LON_AVG,COG_DEG,SPEED_KNOTS,HEADING_DEG,IMO_NUMBER,CALL_SIGN,SHIP_AND_CARGO_TYPE,NAV_SENSOR,DRAUGHT,MMSI_COUNTRY_CD,DIM_BOW,DIM_STERN,DIM_STARBOARD,DIM_PORT,RECEIVER. This dataset is not publicly accessible because: EPA cannot release CBI, or data protected by copyright, patent, or otherwise subject to trade secret restrictions. Request for access to CBI data may be directed to the dataset owner by an authorized person by contacting the party listed. It can be accessed through the following means: Directions for requesting this data from the U.S. Coast Guard can be found at:
https://www.navcen.uscg.gov/?pageName=AISdisclaimer. Format: This data is in the form of a CSV file provided by the U.S. Coast Guard from their NAIS dataset.
the request period was: 01/01/2017-06/30/2017
the upper right bound of the data set is: 38.242°N,  −116.796°W
the lower left bound of the data set is 32.6703°N, −128.296°W
The data was delivered in 5 minute intervals
The fields contained in the data set are:
MSG_TYPE,MMSI,NAME,PERIOD,LAT_AVG,LON_AVG,COG_DEG,SPEED_KNOTS,HEADING_DEG,IMO_NUMBER,CALL_SIGN,SHIP_AND_CARGO_TYPE,NAV_SENSOR,DRAUGHT,MMSI_COUNTRY_CD,DIM_BOW,DIM_STERN,DIM_STARBOARD,DIM_PORT,RECEIVER. Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: ais
Organization: U.S. Environmental Protection Agency
Effects of Increasing Aridity on Ambient Dust and Public Health in the U.S. Southwest Under Climate Change

Supplemental information, excel spreadsheet of data behind figures in the paper, 11 files with code to reproduce the study. 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, climate-change, climate-impacts, drought, health-impacts-assessment, mineral-dust, particulate-matter
Organization: U.S. Environmental Protection Agency
Estimates of Present and Future Asthma Emergency Department Visits Associated With Exposure to Oak, Birch, and Grass Pollen in the United States

Word file with supplemental figures and tables, including data behind figures in the paper. Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: aeroallergens, asthma, climate-change, pollen
Organization: U.S. Environmental Protection Agency
4-Acetoxyphenol as a substrate for acetylcholinesterase-based sensor and its application for As(III) determination

The supplementary data is used to support the interpretation of electrochemical reaction at the interface of working electrode, and reaction features of the immobilized enzyme. The formula for modeling the kinetics of immobilized enzyme was also given in the supplementary material. 

This dataset is associated with the following publication:
Li, T., E. Sahle-Demessie, E. Varughese, and J. Berberich. A disposable acetylcholine esterase sensor for As(iii) determination in groundwater matrix based on 4-acetoxyphenol hydrolysis.   Analytical Methods. RSC Publishing, Cambridge,  UK, 11(40): 5203-5213, (2019).

Tags: amperometric-assay, biosensor, contaminant, cyclic-voltametry, enzyme-activity, real-time-analysis, reversible-first-order-reaction-kinetics, voltammogram-of-hydroquinone
Organization: U.S. Environmental Protection Agency
Data for Adaptation, Sea Level Rise, and Property Prices in the Chesapeake Bay Watershed

Property characteristics and parcel boundaries, shoreline features, and sea level rise inundation vulnerability for the state of Maryland. This dataset is not publicly accessible because: EPA cannot release CBI, or data protected by copyright, patent, or otherwise subject to trade secret restrictions. Request for access to CBI data may be directed to the dataset owner by an authorized person by contacting the party listed. It can be accessed through the following means: Data on property attributes and parcel boundaries from MdProperty View can be accessed at https://planning.maryland.gov/Pages/OurProducts/PropertyMapProducts/MDPropertyViewProducts.aspx 

Data on shoreline features for Anne Arundel County can be accessed at http://ccrm.vims.edu/gis_data_maps/shoreline_inventories/maryland/anne_arundel/annearundel_disclaimer.html

Data on sea level rise inundation vulnerability for Maryland coastal counties can be accessed at https://imap.maryland.gov/ServicesMetadata/ClimMetAtm/SeaLevelRiseVul/ELEV_2FootInundation_CGIS.htm. Format: Property sales and attribute data were obtained from MdProperty View and include numeric data as well as georeferenced parcel data.

Georeferenced data on shoreline features, including adaptation structures, come from a joint program between the Virginia Institute of Marine Science, the Maryland Department of Natural Resources, and the National Oceanic and Atmospheric Agency (NOAA).

Georeferenced sea level rise inundation vulnerability data were produced in a joint project between NOAA, the Maryland Commission on Climate Change, and Towson University. Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: climate-adaptation, hedonic-analysis, sea-level-rise
Organization: U.S. Environmental Protection Agency
PACOM DATA SET Gasifier Municipal Batch Emissions

This dataset reports a variety of emissions from operation of a batch-fed waste gasifier with a combustor. 

This dataset is associated with the following publication:
Aurell, J., M. Barnes, B. Gullett, A. Holder, and R. Eninger. Methodology for Characterizing Emissions from Small (0.5-2 MTD) Batch-Fed Gasification Systems Using Multiple Waste Compositions.   WASTE MANAGEMENT. Elsevier Science Ltd, New York, NY, USA, 87: 398-406, (2019).

Tags: combustor, emissions, gasifier, military, municipal, waste, waste-composition
Organization: U.S. Environmental Protection Agency