Cheminformatics Tools to Access Data for PFAS and Constituents of Fluorine-Free Foams
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A number of cheminformatics tools have been developed in recent years in the Computational Chemistry & Cheminformatics Branch (CCCB) of the Center for Computational Toxicology and Exposure. The DSSTox chemistry database underpins all cheminformatics tools and provides the foundation for multiple Dashboards including the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) and the proof-of-concept Cheminformatics Tools (https://www.epa.gov/chemical-research/cheminformatics). These applications provide access to property, hazard, exposure and safety data. This presentation will give an overview of available tools and how they may serve research applications regarding fluorine-free foams.
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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 ~880,000 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 the database. 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 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 new physicochemical property and environmental fate and transport QSAR prediction models developed for these chemicals. The application of the dashboard to support mass spectrometry non-targeted analysis studies for the identification of PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...
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The EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a publicly accessible website providing access to data for ~770,000 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, product use information extracted from safety data sheets, and integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. The application provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders, including Per- & Polyfluoroalkyl Substances (PFAS) containing thousands of chemicals. A procured testing library of hundreds of PFAS chemicals 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. Several specific search types have been developed 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. 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 developed for these chemicals. The application of the dashboard to support mass spectrometry non-targeted analysis studies for the identification of PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency. The US-EPA CompTox Chemicals Dashboard – an information hub for over five tho...
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EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases and providing accurate linkages of data to chemical structures, exposure and hazard information. The data are being made available via the EPA’s CompTox Chemistry Dashboard (https://comptox.epa.gov/dashboard), a publicly accessible website providing access to data for almost 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 spectroscopy non-targeted screening community, who are generating important data for detecting and assessing environmental exposures to chemicals contained within DSSTox. The application provides access to segregated lists of chemicals that are of specific interests to relevant stakeholders including, for example, scientists interested in algal toxins and hydraulic fracturing chemicals. This presentation will provide an overview of the challenges associated with the curation of data from EPA’s December 2016 Hydraulic Fracturing Drinking Water Assessment Report that represented chemicals reported to be used in hydraulic fracturing fluids and those found in produced water. The data have been integrated into the dashboard with a number of resulting benefits: a searchable database of chemical properties, with hazard and exposure predictions, and open literature. The application of the dashboard to support mass spectrometry non-targeted analysis studies will also be reviewed. This abstract does not reflect U.S. EPA policy.Accessing information for chemicals in hydraulic fracturing fluids using the ...
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Per- and polyfluoroalkyl substances (PFAS) are a group of fluorinated substances that have generated increased public attention due to their potential health hazard and widespread presence in the environment. An attempt to define PFAS and establish standard categories was established in Buck et al. 2011. Since then, various groups, including the Organization for Economic Co-operation and Development and U.S. Environmental Protection Agency, have defined PFAS differently to serve their respective needs. The U.S. EPA’s CompTox Chemicals Dashboard is a public resource providing access to predicted or experimental data for ~900,000 chemical substances, the majority with defined structures, and with data types including hazard, bioactivity, property, and exposure data. With the increased attention given to PFAS, efforts have been dedicated to the assembly and curation of thousands of PFAS substances into the DSSTox database underlying the Dashboard. A set of more than 30 PFAS lists spanning EPA and international regulatory interests, as well as lists pertaining to research activities and analytical methods, are currently delivered via the Dashboard. Depending on the definition of what is deemed to be a PFAS, approximately 6,000 to upwards of 38,000 compounds currently in the Dashboard could be considered PFAS. We have defined an inventory of over 10,000 PFAS structures (the PFASSTRUC list) using a set of clearly defined structural filters that encompass current EPA programmatic interests. This list is serving as a benchmark for the community to apply cheminformatics approaches and better understand and survey the scope of PFAS chemistries of potential concern. PFASSTRUC was compared to several other structure-based definitions of PFAS to investigate what type of structures do and do not meet the definitions and thus what similar structures may be considered PFAS by some but not others. Such resources can help support the PFAS community to better frame the PFAS problem and aid in the development of categorization approaches for PFAS, as well as support the reporting of relevant data for the agency. Abstract does not reflect EPA policy. Comparison of lists of per- and polyfluoroalkyl substances (PFAS) based on di...
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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 ~880,000 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 the database. 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 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 new physicochemical property and environmental fate and transport QSAR prediction models developed for these chemicals. The application of the dashboard to support mass spectrometry non-targeted analysis studies for the identification of PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...
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The EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a publicly accessible website providing access to data for ~770,000 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, product use information extracted from safety data sheets, and integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. The application provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders, including Per- & Polyfluoroalkyl Substances (PFAS) containing thousands of chemicals. A procured testing library of hundreds of PFAS chemicals 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. Several specific search types have been developed 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. 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 developed for these chemicals. The application of the dashboard to support mass spectrometry non-targeted analysis studies for the identification of PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency. The US-EPA CompTox Chemicals Dashboard – an information hub for over five tho...
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EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases and providing accurate linkages of data to chemical structures, exposure and hazard information. The data are being made available via the EPA’s CompTox Chemistry Dashboard (https://comptox.epa.gov/dashboard), a publicly accessible website providing access to data for almost 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 spectroscopy non-targeted screening community, who are generating important data for detecting and assessing environmental exposures to chemicals contained within DSSTox. The application provides access to segregated lists of chemicals that are of specific interests to relevant stakeholders including, for example, scientists interested in algal toxins and hydraulic fracturing chemicals. This presentation will provide an overview of the challenges associated with the curation of data from EPA’s December 2016 Hydraulic Fracturing Drinking Water Assessment Report that represented chemicals reported to be used in hydraulic fracturing fluids and those found in produced water. The data have been integrated into the dashboard with a number of resulting benefits: a searchable database of chemical properties, with hazard and exposure predictions, and open literature. The application of the dashboard to support mass spectrometry non-targeted analysis studies will also be reviewed. This abstract does not reflect U.S. EPA policy.Accessing information for chemicals in hydraulic fracturing fluids using the ...
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Per- and polyfluoroalkyl substances (PFAS) are a group of fluorinated substances that have generated increased public attention due to their potential health hazard and widespread presence in the environment. An attempt to define PFAS and establish standard categories was established in Buck et al. 2011. Since then, various groups, including the Organization for Economic Co-operation and Development and U.S. Environmental Protection Agency, have defined PFAS differently to serve their respective needs. The U.S. EPA’s CompTox Chemicals Dashboard is a public resource providing access to predicted or experimental data for ~900,000 chemical substances, the majority with defined structures, and with data types including hazard, bioactivity, property, and exposure data. With the increased attention given to PFAS, efforts have been dedicated to the assembly and curation of thousands of PFAS substances into the DSSTox database underlying the Dashboard. A set of more than 30 PFAS lists spanning EPA and international regulatory interests, as well as lists pertaining to research activities and analytical methods, are currently delivered via the Dashboard. Depending on the definition of what is deemed to be a PFAS, approximately 6,000 to upwards of 38,000 compounds currently in the Dashboard could be considered PFAS. We have defined an inventory of over 10,000 PFAS structures (the PFASSTRUC list) using a set of clearly defined structural filters that encompass current EPA programmatic interests. This list is serving as a benchmark for the community to apply cheminformatics approaches and better understand and survey the scope of PFAS chemistries of potential concern. PFASSTRUC was compared to several other structure-based definitions of PFAS to investigate what type of structures do and do not meet the definitions and thus what similar structures may be considered PFAS by some but not others. Such resources can help support the PFAS community to better frame the PFAS problem and aid in the development of categorization approaches for PFAS, as well as support the reporting of relevant data for the agency. Abstract does not reflect EPA policy. Comparison of lists of per- and polyfluoroalkyl substances (PFAS) based on di...
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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 Chemistry 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 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 new physicochemical property and environmental fate and transport QSAR prediction models developed for these chemicals. The application of the dashboard to support mass spectrometry non-targeted analysis studies for the identification of PFAS chemicals will also be reviewed. 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 ...
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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 Delivering chemical-associated data via EPA web applications
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High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are utilized to identify emerging contaminants and chemical signatures of interest detected in various media. At the US Environmental Protection Agency the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is an open chemistry resource and web-based application containing data for ~900,000 substances and supports non-targeted and suspect screening analyses. Searching functionality includes identifier searches (e.g. systematic names, trade names and CAS Registry Numbers), mass and formula-based searches and prototype developments include combined substructure-mass/formula searches and searching experimental mass spectral data against predicted fragmentation spectra. A specific type of data mapping in the database uses “MS-Ready” structures, a way to process all registered substances to separate multi-component chemicals into their individual components, removal of stereochemical bonds and desalting and neutralization. This MS-Ready processing supports batch-searching using either mass or formulae to identify candidate chemicals and their mapped substances. A number of chemical lists (https://comptox.epa.gov/dashboard/chemical_lists) have also been developed to support the identification of chemicals related to agrochemistry, specifically pesticides (both active and inert constituents), insecticides and their metabolites and environmental breakdown products). This presentation will provide an overview of how the CompTox Chemicals Dashboard supports mass spectrometry based structure identification and non-targeted analysis of chemicals in agrochemistry. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.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 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.
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
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.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
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program utilizes computational and data-driven approaches that integrate chemistry, exposure and biological data to help characterize potential risks from chemical exposure. 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. The CompTox Chemicals Dashboard website provides access to data associated with ~900,000 chemical substances. New data are added on an ongoing basis, including the registration of new and emerging chemicals, data extracted from the literature, chemicals studied in our labs, and data of interest to specific research projects at the EPA. Hazard and exposure data have been assembled from a large number of public databases and as a result the dashboard surfaces hundreds of thousands of data points. Other data includes experimental and predicted physicochemical property data, in vitro bioassay data for over 4000 chemicals and ~1500 assays, and millions of chemical identifiers (names and CAS Registry Numbers) to facilitate searching. Other integrated modules include an interactive read-across module, real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed. 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 Agency.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
This presentation was made to the University of North Carolina in Chapel Hill on 9/20/21. The presentation was a general introduction to cheminformatics prior to how to navigate the Dashboard.
• An introduction to the dashboard
• Substances vs structures
• Structure formats for data exchange and connectivity (SMILES, InChIs, molfiles)
• Identifiers – CASRN, chemical names, systematic names
• Data curation approaches: substance-structure ambiguity
• ChemReg: substance registration
• Data gathering for systematic reviews
• Curated lists
• Properties/Fate and Transport
• Access to Exposure Data
• Hazard data in the dashboard – ToxVal data (sourced from >40 databases, >50,000 chemicals, >900,000 data points)
• The Executive Summary of data
• Single chemical searches vs Batch searches
Introduction to Cheminformatics: Accessing data through the CompTox Chemicals...
Introduction to Cheminformatics: Accessing data through the CompTox Chemicals...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 AgencyEPA 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 U.S. Environmental Protection Agency (EPA) Computational Toxicology Program utilizes computational and data-driven approaches that integrate chemistry, exposure and biological data to help characterize potential risks from chemical exposure. 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. The CompTox Chemicals Dashboard website provides access to data associated with ~900,000 chemical substances. New data are added on an ongoing basis, including the registration of new and emerging chemicals, data extracted from the literature, chemicals studied in our labs, and data of interest to specific research projects at the EPA. Hazard and exposure data have been assembled from a large number of public databases and as a result the dashboard surfaces hundreds of thousands of data points. Other data includes experimental and predicted physicochemical property data, in vitro bioassay data and millions of chemical identifiers (names and CAS Registry Numbers) to facilitate searching. Other integrated modules include real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed. 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 Agency.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’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a freely available web-based application providing access to data for ~900,000 chemical substances, the majority of these represented as chemical structures. The Dashboard also provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders and, in particular, a list of hundreds of disinfection by-product (DBP) chemicals reported in the literature and detected in the laboratory using mass spectrometric techniques. Many of these chemicals are explicit chemical structures whose structures have been confirmed using purchased or synthesized reference standards. However, some of these chemicals may be ambiguous in nature with no explicit positional isomers being possible to define but the formula and mass spec fragmentation sufficient to define a class of chemicals (e.g. dichlorophenol). Such chemicals may be represented with ambiguous chemical structure forms, so-called Markush structures, and mapped to the individual class members. Chemicals accessible via the Dashboard can include access to a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data, product use information extracted from safety data sheets, and integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. Since DBP chemicals are primarily identified using mass spectrometric techniques specific search types have been developed to directly support the non-targeted screening community, enabling cohesive workflows to support data generation for the detection and assessment of environmental exposures to chemicals contained within the database. This presentation will provide an overview of the Dashboard, the ongoing expansion of the DBP chemical list and specific functionality supporting identification of DBPs by mass spectrometry. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Web-based access to data for >600 disinfection by-products via the EPA CompTo...
Web-based access to data for >600 disinfection by-products via the EPA CompTo...US 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 have served the chemistry community for many years. Several web-based software applications have been developed at the US-EPA and made available to the community to provide access to information regarding mycotoxins. This includes related structures, experimental and predicted properties, hazard data and mass spectrometry analytical data and methods. While the primary software application from the Center is the CompTox Chemicals 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 modules to allow for hazard comparison for sets of chemicals, structure-substructure-similarity searching and batch QSAR prediction of both physicochemical and toxicity endpoints. This presentation will provide an overview of all tools in development that provide access to mycotoxin related data and the integrated nature of the applications based on the underlying chemistry data set. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Data delivery from the US-EPA Center for Computational Toxicology and Exposur...
Data delivery from the US-EPA Center for Computational Toxicology and Exposur...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 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. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will review how the CompTox Chemicals Dashboard via its flexible search capabilities, rich data for ~900,000 chemical substances, and visualization approaches within this open chemistry resource provides a freely available software tool to support structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation given at the Federal Environment Symposium on March 28th 2022.
As part of its mission the Center for Computational Toxicology and Exposure (CCTE) delivers access to chemicals related data via online Dashboards. The CompTox Chemicals Dashboard (available at https://comptox.epa.gov/dashboard) provides access to >900,000 chemicals and associated data including experimental and predicted property data, in vivo hazard data, in vitro bioactivity data, exposure data, and various other data types. The application provides a set of flexible searches allowing for search, visualization and downloads of the data to the desktop for further interrogation. This presentation will provide an overview of the Dashboard and other proof-of-concept applications. For example, the Hazard Comparison Dashboard has a module which allows profiling of chemicals based on toxicity types (https://doi.org/10.1007/s10098-019-01795-w). This presentation will also introduce a number of proof-of-concept modules in development. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Accessing Environmental Chemistry Data via Data Dashboards
Accessing Environmental Chemistry Data via Data DashboardsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are of increasing interest in chemical forensics for the identification of emerging contaminants and chemical signatures of interest. At the US Environmental Protection Agency, our research using HRMS for non-targeted and suspect screening analyses utilizes databases and cheminformatics approaches that are applicable to chemical forensics. The CompTox Chemistry Dashboard is an open chemistry resource and web-based application containing data for ~760,000 substances. Basic functionality for searching through the data is provided through identifier searches, such as systematic name, trade names and CAS Registry Numbers. Advanced Search capabilities supporting mass spectrometry include mass and formula-based searches, combined substructure-mass searches and searching experimental mass spectral data against predicted fragmentation spectra. A specific type of data mapping in the underpinning database, using “MS-Ready” structures, has proven to be a valuable approach for structure identification that links structures that can be identified via HRMS with related substances in the form of salts, and other multi-component mixtures that are available in commerce. This presentation will provide an overview of the CompTox Chemistry Dashboard and demonstrate its utility for supporting structure identification and NTA in chemical forensics. 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
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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 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
The EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a publicly accessible website providing access to data for ~875,000 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, product use information extracted from safety data sheets, and integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. The application provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders, including Per- & Polyfluoroalkyl Substances (PFAS) containing thousands of chemicals. A procured testing library of hundreds of PFAS chemicals annotated into chemical categories has also 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. Several specific search types have been developed 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 the database. 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 developed for these chemicals. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.US-EPA CompTox Chemicals Dashboard – a web-based database and information hub...
US-EPA CompTox Chemicals Dashboard – a web-based database and information hub...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program utilizes computational and data-driven approaches that integrate chemistry, exposure and biological data to help characterize potential risks from chemical exposure. 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. The CompTox Chemicals Dashboard website provides access to data associated with ~900,000 chemical substances. New data are added on an ongoing basis, including the registration of new and emerging chemicals, data extracted from the literature, chemicals studied in our labs, and data of interest to specific research projects at the EPA. Hazard and exposure data have been assembled from a large number of public databases and as a result the dashboard surfaces hundreds of thousands of data points. Other data includes experimental and predicted physicochemical property data, in vitro bioassay data for over 4000 chemicals and 2000 assays, and millions of chemical identifiers (names and CAS Registry Numbers) to facilitate searching. Other integrated modules include an interactive read-across module, real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed. This presentation will provide an overview of the latest release 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 Agency.US-EPA CompTox Chemicals Dashboard – integrating chemistry and biology data t...
US-EPA CompTox Chemicals Dashboard – integrating chemistry and biology data t...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
As part of its mission the Center for Computational Toxicology and Exposure (CCTE) delivers access to chemicals related data via online Dashboards. The CompTox Chemicals Dashboard (available at https://comptox.epa.gov/dashboard) provides access to >900,000 chemicals and associated data including experimental and predicted property data, in vivo hazard data, in vitro bioactivity data, exposure data, and various other data types. The application provides a set of flexible searches allowing for search, visualization and downloads of the data to the desktop for further interrogation. This presentation will provide an overview of the Dashboard and other proof-of-concept applications that are now publicly available (https://www.epa.gov/chemical-research/cheminformatics). For example, the Hazard Comparison module (shown in the figure below) allows profiling of chemicals based on toxicity types (https://doi.org/10.1007/s10098-019-01795-w). This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Accessing Environmental Chemistry Data via Data Dashboards
Accessing Environmental Chemistry Data via Data Dashboards US 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.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
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 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. Each of these depends on the underlying DSSTox chemicals database, a rich source of chemistry data for over 1.2 million chemical substances. This presentation will provide an overview of all tools in development and the integrated nature of the applications based on the underlying chemistry data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection AgencyUtilizing US-EPA Data Dashboards to Support Exposomics research
Utilizing US-EPA Data Dashboards to Support Exposomics researchUS 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 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. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will review how the CompTox Chemicals Dashboard via its flexible search capabilities, rich data for ~875,000 chemical substances, and visualization approaches within this open chemistry resource provides a freely available software tool to support structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are utilized to identify emerging contaminants and chemical signatures of interest detected in various media. At the US Environmental Protection Agency the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is an open chemistry resource and web-based application containing data for ~900,000 substances and supports non-targeted and suspect screening analyses. Searching functionality includes identifier searches (e.g. systematic names, trade names and CAS Registry Numbers), mass and formula-based searches and prototype developments include combined substructure-mass/formula searches and searching experimental mass spectral data against predicted fragmentation spectra. A specific type of data mapping in the database uses “MS-Ready” structures, a way to process all registered substances to separate multi-component chemicals into their individual components, removal of stereochemical bonds and desalting and neutralization. This MS-Ready processing supports batch-searching using either mass or formulae to identify candidate chemicals and their mapped substances. A number of chemical lists (https://comptox.epa.gov/dashboard/chemical_lists) have also been developed to support the identification of chemicals related to agrochemistry, specifically pesticides (both active and inert constituents), insecticides and their metabolites and environmental breakdown products). This presentation will provide an overview of how the CompTox Chemicals Dashboard supports mass spectrometry based structure identification and non-targeted analysis of chemicals in agrochemistry. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.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 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.
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
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.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
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program utilizes computational and data-driven approaches that integrate chemistry, exposure and biological data to help characterize potential risks from chemical exposure. 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. The CompTox Chemicals Dashboard website provides access to data associated with ~900,000 chemical substances. New data are added on an ongoing basis, including the registration of new and emerging chemicals, data extracted from the literature, chemicals studied in our labs, and data of interest to specific research projects at the EPA. Hazard and exposure data have been assembled from a large number of public databases and as a result the dashboard surfaces hundreds of thousands of data points. Other data includes experimental and predicted physicochemical property data, in vitro bioassay data for over 4000 chemicals and ~1500 assays, and millions of chemical identifiers (names and CAS Registry Numbers) to facilitate searching. Other integrated modules include an interactive read-across module, real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed. 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 Agency.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
This presentation was made to the University of North Carolina in Chapel Hill on 9/20/21. The presentation was a general introduction to cheminformatics prior to how to navigate the Dashboard.
• An introduction to the dashboard
• Substances vs structures
• Structure formats for data exchange and connectivity (SMILES, InChIs, molfiles)
• Identifiers – CASRN, chemical names, systematic names
• Data curation approaches: substance-structure ambiguity
• ChemReg: substance registration
• Data gathering for systematic reviews
• Curated lists
• Properties/Fate and Transport
• Access to Exposure Data
• Hazard data in the dashboard – ToxVal data (sourced from >40 databases, >50,000 chemicals, >900,000 data points)
• The Executive Summary of data
• Single chemical searches vs Batch searches
Introduction to Cheminformatics: Accessing data through the CompTox Chemicals...
Introduction to Cheminformatics: Accessing data through the CompTox Chemicals...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 AgencyEPA 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 U.S. Environmental Protection Agency (EPA) Computational Toxicology Program utilizes computational and data-driven approaches that integrate chemistry, exposure and biological data to help characterize potential risks from chemical exposure. 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. The CompTox Chemicals Dashboard website provides access to data associated with ~900,000 chemical substances. New data are added on an ongoing basis, including the registration of new and emerging chemicals, data extracted from the literature, chemicals studied in our labs, and data of interest to specific research projects at the EPA. Hazard and exposure data have been assembled from a large number of public databases and as a result the dashboard surfaces hundreds of thousands of data points. Other data includes experimental and predicted physicochemical property data, in vitro bioassay data and millions of chemical identifiers (names and CAS Registry Numbers) to facilitate searching. Other integrated modules include real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed. 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 Agency.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’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a freely available web-based application providing access to data for ~900,000 chemical substances, the majority of these represented as chemical structures. The Dashboard also provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders and, in particular, a list of hundreds of disinfection by-product (DBP) chemicals reported in the literature and detected in the laboratory using mass spectrometric techniques. Many of these chemicals are explicit chemical structures whose structures have been confirmed using purchased or synthesized reference standards. However, some of these chemicals may be ambiguous in nature with no explicit positional isomers being possible to define but the formula and mass spec fragmentation sufficient to define a class of chemicals (e.g. dichlorophenol). Such chemicals may be represented with ambiguous chemical structure forms, so-called Markush structures, and mapped to the individual class members. Chemicals accessible via the Dashboard can include access to a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data, product use information extracted from safety data sheets, and integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. Since DBP chemicals are primarily identified using mass spectrometric techniques specific search types have been developed to directly support the non-targeted screening community, enabling cohesive workflows to support data generation for the detection and assessment of environmental exposures to chemicals contained within the database. This presentation will provide an overview of the Dashboard, the ongoing expansion of the DBP chemical list and specific functionality supporting identification of DBPs by mass spectrometry. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Web-based access to data for >600 disinfection by-products via the EPA CompTo...
Web-based access to data for >600 disinfection by-products via the EPA CompTo...US 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 have served the chemistry community for many years. Several web-based software applications have been developed at the US-EPA and made available to the community to provide access to information regarding mycotoxins. This includes related structures, experimental and predicted properties, hazard data and mass spectrometry analytical data and methods. While the primary software application from the Center is the CompTox Chemicals 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 modules to allow for hazard comparison for sets of chemicals, structure-substructure-similarity searching and batch QSAR prediction of both physicochemical and toxicity endpoints. This presentation will provide an overview of all tools in development that provide access to mycotoxin related data and the integrated nature of the applications based on the underlying chemistry data set. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Data delivery from the US-EPA Center for Computational Toxicology and Exposur...
Data delivery from the US-EPA Center for Computational Toxicology and Exposur...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 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. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will review how the CompTox Chemicals Dashboard via its flexible search capabilities, rich data for ~900,000 chemical substances, and visualization approaches within this open chemistry resource provides a freely available software tool to support structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation given at the Federal Environment Symposium on March 28th 2022.
As part of its mission the Center for Computational Toxicology and Exposure (CCTE) delivers access to chemicals related data via online Dashboards. The CompTox Chemicals Dashboard (available at https://comptox.epa.gov/dashboard) provides access to >900,000 chemicals and associated data including experimental and predicted property data, in vivo hazard data, in vitro bioactivity data, exposure data, and various other data types. The application provides a set of flexible searches allowing for search, visualization and downloads of the data to the desktop for further interrogation. This presentation will provide an overview of the Dashboard and other proof-of-concept applications. For example, the Hazard Comparison Dashboard has a module which allows profiling of chemicals based on toxicity types (https://doi.org/10.1007/s10098-019-01795-w). This presentation will also introduce a number of proof-of-concept modules in development. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Accessing Environmental Chemistry Data via Data Dashboards
Accessing Environmental Chemistry Data via Data DashboardsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are of increasing interest in chemical forensics for the identification of emerging contaminants and chemical signatures of interest. At the US Environmental Protection Agency, our research using HRMS for non-targeted and suspect screening analyses utilizes databases and cheminformatics approaches that are applicable to chemical forensics. The CompTox Chemistry Dashboard is an open chemistry resource and web-based application containing data for ~760,000 substances. Basic functionality for searching through the data is provided through identifier searches, such as systematic name, trade names and CAS Registry Numbers. Advanced Search capabilities supporting mass spectrometry include mass and formula-based searches, combined substructure-mass searches and searching experimental mass spectral data against predicted fragmentation spectra. A specific type of data mapping in the underpinning database, using “MS-Ready” structures, has proven to be a valuable approach for structure identification that links structures that can be identified via HRMS with related substances in the form of salts, and other multi-component mixtures that are available in commerce. This presentation will provide an overview of the CompTox Chemistry Dashboard and demonstrate its utility for supporting structure identification and NTA in chemical forensics. 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
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Cheminformatics Tools to Access Data for PFAS and Constituents of Fluorine-Free Foams
- 1. Cheminformatics Tools to Access Data for PFAS and Constituents of Fluorine-Free Foams Antony Williams Center for Computational Toxicology & Exposure, U.S. Environmental Protection Agency http://www.orcid.org/0000-0002-2668-4821 November 2023: Sandia National Labs PFAS Workshop The views expressed in this presentation are those of the author and do not necessarily reflect the views or policies of the U.S. EPA
- 2. CCTE Cheminformatics Tools • DSSTox – the chemistry database under all cheminformatics tools • https://doi.org/10.1016/j.comtox.2019.10009 6 1
- 3. CompTox Chemicals Dashboard https://comptox.epa.gov/dashboard 2 • Searching 1.2M chemicals – CAS Numbers, systematic names and synonyms, structures
- 4. CompTox Chemicals Dashboard • A publicly accessible website delivering access to: – ~1.2M chemicals with related property data – Experimental and predicted physicochemical property data – Experimental Human and Ecological hazard data – Integration to “biological assay data” for 1000s of chemicals – Information regarding chemicals in consumer products – Links to other agency websites and public data resources – “Literature” search capability for chemicals using public resources – “Batch searching” for tens to thousands of chemicals – Over 15,000 of the chemicals are classed as PFAS Chemicals (but be cautious regarding the definition of a PFAS”…) 3
- 5. To understand FFF it helps to understand PFAS also 4
- 6. 1 of ~1.2M Chemical Pages 5
- 9. What is PFOS Called? Synonyms, CASRNs and more 8
- 10. Substance Relationship Mappings • Similar compounds - based on structure 9
- 11. Are there Similar Compounds? 127 chemicals >0.8 match factor 10
- 12. Substance Relationship Mappings • Similar compounds - based on structure • Structure mappings - between parent and salts, multicomponent chemicals, isotopomers – Useful for creating structure-based category mappings • Related substances – monomer to polymer, parent to transformation products – Ideal way to create a chemical description of a formulation 11
- 13. Relationships in the data 12
- 14. Chemicals in an AFFF foam 13
- 15. Chemicals in an AFFF foam • We extract data from many sources 14
- 16. How to compare Hazard Data? 15 • Search thousands of chemicals based on CASRN, names and identifiers • Harvest available data including properties, toxicity data, chemical relationships, category mappings, presence in lists
- 17. How to compare Hazard Data? 16
- 18. How to compare Hazard Data? NOT Easy to interpret… 17
- 19. Profiling the toxicity of chemicals MUCH easier… 18 • The Hazard Comparison module profiles toxicity across chemicals • https://www.epa.gov/chemical-research/cheminformatics
- 20. Obtain Data and Profile Any Chemicals • If we have the chemicals in DSSTox data can be retrieved and the chemical profiled • Imagine any FFF mixture where constituents are known – harvest data and profile hazard 19
- 21. Safety Profiling (Work in Progress) • New module in development (NOT public) 20
- 22. Analytical Methods and Open Spectra (Work in Progress) • ~4000 methods extracted 21
- 23. Analytical Methods and Open Spectra (Work in Progress) • ~4000 methods extracted (100 PFAS methods) 22
- 24. Conclusions • CompTox Chemicals Dashboard supports research at EPA in numerous ways – Assembly, integration and curation of chemistry data – Relationships in the data enrich navigation between chemicals – Flexible searches – names, structures, formulae, masses • Proof-of-Concept tools online/in development – Hazard and Safety Profiling – Structure/substructure/similarity search 23
- 28. Contact Interested in a demo and overview of our tools? Contact me: Antony Williams NCCT, US EPA Office of Research and Development, Williams.Antony@epa.gov ORCID: https://orcid.org/0000-0002-2668-4821 27