The US-EPA CompTox Chemicals Dashboard – an information hub for over five thousand per- & polyfluoroalkyl chemical substances
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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.
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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 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.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.PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...
PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...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 ~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.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 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.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 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.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
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.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
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.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
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.Recommended
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 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.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.PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...
PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...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 ~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.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 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.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 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.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
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.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
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.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
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 providing access to experimental and predi...
US-EPA CompTox Chemicals Dashboard providing access to experimental and predi...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Access to both experimental and predicted environmental fate and transport data is facilitated by the US-EPA CompTox Chemicals Dashboard. Providing access to various types of data associated with ~900,000 chemical substances, the dashboard is a web-based application supporting computational toxicology research in environmental chemistry. When experimental physicochemical and fate and transport data are not available, QSAR models developed using curated datasets are used for the prediction of properties. These include: bioaccumulation factors, bioconcentration factors, and biodegradation and fish biotransformation half-lives. For chemicals of interest that are not already registered in the dashboard real-time predictions based on structural inputs are available. This presentation will provide an overview of the dashboard with a focus on the availability of environmental fate and transport data, access to real time predictions, and our ongoing efforts to harvest and curate available experimental data from the literature and online databases. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.New Approach Methods - What is That?
New Approach Methods - What is That?US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation for Texas A&M Superfund Research Center virtual learning series, Big Data in Environmental Science and Toxicology. More details at https://superfund.tamu.edu/big-data-session-2-aug-18-2021/What chemicals constitute the Exposome? Accessing data via the US EPA’s Comp...
What chemicals constitute the Exposome? Accessing data via the US EPA’s Comp...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The CompTox Chemicals Dashboard is an open chemistry resource and web-based application containing data for ~900,000 substances. While it pales in comparison to other online resources containing many tens of millions of chemical substances it represents two decades of effort to aggregate and curate chemical data to deliver access to physicochemical properties and environmental fate and transport data, in vitro and in vivo toxicity data and consumer product data for over 500,000 products. Associated with the chemical substance collections are specific lists based on chemical classes (e.g. polychlorinated biphenyls (PCBs)), usage categories (e.g. flame retardants, pesticides), specific environmental classes of interest (e.g. disinfectant by-products) and regulatory lists (e.g. TSCA, Toxics release inventory data). The underlying database expands daily as a result of the efforts of curators who continue to harvest data from peer-reviewed publications, regulatory documents and relevant online databases. The cheminformatics architecture allows for mapping between parent chemicals and related substances including metabolites and environmental degradants. The dashboard has become a valuable resource in the identification of chemical substances in the environment.
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. Our research using HRMS for non-targeted and suspect screening analyses utilizes Advanced Search capabilities including mass and formula-based searches. 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. These MS-Ready structures have been used as an input set for computational MS-fragmentation to provide a database against which to search experimental data for spectral matching. This presentation will provide an overview of how CompTox Chemicals Dashboard, the underlying data, and how it supports structure identification and non-targeted analysis in chemical forensics. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.
How to place your research questions or results into the context of the "Lega...
How to place your research questions or results into the context of the "Lega...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation for Texas A&M Superfund Research Center virtual learning series, Big Data in Environmental Science and Toxicology. More details at https://superfund.tamu.edu/big-data-session-1-july-14-2021/Does bigger mean better in the world of chemistry databases?
Does bigger mean better in the world of chemistry databases? US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The internet has changed the way we access chemistry data as well as providing access to data that can quickly proliferate and becomes referenceable. Web access to chemical structures and their integration with biological data has become massively enabling with numbers for UniChem, PubChem and ChemSpider reaching 157, 97 and 71 million respectively (at the time of writing). A range of specialist databases small enough to be curated have stand-alone utility and synergies when integrated into the larger collections. These include DrugBank, BindingDB, ChEBI, and many others. Databases of any size have inherent quality challenges but at large scale various forms of “noise” accumulate to problematic levels. The unfortunate consequence is that “bigger gets worse”. This is particularly associated with large uncurated submissions from vendors and automated document extractions (even though these are high-value). Virtual enumerations and circularity between overlapping sources add to the problem. As a result of some of the noise in the larger databases the value becomes highly dependent on the specific applications. An example includes using the databases to support non-targeted analysis. This presentation covers examples of these noise and quality issues and suggests at least some options to ameliorate the problem. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency. 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
The increasing popularity of high mass accuracy non-target mass spectrometry methods has yielded extensive identification efforts based on chemical compound databases. Candidate structures are often retrieved with either exact mass or molecular formula from large resources such as PubChem, ChemSpider or the EPA CompTox Chemistry Dashboard. Additional data (e.g. fragmentation, physicochemical properties, reference and data source information) is then used to select potential candidates, depending on the experimental context. However, these strategies require the presence of substances of interest in these compound databases, which is often not the case as no database can be fully inclusive. A prominent example with clear data gaps are surfactants, used in many products in our daily lives, yet often absent as discrete structures in compound databases. Linear alkylbenzene sulfonates (LAS) are a common, high use and high priority surfactant class that have highly complex transformation behaviour in wastewater. Despite extensive reports in the environmental literature, few of the LAS and none of the related transformation products were reported in any compound databases during an investigation into Swiss wastewater effluents, despite these forming the most intense signals. The LAS surfactant class will be used to demonstrate how the coupling of environmental observations with high resolution mass spectrometry and detailed literature data (expert knowledge) on the transformation of these species can be used to progressively “fill the gaps” in compound databases. The LAS and their transformation products have been added to the CompTox Chemistry Dashboard (https://comptox.epa.gov/) using a combination of “representative structures” and “related structures” starting from the structural information contained in the literature. By adding this information into a centralized open resource, future environmental investigations can now profit from the expert knowledge previously scattered throughout the literature. Note: This abstract does not reflect US EPA policy.Accessing information for chemicals in hydraulic fracturing fluids using the ...
Accessing information for chemicals in hydraulic fracturing fluids using the ...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 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 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.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.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 Chemicals Dashboard as a Data Integration Hub for Environment...
The EPA Comptox Chemicals Dashboard as a Data Integration Hub for Environment...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 involves computational and data-driven approaches that integrate chemistry, exposure and biological data. 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 is a web-based application providing access to data associated with ~~875,000 chemical substances. New data are continuously added to the database on an ongoing basis, along with registration of new and emerging chemicals. This includes data extracted from the literature, identified by our analytical labs, and otherwise of interest to support specific research projects to the agency. By adding these data, with their associated chemical identifiers (names and CAS Registry Numbers), the dashboard uses linking approaches to allow for automated searching of PubMed, Google Scholar and an array of public databases. This presentation will provide an overview of the CompTox Chemicals Dashboard, how it has developed into an integrated data hub for environmental data, and how it can be used for the analysis of emerging chemicals in terms of sourcing related chemicals of interest, and deriving read-across as well as QSAR predictions in real time. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Searching for chemical information using PubChem
Presented at the 257th American Chemical Society (ACS) National Meeting in Orlando, FL (April 1, 2019). [CHED 303]
==== Abstract ====
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical database, which provides information on a broad range of chemical entities, including small molecules, lipids, carbohydrates, and (chemically-modified) amino acid and nucleic acid sequences (including siRNA and miRNA). With three million unique users per month at peak, PubChem is ranked as one of the most visited chemistry websites in the world. A substantial number of PubChem users are between ages 18 and 24, who are likely to be undergraduate or graduate students at academic institutions. Therefore, PubChem has a great potential as an online resource for chemical education. In this talk, we will present “PubChem Search”, a new web interface that allows users to quickly find desired chemical information. This interface supports chemical name search as well as various types of chemical structure search, including identity/similarity search, superstructure/substructure search, and molecular search. Using PubChem Search, it is also possible to search for journal articles or patent documents that mention a given chemical. The hits returned from a search can be downloaded to local machines or further refined or analyzed in conjunction with other PubChem tools and services. In this presentation, we will demonstrate how the PubChem Search interface can be used to search beyond google for chemical information of interest.
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
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.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
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 architecture to support real-time property and toxicity endpoint prediction. This abstract does not reflect U.S. EPA policy.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
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.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.
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
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 Chemicals Dashboard is an open chemistry resource and web-based application containing data for ~900,000 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. These MS-Ready structures have been used as an input set for computational MS-fragmentation to provide a database against which to search experimental data for spectral matching. This presentation will provide an overview of how the CompTox Chemicals Dashboard supports structure identification and non-targeted analysis in chemical forensics. 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 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 AgencyPubChem and Its Applications for Drug Discovery
Presentation delivered at Lehigh University (Bethlehem, PA) on Friday, April 26, 2019.
This presentation provides a brief introduction to PubChem and discusses how to use PubChem for drug discovery. More detailed information on this topic can found in the following paper:
Getting the most out of PubChem for virtual screening.
Expert Opin Drug Discov. 2016 Aug 5; 11(9):843-55.
https://doi.org/10.1080/17460441.2016.1216967
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045798/
Comparison of lists of per- and polyfluoroalkyl substances (PFAS) based on di...
Comparison of lists of per- and polyfluoroalkyl substances (PFAS) based on di...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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. What is a PFAS?..and the challenges associated with defining them
What is a PFAS?..and the challenges associated with defining themUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at the XPAND2022 Annual Meeting for the Household & Commercial Products Association and focused on PFAS chemicals, the definition of what they are, how to categorize and classify them, and how data can be delivered via the CompTox Chemicals Dashboard More Related Content
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US-EPA CompTox Chemicals Dashboard providing access to experimental and predi...
US-EPA CompTox Chemicals Dashboard providing access to experimental and predi...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Access to both experimental and predicted environmental fate and transport data is facilitated by the US-EPA CompTox Chemicals Dashboard. Providing access to various types of data associated with ~900,000 chemical substances, the dashboard is a web-based application supporting computational toxicology research in environmental chemistry. When experimental physicochemical and fate and transport data are not available, QSAR models developed using curated datasets are used for the prediction of properties. These include: bioaccumulation factors, bioconcentration factors, and biodegradation and fish biotransformation half-lives. For chemicals of interest that are not already registered in the dashboard real-time predictions based on structural inputs are available. This presentation will provide an overview of the dashboard with a focus on the availability of environmental fate and transport data, access to real time predictions, and our ongoing efforts to harvest and curate available experimental data from the literature and online databases. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.New Approach Methods - What is That?
New Approach Methods - What is That?US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation for Texas A&M Superfund Research Center virtual learning series, Big Data in Environmental Science and Toxicology. More details at https://superfund.tamu.edu/big-data-session-2-aug-18-2021/What chemicals constitute the Exposome? Accessing data via the US EPA’s Comp...
What chemicals constitute the Exposome? Accessing data via the US EPA’s Comp...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The CompTox Chemicals Dashboard is an open chemistry resource and web-based application containing data for ~900,000 substances. While it pales in comparison to other online resources containing many tens of millions of chemical substances it represents two decades of effort to aggregate and curate chemical data to deliver access to physicochemical properties and environmental fate and transport data, in vitro and in vivo toxicity data and consumer product data for over 500,000 products. Associated with the chemical substance collections are specific lists based on chemical classes (e.g. polychlorinated biphenyls (PCBs)), usage categories (e.g. flame retardants, pesticides), specific environmental classes of interest (e.g. disinfectant by-products) and regulatory lists (e.g. TSCA, Toxics release inventory data). The underlying database expands daily as a result of the efforts of curators who continue to harvest data from peer-reviewed publications, regulatory documents and relevant online databases. The cheminformatics architecture allows for mapping between parent chemicals and related substances including metabolites and environmental degradants. The dashboard has become a valuable resource in the identification of chemical substances in the environment.
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. Our research using HRMS for non-targeted and suspect screening analyses utilizes Advanced Search capabilities including mass and formula-based searches. 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. These MS-Ready structures have been used as an input set for computational MS-fragmentation to provide a database against which to search experimental data for spectral matching. This presentation will provide an overview of how CompTox Chemicals Dashboard, the underlying data, and how it supports structure identification and non-targeted analysis in chemical forensics. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.
How to place your research questions or results into the context of the "Lega...
How to place your research questions or results into the context of the "Lega...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation for Texas A&M Superfund Research Center virtual learning series, Big Data in Environmental Science and Toxicology. More details at https://superfund.tamu.edu/big-data-session-1-july-14-2021/Does bigger mean better in the world of chemistry databases?
Does bigger mean better in the world of chemistry databases? US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The internet has changed the way we access chemistry data as well as providing access to data that can quickly proliferate and becomes referenceable. Web access to chemical structures and their integration with biological data has become massively enabling with numbers for UniChem, PubChem and ChemSpider reaching 157, 97 and 71 million respectively (at the time of writing). A range of specialist databases small enough to be curated have stand-alone utility and synergies when integrated into the larger collections. These include DrugBank, BindingDB, ChEBI, and many others. Databases of any size have inherent quality challenges but at large scale various forms of “noise” accumulate to problematic levels. The unfortunate consequence is that “bigger gets worse”. This is particularly associated with large uncurated submissions from vendors and automated document extractions (even though these are high-value). Virtual enumerations and circularity between overlapping sources add to the problem. As a result of some of the noise in the larger databases the value becomes highly dependent on the specific applications. An example includes using the databases to support non-targeted analysis. This presentation covers examples of these noise and quality issues and suggests at least some options to ameliorate the problem. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency. 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
The increasing popularity of high mass accuracy non-target mass spectrometry methods has yielded extensive identification efforts based on chemical compound databases. Candidate structures are often retrieved with either exact mass or molecular formula from large resources such as PubChem, ChemSpider or the EPA CompTox Chemistry Dashboard. Additional data (e.g. fragmentation, physicochemical properties, reference and data source information) is then used to select potential candidates, depending on the experimental context. However, these strategies require the presence of substances of interest in these compound databases, which is often not the case as no database can be fully inclusive. A prominent example with clear data gaps are surfactants, used in many products in our daily lives, yet often absent as discrete structures in compound databases. Linear alkylbenzene sulfonates (LAS) are a common, high use and high priority surfactant class that have highly complex transformation behaviour in wastewater. Despite extensive reports in the environmental literature, few of the LAS and none of the related transformation products were reported in any compound databases during an investigation into Swiss wastewater effluents, despite these forming the most intense signals. The LAS surfactant class will be used to demonstrate how the coupling of environmental observations with high resolution mass spectrometry and detailed literature data (expert knowledge) on the transformation of these species can be used to progressively “fill the gaps” in compound databases. The LAS and their transformation products have been added to the CompTox Chemistry Dashboard (https://comptox.epa.gov/) using a combination of “representative structures” and “related structures” starting from the structural information contained in the literature. By adding this information into a centralized open resource, future environmental investigations can now profit from the expert knowledge previously scattered throughout the literature. Note: This abstract does not reflect US EPA policy.Accessing information for chemicals in hydraulic fracturing fluids using the ...
Accessing information for chemicals in hydraulic fracturing fluids using the ...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 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 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.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.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 Chemicals Dashboard as a Data Integration Hub for Environment...
The EPA Comptox Chemicals Dashboard as a Data Integration Hub for Environment...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 involves computational and data-driven approaches that integrate chemistry, exposure and biological data. 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 is a web-based application providing access to data associated with ~~875,000 chemical substances. New data are continuously added to the database on an ongoing basis, along with registration of new and emerging chemicals. This includes data extracted from the literature, identified by our analytical labs, and otherwise of interest to support specific research projects to the agency. By adding these data, with their associated chemical identifiers (names and CAS Registry Numbers), the dashboard uses linking approaches to allow for automated searching of PubMed, Google Scholar and an array of public databases. This presentation will provide an overview of the CompTox Chemicals Dashboard, how it has developed into an integrated data hub for environmental data, and how it can be used for the analysis of emerging chemicals in terms of sourcing related chemicals of interest, and deriving read-across as well as QSAR predictions in real time. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Searching for chemical information using PubChem
Presented at the 257th American Chemical Society (ACS) National Meeting in Orlando, FL (April 1, 2019). [CHED 303]
==== Abstract ====
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical database, which provides information on a broad range of chemical entities, including small molecules, lipids, carbohydrates, and (chemically-modified) amino acid and nucleic acid sequences (including siRNA and miRNA). With three million unique users per month at peak, PubChem is ranked as one of the most visited chemistry websites in the world. A substantial number of PubChem users are between ages 18 and 24, who are likely to be undergraduate or graduate students at academic institutions. Therefore, PubChem has a great potential as an online resource for chemical education. In this talk, we will present “PubChem Search”, a new web interface that allows users to quickly find desired chemical information. This interface supports chemical name search as well as various types of chemical structure search, including identity/similarity search, superstructure/substructure search, and molecular search. Using PubChem Search, it is also possible to search for journal articles or patent documents that mention a given chemical. The hits returned from a search can be downloaded to local machines or further refined or analyzed in conjunction with other PubChem tools and services. In this presentation, we will demonstrate how the PubChem Search interface can be used to search beyond google for chemical information of interest.
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
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.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
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 architecture to support real-time property and toxicity endpoint prediction. This abstract does not reflect U.S. EPA policy.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
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.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.
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
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 Chemicals Dashboard is an open chemistry resource and web-based application containing data for ~900,000 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. These MS-Ready structures have been used as an input set for computational MS-fragmentation to provide a database against which to search experimental data for spectral matching. This presentation will provide an overview of how the CompTox Chemicals Dashboard supports structure identification and non-targeted analysis in chemical forensics. 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 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 AgencyPubChem and Its Applications for Drug Discovery
Presentation delivered at Lehigh University (Bethlehem, PA) on Friday, April 26, 2019.
This presentation provides a brief introduction to PubChem and discusses how to use PubChem for drug discovery. More detailed information on this topic can found in the following paper:
Getting the most out of PubChem for virtual screening.
Expert Opin Drug Discov. 2016 Aug 5; 11(9):843-55.
https://doi.org/10.1080/17460441.2016.1216967
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045798/
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Comparison of lists of per- and polyfluoroalkyl substances (PFAS) based on di...
Comparison of lists of per- and polyfluoroalkyl substances (PFAS) based on di...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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. What is a PFAS?..and the challenges associated with defining them
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This presentation was given at the XPAND2022 Annual Meeting for the Household & Commercial Products Association and focused on PFAS chemicals, the definition of what they are, how to categorize and classify them, and how data can be delivered via the CompTox Chemicals Dashboard Cheminformatics Tools to Access Data for PFAS and Constituents of Fluorine-Fr...
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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. Delivering chemical-associated data via EPA web applications
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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.EPA CompTox chemicals dashboard: An online resource for environmental chemists
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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.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 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.Informatics Approaches supporting UVCB Chemicals in the US-EPA CompTox Chemic...
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US-EPA Chemicals Dashboard – an integrated data hub for environmental scienceUS 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.Toxicological information in PubChem
Presented at the Fall 2020 American Chemical Society (ACS) National Meeting (Virtual) on August 20, 2020.
Sunghwan Kim, Jian Zhang, Paul Thiessen, Asta Gindulyte, Pertti J. Hakkinen & Evan Bolton
National Library of Medicine, National Institutes of Health, Rockville, Maryland, United States
==== Abstract ====
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical information resource at the U.S. National Institutes of Health. It collects chemical information from 700+ data sources and disseminates the collected data to the public free of charge. Arguably, PubChem contains the largest amount of chemical information available in the public domain, with more than 250 million depositor-provided substance descriptions, 100 million unique chemical structures, and 265 million bioactivity outcomes from one million assays covering around twenty thousand unique protein target sequences.
Included in the many types of content in PubChem is toxicological information about chemicals, e.g., human and animal toxicity, ecotoxicity, exposure limits, exposure symptoms, and antidote & emergency treatment. Notably, a substantial amount of toxicological information from resources formerly offered by the TOXicology data NETwork (TOXNET) is now integrated into PubChem, e.g., the Hazardous Substances Data Bank (HSDB), LactMed, and LiverTox. In addition, PubChem contains a large amount of bioactivity and toxicity screening data that can be used to build toxicity prediction models based on statistical and machine-learning approaches. This presentation provides an overview of PubChem’s toxicological information as well as tools and services that help users exploit this information. It also describes how open data in PubChem can be used to develop prediction models for chemical toxicity.
Cheminformatics Support for MS Supporting Exposomics
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A presentation given at the 5th Metabolomics of North America webinar on September 8th 2023. Provides an overview of the cheminformatics support provided by the DSSTox database, CompTox Chemicals Dashboard and multiple other web-based applications in development Accessing Environmental Chemistry Data via Data Dashboards
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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.US-EPA Cheminformatics Support for Delivering Data Related to Chemicals of E...
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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 involves computational and data-driven approaches that integrate chemistry, exposure and biological data. 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 Chemistry Dashboard is a web-based application providing access to data associated with ~760,000 chemical substances. New data are continuously added to the database on an ongoing basis, along with registration of new and emerging chemicals. This includes data extracted from the literature, identified by our analytical labs, and otherwise of interest to support specific research projects to the agency. By adding these data, with their associated chemical identifiers (names and CAS Registry Numbers), the dashboard uses linking approaches to allow for automated searching of PubMed, Google Scholar and an array of public databases. This presentation will provide an overview of the Dashboard, how it has developed into an integrated data hub for environmental data, and how it can be used for the analysis of emerging chemicals in terms of sourcing related chemicals of interest, and deriving read-across as well as QSAR predictions in real time. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.
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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. PubChem as a resource for chemical information training
Presented at the 257th American Chemical Society (ACS) National Meeting in Orlando, FL (March 31, 2019). [CINF 13]
==== Abstract ====
Libraries at many large academic institutions provide chemical information training programs for students. However, these programs are based on commercial chemical information resources, which come with non-trivial subscription fees. These fees are often too expensive for small organizations, including many primarily undergraduate institutions (PUIs) and community colleges (CCs). It leads to disparity in access to chemical information as well as learning opportunities among students. This issue may be addressed at least in part by developing free online training programs based on public chemical databases, such as PubChem (https://pubchem.ncbi.nlm.nih.gov). PubChem has a great potential as an online resource for chemical education, but it also has important issues that students and teachers should keep in mind, such as data accuracy, data provenance, structure standardization, terminologies and so on. In this presentation, we will discuss various aspects of PubChem as a resource for chemical information training.
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- 1. US-EPA Comptox Chemicals Dashboard: an information hub for over five thousand per- & polyfluoroalkyl chemical substances Antony Williams, Chris Grulke, Grace Patlewicz, and Ann Richard National Center for Computational Toxicology, U.S. Environmental Protection Agency, RTP, NC Spring 2019 ACS Spring Meeting, Orlando http://www.orcid.org/0000-0002-2668-4821 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. Limit notetaking if you wish www.slideshare.net/AntonyWilliams
- 3. CompTox Chemicals Dashboard • A publicly accessible website delivering access: – ~875,000 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 consumer products containing chemicals – Links to other agency websites and public data resources – “Literature” searches for chemicals using public resources – “Batch searching” for thousands of chemicals – Real time prediction of physchem and toxicity endpoints – Over 5,000 of the chemicals are classed as PFAS Chemicals 2
- 4. EPA activities around PFAS chemicals https://www.epa.gov/pfas 3
- 7. 1 of ~875,000 Chemical Pages 6
- 12. Detailed OPERA Prediction Reports 11
- 13. PFAS Literature Data Extraction • Physicochemical property and environmental fate and transport data has been extracted from the literature • OPERA models have been rebuilt with these data for new predictions • Dramatic improvements in predictions for physchem endpoints – logP, AqSol, VP 12
- 14. Hazard Data – Human and Eco 13
- 15. Hazard Data from “ToxVal_DB” • ToxVal Database contains following data: –~30,000 chemicals –~750,000 toxicity values –~30 sources of data –~21,000 sub-sources –~4500 journals cited –~70,000 literature citations 14
- 17. What is PFOS Called? 16
- 18. Literature Searching - PubMed 17
- 19. Literature Searching - PubMed 18
- 20. Are there Similar Compounds? 19
- 21. Relationships in the data 20
- 22. 9 salt forms of PFOS (and the ion) 21
- 27. A List of Lists of Chemicals https://comptox.epa.gov/dashboard/chemical_lists 26
- 28. The OECD List of PFAS http://www.oecd.org/chemicalsafety/portal-perfluorinated-chemicals/ 27
- 29. The OECD List of PFAS http://www.oecd.org/chemicalsafety/portal-perfluorinated-chemicals/ 28
- 32. Markush Chemicals • PFOS is a member of linear perfluoroalkyl sulfonates 31
- 33. …and their Markush Children… • Linear perfluoroalkyl sulfonates has children… 32
- 34. PFAS Categories in Development 33
- 35. PFAS Categories in Development 34
- 37. 36
- 40. 2 Chemicals match the formula 39
- 42. 23 Chemicals match the formula 41
- 43. Work in progress • Development of a high-throughput screening library and collection of physical samples (~430) • 150 PFAS for screening based on categories, diversity, exposure considerations, procurability and testability, availability of existing toxicity data 42
- 44. Supporting future work • 1. Mobility: A wide and dynamic distribution of short chain PFAS due to their high polarity, persistency and volatility. (OPERA Predictions) • 2. Substitution of regulated substances: The ban or restrictions of individual molecules will lead to a replacement with substitutes of similar concern. (Database content and Markush Enumeration) • 3. Increase in structural diversity of existing PFAS molecules: Introduction of e.g., hydrogens and chlorine atoms instead of fluorine, as well as branching and cross-linking lead to a high versatility of unknown target molecules. (Database content) • 4. Unknown “Dark Matter”: The amount, identity, formation pathways, and transformation dynamics of polymers and PFAS precursors are largely unknown. (Working with agency analytical scientists and collaborators to link and host data) 43Front Chem. 2018; 6: 103.
- 45. Conclusions • CompTox Chemicals Dashboard supports PFAS research at EPA in numerous ways – Delivery of curated lists of PFAS chemicals (growing) – Flexible search capabilities – support for Mass Spec – Relationships in the data enrich navigation between chemicals • Ongoing research efforts for PFAS chemicals – Physical library of 100s of chemicals has been acquired – High-throughput screening of ~150 chemicals – Classification approaches and Markush representations 44
- 46. Acknowledgements EPA-RTP • An enormous team of contributors from NCCT, especially the IT software development team • Our curation team for their care and focus on data quality • Multiple centers and laboratories across the EPA • Many public domain databases and open data contributors
- 47. Contact Antony Williams NCCT, US EPA Office of Research and Development, Williams.Antony@epa.gov ORCID: https://orcid.org/0000-0002-2668-4821 46 https://doi.org/10.1186/s13321-017-0247-6