Bringing it all together: A Web-based Database for Chemical and Biological Data to Support Environmental Toxicology
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The EPA Comptox Chemistry Dashboard is a web-based application providing access to a set of data resources provided by the National Center of Computational Toxicology. Sitting on a foundation of chemistry data for ~750,000 chemical substances the application integrates bioassay screening results, physicochemical and toxicological endpoints (both experimental and predicted) and consumer product and functional use data. By integrating a series of other EPA and public databases (e.g. ECOTOX, the EPA Substance Registry Service, EPA’s ChemView and PubChem), the dashboard provides a hub for connecting to other releases of value to environmental scientists and toxicologists. The underpinning architecture has been developed in a manner allowing for the release of the dashboard as a public resource, as well as for delivering applications used inside confidential business information environments. These applications are being assessed for potential applications to support risk decisions. This presentation will provide an overview of the dashboard focusing specifically on the most recent functionality supporting deeper integration to the ToxCast bioassay data and exposure data and predictions available via the dashboard. This abstract does not reflect U.S. EPA policy.
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![Innovative Research for a Sustainable Futurewww.epa.gov/research
ORCID: 0000-0002-2668-4821
Antony Williams l williams.antony@epa.gov l 919-541-1033
Bringing it all together: A web-based database for chemical and
biological data to support environmental toxicology
Antony Williams1, Chris Grulke1, Sean Watford1, Rebecca Jolley1, Jeremy Dunne1,
Elizabeth Edmiston1 and Jeff Edwards1
1U.S. Environmental Protection Agency, Office of Research and Development, National Center for Computational Toxicology, Research Triangle Park, NC
ACS Fall 2017
Washington, DC
August 20-24, 2017
The EPA Comptox Chemistry Dashboard is a web-based application
providing access to a set of data resources provided by the National
Center of Computational Toxicology. Diverse data types associated
with ~760,000 chemical substances are delivered through the
application. These data include bioassay screening results (associated
with the ToxCast project), physicochemical and toxicological endpoints
(both experimental and predicted), and consumer product and
functional use data. Access to tens of millions of predicted property
values associated with the chemicals on the dashboard includes
detailed calculation reports for the OPERA models [1].
The dashboard is an integration hub for ~70 public resources using
cross website linking. This helps the user navigate to other data and
information for a particular chemical on other websites. The application
also provides integrated literature searches for chemical related
information using Google Scholar and PubMed.
Advanced searching capabilities provide molecular formula and mass-
based searching to support non-targeted analysis for mass
spectrometry, a key area of research at the US Environmental
Protection Agency. A batch search also allows users to search using
inputs of thousands of chemical names or CAS Registry Numbers and
download details regarding the availability of bioassay, exposure and
toxicity data.
Much of the data on the dashboard is available as Open Data via a
downloads page. This allows third parties to integrate these data into
their own applications and link back to the dashboard chemical pages.
The underpinning architecture has been developed in a manner
allowing for the release of the dashboard as a public resource as well
as for delivering research applications internal to the U.S. EPA.
Specifically the dashboard, and new modules are being assessed for
potential applications to support risk assessment.
The CompTox Chemistry Dashboard
Abstract
For records with chemical
structure representations, various
inherent properties (e.g. formula
and mass) and predicted
physicochemical properties (logP,
water solubility etc.) are provided.
The landing page of the
dashboard is a simple text entry
box allowing a type-ahead search
for systematic, trade and trivial
names, CAS Registry Numbers
and InChIs.
Dashboard Entry Page
Chemical Record Page: Atrazine
Chemical Properties Panel
Where possible, links are
provided to related Wikipedia
articles. An associated mol file is
available for download to the
desktop, and a summary report
containing record data can be
provided as a PDF file.
Accessing ~100 Million Predicted Properties Online
Future Work
The dashboard provides access to ~760,000 chemicals and integrates
curated experimental data [1] used to produce OPEn saR Application
(OPERA) models. All chemicals were passed through the prediction
models and detailed model reports showing global and local
applicability domains and nearest neighbor results are displayed in the
application. The QSAR Modeling Report Formats (QMRF) for each
model are available for each predicted endpoint.
References
1. Mansouri et al. An automated curation procedure for addressing
chemical errors and inconsistencies in public datasets in QSAR
modelling, SAR QSAR Environ Res. 2016 Nov;27(11):939-965.
2. EPA Toxicity Estimation Software Tool (T.E.S.T.) software
http://www.epa.gov/chemical-research/toxicity-estimation-software-tool-test
• Continue to expand the data in terms of chemicals, toxicity data,
additional experimental data.
• Provide access to the data via a suite of web services and fully
documented API.
• Release NCCT models as interactive online prediction tools in the
near future via the dashboard.
A summary of available chemical
properties for Bisphenol A
The MP prediction model report for
BPA – including nearest neighbors.
Problem Definition and Goals
Problem: There are many freely available data available online to
support computational toxicology in environmental science, but an
easy way to access available data across multiple sites is lacking.
Goals: To deliver online access via a simple to use web-based
interface supporting diverse types of data associated with
environmental chemistry, and specifically computational toxicology. To
make the data available for ~760,000 chemical substances available
as downloadable data for reuse and repurposing in other databases.
Toxicity Values Panel
Bioassays: ToxCast Data
The Toxicity Values tab provides
access to data assembled from a
series of public resources
including EPA data (i.e. IRIS and
PPRTV reports, ToxRef DB). Data
can be downloaded as TSV and
Excel files.
The ToxCast Bioassay data
measured over the past decade is
accessible via the dashboard
under the Bioassays Tab.
PubChem bioassays data are
also available. Data can be
downloaded as Excel files.
Future Work
The authors would like to acknowledge specific colleagues within our
center for their contributions to the development of the dashboard: Todd
Martin, Nancy Baker, Richard Judson and John Wambaugh.
This presentation does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.
Predicted data from the EPA’s Toxicity Estimation Software Tool
(T.E.S.T) [2] is also available. This includes physicochemical and
toxicity prediction models.](https://image.slidesharecdn.com/bringingitalltogetherasawebbaseddatabaseposterv3final-170823021837/85/Bringing-it-all-together-A-Web-based-Database-for-Chemical-and-Biological-Data-to-Support-Environmental-Toxicology-1-320.jpg)
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The National Center for Computational Toxicology at the EPA has developed the CompTox Chemistry Dashboard to provide public access to toxicity and chemical property data. The dashboard integrates data from high-throughput screening, predicted properties, chemical hazard assessments, literature searches, and exposure information for over 760,000 chemicals. It allows users to search for chemicals individually or in batches, access detailed chemical pages, view predicted and experimental properties, and download open data. The dashboard is meant to be an integration hub that makes NCCT's data and models more accessible and reusable to other scientists.Using the US EPA’s CompTox Chemistry Dashboard for structure identification a...
Using the US EPA’s CompTox Chemistry Dashboard for structure identification a...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are advancing the identification of emerging contaminants in environmental matrices, improving the means by which exposure analyses can be conducted. However, confidence in structure identification of unknowns in NTA presents challenges to analytical chemists. Structure identification requires integration of complementary data types such as reference databases, fragmentation prediction tools, and retention time prediction models. The goal of this research is to optimize and implement structure identification functionality within the US EPA’s CompTox Chemistry Dashboard, an open chemistry resource and web application containing data for ~760,000 substances. Rank-ordering the number of sources associated with chemical records within the Dashboard (Data Source Ranking) improves the identification of unknowns by bringing the most likely candidate structures to the top of a search results list. Database searching has been further optimized with the generation of MS-Ready Structures. MS-Ready structures are de-salted, stripped of stereochemistry, and mixture separated to replicate the form of a chemical observed via HRMS. Functionality to conduct batch searching of molecular formulae and monoisotopic masses was designed and released to improve searching efforts. Finally, a scoring-based identification scheme was developed, optimized, and surfaced via the Dashboard using multiple data streams contained within the database underlying the Dashboard. The scoring-based identification scheme improved the identification of unknowns over previous efforts using data source ranking alone. Combining these steps within an open chemistry resource provides a freely available software tool for structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. A new web application, the CompTox Chemistry Dashboard provides access to data associated with ~720,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists.
The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identification based on non-targeted analysis studies using mass spectrometry. Chemical identification using both mass and formula-based searching utilizes rank-ordering of results via functional use statistics, thereby providing a solution to help prioritize chemicals for further review when detected in environmental media.
This presentation will provide an overview of the CompTox Dashboard, its capabilities for delivering data to the environmental toxicology community and how the architecture provides a foundation for the development of additional applications to support chemical risk assessment. This abstract does not reflect U.S. EPA policy.
Structure identification by Mass Spectrometry Non-Targeted Analysis using the...
Structure identification by Mass Spectrometry Non-Targeted Analysis using the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Identification of unknowns in mass spectrometry based non-targeted analyses (NTA) requires the integration of complementary pieces of data to arrive at a confident, consensus structure. Researchers use chemical reference databases, spectral matching, fragment prediction tools, retention time prediction tools, and a variety of other data to arrive at tentative, probable, and confirmed, if possible, identifications. With the diverse, robust data contained within the US EPA’s CompTox Chemistry Dashboard (https://comptox.epa.gov), the goal of this research is to identify and implement a harmonized identification tool and workflow using previously generated chemistry data. Data has been compiled from product use, functional use prediction models, environmental media occurrence prediction models, and PubMed references, among other sources. We will report on our development of a visualization tool whereby users can visualize the relative contribution of identification-based metrics on a list of candidate structures and observe the greatest likelihood of occurrence. These data and visualization tools support NTA identification via the Dashboard and demonstrate an open, accessible tool for all users of HRMS data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Development of a Tool for Systematic Integration of Traditional and New Appro...
Development of a Tool for Systematic Integration of Traditional and New Appro...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Multiple regulatory bodies (EPA, ECHA, Health Canada) are currently tasked with prioritizing chemicals for data collection and risk assessments. These prioritization efforts are in response to regulatory mandates to identify chemicals for further assessment. We have developed a web-based application that enables a rapid, flexible and transparent prioritization process. The tool includes multiple data streams related to human and ecological hazard, exposure, and physicochemical properties (persistence and bioaccumulation). For human hazard, the data streams include quantitative points of departure (PODs) that are compiled from multiple sources such as EPA ToxRefDB, ECHA, COSMOS; estimated PODs from high-throughput in vitro screening assays and computational models; and qualitative measurements and predictions of specific endpoints (e.g., genotoxicity, endocrine activity). For ecological hazard, quantitative PODs are taken from the EPA ECOTOX database. Exposure information includes production volume, quantitative predictions using the EPA ExpoCast and SHEDS models, biomonitoring data, and qualitative information such as media occurrence, use profiles and likelihood of consumer and childhood exposures. The use of the tool is illustrated by prioritizing chemicals related to TSCA and the Safer Choice Ingredient List. The underpinning data streams for this application are already available in the EPA CompTox Chemistry Dashboard and have been repurposed to deliver this application. This is in keeping with our overarching software development methodology of providing multiple “building blocks” in the form of databases, web services and visualization components to deliver fit-for purpose applications to the relevant audiences. This abstract does not necessarily represent U.S. EPA policy.Chemical identification of unknowns in high resolution mass spectrometry usin...
Chemical identification of unknowns in high resolution mass spectrometry usin...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted and suspect screening studies using high resolution mass spectrometry (HRMS) have revolutionized the detection of chemicals in complex matrices. However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. The US EPA has developed functionality within the CompTox Chemicals Dashboard (https://comptox.epa.gov) to address challenges related to data processing and analysis in HRMS. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will introduce the tools and combined workflow, including visualization and access via the CompTox Chemicals Dashboard. These tools, data, and visualization approaches within an open chemistry resource provides a publicly available software tool to support structure identification and non-targeted analyses. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.US-EPA Chemicals Dashboard and Applications to Digital Design of Molecules
US-EPA Chemicals Dashboard and Applications to Digital Design of MoleculesUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation at: Digital design of molecules and formulations (https://www.soci.org/events/ai-and-digitalisation/digital-design-of-molecules-and-formulations). The Chemicals Dashboard is a free web-based application from the United States Environmental Protection Agency that provides various types of data for ~900,000 chemicals. These data include physicochemical properties, in vivo and in vitro toxicity data and information regarding the presence of chemicals in commercial products, including formulation data where available. The dashboard allows for sourcing of data associated with singleton chemicals or a batch mode for downloading data for thousands of chemicals at a time. This presentation will provide an overview of the Dashboard, the myriad of data sources underpinning the application and potential applications of the dashboard.The EPA CompTox Chemistry Dashboard and Underpinning Software Architecture
The EPA CompTox Chemistry Dashboard and Underpinning Software Architecture US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The CompTox Chemistry Dashboard was developed by the Environmental Protection Agency’s National Center for Computational Toxicology. This dashboard has been architected in a manner that allows for the deployment of multiple “applications”, both as publicly available databases, and for deployment under the constraints of confidential business information (CBI). The public dashboard provide access to multiple types of data for ~750,000 chemicals. This includes, when available for a chemical substance, physicochemical parameters, toxicity and bioassay data, consumer use and analytical data. Fate, exposure, and hazard calculations can benefit from access to the data aggregation and curation efforts that underpin the public dashboard. Also, regulators can benefit from the integration of their own data within their closed infrastructure environments. This presentation will provide a review of the chemistry dashboard architecture and its present application providing access to data to the research and regulatory communities. We will also review present developments in the area of delivering an application programming interface, web services, and software components for integration into third party applications providing access to the data exposed via the dashboard. This abstract does not reflect U.S. EPA policy.US-EPA Chemicals Dashboard – an integrated data hub for environmental science
US-EPA Chemicals Dashboard – an integrated data hub for environmental scienceUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The US-EPA Chemicals Dashboard is an integrated data hub providing centralized access to environmental chemistry data to support EPA and partner decision making. It contains nearly 900,000 chemical substances with experimental and predicted physical/chemical properties, hazard, exposure, and toxicity data. Users can perform various search types including basic searches by chemical name/identifier, structure-based searches, and batch searches for lists of chemicals. Detailed chemical pages display curated data from sources like ToxCast/Tox21 along with linked analogous chemicals and real-time predictive models. The goal is to improve efficiency in chemical risk assessment through easy access to this centralized chemical data resource.Structure identification approaches using the EPA CompTox Chemicals Dashboard...
Structure identification approaches using the EPA CompTox Chemicals Dashboard...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The document discusses how the EPA's CompTox Chemicals Dashboard can be used to support mass spectrometry analyses for structure identification. The Dashboard contains data on over 800,000 chemicals including properties, lists, and links to other resources. It allows searching by formula, structure, and mass to find related chemicals. Candidate structures can be ranked using metadata. Predicted mass spectra from over 800,000 structures may also be accessible. The Dashboard integrates data to help identify unknown chemicals detected by mass spectrometry.US-EPA CompTox Chemicals Dashboard as a web-based data resource to help ident...
US-EPA CompTox Chemicals Dashboard as a web-based data resource to help ident...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted screening, targeted screening and suspect screening, as well as “Known Unknowns” and “Unknown Unknowns” are now common terms in the field of water analysis. While data processing can be highly automated, the identification of chemicals from extracted masses, formulae or fragmentation utilizes reference spectral libraries or identification and ranking of tentative candidate lists from large structure libraries. The US-EPA CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) provides access to data for ~875,000 substances, searchable by mass and formula and then ranked using associated meta-data. Cheminformatics approaches are also utilized to provide mapped relationships between individual substances and their “MS-Ready” (desalted, non-stereospecific) forms. This presentation will review how the freely available Dashboard application can be utilized to support structure identification using mass spectrometry and our efforts to enhance the application using computational spectral fragmentation and access to predicted data such as relative retention time index values and computed collision cross section values to support ion mobility spectrometry. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental C...
EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental C...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The US EPA CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a web-based application providing access to ~875,000 chemical substances and diverse data types including physicochemical property, toxicity and EPA’s ToxCast data. This presentation provided a live demo of the application and its benefits to members of ACS AGRO.The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Env...
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Env...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrate advances in biology, chemistry, exposure and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, legacy in vivo animal data, consumer use and production information, exposure models and chemical structure databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data, but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. Our web application, the CompTox Chemistry Dashboard provides access to data associated with ~750,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists.
The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identification based on non-targeted analysis studies using mass spectrometry. Chemical identification using both mass and formula-based searching utilizes rank-ordering of results via functional use statistics, thereby providing a solution to help prioritize chemicals for further review when detected in environmental media.
This presentation will provide an overview of the dashboard, its capabilities for delivering data to the environmental chemistry community and how the architecture provides a foundation for the development of additional applications to support chemical risk assessment. This abstract does not reflect U.S. EPA policy.
US-EPA Chemicals Dashboard – an integrated data hub for environmental science
US-EPA Chemicals Dashboard – an integrated data hub for environmental scienceUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The US-EPA Chemicals Dashboard is a web-based database and integrated data hub containing information on over 875,000 chemical substances. It includes experimental and predicted physicochemical properties, in vivo toxicity data, in vitro bioactivity screening results, and links to external resources. Key features include search capabilities, chemical profiles with summarized toxicity information, modules for literature searching and read-across, and batch searching and downloading of data for multiple chemicals. The goal is to provide a transparent, integrated resource to support computational toxicology and exposure science. Ongoing efforts focus on expanding the breadth of data and ensuring data quality through expert curation.US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for ...
US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Chemical risk assessment is both time-consuming and difficult because it requires the assembly of data for chemicals generally distributed across multiple sources. The US EPA CompTox Chemistry Dashboard is a publicly accessible web-based application providing access to various data streams on ~760,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, consumer product and functional use information and a myriad of related data of value to environmental scientists and toxicologists. At this stage of development, the public dashboard provides access to almost 20 predicted physicochemical and environmental fate and transport endpoints with full transparency in terms of model performance. Experimental and predicted human and ecological toxicity data are also available, as are in vitro to in vivo extrapolation dosimetry predictions and predicted exposure and functional use. In parallel to the CompTox Chemistry Dashboard we are developing RapidTox, a web-based application that enables a rapid, flexible and transparent prioritization process for sets of chemicals using several previously used workflows focused on scoring of traditional risk metrics and the inclusion of alternative hazard and exposure estimates. This presentation will give an overview of the CompTox Chemistry Dashboard, RapidTox, our approaches to building transparent and open prediction models, and our efforts to provide access to real time predictions. This abstract does not necessarily represent U.S. EPA policy.Adding complex expert knowledge into chemical database and transforming surfa...
Adding complex expert knowledge into chemical database and transforming surfa...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This document discusses adding complex expert knowledge about surfactants to chemical databases to aid in the identification of unknown compounds from wastewater samples. It describes how over 60% of peaks detected by high resolution mass spectrometry in wastewater samples are unknown. Literature data on surfactant properties and spectra were compiled and added to databases to support the identification of homologous series and complex mixtures present. A list of surfactants was developed and incorporated into toxicity databases to enable in silico modeling and computational mass spectrometry approaches to aid non-target screening. International collaboration is helping to establish a global exchange of suspect lists to support the identification of unknown contaminants.The US-EPA CompTox Chemicals Dashboard – an online data integration hub suppo...
The US-EPA CompTox Chemicals Dashboard – an online data integration hub suppo...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are advancing the identification of emerging contaminants in environmental matrices, improving the means by which exposure analyses can be conducted. However, confidence in structure identification of unknowns in NTA presents challenges to analytical chemists. Structure identification requires integration of complementary data types such as reference databases (either commercial or open databases), fragmentation prediction tools, and retention time prediction models. One goal of our research is to optimize and implement structure identification functionality within the US EPA’s CompTox Chemicals Dashboard, an open chemistry resource and web application containing data for ~900,000 substances. Database searching using mass or formula-based inputs has been optimized for structure identification using “MS-Ready Structures”: de-salted, stripped of stereochemistry, and mixture separated to replicate the form of a chemical observed via HRMS. Functionality to conduct batch searching of molecular formulae and monoisotopic masses has also been implemented. While the increasing number of free online databases are of value to support chemical structure verification and elucidation there are known issues regarding data quality and careful data curation is a very necessary part of the development of these resources. This presentation will provide an overview of our latest enhancements to the dashboard to support mass spectrometry, incorporation of specific datasets (e.g., to support breath research (the volatilome) and household dust analysis), and the value of metadata and predicted fragmentation spectral matching to support structure identification. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Delivering an integrated data hub for per- and polyfluoroalkyl (PFAS) chemica...
Delivering an integrated data hub for per- and polyfluoroalkyl (PFAS) chemica...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
There is increasing interest in the environmental impact of per- and polyfluoroalkyl substances (PFAS) chemicals and the aggregation of related data provides both agency and public access to support research. The US-EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a publicly accessible website providing access to data for ~900,000 chemical substances, including thousands of PFAS chemicals. The dashboard provides access to a wide array of experimental and predicted physicochemical properties, in vitro bioactivity and in vivo toxicity data, product use information and integrated linkages to a growing list of literature, toxicology, and analytical chemistry websites. The assembly of data has required hundreds of hours of manual curation and data checking to deliver a number of segregated lists of PFAS chemicals. Experimental data extracted from literature articles has allowed the optimization of QSAR models for the prediction of properties such as logP (octanol-water partition) and aqueous solubility. This presentation will provide an overview of the dashboard, the ongoing expansion of the PFAS chemical library, with associated categorization, and new physicochemical property and environmental fate and transport QSAR prediction models being developed for these chemicals. Our progress in the measurement and analysis of bioactivity data for PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.More Related Content
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EPA CompTox chemicals dashboard: An online resource for environmental chemists
EPA CompTox chemicals dashboard: An online resource for environmental chemists US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Chemicals Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Chemicals Dashboard and its value to the community as an informational hub. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Applications of the US EPA’s CompTox Chemistry Dashboard to support structure...
Applications of the US EPA’s CompTox Chemistry Dashboard to support structure...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This document discusses the CompTox Chemistry Dashboard, a publicly accessible website developed by the US EPA's National Center for Computational Toxicology. The dashboard provides data on over 760,000 chemicals, including physicochemical properties, bioactivity data, and links to other resources. It supports applications in structure identification and chemical forensics using mass spectrometry through features like batch searching by formula or mass, MS-ready chemical mappings, and predicted mass spectra. The dashboard is being expanded to include additional prediction models and web services to further enable non-targeted analysis using mass spectrometry data.Delivering access to chemistry and bioassay data from the National Center for...
Delivering access to chemistry and bioassay data from the National Center for...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Researchers at EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The goal of this research program is to quickly evaluate thousands of chemicals, but at a much reduced cost and shorter time frame relative to traditional approaches. The data generated by the Center includes characterization of thousands of chemicals across hundreds of high-throughput screening assays, consumer use and production information, pharmacokinetic properties, literature data, physical-chemical properties as well as the predictive computational modeling of toxicity and exposure. We have developed a number of databases and applications to deliver the data to the public, academic community, industry stakeholders, and regulators. This presentation will provide an overview of our work to develop an architecture that integrates diverse large-scale data from the chemical and biological domains, our approaches to disseminate these data, and the delivery of models supporting predictive computational toxicology. In particular, this presentation will review our new CompTox Chemistry Dashboard and the developing software architecture. This abstract does not reflect U.S. EPA policy.CompTox Chemicals Dashboard: Data and tools to support chemical and environme...
CompTox Chemicals Dashboard: Data and tools to support chemical and environme...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Information and data on chemicals is used by scientists to evaluate potential health and ecological risks due to environmental exposures. EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov) helps evaluate the safety of chemicals by providing public access to a variety of information on over 760,000 chemicals. Within the Dashboard, users can access chemical structures, chemistry information, toxicity data, hazard data, exposure information, and additional links to relevant websites and applications. These data are compiled from sources including EPA’s computational toxicology research databases, from public domain databases and with collaborators across the world. Chemical lists have been added that provide access to various classes of chemicals and project-based datasets are under constant development. Specific functionality has been delivered within the Dashboard to support mass spectrometry including “MS-ready forms” of chemical substances that would be detectable by mass spectrometry. Workflows have been developed to assist in candidate identification and have now been proven with multiple published studies. An integration path between the dashboard and MetFrag has also been established to provide users the significant benefits resulting from the marriage between the two applications. The datasets underpinning the dashboard are freely available (https://comptox.epa.gov/dashboard/downloads) for integration into third party databases. This presentation will provide an overview of the available data types and functionality of the dashboard prior to examining how it is developing to support mass spectrometry based analyses within the agency and for the community in general. This will include a review of our research efforts to enhance the dashboard using in silico MS/MS fragmentation prediction for spectral matching. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.New developments in delivering public access to data from the National Center...
New developments in delivering public access to data from the National Center...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The National Center for Computational Toxicology at the EPA has developed the CompTox Chemistry Dashboard to provide public access to toxicity and chemical property data. The dashboard integrates data from high-throughput screening, predicted properties, chemical hazard assessments, literature searches, and exposure information for over 760,000 chemicals. It allows users to search for chemicals individually or in batches, access detailed chemical pages, view predicted and experimental properties, and download open data. The dashboard is meant to be an integration hub that makes NCCT's data and models more accessible and reusable to other scientists.Using the US EPA’s CompTox Chemistry Dashboard for structure identification a...
Using the US EPA’s CompTox Chemistry Dashboard for structure identification a...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are advancing the identification of emerging contaminants in environmental matrices, improving the means by which exposure analyses can be conducted. However, confidence in structure identification of unknowns in NTA presents challenges to analytical chemists. Structure identification requires integration of complementary data types such as reference databases, fragmentation prediction tools, and retention time prediction models. The goal of this research is to optimize and implement structure identification functionality within the US EPA’s CompTox Chemistry Dashboard, an open chemistry resource and web application containing data for ~760,000 substances. Rank-ordering the number of sources associated with chemical records within the Dashboard (Data Source Ranking) improves the identification of unknowns by bringing the most likely candidate structures to the top of a search results list. Database searching has been further optimized with the generation of MS-Ready Structures. MS-Ready structures are de-salted, stripped of stereochemistry, and mixture separated to replicate the form of a chemical observed via HRMS. Functionality to conduct batch searching of molecular formulae and monoisotopic masses was designed and released to improve searching efforts. Finally, a scoring-based identification scheme was developed, optimized, and surfaced via the Dashboard using multiple data streams contained within the database underlying the Dashboard. The scoring-based identification scheme improved the identification of unknowns over previous efforts using data source ranking alone. Combining these steps within an open chemistry resource provides a freely available software tool for structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. A new web application, the CompTox Chemistry Dashboard provides access to data associated with ~720,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists.
The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identification based on non-targeted analysis studies using mass spectrometry. Chemical identification using both mass and formula-based searching utilizes rank-ordering of results via functional use statistics, thereby providing a solution to help prioritize chemicals for further review when detected in environmental media.
This presentation will provide an overview of the CompTox Dashboard, its capabilities for delivering data to the environmental toxicology community and how the architecture provides a foundation for the development of additional applications to support chemical risk assessment. This abstract does not reflect U.S. EPA policy.
Structure identification by Mass Spectrometry Non-Targeted Analysis using the...
Structure identification by Mass Spectrometry Non-Targeted Analysis using the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Identification of unknowns in mass spectrometry based non-targeted analyses (NTA) requires the integration of complementary pieces of data to arrive at a confident, consensus structure. Researchers use chemical reference databases, spectral matching, fragment prediction tools, retention time prediction tools, and a variety of other data to arrive at tentative, probable, and confirmed, if possible, identifications. With the diverse, robust data contained within the US EPA’s CompTox Chemistry Dashboard (https://comptox.epa.gov), the goal of this research is to identify and implement a harmonized identification tool and workflow using previously generated chemistry data. Data has been compiled from product use, functional use prediction models, environmental media occurrence prediction models, and PubMed references, among other sources. We will report on our development of a visualization tool whereby users can visualize the relative contribution of identification-based metrics on a list of candidate structures and observe the greatest likelihood of occurrence. These data and visualization tools support NTA identification via the Dashboard and demonstrate an open, accessible tool for all users of HRMS data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Development of a Tool for Systematic Integration of Traditional and New Appro...
Development of a Tool for Systematic Integration of Traditional and New Appro...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Multiple regulatory bodies (EPA, ECHA, Health Canada) are currently tasked with prioritizing chemicals for data collection and risk assessments. These prioritization efforts are in response to regulatory mandates to identify chemicals for further assessment. We have developed a web-based application that enables a rapid, flexible and transparent prioritization process. The tool includes multiple data streams related to human and ecological hazard, exposure, and physicochemical properties (persistence and bioaccumulation). For human hazard, the data streams include quantitative points of departure (PODs) that are compiled from multiple sources such as EPA ToxRefDB, ECHA, COSMOS; estimated PODs from high-throughput in vitro screening assays and computational models; and qualitative measurements and predictions of specific endpoints (e.g., genotoxicity, endocrine activity). For ecological hazard, quantitative PODs are taken from the EPA ECOTOX database. Exposure information includes production volume, quantitative predictions using the EPA ExpoCast and SHEDS models, biomonitoring data, and qualitative information such as media occurrence, use profiles and likelihood of consumer and childhood exposures. The use of the tool is illustrated by prioritizing chemicals related to TSCA and the Safer Choice Ingredient List. The underpinning data streams for this application are already available in the EPA CompTox Chemistry Dashboard and have been repurposed to deliver this application. This is in keeping with our overarching software development methodology of providing multiple “building blocks” in the form of databases, web services and visualization components to deliver fit-for purpose applications to the relevant audiences. This abstract does not necessarily represent U.S. EPA policy.Chemical identification of unknowns in high resolution mass spectrometry usin...
Chemical identification of unknowns in high resolution mass spectrometry usin...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted and suspect screening studies using high resolution mass spectrometry (HRMS) have revolutionized the detection of chemicals in complex matrices. However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. The US EPA has developed functionality within the CompTox Chemicals Dashboard (https://comptox.epa.gov) to address challenges related to data processing and analysis in HRMS. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will introduce the tools and combined workflow, including visualization and access via the CompTox Chemicals Dashboard. These tools, data, and visualization approaches within an open chemistry resource provides a publicly available software tool to support structure identification and non-targeted analyses. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.US-EPA Chemicals Dashboard and Applications to Digital Design of Molecules
US-EPA Chemicals Dashboard and Applications to Digital Design of MoleculesUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation at: Digital design of molecules and formulations (https://www.soci.org/events/ai-and-digitalisation/digital-design-of-molecules-and-formulations). The Chemicals Dashboard is a free web-based application from the United States Environmental Protection Agency that provides various types of data for ~900,000 chemicals. These data include physicochemical properties, in vivo and in vitro toxicity data and information regarding the presence of chemicals in commercial products, including formulation data where available. The dashboard allows for sourcing of data associated with singleton chemicals or a batch mode for downloading data for thousands of chemicals at a time. This presentation will provide an overview of the Dashboard, the myriad of data sources underpinning the application and potential applications of the dashboard.The EPA CompTox Chemistry Dashboard and Underpinning Software Architecture
The EPA CompTox Chemistry Dashboard and Underpinning Software Architecture US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The CompTox Chemistry Dashboard was developed by the Environmental Protection Agency’s National Center for Computational Toxicology. This dashboard has been architected in a manner that allows for the deployment of multiple “applications”, both as publicly available databases, and for deployment under the constraints of confidential business information (CBI). The public dashboard provide access to multiple types of data for ~750,000 chemicals. This includes, when available for a chemical substance, physicochemical parameters, toxicity and bioassay data, consumer use and analytical data. Fate, exposure, and hazard calculations can benefit from access to the data aggregation and curation efforts that underpin the public dashboard. Also, regulators can benefit from the integration of their own data within their closed infrastructure environments. This presentation will provide a review of the chemistry dashboard architecture and its present application providing access to data to the research and regulatory communities. We will also review present developments in the area of delivering an application programming interface, web services, and software components for integration into third party applications providing access to the data exposed via the dashboard. This abstract does not reflect U.S. EPA policy.US-EPA Chemicals Dashboard – an integrated data hub for environmental science
US-EPA Chemicals Dashboard – an integrated data hub for environmental scienceUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The US-EPA Chemicals Dashboard is an integrated data hub providing centralized access to environmental chemistry data to support EPA and partner decision making. It contains nearly 900,000 chemical substances with experimental and predicted physical/chemical properties, hazard, exposure, and toxicity data. Users can perform various search types including basic searches by chemical name/identifier, structure-based searches, and batch searches for lists of chemicals. Detailed chemical pages display curated data from sources like ToxCast/Tox21 along with linked analogous chemicals and real-time predictive models. The goal is to improve efficiency in chemical risk assessment through easy access to this centralized chemical data resource.Structure identification approaches using the EPA CompTox Chemicals Dashboard...
Structure identification approaches using the EPA CompTox Chemicals Dashboard...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The document discusses how the EPA's CompTox Chemicals Dashboard can be used to support mass spectrometry analyses for structure identification. The Dashboard contains data on over 800,000 chemicals including properties, lists, and links to other resources. It allows searching by formula, structure, and mass to find related chemicals. Candidate structures can be ranked using metadata. Predicted mass spectra from over 800,000 structures may also be accessible. The Dashboard integrates data to help identify unknown chemicals detected by mass spectrometry.US-EPA CompTox Chemicals Dashboard as a web-based data resource to help ident...
US-EPA CompTox Chemicals Dashboard as a web-based data resource to help ident...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted screening, targeted screening and suspect screening, as well as “Known Unknowns” and “Unknown Unknowns” are now common terms in the field of water analysis. While data processing can be highly automated, the identification of chemicals from extracted masses, formulae or fragmentation utilizes reference spectral libraries or identification and ranking of tentative candidate lists from large structure libraries. The US-EPA CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) provides access to data for ~875,000 substances, searchable by mass and formula and then ranked using associated meta-data. Cheminformatics approaches are also utilized to provide mapped relationships between individual substances and their “MS-Ready” (desalted, non-stereospecific) forms. This presentation will review how the freely available Dashboard application can be utilized to support structure identification using mass spectrometry and our efforts to enhance the application using computational spectral fragmentation and access to predicted data such as relative retention time index values and computed collision cross section values to support ion mobility spectrometry. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental C...
EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental C...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The US EPA CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a web-based application providing access to ~875,000 chemical substances and diverse data types including physicochemical property, toxicity and EPA’s ToxCast data. This presentation provided a live demo of the application and its benefits to members of ACS AGRO.The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Env...
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Env...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrate advances in biology, chemistry, exposure and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, legacy in vivo animal data, consumer use and production information, exposure models and chemical structure databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data, but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. Our web application, the CompTox Chemistry Dashboard provides access to data associated with ~750,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists.
The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identification based on non-targeted analysis studies using mass spectrometry. Chemical identification using both mass and formula-based searching utilizes rank-ordering of results via functional use statistics, thereby providing a solution to help prioritize chemicals for further review when detected in environmental media.
This presentation will provide an overview of the dashboard, its capabilities for delivering data to the environmental chemistry community and how the architecture provides a foundation for the development of additional applications to support chemical risk assessment. This abstract does not reflect U.S. EPA policy.
US-EPA Chemicals Dashboard – an integrated data hub for environmental science
US-EPA Chemicals Dashboard – an integrated data hub for environmental scienceUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The US-EPA Chemicals Dashboard is a web-based database and integrated data hub containing information on over 875,000 chemical substances. It includes experimental and predicted physicochemical properties, in vivo toxicity data, in vitro bioactivity screening results, and links to external resources. Key features include search capabilities, chemical profiles with summarized toxicity information, modules for literature searching and read-across, and batch searching and downloading of data for multiple chemicals. The goal is to provide a transparent, integrated resource to support computational toxicology and exposure science. Ongoing efforts focus on expanding the breadth of data and ensuring data quality through expert curation.US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for ...
US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Chemical risk assessment is both time-consuming and difficult because it requires the assembly of data for chemicals generally distributed across multiple sources. The US EPA CompTox Chemistry Dashboard is a publicly accessible web-based application providing access to various data streams on ~760,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, consumer product and functional use information and a myriad of related data of value to environmental scientists and toxicologists. At this stage of development, the public dashboard provides access to almost 20 predicted physicochemical and environmental fate and transport endpoints with full transparency in terms of model performance. Experimental and predicted human and ecological toxicity data are also available, as are in vitro to in vivo extrapolation dosimetry predictions and predicted exposure and functional use. In parallel to the CompTox Chemistry Dashboard we are developing RapidTox, a web-based application that enables a rapid, flexible and transparent prioritization process for sets of chemicals using several previously used workflows focused on scoring of traditional risk metrics and the inclusion of alternative hazard and exposure estimates. This presentation will give an overview of the CompTox Chemistry Dashboard, RapidTox, our approaches to building transparent and open prediction models, and our efforts to provide access to real time predictions. This abstract does not necessarily represent U.S. EPA policy.Adding complex expert knowledge into chemical database and transforming surfa...
Adding complex expert knowledge into chemical database and transforming surfa...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This document discusses adding complex expert knowledge about surfactants to chemical databases to aid in the identification of unknown compounds from wastewater samples. It describes how over 60% of peaks detected by high resolution mass spectrometry in wastewater samples are unknown. Literature data on surfactant properties and spectra were compiled and added to databases to support the identification of homologous series and complex mixtures present. A list of surfactants was developed and incorporated into toxicity databases to enable in silico modeling and computational mass spectrometry approaches to aid non-target screening. International collaboration is helping to establish a global exchange of suspect lists to support the identification of unknown contaminants.What's hot (20)
EPA CompTox chemicals dashboard: An online resource for environmental chemists
EPA CompTox chemicals dashboard: An online resource for environmental chemists
Applications of the US EPA’s CompTox Chemistry Dashboard to support structure...
Applications of the US EPA’s CompTox Chemistry Dashboard to support structure...
Delivering access to chemistry and bioassay data from the National Center for...
Delivering access to chemistry and bioassay data from the National Center for...
CompTox Chemicals Dashboard: Data and tools to support chemical and environme...
CompTox Chemicals Dashboard: Data and tools to support chemical and environme...
New developments in delivering public access to data from the National Center...
New developments in delivering public access to data from the National Center...
Using the US EPA’s CompTox Chemistry Dashboard for structure identification a...
Using the US EPA’s CompTox Chemistry Dashboard for structure identification a...
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...
Structure identification by Mass Spectrometry Non-Targeted Analysis using the...
Structure identification by Mass Spectrometry Non-Targeted Analysis using the...
Development of a Tool for Systematic Integration of Traditional and New Appro...
Development of a Tool for Systematic Integration of Traditional and New Appro...
Chemical identification of unknowns in high resolution mass spectrometry usin...
Chemical identification of unknowns in high resolution mass spectrometry usin...
US-EPA Chemicals Dashboard and Applications to Digital Design of Molecules
US-EPA Chemicals Dashboard and Applications to Digital Design of Molecules
The EPA CompTox Chemistry Dashboard and Underpinning Software Architecture
The EPA CompTox Chemistry Dashboard and Underpinning Software Architecture
US-EPA Chemicals Dashboard – an integrated data hub for environmental science
US-EPA Chemicals Dashboard – an integrated data hub for environmental science
Structure identification approaches using the EPA CompTox Chemicals Dashboard...
Structure identification approaches using the EPA CompTox Chemicals Dashboard...
US-EPA CompTox Chemicals Dashboard as a web-based data resource to help ident...
US-EPA CompTox Chemicals Dashboard as a web-based data resource to help ident...
EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental C...
EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental C...
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Env...
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Env...
US-EPA Chemicals Dashboard – an integrated data hub for environmental science
US-EPA Chemicals Dashboard – an integrated data hub for environmental science
US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for ...
US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for ...
Adding complex expert knowledge into chemical database and transforming surfa...
Adding complex expert knowledge into chemical database and transforming surfa...
Similar to Bringing it all together: A Web-based Database for Chemical and Biological Data to Support Environmental Toxicology
The US-EPA CompTox Chemicals Dashboard – an online data integration hub suppo...
The US-EPA CompTox Chemicals Dashboard – an online data integration hub suppo...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are advancing the identification of emerging contaminants in environmental matrices, improving the means by which exposure analyses can be conducted. However, confidence in structure identification of unknowns in NTA presents challenges to analytical chemists. Structure identification requires integration of complementary data types such as reference databases (either commercial or open databases), fragmentation prediction tools, and retention time prediction models. One goal of our research is to optimize and implement structure identification functionality within the US EPA’s CompTox Chemicals Dashboard, an open chemistry resource and web application containing data for ~900,000 substances. Database searching using mass or formula-based inputs has been optimized for structure identification using “MS-Ready Structures”: de-salted, stripped of stereochemistry, and mixture separated to replicate the form of a chemical observed via HRMS. Functionality to conduct batch searching of molecular formulae and monoisotopic masses has also been implemented. While the increasing number of free online databases are of value to support chemical structure verification and elucidation there are known issues regarding data quality and careful data curation is a very necessary part of the development of these resources. This presentation will provide an overview of our latest enhancements to the dashboard to support mass spectrometry, incorporation of specific datasets (e.g., to support breath research (the volatilome) and household dust analysis), and the value of metadata and predicted fragmentation spectral matching to support structure identification. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Delivering an integrated data hub for per- and polyfluoroalkyl (PFAS) chemica...
Delivering an integrated data hub for per- and polyfluoroalkyl (PFAS) chemica...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
There is increasing interest in the environmental impact of per- and polyfluoroalkyl substances (PFAS) chemicals and the aggregation of related data provides both agency and public access to support research. The US-EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a publicly accessible website providing access to data for ~900,000 chemical substances, including thousands of PFAS chemicals. The dashboard provides access to a wide array of experimental and predicted physicochemical properties, in vitro bioactivity and in vivo toxicity data, product use information and integrated linkages to a growing list of literature, toxicology, and analytical chemistry websites. The assembly of data has required hundreds of hours of manual curation and data checking to deliver a number of segregated lists of PFAS chemicals. Experimental data extracted from literature articles has allowed the optimization of QSAR models for the prediction of properties such as logP (octanol-water partition) and aqueous solubility. This presentation will provide an overview of the dashboard, the ongoing expansion of the PFAS chemical library, with associated categorization, and new physicochemical property and environmental fate and transport QSAR prediction models being developed for these chemicals. Our progress in the measurement and analysis of bioactivity data for PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Proof-of-Concept Publicly Accessible Data Dashboards from the US-EPA.pptx
Proof-of-Concept Publicly Accessible Data Dashboards from the US-EPA.pptxUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The US-EPA first delivered the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) to the community in 2016 and it has become one of the definitive online resources for sourcing chemical toxicity data. Used by thousands of scientists a day, the stability, uptime and data quality for such a production resource is critical. The assembly of increasingly diverse data types and approaches to interrogating and delivering such data is best investigated by the delivery of proof-of-concept applications for community feedback. This has been achieved by the delivery of the EPA Cheminformatics Modules (https://www.epa.gov/comptox-tools/cheminformatics).
Methods
The Cheminformatics Modules suite of tools is available to the community and delivers novel approaches for the hazard profiling of chemicals, QSAR batch prediction of physiochemical properties and toxicological endpoints, structure alerts based on structure and substructure, and profiling of chemicals using ToxPrint chemotypes using enrichment statistics associated with ToxCast in vitro bioactivity screening. These modules provide access to new capabilities not presently available to users of the Dashboard and enable new analyses for users interested in applications of computational toxicology data and resources.
Results
The Cheminformatics Modules have been used by multiple EPA regional offices, program offices and state offices to source data and perform analyses in terms of alternatives assessment for chlorinated solvents, aggregation of data related to chemicals of emerging concern (e.g., 6PPD and related phenylenediamines) and to support the development of state specific prioritization lists for chemicals. The modules are being used to provide access to data for emergency responders and onsite coordinators and is presently being expanded with safety data sourced from PubChem to provide GHS data, transportation details, and details regarding regulatory screening levels associated with federal and state specific guidelines. The ease of use of the modules has made the harvesting of data faster and easier for a breadth of general stakeholders as screening data for use in potential decision making.
Conclusions
The delivery of chemistry, toxicity, exposure and related data from the US-EPA’s Center for Computational Toxicology and Exposure to the community is facilitated using a number of web-based applications. Proof-of-concept tools provide a means by which to deliver novel search, visualization and data delivery approaches for testing and feedback prior to adding the capabilities into production-level tools.
This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Accessing information for Per- & Polyfluoroalkyl Substances using the US EPA ...
Accessing information for Per- & Polyfluoroalkyl Substances using the US EPA ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases within the DSSTox project, and providing accurate linkages of data to chemical structures, exposure and hazard information. The data are made available via the EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard), a publicly accessible website providing access to data for ~760,000 chemical substances, the majority of these represented as chemical structures. The web application delivers a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data, as well as integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. In addition, several specific search types are in development to directly support the mass spectrometry non-targeted screening community, enabling cohesive workflows to support data generation for the detection and assessment of environmental exposures to chemicals contained within DSSTox. The application provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders, including, for example, scientists interested in Per- & Polyfluoroalkyl Substances (PFAS). Added lists include those sourced from the European Union as well as developed in-house and now containing thousands of chemicals. A procured testing library of hundreds of PFAS chemicals, with a portion of the list annotated into chemical categories, has been integrated into the dashboard with a number of resulting benefits: a searchable database of chemical properties, with hazard and exposure predictions, and links to the open literature. This presentation will provide an overview of the dashboard, the developing library of PFAS chemicals and associated categorization, and efforts underway to develop new physicochemical property and environmental fate and transport QSAR prediction models developed for these chemicals. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Sourcing chemical hazard and safety data for PFAS chemicals via a US-EPA onli...
Sourcing chemical hazard and safety data for PFAS chemicals via a US-EPA onli...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
In recent years the Center for Computational Toxicology and Exposure at the US Environmental Protection Agency has delivered a number of valuable web-based applications which provide access to a myriad of data types for hundreds of thousands of chemicals. The data include property data, in vivo and in vitro hazard data, exposure data, and numerous other data types of interest to the scientific community. To date the preeminent application delivered by the center is the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) which presently delivers data for over 1.2 million chemicals. One aspect of delivering highly functional mature production software systems is the development of proof-of-concept applications to garner community interest in novel ways of interrogating and visualizing data. These tools include the Hazard Profile and Safety Profile modules which integrate publicly available data streams into a web-based interface delivering information regarding nine categories of GHS data (the Globally Harmonized System of Classification and Labeling of Chemicals), details regarding measures of accidental release (including cleanup and disposal), and firefighting measures. This presentation will provide an overview of publicly available proof-of-concept modules and new tools in development delivering access to chemistry-related data to a variety of stakeholders. Specific examples will be provided regarding how data for PFAS chemicals and those chemicals associated with AFFF mixtures can be sourced from the tools. Disclaimer: The views expressed in this article are those of the authors and do not necessarily represent the views or policies of the US EPA.Targeted Lists of Chemicals to Support Non-Targeted Analysis via the US-EPA C...
Targeted Lists of Chemicals to Support Non-Targeted Analysis via the US-EPA C...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted analysis (NTA) uses high-resolution mass spectrometry to better understand the identity of a wide variety of chemicals present in environmental samples (and other matrices). However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. Analysis of the resultant mass spectrometry information relies on cheminformatics to identify and rank chemicals and the US EPA has developed functionality within the US-EPA CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) to address challenges related to this analysis. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. A number of chemical lists (https://comptox.epa.gov/dashboard/chemical_lists) have also been developed to support specific applications including the identification of chemicals in human breath (i.e., the volatilome), chemicals in human media (e.g., blood, saliva), and in water. Other lists include PFAS (per- and polyfluoroalkyl substances) chemicals and toxins (e.g.. microcystins and cyanotoxins). Combining the synergies of a database containing ~900,000 chemicals with over 200 segregated chemical lists with dashboard search functionality into a comprehensive workflow provides a powerful tool to support NTA. This poster will review how the CompTox Chemicals Dashboard provides a freely available web-based application to support structure identification and NTA and how expansion of the types of data hosted in the database can support different targeted and non-targeted projects. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Precompetitive preclinical ADME/tox data and set it free on the web to facili...
Precompetitive preclinical ADME/tox data and set it free on the web to facili...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The document proposes making preclinical absorption, distribution, metabolism, excretion and toxicity (ADME/Tox) data freely available online to facilitate drug development. Such preclinical data is currently expensive to generate but is pre-competitive in nature. The authors suggest curating literature and patent data, soliciting data donations from pharmaceutical companies, and expanding databases like ChemSpider to include ADME/Tox data. This would help researchers avoid repeating failed studies and improve computational modeling of drug properties.Delivering chemical-associated data via EPA web applications
Delivering chemical-associated data via EPA web applicationsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at the conference: "Cheminformatics Resources of U.S. Governmental Organizations" and focuses on the CompTox Chemicals Dashboard and the sharing of our data https://www.fda.gov/news-events/fda-meetings-conferences-and-workshops/cheminformatics-resources-us-governmental-organizations-05092022#event-information Energy files
EnergyFiles is a virtual library of energy-related scientific and technical information created by the US Department of Energy. It provides access to various collections including journal articles, technical reports, electronic preprints, and bibliographic databases containing over 2 million records. The Energy Citations Database within EnergyFiles contains citations and abstracts of literature from fields related to the work of the Department of Energy. Users can search individual databases or search across multiple collections simultaneously through the EnergyFiles portal.
EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental C...
EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental C...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The CompTox Chemicals Dashboard (available at https://comptox.epa.gov/dashboard) is the latest in a suite of dashboards that have been delivered to the community by EPA’s National Center for Computational Toxicology. The dashboard delivers access to data for >875,000 chemicals and includes experimental and predicted physicochemical properties, hazard and exposure data, access to Toxcast/Tox21 bioactivity screening data and provides a link farm to dozens of other online resources. The dashboard delivers access to data with a variety of powerful search capabilities including searching by chemical identifier (e.g. CAS Number or Name), by commercial product type, or by mass or formula. Searches can be performed one chemical at a time or in batches of thousands. Whether you are a chemist, an analytical scientist or a toxicologist the dashboard is of value as it seamlessly integrates data from dozens of databases into a web-based user experience. Other integrated modules include real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed and almost 30 million publication abstracts. The data and functionality available via the dashboard can be of value in terms of decontamination by providing access to data to assist in detection (specifically via mass spectrometric detection), accessing literature and potential decontamination approaches associated with specific chemicals, and access to toxicity values for chemicals such as Military Exposure Guidelines. This presentation will provide an overview of the CompTox Chemicals Dashboard and how it has developed into an integrated data hub for environmental data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection AgencyDelivering The Benefits of Chemical-Biological Integration in Computational T...
Delivering The Benefits of Chemical-Biological Integration in Computational T...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Researchers at EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The goal of this research program is to quickly evaluate thousands of chemicals, but at a much reduced cost and shorter time frame relative to traditional approaches. The data generated by the Center includes characterization of thousands of chemicals across hundreds of high-throughput screening assays, consumer use and production information, pharmacokinetic properties, literature data, physical-chemical properties as well as the predictive computational modeling of toxicity and exposure. We have developed a number of databases and applications to deliver the data to the public, academic community, industry stakeholders, and regulators. This presentation will provide an overview of our work to develop an architecture that integrates diverse large-scale data from the chemical and biological domains, our approaches to disseminate these data, and the delivery of models supporting predictive computational toxicology. In particular, this presentation will review our new publicly-accessible CompTox Dashboard as the first application built on our newly developed architecture. This abstract does not reflect U.S. EPA policy. DMCM2018 Community Resources Connecting Chemistry and Toxicity Knowledge
Community Resources Connecting Chemistry and Toxicity Knowledge to Environmental Observations presented at the Disease Map Community Meeting 2018 in Paris
Delivering The Benefits of Chemical-Biological Integration in Computational T...
Delivering The Benefits of Chemical-Biological Integration in Computational T...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Researchers at the EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The intention of this research program is to quickly evaluate thousands of chemicals for potential risk but with much reduced cost relative to historical approaches. This work involves computational and data driven approaches including high-throughput screening, modeling, text-mining and the integration of chemistry, exposure and biological data. We have developed a number of databases and applications that are delivering on the vision of developing a deeper understanding of chemicals and their effects on exposure and biological processes that are supporting a large community of scientists in their research efforts. This presentation will provide an overview of our work to bring together diverse large scale data from the chemical and biological domains, our approaches to integrate and disseminate these data, and the delivery of models supporting computational toxicology. This abstract does not reflect U.S. EPA policy.ChemSpider as a hub for online chemical information resources
ChemSpider as a hub for online chemical information resources US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The World Wide Web continues to have an expanding and profound effect on providing access to chemical information. A chemist may wish to know a variety of information about a given chemical compound including physical and chemical properties, molecular structure, spectral data, synthetic methods, known reactions, safety information, and systematic nomenclature and chemical names. In the past, having access to this variety of information required a small library of different reference works, since no one resource contained all this data. This was problematic both in terms of cost and physical space for storage. Now there is a single web site that not only provides all this information for millions of compounds but also is free. This website is the Royal Society of Chemistry’s ChemSpider 2015-02-10 The Open PHACTS Discovery Platform: Semantic Data Integration for ...
The Open PHACTS Discovery Platform integrates multiple biomedical data resources into a single open access point using semantic web technology. It is guided by business questions from pharmaceutical companies to integrate data from sources like ChEMBL, DrugBank, UniProt, and more. The platform is run as a public-private partnership through 2021 to support drug discovery.
The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...
The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
As part of our efforts to develop a public platform to provide access to predictive models we have attempted to disentangle the influence of the quality versus quantity of data available to develop and validate QSAR models. Using a thorough manual review of the data underlying the well-known EPI Suite software, we developed automated processes for the validation of the data using a KNIME workflow. This includes: approaches to validate different chemical structure representations (e.g. molfile and SMILES), identifiers (chemical names and registry numbers), and methods to standardize the data into QSAR-consumable formats for modeling. Our efforts to quantify and segregate data into various quality categories has allowed us to thoroughly investigate the resulting models developed from these data slices, as well as allowing us to examine whether or not efforts into the development of large high-quality datasets has the expected pay-off in terms of prediction performance. Machine-learning approaches have been applied to create a series of models that have been used to generate predicted physicochemical and environmental parameters for over 700,000 chemicals. These data are available online via the EPA’s iCSS Chemistry Dashboard. This abstract does not reflect U.S. EPA policy.Chemistry data delivery from the US-EPA to support environmental chemistry
Chemistry data delivery from the US-EPA to support environmental chemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
In recent years, the growth of scientific data and the increasing need for data sharing and collaboration in the field of environmental chemistry has led to the creation of various software and databases that facilitate research and development into the safety and toxicity of chemicals. The US-EPA Center for Computational Toxicology and Exposure has been developing software and databases that serve the chemistry community for many years. This presentation will focus on several web-based software applications which have been developed at the US-EPA and made available to the community. While the primary software application from the Center is the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard), almost a dozen proof-of-concept applications have been built serving various capabilities. The publicly accessible Cheminformatics Modules (https://www.epa.gov/chemical-research/cheminformatics) provides access to six individual modules to allow for hazard comparison for sets of chemicals, structure-substructure-similarity searching, structure alerts and batch QSAR prediction of both physicochemical and toxicity endpoints. A number of other applications in development include a chemical transformations database and a database of analytical methods and open mass spectral data. Each of these depends on the underlying DSSTox chemicals database, a rich source of chemistry data for over 1.2 million chemical substances. To further extend the accessibility and usability of this vast repository, we have developed RESTful Public APIs hosted on the secure cloud.gov environment, enabling seamless integration of this rich data into computational biology pipelines and web visualizations. We will provide an overview of all tools in development, the integrated nature of the applications based on the underlying chemistry data, and the API which is now publicly available. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.US EPA CompTox Chemicals Dashboard Data Integration Hub to Support Environmen...
US EPA CompTox Chemicals Dashboard Data Integration Hub to Support Environmen...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
A presentation given at the Global Marine Summit at UNC Wilmington on October 9th 2019. The focus of the presentation was an overview of the EPA CompTox Chemicals Dashboard with a specific focus on providing access to data to chemicals such as algal toxins and mycotoxins. Web-based access to experimental and predicted data for environmental fate, t...
Web-based access to experimental and predicted data for environmental fate, t...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This document describes the CompTox Chemistry Dashboard, a publicly accessible website developed by the EPA's National Center for Computational Toxicology that provides data on over 762,000 chemicals. The dashboard contains experimental and predicted physicochemical property data, environmental fate and transport data, toxicity data, and models. It allows users to search, view detailed chemical pages, access prediction reports, perform batch searches, and will integrate additional predicted properties and data in the future. The goal is to provide a central resource for computational toxicology data to support chemical safety assessments.Delivering web-based access to data and algorithms to support computational t...
Delivering web-based access to data and algorithms to support computational t...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The US-EPA National Center for Computational Toxicity (NCCT) has been generating data and building software applications and web-based chemistry databases for over a decade. During this period the center has analyzed thousands of chemicals in hundreds of bioassays, has researched high-throughput physicochemical property measurements and investigated approaches for high throughput toxicokinetics. NCCT continues to expand the battery of assays and number of chemicals under examination and is now investigating the application of transcriptomics. In parallel to these experimental efforts, and to support our efforts to develop new approaches to prioritize chemicals based on potential human health risks, we aggregate and curate data streams of various types to support prediction models. Over the past few years some of the data have been delivered through prototype web-based “dashboards” for public consumption. The latest of these web applications, the CompTox Chemicals Dashboard, is an integrated access point to obtain information associated with 875,000 chemical substances and providing experimental and predicted data of various types. This includes physicochemical and fate and transport data, bioactivity data, exposure data and integrated literature searches. Real-time predictions and generalized read-across are possible and advanced search capabilities are available to support EPA-related projects including mass spectrometry non-targeted analysis. This presentation will provide an overview of the CompTox Chemicals Dashboard and the its role in delivering access to the outputs of NCCT. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Similar to Bringing it all together: A Web-based Database for Chemical and Biological Data to Support Environmental Toxicology (20)
The US-EPA CompTox Chemicals Dashboard – an online data integration hub suppo...
The US-EPA CompTox Chemicals Dashboard – an online data integration hub suppo...
Delivering an integrated data hub for per- and polyfluoroalkyl (PFAS) chemica...
Delivering an integrated data hub for per- and polyfluoroalkyl (PFAS) chemica...
Proof-of-Concept Publicly Accessible Data Dashboards from the US-EPA.pptx
Proof-of-Concept Publicly Accessible Data Dashboards from the US-EPA.pptx
Accessing information for Per- & Polyfluoroalkyl Substances using the US EPA ...
Accessing information for Per- & Polyfluoroalkyl Substances using the US EPA ...
Sourcing chemical hazard and safety data for PFAS chemicals via a US-EPA onli...
Sourcing chemical hazard and safety data for PFAS chemicals via a US-EPA onli...
Targeted Lists of Chemicals to Support Non-Targeted Analysis via the US-EPA C...
Targeted Lists of Chemicals to Support Non-Targeted Analysis via the US-EPA C...
Precompetitive preclinical ADME/tox data and set it free on the web to facili...
Precompetitive preclinical ADME/tox data and set it free on the web to facili...
Delivering chemical-associated data via EPA web applications
Delivering chemical-associated data via EPA web applications
EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental C...
EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental C...
Delivering The Benefits of Chemical-Biological Integration in Computational T...
Delivering The Benefits of Chemical-Biological Integration in Computational T...
DMCM2018 Community Resources Connecting Chemistry and Toxicity Knowledge
DMCM2018 Community Resources Connecting Chemistry and Toxicity Knowledge
Delivering The Benefits of Chemical-Biological Integration in Computational T...
Delivering The Benefits of Chemical-Biological Integration in Computational T...
ChemSpider as a hub for online chemical information resources
ChemSpider as a hub for online chemical information resources
2015-02-10 The Open PHACTS Discovery Platform: Semantic Data Integration for ...
2015-02-10 The Open PHACTS Discovery Platform: Semantic Data Integration for ...
The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...
The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...
Chemistry data delivery from the US-EPA to support environmental chemistry
Chemistry data delivery from the US-EPA to support environmental chemistry
US EPA CompTox Chemicals Dashboard Data Integration Hub to Support Environmen...
US EPA CompTox Chemicals Dashboard Data Integration Hub to Support Environmen...
Web-based access to experimental and predicted data for environmental fate, t...
Web-based access to experimental and predicted data for environmental fate, t...
Delivering web-based access to data and algorithms to support computational t...
Delivering web-based access to data and algorithms to support computational t...
Recently uploaded
Compexometric titration/Chelatorphy titration/chelating titration
Classification
Metal ion ion indicators
Masking and demasking reagents
Estimation of Magnisium sulphate
Calcium gluconate
Complexometric Titration/ chelatometry titration/chelating titration, introduction, Types-
1.Direct Titration
2.Back Titration
3.Replacement Titration
4.Indirect Titration
Masking agent, Demasking agents
formation of complex
comparition between masking and demasking agents,
Indicators/Metal ion indicators/ Metallochromic indicators/pM indicators,
Visual Technique,PM indicators (metallochromic), Indicators of pH, Redox Indicators
Instrumental Techniques-Photometry
Potentiometry
Miscellaneous methods.
Complex titration with EDTA.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
在线办理(salfor毕业证书)索尔福德大学毕业证毕业完成信一模一样
学校原件一模一样【微信：741003700 】《(salfor毕业证书)索尔福德大学毕业证》【微信：741003700 】学位证，留信认证（真实可查，永久存档）原件一模一样纸张工艺/offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。
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Travis Hills of MN is Making Clean Water Accessible to All Through High Flux ...
By harnessing the power of High Flux Vacuum Membrane Distillation, Travis Hills from MN envisions a future where clean and safe drinking water is accessible to all, regardless of geographical location or economic status.
Micronuclei test.M.sc.zoology.fisheries.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
Mending Clothing to Support Sustainable Fashion_CIMaR 2024.pdf
Ozturkcan, S., Berndt, A., & Angelakis, A. (2024). Mending clothing to support sustainable fashion. Presented at the 31st Annual Conference by the Consortium for International Marketing Research (CIMaR), 10-13 Jun 2024, University of Gävle, Sweden.
Authoring a personal GPT for your research and practice: How we created the Q...
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
11.1 Role of physical biological in deterioration of grains.pdf
Storagedeteriorationisanyformoflossinquantityandqualityofbio-materials.
Themajorcausesofdeteriorationinstorage
•Physical
•Biological
•Mechanical
•Chemical
Storageonlypreservesquality.Itneverimprovesquality.
Itisadvisabletostartstoragewithqualityfoodproduct.Productwithinitialpoorqualityquicklydepreciates
The debris of the ‘last major merger’ is dynamically young
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
Immersive Learning That Works: Research Grounding and Paths Forward
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
Farming systems analysis: what have we learnt?.pptx
Presentation given at the official farewell of Prof Ken Gillet at Wageningen on 13 June 2024
Recently uploaded (20)
Compexometric titration/Chelatorphy titration/chelating titration
Compexometric titration/Chelatorphy titration/chelating titration
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
Travis Hills of MN is Making Clean Water Accessible to All Through High Flux ...
Travis Hills of MN is Making Clean Water Accessible to All Through High Flux ...
Mending Clothing to Support Sustainable Fashion_CIMaR 2024.pdf
Mending Clothing to Support Sustainable Fashion_CIMaR 2024.pdf
Basics of crystallography, crystal systems, classes and different forms
Basics of crystallography, crystal systems, classes and different forms
Authoring a personal GPT for your research and practice: How we created the Q...
Authoring a personal GPT for your research and practice: How we created the Q...
11.1 Role of physical biological in deterioration of grains.pdf
11.1 Role of physical biological in deterioration of grains.pdf
The debris of the ‘last major merger’ is dynamically young
The debris of the ‘last major merger’ is dynamically young
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Immersive Learning That Works: Research Grounding and Paths Forward
Immersive Learning That Works: Research Grounding and Paths Forward
Farming systems analysis: what have we learnt?.pptx
Farming systems analysis: what have we learnt?.pptx
Juaristi, Jon. - El canon espanol. El legado de la cultura española a la civi...
Juaristi, Jon. - El canon espanol. El legado de la cultura española a la civi...
Bringing it all together: A Web-based Database for Chemical and Biological Data to Support Environmental Toxicology
- 1. Innovative Research for a Sustainable Futurewww.epa.gov/research ORCID: 0000-0002-2668-4821 Antony Williams l williams.antony@epa.gov l 919-541-1033 Bringing it all together: A web-based database for chemical and biological data to support environmental toxicology Antony Williams1, Chris Grulke1, Sean Watford1, Rebecca Jolley1, Jeremy Dunne1, Elizabeth Edmiston1 and Jeff Edwards1 1U.S. Environmental Protection Agency, Office of Research and Development, National Center for Computational Toxicology, Research Triangle Park, NC ACS Fall 2017 Washington, DC August 20-24, 2017 The EPA Comptox Chemistry Dashboard is a web-based application providing access to a set of data resources provided by the National Center of Computational Toxicology. Diverse data types associated with ~760,000 chemical substances are delivered through the application. These data include bioassay screening results (associated with the ToxCast project), physicochemical and toxicological endpoints (both experimental and predicted), and consumer product and functional use data. Access to tens of millions of predicted property values associated with the chemicals on the dashboard includes detailed calculation reports for the OPERA models [1]. The dashboard is an integration hub for ~70 public resources using cross website linking. This helps the user navigate to other data and information for a particular chemical on other websites. The application also provides integrated literature searches for chemical related information using Google Scholar and PubMed. Advanced searching capabilities provide molecular formula and mass- based searching to support non-targeted analysis for mass spectrometry, a key area of research at the US Environmental Protection Agency. A batch search also allows users to search using inputs of thousands of chemical names or CAS Registry Numbers and download details regarding the availability of bioassay, exposure and toxicity data. Much of the data on the dashboard is available as Open Data via a downloads page. This allows third parties to integrate these data into their own applications and link back to the dashboard chemical pages. The underpinning architecture has been developed in a manner allowing for the release of the dashboard as a public resource as well as for delivering research applications internal to the U.S. EPA. Specifically the dashboard, and new modules are being assessed for potential applications to support risk assessment. The CompTox Chemistry Dashboard Abstract For records with chemical structure representations, various inherent properties (e.g. formula and mass) and predicted physicochemical properties (logP, water solubility etc.) are provided. The landing page of the dashboard is a simple text entry box allowing a type-ahead search for systematic, trade and trivial names, CAS Registry Numbers and InChIs. Dashboard Entry Page Chemical Record Page: Atrazine Chemical Properties Panel Where possible, links are provided to related Wikipedia articles. An associated mol file is available for download to the desktop, and a summary report containing record data can be provided as a PDF file. Accessing ~100 Million Predicted Properties Online Future Work The dashboard provides access to ~760,000 chemicals and integrates curated experimental data [1] used to produce OPEn saR Application (OPERA) models. All chemicals were passed through the prediction models and detailed model reports showing global and local applicability domains and nearest neighbor results are displayed in the application. The QSAR Modeling Report Formats (QMRF) for each model are available for each predicted endpoint. References 1. Mansouri et al. An automated curation procedure for addressing chemical errors and inconsistencies in public datasets in QSAR modelling, SAR QSAR Environ Res. 2016 Nov;27(11):939-965. 2. EPA Toxicity Estimation Software Tool (T.E.S.T.) software http://www.epa.gov/chemical-research/toxicity-estimation-software-tool-test • Continue to expand the data in terms of chemicals, toxicity data, additional experimental data. • Provide access to the data via a suite of web services and fully documented API. • Release NCCT models as interactive online prediction tools in the near future via the dashboard. A summary of available chemical properties for Bisphenol A The MP prediction model report for BPA – including nearest neighbors. Problem Definition and Goals Problem: There are many freely available data available online to support computational toxicology in environmental science, but an easy way to access available data across multiple sites is lacking. Goals: To deliver online access via a simple to use web-based interface supporting diverse types of data associated with environmental chemistry, and specifically computational toxicology. To make the data available for ~760,000 chemical substances available as downloadable data for reuse and repurposing in other databases. Toxicity Values Panel Bioassays: ToxCast Data The Toxicity Values tab provides access to data assembled from a series of public resources including EPA data (i.e. IRIS and PPRTV reports, ToxRef DB). Data can be downloaded as TSV and Excel files. The ToxCast Bioassay data measured over the past decade is accessible via the dashboard under the Bioassays Tab. PubChem bioassays data are also available. Data can be downloaded as Excel files. Future Work The authors would like to acknowledge specific colleagues within our center for their contributions to the development of the dashboard: Todd Martin, Nancy Baker, Richard Judson and John Wambaugh. This presentation does not necessarily represent the views or policies of the U.S. Environmental Protection Agency. Predicted data from the EPA’s Toxicity Estimation Software Tool (T.E.S.T) [2] is also available. This includes physicochemical and toxicity prediction models.