Web-based access to data for >600 disinfection by-products via the EPA CompTox Chemicals Dashboard
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The US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a freely available web-based application providing access to data for ~900,000 chemical substances, the majority of these represented as chemical structures. The Dashboard also provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders and, in particular, a list of hundreds of disinfection by-product (DBP) chemicals reported in the literature and detected in the laboratory using mass spectrometric techniques. Many of these chemicals are explicit chemical structures whose structures have been confirmed using purchased or synthesized reference standards. However, some of these chemicals may be ambiguous in nature with no explicit positional isomers being possible to define but the formula and mass spec fragmentation sufficient to define a class of chemicals (e.g. dichlorophenol). Such chemicals may be represented with ambiguous chemical structure forms, so-called Markush structures, and mapped to the individual class members. Chemicals accessible via the Dashboard can include access to a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data, product use information extracted from safety data sheets, and integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. Since DBP chemicals are primarily identified using mass spectrometric techniques specific search types have been developed to directly support the non-targeted screening community, enabling cohesive workflows to support data generation for the detection and assessment of environmental exposures to chemicals contained within the database. This presentation will provide an overview of the Dashboard, the ongoing expansion of the DBP chemical list and specific functionality supporting identification of DBPs by mass spectrometry. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.
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There is a growing need for rapid chemical screening and prioritization to inform regulatory decision-making on thousands of chemicals in the environment. We have previously used high-resolution mass spectrometry to examine household vacuum dust samples using liquid chromatography time-of-flight mass spectrometry (LC-TOF/MS). Using a combination of exact mass, isotope distribution, and isotope spacing, molecular features were matched with a list of chemical formulas from the EPA’s Distributed Structure-Searchable Toxicity (DSSTox) database. This has further developed our understanding of how openly available chemical databases, together with the appropriate searches, could be used for the purpose of compound identification. We report here on the utility of the EPA’s iCSS Chemistry Dashboard for the purpose of compound identification using searches against a database of over 720,000 chemicals. We also examine the benefits of QSAR prediction for the purpose of retention time prediction to allow for alignment of both chromatographic and mass spectral properties. This abstract does not reflect U.S. EPA policy.Development of a Tool for Systematic Integration of Traditional and New Appro...
Development of a Tool for Systematic Integration of Traditional and New Appro...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Multiple regulatory bodies (EPA, ECHA, Health Canada) are currently tasked with prioritizing chemicals for data collection and risk assessments. These prioritization efforts are in response to regulatory mandates to identify chemicals for further assessment. We have developed a web-based application that enables a rapid, flexible and transparent prioritization process. The tool includes multiple data streams related to human and ecological hazard, exposure, and physicochemical properties (persistence and bioaccumulation). For human hazard, the data streams include quantitative points of departure (PODs) that are compiled from multiple sources such as EPA ToxRefDB, ECHA, COSMOS; estimated PODs from high-throughput in vitro screening assays and computational models; and qualitative measurements and predictions of specific endpoints (e.g., genotoxicity, endocrine activity). For ecological hazard, quantitative PODs are taken from the EPA ECOTOX database. Exposure information includes production volume, quantitative predictions using the EPA ExpoCast and SHEDS models, biomonitoring data, and qualitative information such as media occurrence, use profiles and likelihood of consumer and childhood exposures. The use of the tool is illustrated by prioritizing chemicals related to TSCA and the Safer Choice Ingredient List. The underpinning data streams for this application are already available in the EPA CompTox Chemistry Dashboard and have been repurposed to deliver this application. This is in keeping with our overarching software development methodology of providing multiple “building blocks” in the form of databases, web services and visualization components to deliver fit-for purpose applications to the relevant audiences. This abstract does not necessarily represent U.S. EPA policy.Delivering The Benefits of Chemical-Biological Integration in Computational T...
Delivering The Benefits of Chemical-Biological Integration in Computational T...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Researchers at EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The goal of this research program is to quickly evaluate thousands of chemicals, but at a much reduced cost and shorter time frame relative to traditional approaches. The data generated by the Center includes characterization of thousands of chemicals across hundreds of high-throughput screening assays, consumer use and production information, pharmacokinetic properties, literature data, physical-chemical properties as well as the predictive computational modeling of toxicity and exposure. We have developed a number of databases and applications to deliver the data to the public, academic community, industry stakeholders, and regulators. This presentation will provide an overview of our work to develop an architecture that integrates diverse large-scale data from the chemical and biological domains, our approaches to disseminate these data, and the delivery of models supporting predictive computational toxicology. In particular, this presentation will review our new publicly-accessible CompTox Dashboard as the first application built on our newly developed architecture. This abstract does not reflect U.S. EPA policy. 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.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.The US-EPA CompTox Chemicals Dashboard – a key player in the domain of Open S...
The US-EPA CompTox Chemicals Dashboard – a key player in the domain of Open S...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are advancing the identification of emerging contaminants in environmental matrices, improving the means by which exposure analyses can be conducted. However, confidence in structure identification of unknowns in NTA presents challenges to analytical chemists. Structure identification requires integration of complementary data types such as reference databases (either commercial or open databases), fragmentation prediction tools, and retention time prediction models. One goal of our research is to optimize and implement structure identification functionality within the US EPA’s CompTox Chemicals Dashboard, an open chemistry resource and web application containing data for ~900,000 substances. Database searching using mass or formula-based inputs has been optimized for structure identification using “MS-Ready Structures”: de-salted, stripped of stereochemistry, and mixture separated to replicate the form of a chemical observed via HRMS. Functionality to conduct batch searching of molecular formulae and monoisotopic masses has also been implemented. While the increasing number of free online databases are of value to support chemical structure verification and elucidation there are known issues regarding data quality and careful data curation is a very necessary part of the development of these resources. This presentation will provide an overview of our latest enhancements to the dashboard to support mass spectrometry, incorporation of specific datasets (i.e. to support breath research and household dust analysis) and the value of metadata and predicted fragmentation spectral matching to support structure identification. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Open PHACTS Chemistry Platform Update and Learnings
Open PHACTS Chemistry Platform Update and Learnings US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was a webinar update to the Open PHACTS community regarding the release of the OPen PHACTS open source components of the Chemical Registration System and, more specifically, the Chemical validation and Standardization Platform. The need for a community set of rules was driven home with the Chemical validation and Standardization Platform potentially being an example platform for the rules. TRIANGLE AREA MASS SPECTOMETRY MEETING: Structure Identification Approaches U...
TRIANGLE AREA MASS SPECTOMETRY MEETING: Structure Identification Approaches U...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at a TRIANGLE AREA MASS SPECTOMETRY meeting on 01/29/2019 in Research Triangle Park, North Carolina to provide a general overview of the CompTox Chemicals Dashboard to an audience of mass spectrometrists and people interested in the capabilities of the dashboard for chemical forensics, structure identification etc.Structure Identification Using High Resolution Mass Spectrometry Data and the...
Structure Identification Using High Resolution Mass Spectrometry Data and the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The iCSS CompTox Chemistry Dashboard is a publicly accessible dashboard provided by the National Center for Computation Toxicology at the US-EPA. It serves a number of purposes, including providing a chemistry database underpinning many of our public-facing projects (e.g. ToxCast and ExpoCast). The available data and searches provide a valuable path to structure identification using mass spectrometry as the source data. With an underlying database of over 720,000 chemicals, the dashboard has already been used to assist in identifying chemicals present in house dust. This poster reviews the benefits of the EPA’s platform and underlying algorithms used for the purpose of compound identification using high-resolution mass spectrometry data. Standard approaches for both mass and formula lookup are available but the dashboard delivers a novel approach for hit ranking based on functional use of the chemicals. The focus on high-quality data, novel ranking approaches and integration to other resources of value to mass spectrometrists makes the CompTox Dashboard a valuable resource for the identification of environmental chemicals. This abstract does not reflect U.S. EPA policy.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.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.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.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.US EPA CompTox Chemicals Dashboard Data Integration Hub to Support Environmen...
US EPA CompTox Chemicals Dashboard Data Integration Hub to Support Environmen...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
A presentation given at the Global Marine Summit at UNC Wilmington on October 9th 2019. The focus of the presentation was an overview of the EPA CompTox Chemicals Dashboard with a specific focus on providing access to data to chemicals such as algal toxins and mycotoxins. More Related Content
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Chemical identification of unknowns in high resolution mass spectrometry usin...
Chemical identification of unknowns in high resolution mass spectrometry usin...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted and suspect screening studies using high resolution mass spectrometry (HRMS) have revolutionized the detection of chemicals in complex matrices. However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. The US EPA has developed functionality within the CompTox Chemicals Dashboard (https://comptox.epa.gov) to address challenges related to data processing and analysis in HRMS. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will introduce the tools and combined workflow, including visualization and access via the CompTox Chemicals Dashboard. These tools, data, and visualization approaches within an open chemistry resource provides a publicly available software tool to support structure identification and non-targeted analyses. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.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.US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for ...
US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Chemical risk assessment is both time-consuming and difficult because it requires the assembly of data for chemicals generally distributed across multiple sources. The US EPA CompTox Chemistry Dashboard is a publicly accessible web-based application providing access to various data streams on ~760,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, consumer product and functional use information and a myriad of related data of value to environmental scientists and toxicologists. At this stage of development, the public dashboard provides access to almost 20 predicted physicochemical and environmental fate and transport endpoints with full transparency in terms of model performance. Experimental and predicted human and ecological toxicity data are also available, as are in vitro to in vivo extrapolation dosimetry predictions and predicted exposure and functional use. In parallel to the CompTox Chemistry Dashboard we are developing RapidTox, a web-based application that enables a rapid, flexible and transparent prioritization process for sets of chemicals using several previously used workflows focused on scoring of traditional risk metrics and the inclusion of alternative hazard and exposure estimates. This presentation will give an overview of the CompTox Chemistry Dashboard, RapidTox, our approaches to building transparent and open prediction models, and our efforts to provide access to real time predictions. This abstract does not necessarily represent U.S. EPA policy.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.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.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.The US-EPA CompTox Chemicals Dashboard to support Non-Targeted Analysis
The US-EPA CompTox Chemicals Dashboard to support Non-Targeted AnalysisUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at the ASMS Sanibel Conference "Unraveling the Exposome" and provided a general overview of the dashboard and how it integrates to many of the projects that we support but with a special focus on list generation, mass and formula searching based on MS-Ready structures and some of the prototypes that we have been developing to support non-targeted analysis.Structure Identification Using High Resolution Mass Spectrometry Data and the...
Structure Identification Using High Resolution Mass Spectrometry Data and the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The iCSS CompTox Dashboard is a publicly accessible dashboard provided by the National Center for Computation Toxicology at the US-EPA. It serves a number of purposes, including providing a chemistry database underpinning many of our public-facing projects (e.g. ToxCast and ExpoCast). The available data and searches provide a valuable path to structure identification using mass spectrometry as the source data. With an underlying database of over 720,000 chemicals, the dashboard has already been used to assist in identifying chemicals present in house dust. However, it can also be applied to many other purposes, e.g., the identification of agrochemicals in waste streams. This presentation will provide a review of the EPA’s platform and underlying algorithms used for the purpose of compound identification using high-resolution mass spectrometry data. In order to examine its performance for structure identification, especially in terms of rank-ordering database hits, we have compared it with the ChemSpider database, a well-regarded public database that has become one of the community standards for structure identification. The study has shown that the CompTox Dashboard outperforms ChemSpider in terms of structure identification and ranking providing improved outcomes for mass spectrometry analysis of “known unknowns”. Environmental Chemistry Compound Identification Using High Resolution Mass Sp...
Environmental Chemistry Compound Identification Using High Resolution Mass Sp...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
There is a growing need for rapid chemical screening and prioritization to inform regulatory decision-making on thousands of chemicals in the environment. We have previously used high-resolution mass spectrometry to examine household vacuum dust samples using liquid chromatography time-of-flight mass spectrometry (LC-TOF/MS). Using a combination of exact mass, isotope distribution, and isotope spacing, molecular features were matched with a list of chemical formulas from the EPA’s Distributed Structure-Searchable Toxicity (DSSTox) database. This has further developed our understanding of how openly available chemical databases, together with the appropriate searches, could be used for the purpose of compound identification. We report here on the utility of the EPA’s iCSS Chemistry Dashboard for the purpose of compound identification using searches against a database of over 720,000 chemicals. We also examine the benefits of QSAR prediction for the purpose of retention time prediction to allow for alignment of both chromatographic and mass spectral properties. This abstract does not reflect U.S. EPA policy.Development of a Tool for Systematic Integration of Traditional and New Appro...
Development of a Tool for Systematic Integration of Traditional and New Appro...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Multiple regulatory bodies (EPA, ECHA, Health Canada) are currently tasked with prioritizing chemicals for data collection and risk assessments. These prioritization efforts are in response to regulatory mandates to identify chemicals for further assessment. We have developed a web-based application that enables a rapid, flexible and transparent prioritization process. The tool includes multiple data streams related to human and ecological hazard, exposure, and physicochemical properties (persistence and bioaccumulation). For human hazard, the data streams include quantitative points of departure (PODs) that are compiled from multiple sources such as EPA ToxRefDB, ECHA, COSMOS; estimated PODs from high-throughput in vitro screening assays and computational models; and qualitative measurements and predictions of specific endpoints (e.g., genotoxicity, endocrine activity). For ecological hazard, quantitative PODs are taken from the EPA ECOTOX database. Exposure information includes production volume, quantitative predictions using the EPA ExpoCast and SHEDS models, biomonitoring data, and qualitative information such as media occurrence, use profiles and likelihood of consumer and childhood exposures. The use of the tool is illustrated by prioritizing chemicals related to TSCA and the Safer Choice Ingredient List. The underpinning data streams for this application are already available in the EPA CompTox Chemistry Dashboard and have been repurposed to deliver this application. This is in keeping with our overarching software development methodology of providing multiple “building blocks” in the form of databases, web services and visualization components to deliver fit-for purpose applications to the relevant audiences. This abstract does not necessarily represent U.S. EPA policy.Delivering The Benefits of Chemical-Biological Integration in Computational T...
Delivering The Benefits of Chemical-Biological Integration in Computational T...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Researchers at EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The goal of this research program is to quickly evaluate thousands of chemicals, but at a much reduced cost and shorter time frame relative to traditional approaches. The data generated by the Center includes characterization of thousands of chemicals across hundreds of high-throughput screening assays, consumer use and production information, pharmacokinetic properties, literature data, physical-chemical properties as well as the predictive computational modeling of toxicity and exposure. We have developed a number of databases and applications to deliver the data to the public, academic community, industry stakeholders, and regulators. This presentation will provide an overview of our work to develop an architecture that integrates diverse large-scale data from the chemical and biological domains, our approaches to disseminate these data, and the delivery of models supporting predictive computational toxicology. In particular, this presentation will review our new publicly-accessible CompTox Dashboard as the first application built on our newly developed architecture. This abstract does not reflect U.S. EPA policy. 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.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.The US-EPA CompTox Chemicals Dashboard – a key player in the domain of Open S...
The US-EPA CompTox Chemicals Dashboard – a key player in the domain of Open S...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are advancing the identification of emerging contaminants in environmental matrices, improving the means by which exposure analyses can be conducted. However, confidence in structure identification of unknowns in NTA presents challenges to analytical chemists. Structure identification requires integration of complementary data types such as reference databases (either commercial or open databases), fragmentation prediction tools, and retention time prediction models. One goal of our research is to optimize and implement structure identification functionality within the US EPA’s CompTox Chemicals Dashboard, an open chemistry resource and web application containing data for ~900,000 substances. Database searching using mass or formula-based inputs has been optimized for structure identification using “MS-Ready Structures”: de-salted, stripped of stereochemistry, and mixture separated to replicate the form of a chemical observed via HRMS. Functionality to conduct batch searching of molecular formulae and monoisotopic masses has also been implemented. While the increasing number of free online databases are of value to support chemical structure verification and elucidation there are known issues regarding data quality and careful data curation is a very necessary part of the development of these resources. This presentation will provide an overview of our latest enhancements to the dashboard to support mass spectrometry, incorporation of specific datasets (i.e. to support breath research and household dust analysis) and the value of metadata and predicted fragmentation spectral matching to support structure identification. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Open PHACTS Chemistry Platform Update and Learnings
Open PHACTS Chemistry Platform Update and Learnings US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was a webinar update to the Open PHACTS community regarding the release of the OPen PHACTS open source components of the Chemical Registration System and, more specifically, the Chemical validation and Standardization Platform. The need for a community set of rules was driven home with the Chemical validation and Standardization Platform potentially being an example platform for the rules. TRIANGLE AREA MASS SPECTOMETRY MEETING: Structure Identification Approaches U...
TRIANGLE AREA MASS SPECTOMETRY MEETING: Structure Identification Approaches U...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at a TRIANGLE AREA MASS SPECTOMETRY meeting on 01/29/2019 in Research Triangle Park, North Carolina to provide a general overview of the CompTox Chemicals Dashboard to an audience of mass spectrometrists and people interested in the capabilities of the dashboard for chemical forensics, structure identification etc.Structure Identification Using High Resolution Mass Spectrometry Data and the...
Structure Identification Using High Resolution Mass Spectrometry Data and the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The iCSS CompTox Chemistry Dashboard is a publicly accessible dashboard provided by the National Center for Computation Toxicology at the US-EPA. It serves a number of purposes, including providing a chemistry database underpinning many of our public-facing projects (e.g. ToxCast and ExpoCast). The available data and searches provide a valuable path to structure identification using mass spectrometry as the source data. With an underlying database of over 720,000 chemicals, the dashboard has already been used to assist in identifying chemicals present in house dust. This poster reviews the benefits of the EPA’s platform and underlying algorithms used for the purpose of compound identification using high-resolution mass spectrometry data. Standard approaches for both mass and formula lookup are available but the dashboard delivers a novel approach for hit ranking based on functional use of the chemicals. The focus on high-quality data, novel ranking approaches and integration to other resources of value to mass spectrometrists makes the CompTox Dashboard a valuable resource for the identification of environmental chemicals. This abstract does not reflect U.S. EPA policy.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.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.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.What's hot (20)
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Chemical identification of unknowns in high resolution mass spectrometry usin...
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US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for ...
US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for ...
Using the US EPA’s CompTox Chemistry Dashboard for structure identification a...
Using the US EPA’s CompTox Chemistry Dashboard for structure identification a...
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Structure identification by Mass Spectrometry Non-Targeted Analysis using the...
New developments in delivering public access to data from the National Center...
New developments in delivering public access to data from the National Center...
The US-EPA CompTox Chemicals Dashboard to support Non-Targeted Analysis
The US-EPA CompTox Chemicals Dashboard to support Non-Targeted Analysis
Structure Identification Using High Resolution Mass Spectrometry Data and the...
Structure Identification Using High Resolution Mass Spectrometry Data and the...
Environmental Chemistry Compound Identification Using High Resolution Mass Sp...
Environmental Chemistry Compound Identification Using High Resolution Mass Sp...
Development of a Tool for Systematic Integration of Traditional and New Appro...
Development of a Tool for Systematic Integration of Traditional and New Appro...
Delivering The Benefits of Chemical-Biological Integration in Computational T...
Delivering The Benefits of Chemical-Biological Integration in Computational T...
Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...
The US-EPA CompTox Chemicals Dashboard – a key player in the domain of Open S...
The US-EPA CompTox Chemicals Dashboard – a key player in the domain of Open S...
Open PHACTS Chemistry Platform Update and Learnings
Open PHACTS Chemistry Platform Update and Learnings
TRIANGLE AREA MASS SPECTOMETRY MEETING: Structure Identification Approaches U...
TRIANGLE AREA MASS SPECTOMETRY MEETING: Structure Identification Approaches U...
Structure Identification Using High Resolution Mass Spectrometry Data and the...
Structure Identification Using High Resolution Mass Spectrometry Data and the...
US-EPA CompTox Chemicals Dashboard – integrating chemistry and biology data t...
US-EPA CompTox Chemicals Dashboard – integrating chemistry and biology data t...
Accessing information for Per- & Polyfluoroalkyl Substances using the US EPA ...
Accessing information for Per- & Polyfluoroalkyl Substances using the US EPA ...
Adding complex expert knowledge into chemical database and transforming surfa...
Adding complex expert knowledge into chemical database and transforming surfa...
Similar to Web-based access to data for >600 disinfection by-products via the EPA CompTox Chemicals Dashboard
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.US EPA CompTox Chemicals Dashboard Data Integration Hub to Support Environmen...
US EPA CompTox Chemicals Dashboard Data Integration Hub to Support Environmen...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
A presentation given at the Global Marine Summit at UNC Wilmington on October 9th 2019. The focus of the presentation was an overview of the EPA CompTox Chemicals Dashboard with a specific focus on providing access to data to chemicals such as algal toxins and mycotoxins. 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.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.US-EPA Chemicals Dashboard and Applications to Digital Design of Molecules
US-EPA Chemicals Dashboard and Applications to Digital Design of MoleculesUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation at: Digital design of molecules and formulations (https://www.soci.org/events/ai-and-digitalisation/digital-design-of-molecules-and-formulations). The Chemicals Dashboard is a free web-based application from the United States Environmental Protection Agency that provides various types of data for ~900,000 chemicals. These data include physicochemical properties, in vivo and in vitro toxicity data and information regarding the presence of chemicals in commercial products, including formulation data where available. The dashboard allows for sourcing of data associated with singleton chemicals or a batch mode for downloading data for thousands of chemicals at a time. This presentation will provide an overview of the Dashboard, the myriad of data sources underpinning the application and potential applications of the dashboard.Delivering web-based access to data and algorithms to support computational t...
Delivering web-based access to data and algorithms to support computational t...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The US-EPA National Center for Computational Toxicity (NCCT) has been generating data and building software applications and web-based chemistry databases for over a decade. During this period the center has analyzed thousands of chemicals in hundreds of bioassays, has researched high-throughput physicochemical property measurements and investigated approaches for high throughput toxicokinetics. NCCT continues to expand the battery of assays and number of chemicals under examination and is now investigating the application of transcriptomics. In parallel to these experimental efforts, and to support our efforts to develop new approaches to prioritize chemicals based on potential human health risks, we aggregate and curate data streams of various types to support prediction models. Over the past few years some of the data have been delivered through prototype web-based “dashboards” for public consumption. The latest of these web applications, the CompTox Chemicals Dashboard, is an integrated access point to obtain information associated with 875,000 chemical substances and providing experimental and predicted data of various types. This includes physicochemical and fate and transport data, bioactivity data, exposure data and integrated literature searches. Real-time predictions and generalized read-across are possible and advanced search capabilities are available to support EPA-related projects including mass spectrometry non-targeted analysis. This presentation will provide an overview of the CompTox Chemicals Dashboard and the its role in delivering access to the outputs of NCCT. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental C...
EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental C...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The US EPA CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a web-based application providing access to ~875,000 chemical substances and diverse data types including physicochemical property, toxicity and EPA’s ToxCast data. This presentation provided a live demo of the application and its benefits to members of ACS AGRO.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.Accessing Environmental Chemistry Data via Data Dashboards
Accessing Environmental Chemistry Data via Data Dashboards US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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.Cheminformatics approaches to support chemical identification delivered via t...
Cheminformatics approaches to support chemical identification delivered via t...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The identification of chemicals in environment media depends on the application of analytical methods, the primary approach being one of the multiple mass spectrometry techniques. Cheminformatics solutions are critical to supporting the chemical identification process. This includes the assembly of large chemical substance databases, prioritization ranking of potential candidate search hits, and search approaches that support both targeted and non-targeted screening approaches. The US Environmental Protection Agency CompTox Chemicals Dashboard is a web-based application providing access to data for over 760,000 chemical substances. This includes access to physicochemical property, environmental fate and transport data, both human and ecological toxicity data, information regarding chemicals contained in products in commerce, and in vitro bioactivity data. Searches are allowed based on chemical identifiers, product and use, genes and assays associated with the EPA ToxCast assays and, specific to supporting mass spectrometry, searches based on masses and formulae. These searches make use of a novel “MS-Ready structures” approach collapsing chemicals related as mixtures, salts, stereoforms and isotopomers. The dashboard supports both singleton or batch searching by accurate mass/chemical formula, supported by MS-ready structures, and utilizes rich meta data to facilitate candidate ranking and the prioritization of chemicals of concern based on toxicity and exposure data. The dashboard also hosts tens of chemical lists that have been assembled from public databases, many supporting non-targeted analysis and mass spectrometry databases.
This presentation will provide an overview of the dashboard and will review our latest research into structure identification by searching experimental mass spectrometry data against predicted fragmentation spectra for LC-MS (positive and negative ion mode) and GC-MS (EI), a total of 3 million predicted spectra. We will also provide an overview of our progress supporting structure and substructure searching, using mass and formula-based filtering, and report on the latest applications of the dashboard to support structure identification projects of interest to the EPA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Integrating Mass Spectrometry Non-Targeted Analysis and Computational Toxico...
Integrating Mass Spectrometry Non-Targeted Analysis and Computational Toxico...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at an SoT "Medical Device and Combination Product / Computational Toxicology Webinar" and covers "Integrating Mass Spectrometry Non-Targeted Analysis and Computational Toxicology to Characterize Chemicals"Accessing Environmental Chemistry Data via Data Dashboards
Accessing Environmental Chemistry Data via Data DashboardsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation given at the Federal Environment Symposium on March 28th 2022.
As part of its mission the Center for Computational Toxicology and Exposure (CCTE) delivers access to chemicals related data via online Dashboards. The CompTox Chemicals Dashboard (available at https://comptox.epa.gov/dashboard) provides access to >900,000 chemicals and associated data including experimental and predicted property data, in vivo hazard data, in vitro bioactivity data, exposure data, and various other data types. The application provides a set of flexible searches allowing for search, visualization and downloads of the data to the desktop for further interrogation. This presentation will provide an overview of the Dashboard and other proof-of-concept applications. For example, the Hazard Comparison Dashboard has a module which allows profiling of chemicals based on toxicity types (https://doi.org/10.1007/s10098-019-01795-w). This presentation will also introduce a number of proof-of-concept modules in development. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Applications of the US EPA’s CompTox chemicals dashboard to support structure...
Applications of the US EPA’s CompTox chemicals 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 ~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 Chemicals 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.CompTox Chemicals Dashboard: Data and tools to support chemical and environme...
CompTox Chemicals Dashboard: Data and tools to support chemical and environme...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Information and data on chemicals is used by scientists to evaluate potential health and ecological risks due to environmental exposures. EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov) helps evaluate the safety of chemicals by providing public access to a variety of information on over 760,000 chemicals. Within the Dashboard, users can access chemical structures, chemistry information, toxicity data, hazard data, exposure information, and additional links to relevant websites and applications. These data are compiled from sources including EPA’s computational toxicology research databases, from public domain databases and with collaborators across the world. Chemical lists have been added that provide access to various classes of chemicals and project-based datasets are under constant development. Specific functionality has been delivered within the Dashboard to support mass spectrometry including “MS-ready forms” of chemical substances that would be detectable by mass spectrometry. Workflows have been developed to assist in candidate identification and have now been proven with multiple published studies. An integration path between the dashboard and MetFrag has also been established to provide users the significant benefits resulting from the marriage between the two applications. The datasets underpinning the dashboard are freely available (https://comptox.epa.gov/dashboard/downloads) for integration into third party databases. This presentation will provide an overview of the available data types and functionality of the dashboard prior to examining how it is developing to support mass spectrometry based analyses within the agency and for the community in general. This will include a review of our research efforts to enhance the dashboard using in silico MS/MS fragmentation prediction for spectral matching. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.EPA’s CompTox Chemicals Dashboard, a tool with information on ~900,000 chemicals
EPA’s CompTox Chemicals Dashboard, a tool with information on ~900,000 chemicalsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The US-EPA CompTox Chemicals Dashboard provides access to data associated with ~900,000 chemical substances. Available data include experimental and predicted physicochemical properties, environmental fate and transport data, in vivo and in silico toxicity data, in vitro bioassay data, exposure data and a variety of other types of information. The data are under continuous expansion and curation and the experimental data have been used to develop QSAR and QSPR models. A number of these models are available via a web interface so that users can submit a chemical structure and predict properties in real time. The dashboard also provides access to pre-compiled chemical lists and categories, including pesticides, and chemicals detected in the environment via non-targeted mass spectrometry analysis. The data are searchable using chemical identifiers (systematic names, trade names, CAS Registry Numbers), by structure, mass and formula. Batch searches allow for data associated with thousands of chemicals to be obtained in a few seconds, with just a few button clicks, and downloaded to the desktop in formats including spreadsheets and chemical structure file formats. This presentation will provide an overview of the Dashboard and its applications to accessing source data associated with agriculturally related chemicals. 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.Delivering chemical-associated data via EPA web applications
Delivering chemical-associated data via EPA web applicationsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at the conference: "Cheminformatics Resources of U.S. Governmental Organizations" and focuses on the CompTox Chemicals Dashboard and the sharing of our data https://www.fda.gov/news-events/fda-meetings-conferences-and-workshops/cheminformatics-resources-us-governmental-organizations-05092022#event-information Cheminformatics Support for MS Supporting Exposomics
Cheminformatics Support for MS Supporting ExposomicsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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 EPA CompTox chemicals dashboard: An online resource for environmental chemists
EPA CompTox chemicals dashboard: An online resource for environmental chemists US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Chemicals Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Chemicals Dashboard and its value to the community as an informational hub. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.The EPA CompTox Dashboard as a Data Integration Hub for Environmental Chemist...
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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Web-based access to data for >600 disinfection by-products via the EPA CompTox Chemicals Dashboard
- 1. Web-based access to data for >600 disinfection by-products via the EPA CompTox Chemicals Dashboard Antony Williams1, Chris Grulke1 and Susan Richardson2 1Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, RTP, NC 2University of South Carolina, Department of Chemistry and Biochemistry, Columbia, SC 29208 August 2021 ACS Fall Meeting, Atlanta 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. 1 EPA’s CompTox Chemicals Dashboard A publicly accessible website delivering: - ~883,000 chemicals with related property data - Experimental and predicted physicochemical property data - Integration to “biological assay data” for 1000’s 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 - Downloadable Open Data for reuse and repurposing
- 3. A single app integrating… 2 2 SEARCH TOX DATA BIOACTIVITY SIMILARITY READ-ACROSS PUBMED BATCH SEARCH
- 4. CompTox Chemicals Dashboard https://comptox.epa.gov/dashboard 3 883k Chemical Substances >906k in the next release
- 5. EPA Drinking Water Requirements 4
- 6. Chemical Lists on the Dashboard >300 lists and growing 5
- 8. The advantage of lists • Pulls a relevant dataset of chemicals into a single list • Download of the file provides relevant data to user: structure, CASRN, Names, InChI • “Send to batch” provides access to all other data of interest – hazard, in vitro bioactivity, exposure, properties, relationship mappings to salts and so much more 7
- 9. Disinfectants • Where do you find the best list? You ask an expert who reviews the science! • Extract, register and map the data between parents and by-products 8
- 10. Download File – SDF 9
- 11. Download File – Excel 10 Masses and Formulae support Mass Spectrometry
- 15. MS-Ready Structures for Formula Search 14
- 17. 16
- 20. MS-Ready Mappings • EXACT Formula: C10H16N2O8: 3 Hits 19
- 21. MS-Ready Mappings • Same Input Formula: C10H16N2O8 • MS Ready Formula Search: 125 Chemicals 20
- 22. MS-Ready Mappings • 125 chemicals returned in total – 8 of the 125 are single component chemicals – 3 of the 8 are isotope-labeled – 3 are neutral compounds and 2 are charged 21
- 24. Data Source Ranking of “known unknowns” 23 • Mass and/or formula is for an unknown chemical but contained within a reference database • Most likely candidate chemicals have the most associated data sources, most associated lit. articles or both C14H22N2O3 266.16304 Chemical Reference Database Sorted candidate structures
- 25. Is a bigger database better? 24 • ChemSpider was 26 million chemicals then • Much BIGGER today • Is bigger better??
- 26. Using Metadata for Ranking • Use available metadata to rank candidates – Associated data sources • Associated lists in the underlying database • Associated data sources in PubChem • Specific types (e.g. water, surfactants, pesticides etc.) – Number of associated literature articles (Pubmed) – Chemicals in the environment – the number of products/categories containing the chemical is a very important source of data 25
- 27. Comparing Search Performance 26 • Dashboard content was 720k chemicals • Only 3% of ChemSpider size • What was the comparison in performance?
- 28. SAME dataset for comparison 27
- 29. How did performance compare? 28 For the same 162 chemicals, Dashboard outperforms ChemSpider
- 30. How did performance compare? 29
- 31. Batch Searching • Singleton searches are useful but we work with thousands of masses and formulae! • Typical questions – What is the list of chemicals for the formula CxHyOz – What is the list of chemicals for a mass +/- error – Can I get chemical lists in Excel files? In SDF files? – Can I include properties in the download file? 30
- 33. Searching batches using MS-Ready Formula (or mass) searching 32
- 34. In Progress 33
- 35. Work in Progress • Predicted Spectra for candidate ranking – Viewing and Downloading pre-predicted spectra – Search spectra against the database 34
- 36. Predicted Mass Spectra http://cfmid.wishartlab.com/ • MS/MS spectra prediction for ESI+, ESI-, and EI • Predictions generated and stored for >800,000 structures, to be accessible via Dashboard 35
- 37. Search Expt. vs. Predicted Spectra
- 38. • Predictions generated and stored for >700,000 structures • Python code to score experimental vs predicted spectra • Cosine dot product match score calculation August 26, 2019 Nontargeted screening of wastewater for water reuse using mass spectrometry Current Advances in Water Analysis 37 CFM-ID Predicted Library Available
- 40. Conclusion • Dashboard access to data for ~875,000 chemicals • MS-Ready data facilitates structure identification • Related metadata facilitates candidate ranking 39 • Relationship mappings and chemical lists of great utility • Dashboard and contents are one part of the solution • New API and Web Services are in development
- 41. Acknowledgements • CCTE IT development team • All scientists within CCTE that provide data and feedback on the Dashboard • Ann Richard and the CCTE curation team
- 42. Contact Antony Williams US EPA Office of Research and Development National Center for Computational Toxicology EMAIL: Williams.Antony@epa.gov ORCID: https://orcid.org/0000-0002-2668-4821 41
Editor's Notes
- Clarify it’s a mockup in progress