AndreaBozzo/ceres-open-data-index huggingface dataset:
Structural alerts for protein binding

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. 

This dataset is associated with the following publication:
Nelms, M., R. Lougee, D. Roberts, A. Richard, and G. Patlewicz. Comparing and contrasting the coverage of publicly available structural alerts for protein binding.   Computational Toxicology. Elsevier B.V., Amsterdam,  NETHERLANDS, 12: 100100, (2019).

Tags: dsstox, protein-binding, reaction-mechanistic-domains, structural-alerts, tox21, toxcast, toxprint-enrichments
Organization: U.S. Environmental Protection Agency
An evaluation of the performance of selected (Q)SARs/expert systems for predicting acute oral toxicity

Acute rat oral toxicity lethality data files, processed prediction files from 2 expert systems. 

This dataset is associated with the following publication:
Nelms, M., A. Karmaus, and G. Patlewicz. An evaluation of the performance of selected (Q)SARs/expert systems for predicting acute oral toxicity.   Computational Toxicology. Elsevier B.V., Amsterdam,  NETHERLANDS, 16(November 2020): 100135, (2020).

Tags: chemical-safety-research, curated-data, models, pharmacokinetics
Organization: U.S. Environmental Protection Agency
Metadata:  Data sets, data type, and data source for all pathway surrogates

Data sets, data type, and data source for all pathway surrogates used for determining the “index of invasion pressure”. 

This dataset is associated with the following publication:
Tucker, A., L. Chadderton, G. Annis, A. Davidson, J. Bossenbroek, S. Hensler, M. Hoff, J. Hoffman, E. Jensen, D. Kashian, S. LeSage, and T. Strakosh. A framework for aquatic invasive species surveillance site selection and prioritization in the US waters of the Laurentian Great Lakes.   Management of Biological Invasions. Regional Euro-Asian Biological Invasions Centre, Helsinki,  FINLAND, 11(3): 607–632, (2020).

Tags: aquatic-invasive-species, laurentian-great-lakes, monitoring, surveillance
Organization: U.S. Environmental Protection Agency
Variability in in vivo studies: Defining the upper limit of performance for predictions of systemic effect levels (ORD-034452)

The data used are from curation of legacy studies and stored in ToxRefDB. 

This dataset is associated with the following publication:
Pham, L.L., S. Watford, P. Pradeep, M. Martin, R. Thomas, R. Judson, W. Setzer, and K. Paul-Friedman. Variability in in vivo studies: Defining the upper limit of performance for predictions of systemic effect levels.   Computational Toxicology. Elsevier B.V., Amsterdam,  NETHERLANDS, 15(August 2020): 100126, (2020).

Tags: in-vivo-data, predictive-models, toxrefdb, uncertainty, variance
Organization: U.S. Environmental Protection Agency
IWIICI MatSu

Index of watershed integrity / Index of catchment integrity scores, along with component index scores and landscape metric values, for NHDPlusHR catchments in the Matanuska-Susitna Basin in Alaska. 

This dataset is associated with the following publication:
Aho, K., J. Flotemersch, S. Leibowitz, M. LaCroix, and M. Weber. Applying the index of watershed integrity to the Matanuska–Susitna basin.   Arctic, Antarctic, and Alpine Research. Taylor & Francis Group, London,  UK, 52(1): 435-449, (2020).

Tags: catchment-integrity, cold-climate-hydrology, sub-arctic, watershed-integrity
Organization: U.S. Environmental Protection Agency
RJudson_Mansouri_CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity

Data and supplemental files from COMPARA (A large-scale modeling project). COMPARA combined multiple models developed in collaboration with modelers and computational toxicology scientists from 25 international groups to predict androgen receptor activity of a common set of 55,450 chemical structures. Quantitative structure-activity relationship models and docking approaches were employed to build a total of 91 predictive models for binding, agonist, and antagonist. The consensus values for agonist and antagonist activity are being made public through the CompTox Chemicals Dashboard. 

This dataset is associated with the following publication:
Mansouri, K., N. Kleinstreuer, R. Judson, A. Williams, I. Shah, and A. Richard. CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity.   ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA, 128(2): 27002, (2020).

Tags: actor, androgen-receptor, compara, computational-toxicology, edsp, qsar-models, toxcast
Organization: U.S. Environmental Protection Agency
WRF-ACI-Paper-2

all data are in netCDF format for all figures and tables. 

This dataset is associated with the following publication:
Glotfelty, T., K. Alapaty, J. He, P. Hawbecker, X. Song, and G. Zhang. Studying Scale Dependency of Aerosol Cloud Interactions using Scale-Aware Cloud Formulations.   Monthly Weather Review. American Meteorological Society, Boston, MA, USA,  1-57, (2020).

Tags: aerosol-indirect-effects, aerosol-radiative-forcing, numerical-weather-prediction, precipitation-cloud-life-cloud-cover, spatial-dependency-of-aerosol-indirect-effects
Organization: U.S. Environmental Protection Agency
Zika Brownsville PYW SolarProject

This file contains statistics on the spatial clustering of the internal rate of return for residential rooftop solar over a 20 year period.  Specifically, the IRR per roof was calculated using solar irradiance profile and estimated cash flows for each house.  Spatial clustering was determined by using the the Getis Ord Gi* test from ArcGIS 10.5. 

This dataset is associated with the following publication:
Mangiante, M., P. Whung, L. Zhou, A. Cepada, E. Campirano, D. Licon, R. Lawrence, and M. Torres. Economic and technical assessment of rooftop solar photovoltaic potential in Brownsville, Texas, U.S.A.   Computers, Environment and Urban Systems. Elsevier Science Ltd, New York, NY, USA, 80: 101450, (2020).

Tags: brownsville, geographic-information-systems, internal-rate-of-return, irr, lidar, photovoltaic-economic-potential, residential-rooftop-photovoltaics, solar-potential, spatial-clustering
Organization: U.S. Environmental Protection Agency
Clean Air Status and Trends Network (CASTNET) Weekly Ambient Concentrations

Weekly average air concentrations from CASTNET filter pack data in standard Tuesday 9:00 AM - Tuesday 8:00 AM weeks. The data are collected using an open face, 3-stage filter pack. Data include aerosol concentrations of sulfate, nitrate, ammonium, calcium, sodium, potassium, magnesium and chloride and gaseous concentrations of sulfur dioxide and nitric acid. The QAPP and associated SOPs can be found on the CASTNET website: www.epa.gov/castnet/documents-reports. Site location information is included with this dataset. 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-monitoring, ambient-air, ambient-air-quality, clean-air-status-and-trends-network-castnet
Organization: U.S. Environmental Protection Agency
Long-term trends in reactive N deposition in the U.S.

Data presented in this manuscript are publicly available per the links provided.  These include the US EPA National Emissions Inventory, US EPA Clean Air Status and Trends Network, National Atmospheric Deposition Ammonia Monitoring Network and National Atmospheric Deposition Program Total Deposition Maps. 

This dataset is associated with the following publication:
Beachley, G., C. Rogers, T. Lavery, J. Walker, and M. Puchalski. Long-term trends in reactive N deposition in the U.S..   ENVIRONMENTAL MANAGEMENT. Springer-Verlag, New York, NY, USA,  0, (2019).

Tags: ammonia, atmospheric-deposition, bidirectional-flux, castnet, deposition, micrometeorology, nadp, nitrogen, nitrogen-oxides, reactive-nitrogen, sulfur
Organization: U.S. Environmental Protection Agency
PISA Data Analysis Manual: SPSS, Second Edition

The OECD Programme for International Student Assessment (PISA) surveys collected data on students’ performances in reading, mathematics and science, as well as contextual information on students’ background, home characteristics and school factors which could influence performance. This publication includes detailed information on how to analyse the PISA data, enabling researchers to both reproduce the initial results and to undertake further analyses. In addition to the inclusion of the necessary techniques, the manual also includes a detailed account of the PISA 2006 database and worked examples providing full syntax in SPSS.

Tags: __
Organization: Department of State
Need for Improved Monitoring of Spatial and Temporal Trends of Reduced Nitrogen

Data in Figure 1 are from publicly available databases including county-level ammonia (NH3) emissions from the US EPA National Emissions Inventory (https://www.epa.gov/air-emissions-inventories/2014-national-emissions-inventory-nei-data), ambient ammonium (NH4+) aerosol concentrations from the US EPA Clean Air Status and Trends Network (https://java.epa.gov/castnet/clearsession.do), and ambient NH3 concentrations from the National Atmospheric Deposition Program Ammonia Monitoring Network (AMoN) (http://nadp.slh.wisc.edu/data/AMoN/)

Satellite observations of NH3 from the Infrared Atmospheric Sounding Instrument (IASI V2.2R) shown in Figure 2 are also publicly available (https://en.aeris-data.fr/metadata/?dc9dcce0-9324-451b-8d79-2d6df3094068).

Diurnal profiles of ambient NH3 at different sites across the U.S. are summarized in Figure 3. Data from sites operated by EPA Office of Research and Development are attached as a spreadsheet with accompanying data dictionary.  Greg Beachley (Beachley.gregory) is the contact for data from the Charleston, SC; Beltsville, MD and Bondville, IL sites.  Katherine Benedict (Katherine.Benedict@colostate.edu) is the contact for data from the RMNP; Fort Collins, CO and  Greeley, CO sites. 

This dataset is associated with the following publication:
Puchalski, M., J. Walker, G. Beachley, M. Zondlo, K. Benedict, R. Grant, B. Schichtel, C. Rogers, A. Leytem, J. Rice, K. Morris, J. Schauer, and R. Wang. Need for Improved Monitoring of Spatial and Temporal Trends of Reduced Nitrogen.   ENVIRONMENTAL MANAGEMENT. Springer-Verlag, New York, NY, USA,  0, (2019).

Tags: bidirectional-flux, deposition, micrometeorology, nitrogen, sulfur
Organization: U.S. Environmental Protection Agency
CMAQ predicted concentration file

CMAQ predicted concentration file. 

This dataset is associated with the following publication:
Li, Q., R. Borge, G. Sarwar, D. de la Paz, B. Gantt, J. Domingo, C. Cuevas, and A. Saiz-Lopez. Impact of halogen chemistry on air quality in coastal and continental Europe: application of CMAQ model and implication for regulation.   Atmospheric Chemistry and Physics. Copernicus Publications, Katlenburg-Lindau,  GERMANY, 19(24): 15321-15337, (2019).

Tags: atmospheric-chemistry, bromine, cmaq, iodine, ozone
Organization: U.S. Environmental Protection Agency
Bisphenol A activates EGFR and ERK promoting proliferation, tumor spheroid formation and resistance to EGFR pathway inhibition in estrogen receptor-negative inflammatory breast cancer cells

Raw data and figures for Bisphenol A activates EGFR and ERK promoting proliferation, tumor spheroid formation and resistance to EGFR pathway inhibition in estrogen receptor-negative inflammatory breast cancer cells manuscript. 

This dataset is associated with the following publication:
Sauer, S.J., M. Tarpley, I. Shah , A.V. Save, H.K. Lyerly, S.R. Patierno, K.P. Williams, and G.R. Devi. (Carcinogenesis) Bisphenol A activates EGFR and ERK promoting proliferation, tumor spheroid formation and resistance to EGFR pathway inhibition in estrogen receptornegative inflammatory breast cancer cells.   CARCINOGENESIS. Oxford University Press, Cary, NC, USA, 38(3): 252–260, (2017).

Tags: bpa, estrogen-receptor, expocast, exposure
Organization: U.S. Environmental Protection Agency
Abstract Sifter: a comprehensive front-end system to PubMed

The Abstract Sifter is a Microsoft Excel based application that enhances existing search capabilities of PubMed. The Abstract Sifter assists researchers to search effectively, triage results, and keep track of articles of interest. The tool implements an innovative “sifter” functionality for relevance ranking, giving the researcher a way to find articles of interest quickly. The tool also gives researchers a view of the literature landscape for a set of entities such as chemicals or genes. The Abstract Sifter is available as a Microsoft Excel macro-enabled workbook application. 

This dataset is associated with the following publication:
Baker, N., T. Knudsen, and A. Williams. Abstract Sifter: a comprehensive front-end system to PubMed (F1000 Research).   F1000 Research. Faculty of 1000, London,  UK, 6: 1-10, (2017).

Tags: biology, chemistry, document-retrieval, expocast, exposure, microsoft-excel, pubmed, toxicology, visual-basic-for-applications
Organization: U.S. Environmental Protection Agency
Characterizing cleft palate toxicants using ToxCast data, chemical structure, and the biomedical literature

A data set of 500 chemicals evaluated for their ability to induce cleft palate in animal prenatal developmental studies was compiled from Toxicity Reference Database and the biomedical literature, which included 63 cleft palate active and 437 inactive chemicals. To characterize the potential molecular targets for chemical‐induced cleft palate, we mined the ToxCast high‐throughput screening database for patterns and linkages in bioactivity profiles and chemical structural descriptors. The following datasets can be obtained via the links and files in the Data section: Phase II ToxCast assay data results (Judson et al., 2010); The Gene Score data set derived from ToxCast; ToxRefDB version 1 (Knudsen et al., 2009; Martin, Judson, et al., 2009); The ToxPrint chemotypes (Yang et al., 2015). 

This dataset is associated with the following publication:
Baker, N., N. Sipes, J. Franzosa, D. Belair, B. Abbott, R. Judson, and T. Knudsen. Characterizing cleft palate toxicants using ToxCast data, chemical structure, and the biomedical literature.   Birth Defects Research. John Wiley & Sons, Inc., Hoboken, NJ, USA,  1-21, (2019).

Tags: adverse-outcome-pathway, cleft-palate, developmental-toxicity, genes, machine-learning, tipping-points, toxcast, vembryo, virtual-embryo, virtual-tissues
Organization: U.S. Environmental Protection Agency
Dataset for ORD-037038: Constitutive expression of human CYPs

The raw values used to create figures 1 and 2 and table 3. 

This dataset is associated with the following publication:
Liu, J., Y. Lu, C. Corton, and C. Klaassen. Expression of cytochrome P450 isozyme transcripts and activities in human livers.   XENOBIOTICA. Taylor & Francis, Inc., Philadelphia, PA, USA, 51(3): 279-286, (2021).

Tags: age-related-susceptibility, cyp, cytochrome-p450, liver, susceptibility
Organization: U.S. Environmental Protection Agency
WRF-ACI-Paper-1

Data for all tables and figures are in netCDF format. 

This dataset is associated with the following publication:
Glotfelty, T., K. Alapaty, J. He, P. Hawbecker, X. Song, and G. Zhang. The Weather Research and Forecasting Model with Aerosol–Cloud Interactions (WRF-ACI): Development, Evaluation, and Initial Application.   Monthly Weather Review. American Meteorological Society, Boston, MA, USA, 147(5): 1491-1511, (2019).

Tags: aerosol-indirect-effects, aerosol-radiative-forcing, numerical-weather-prediction, precipitation-cloud-life-cloud-cover
Organization: U.S. Environmental Protection Agency
Increasing importance of organosulfur species for aerosol properties and future air quality

Link to IMPROVE network ambient data used in Figure 2a. 

This dataset is associated with the following publication:
Riva, M., Y. Chen, Y. Zhang, Z. Lei, N.E. Olson, H.C. Boyer, S. Narayan, L.D. Yee, H.S. Green, T. Cui, Z. Zhang, K. Baumann, M. Fort, E. Edgerton, S.H. Budisulistiorini, C.A. Rose, I.O. Ribeiro, R.L. e Oliveira, E.O. dos Santos, C.M.D. Machado, S. Szopa, Y. Zhao, E.G. Alves, S.S. de Sá, W. Hu, E.M. Knipping, S.L. Shaw, S. Duvoisin Junior, R.A.F. de Souza, B.B. Palm, J. Jimenez, M. Glasius, A.H. Goldstein, H. Pye, A. Gold, B.J. Turpin, W. Vizuete, S.T. Martin, J.A. Thornton, C.S. Dutcher, A.P. Ault, and J.D. Surratt. Increasing Isoprene Epoxydiol-to-Inorganic Sulfate Aerosol Ratio Results in Extensive Conversion of Inorganic Sulfate to Organosulfur Forms: Implications for Aerosol Physicochemical Properties.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 53(15): 8682-8694, (2019).

Tags: biogenic-voc, epoxide, iepox, isoprene, organosulfate, pm2-5, pm2-5-air-quality-modeling, semivolatile-organic-compounds-svocs, soa, sulfate, sulfur
Organization: U.S. Environmental Protection Agency
Judson_RefChem_InVitro_Assays

This supplemental material describes two sets of methods; first, it briefly describes the process used to create the EPA’s LitDB database, and second, it describes how a subset of records were extracted from LitDB to be included in the reference chemical database RefChemDB.  LitDB is a database of data elements extracted from the xml download of all MEDLINE PubMed records. Perl scripts are used to extract the identifying information from each citation record, information like title, abstract, authors and PubMed ID.  Additionally, the MeSH (Medical subject heading) terms are extracted with subheadings (also known as qualifiers).  
The Perl scripts extract to text files which are then loaded into a mysql database. 
The MeSH heading and descriptor tree files are also downloaded into mysql tables. They are available at https://www.nlm.nih.gov/mesh/filelist.html.   
To make the data more useful for research in chemicals, the data is passed stepwise through a series of algorithms. 

This dataset is associated with the following publication:
Judson, R., R. Thomas, N. Baker, A. Simha, X.M. Howey, C. Marable, N. Kleinstreuer, and K. Houck. Workflow for Defining Reference Chemicals for Assessing Performance of In Vitro Assays (Altex).   ALTEX. Society ALTEX Edition, Kuesnacht,  SWITZERLAND, 36(2): 261-276, (2019).

Tags: high-throughput-screening, high-throughput-toxicology, toxcast
Organization: U.S. Environmental Protection Agency
Mosaic Land Use in WRF-Noah LSM

Analyzed output from WRF runs which use the Noah land surface model's default treatment of land use and the more novel, mosaic land use representation. 

This dataset is associated with the following publication:
Mallard, M., and T. Spero. Effects of Mosaic Land Use on Dynamically Downscaled WRF Simulations of the Contiguous U.S.   JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES. American Geophysical Union, Washington, DC, USA, 124(16): 9117-9140, (2019).

Tags: dynamical-downscaling, land-use, mosaic-land-use, noah-lsm, wpf
Organization: U.S. Environmental Protection Agency
Saili_AOP43_Systems Modeling of Developmental Vascular Toxicity

The AOP concept was used to translate ToxCast high-throughput screening data into a ToxPi matrix of 1058 chemicals x 24 features ordered by predicted potential to disrupt angiogenesis. 

This dataset is associated with the following publication:
Saili, K., J. Franzosa, N. Baker, R. Ellis-Hutchings, R. Settivari, E. Carney, R. Spencer, T. Zurlinden, N. Kleinstreuer, S. Li, M. Xia, and T. Knudsen. Systems Modeling of Developmental Vascular Toxicity.   Current Opinion in Toxicology. Elsevier BV, AMSTERDAM,  NETHERLANDS, 15(1): 55-63, (2019).

Tags: 5hpp-33, adverse-outcome-pathway, angiogenesis, tipping-points, tnp-470, tox21, toxcast, vembryo, virtual-embryo, virtual-tissues
Organization: U.S. Environmental Protection Agency
Revision of National Index of Watershed Integrity

Datasets contain original and revised Index of Watershed Integrity (IWI) and Index of Catchment Integrity (ICI), as well as sub-components that were used to develop the indices and water quality data used to revise and/or evaluate the indices. 

This dataset is associated with the following publication:
Johnson, Z.C., S. Leibowitz, and R.A. Hill. Revising the index of watershed integrity national maps.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 651: 2615-2630, (2018).

Tags: aquatic-condition, catchment-integrity, catchments, conus, ici, iwi, national-aquatic-resource-surveys, national-hydrography-dataset, national-hydrography-dataset-plus-nhdplus, random-forests, spatial-prediction, streams, watershed-integrity, watershed-metrics, watersheds
Organization: U.S. Environmental Protection Agency
Generalised Read-Across (GenRA) refinements

These new analysis builds on the baseline GenRA approach and presents a proof of concept of how other contexts of similarity namely physchem can be implemented into a search strategy for identification of analogues and how this impacts performance of read-across. Chemicals Involved: Same ToxRef dataset as used in the original GenRA manuscript. 

This dataset is associated with the following publication:
Helman, G., I. Shah, and G. Patlewicz. Extending the Generalised Read-Across approach (GenRA): A systematic analysis of the impact of physicochemical property information on read-across performance.   Computational Toxicology. Elsevier B.V., Amsterdam,  NETHERLANDS, 8: 34-50, (2018).

Tags: dsstox, generalised-read-across, genra, physiochemical-parameters, read-across, toxcast
Organization: U.S. Environmental Protection Agency
Data contributed by EPA/ORD/NERL/CED researchers to the manuscript "Attributing Differences in the Fate of Lateral Boundary Ozone in AQMEII3 Models to Physical Process Representations"

This dataset contains the data used in the Figures and Tables of the manuscript “Attributing Differences in the Fate of Lateral Boundary Ozone in AQMEII3 Models to Physical Process Representations ". 

This dataset is associated with the following publication:
Liu, P., C. Hogrefe, U. Im, J. Christensen, J. Bieser, U. Nopmongcol, G. Yarwood, R. Mathur, S. Roselle, and T. Spero. Attributing differences in the fate of lateral boundary ozone in AQMEII3 models to physical process representations.   Atmospheric Chemistry and Physics. Copernicus Publications, Katlenburg-Lindau,  GERMANY, 18(23): 17157-17175, (2018).

Tags: boundary-conditions, model-intercomparison, tracers, vertical-mixing
Organization: U.S. Environmental Protection Agency
Data for tables and figures

A zipped and tarred file which contains netCDF files needed to replicate all tables and figures shown in the referenced journal article. 

This dataset is associated with the following publication:
Mallard, M., T. Spero, and S. Taylor. Examining WRF’s Sensitivity to Contemporary Land-Use Datasets across the Contiguous United States Using Dynamical Downscaling.   JOURNAL OF APPLIED METEOROLOGY AND CLIMATOLOGY. American Meteorological Society, Boston, MA, USA, 57(11): 2561-2583, (2018).

Tags: land-use, national-land-cover-database-nlcd, usgs, wrf
Organization: U.S. Environmental Protection Agency