Structure Identification Using High Resolution Mass Spectrometry Data and the EPA’s Chemistry Dashboard
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The iCSS 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. 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. We will also discuss progress towards a high-throughput non-targeted analysis platform for use by the mass spectrometry community. This abstract does not reflect U.S. EPA policy.
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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.The EPA iCSS Chemistry Dashboard to Support Compound Identification Using Hig...
The EPA iCSS Chemistry Dashboard to Support Compound Identification Using Hig...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Researchers at the EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The intention of this research program is to quickly evaluate thousands of chemicals for potential risk but with much reduced cost relative to historical approaches. This work involves computational and data driven approaches including high-throughput screening, modeling, text-mining and the integration of chemistry, exposure and biological data. We have developed a number of databases and applications that are delivering on the vision of developing a deeper understanding of chemicals and their effects on exposure and biological processes that are supporting a large community of scientists in their research efforts. This presentation will provide an overview of our work to bring together diverse large scale data from the chemical and biological domains, our approaches to integrate and disseminate these data, and the delivery of models supporting computational toxicology. This abstract does not reflect U.S. EPA policy.Delivering The Benefits of Chemical-Biological Integration in Computational T...
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As part of our efforts to develop a public platform to provide access to predictive models we have attempted to disentangle the influence of the quality versus quantity of data available to develop and validate QSAR models. Using a thorough manual review of the data underlying the well-known EPI Suite software, we developed automated processes for the validation of the data using a KNIME workflow. This includes: approaches to validate different chemical structure representations (e.g. molfile and SMILES), identifiers (chemical names and registry numbers), and methods to standardize the data into QSAR-consumable formats for modeling. Our efforts to quantify and segregate data into various quality categories has allowed us to thoroughly investigate the resulting models developed from these data slices, as well as allowing us to examine whether or not efforts into the development of large high-quality datasets has the expected pay-off in terms of prediction performance. Machine-learning approaches have been applied to create a series of models that have been used to generate predicted physicochemical and environmental parameters for over 700,000 chemicals. These data are available online via the EPA’s iCSS Chemistry Dashboard. This abstract does not reflect U.S. EPA policy.The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...
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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. Delivering The Benefits of Chemical-Biological Integration in Computational T...
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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.Environmental Chemistry Compound Identification Using High Resolution Mass Sp...
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The construction of QSAR models is critically dependent on the quality of available data. As part of our efforts to develop public platforms to provide access to predictive models, we have attempted to discriminate the influence of the quality versus quantity of data available to develop and validate QSAR models. We have focused our efforts on the widely used EPISuite software that was initially developed over two decades ago. Specific examples of quality issues for the EPISuite data include multiple records for the same chemical structure with different measured property values, inconsistency between the structure, chemical name and CAS registry number for single records, the inability to convert the SMILES strings into chemical structures, hypervalency in the chemical structures and the absence of stereochemistry for thousands of data records. Relative to the era of EPISuite development, modern cheminformatics tools allow for more advanced capabilities in terms of chemical structure representation and storage, as well as enabling automated data validation and standardization approaches to examine data quality. This presentation will review both our manual and automated approaches to examining key datasets related to the EPISuite training and test data. This includes approaches to validate between chemical structure representations (e.g. molfile and SMILES) and identifiers (chemical names and registry numbers), as well as approaches to standardize the data into QSAR-consumable formats for modeling. We have quantified and segregated the data into various quality categories to allow us to thoroughly investigate the resulting models that can be developed from these data slices and to examine to what extent efforts into the development of large high-quality datasets have the expected pay-off in terms of prediction performance. This abstract does not reflect U.S. EPA policy. The influence of data curation on QSAR Modeling – examining issues of qualit...
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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.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”. 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
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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.The EPA iCSS Chemistry Dashboard to Support Compound Identification Using Hig...
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Researchers at the EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The intention of this research program is to quickly evaluate thousands of chemicals for potential risk but with much reduced cost relative to historical approaches. This work involves computational and data driven approaches including high-throughput screening, modeling, text-mining and the integration of chemistry, exposure and biological data. We have developed a number of databases and applications that are delivering on the vision of developing a deeper understanding of chemicals and their effects on exposure and biological processes that are supporting a large community of scientists in their research efforts. This presentation will provide an overview of our work to bring together diverse large scale data from the chemical and biological domains, our approaches to integrate and disseminate these data, and the delivery of models supporting computational toxicology. This abstract does not reflect U.S. EPA policy.Delivering The Benefits of Chemical-Biological Integration in Computational T...
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As part of our efforts to develop a public platform to provide access to predictive models we have attempted to disentangle the influence of the quality versus quantity of data available to develop and validate QSAR models. Using a thorough manual review of the data underlying the well-known EPI Suite software, we developed automated processes for the validation of the data using a KNIME workflow. This includes: approaches to validate different chemical structure representations (e.g. molfile and SMILES), identifiers (chemical names and registry numbers), and methods to standardize the data into QSAR-consumable formats for modeling. Our efforts to quantify and segregate data into various quality categories has allowed us to thoroughly investigate the resulting models developed from these data slices, as well as allowing us to examine whether or not efforts into the development of large high-quality datasets has the expected pay-off in terms of prediction performance. Machine-learning approaches have been applied to create a series of models that have been used to generate predicted physicochemical and environmental parameters for over 700,000 chemicals. These data are available online via the EPA’s iCSS Chemistry Dashboard. This abstract does not reflect U.S. EPA policy.The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...
The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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. Delivering The Benefits of Chemical-Biological Integration in Computational T...
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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.Environmental Chemistry Compound Identification Using High Resolution Mass Sp...
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The construction of QSAR models is critically dependent on the quality of available data. As part of our efforts to develop public platforms to provide access to predictive models, we have attempted to discriminate the influence of the quality versus quantity of data available to develop and validate QSAR models. We have focused our efforts on the widely used EPISuite software that was initially developed over two decades ago. Specific examples of quality issues for the EPISuite data include multiple records for the same chemical structure with different measured property values, inconsistency between the structure, chemical name and CAS registry number for single records, the inability to convert the SMILES strings into chemical structures, hypervalency in the chemical structures and the absence of stereochemistry for thousands of data records. Relative to the era of EPISuite development, modern cheminformatics tools allow for more advanced capabilities in terms of chemical structure representation and storage, as well as enabling automated data validation and standardization approaches to examine data quality. This presentation will review both our manual and automated approaches to examining key datasets related to the EPISuite training and test data. This includes approaches to validate between chemical structure representations (e.g. molfile and SMILES) and identifiers (chemical names and registry numbers), as well as approaches to standardize the data into QSAR-consumable formats for modeling. We have quantified and segregated the data into various quality categories to allow us to thoroughly investigate the resulting models that can be developed from these data slices and to examine to what extent efforts into the development of large high-quality datasets have the expected pay-off in terms of prediction performance. This abstract does not reflect U.S. EPA policy. The influence of data curation on QSAR Modeling – examining issues of qualit...
The influence of data curation on QSAR Modeling – examining issues of qualit...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.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”. 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
This presentation highlights known challenges with the production of high quality chemical databases and outline recent efforts made to address these challenges. Specific examples will be provided illustrating these challenges within the U.S. Environmental Protection Agency (EPA) Computational Toxicology Program. This includes consolidating EPA’s ACToR and DSSTox databases, augmenting computed properties and list search features, and introducing quality metrics to assess confidence in chemical structure assignments across hundreds of thousands of chemical substance records. The past decade has seen enormous investments in the generation and release of data from studies of chemicals and their toxicological effects. There is, however, commonly little concern given to provenance and, more generally, to the quality of the data. The presentation will emphasize the importance of rigorous data review procedures, progress in web-based public access to accurate chemical data sets for use in predictive modeling, and the benefits that these efforts will deliver to toxicologists to embrace the “Big Data” era.
This abstract does not necessarily represent the views of the U.S. Environmental Protection Agency.
The needs for chemistry standards, database tools and data curation at the ch...
The needs for chemistry standards, database tools and data curation at the ch...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The development of QSAR models is critically dependent on the quality of available data. As part of our efforts to develop public platforms to provide access to predictive models, we have attempted to discriminate the influence of the quality versus quantity of data available to develop and validate QSAR models. We have focused our efforts on the widely used EPISuite software that was initially developed over two decades ago and, specifically, on the PHYSPROP dataset used to train the EPISuite prediction models. This presentation will review our approaches to examining key datasets, the delivery of curated data and the development of machine-learning models for thirteen separate property endpoints of interest to environmental science. We will also review how these data will be made freely accessible to the community via a new “chemistry dashboard”. This abstract does not reflect U.S. EPA policyAn examination of data quality on QSAR Modeling in regards to the environment...
An examination of data quality on QSAR Modeling in regards to the environment...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.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
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.Structure identification by Mass Spectrometry Non-Targeted Analysis using the...
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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. 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
EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases and providing accurate linkages of data to chemical structures, exposure and hazard information. The data are being made available via the EPA’s CompTox Chemistry Dashboard (https://comptox.epa.gov/dashboard), a publicly accessible website providing access to data for almost 760,000 chemical substances, the majority of these represented as chemical structures. The web application delivers a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data as well as integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. In addition, several specific search types are in development to directly support the mass spectroscopy non-targeted screening community, who are generating important data for detecting and assessing environmental exposures to chemicals contained within DSSTox. The application provides access to segregated lists of chemicals that are of specific interests to relevant stakeholders including, for example, scientists interested in algal toxins and hydraulic fracturing chemicals. This presentation will provide an overview of the challenges associated with the curation of data from EPA’s December 2016 Hydraulic Fracturing Drinking Water Assessment Report that represented chemicals reported to be used in hydraulic fracturing fluids and those found in produced water. The data have been integrated into the dashboard with a number of resulting benefits: a searchable database of chemical properties, with hazard and exposure predictions, and open literature. The application of the dashboard to support mass spectrometry non-targeted analysis studies will also be reviewed. This abstract does not reflect U.S. EPA policy.Accessing information for chemicals in hydraulic fracturing fluids using the ...
Accessing information for chemicals in hydraulic fracturing fluids using the ...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.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
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.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
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.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
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.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
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.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
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.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
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.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
Non-targeted analysis (NTA) uses high-resolution mass spectrometry to better understand the identity of a wide variety of chemicals present in environmental samples (and other matrices). However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. Analysis of the resultant mass spectrometry information relies on cheminformatics to identify and rank chemicals and the US EPA has developed functionality within the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) to address challenges related to this analysis. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will review how the CompTox Chemicals Dashboard via its flexible search capabilities, rich data for ~900,000 chemical substances, and visualization approaches within this open chemistry resource provides a freely available software tool to support structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are utilized to identify emerging contaminants and chemical signatures of interest detected in various media. At the US Environmental Protection Agency the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is an open chemistry resource and web-based application containing data for ~900,000 substances and supports non-targeted and suspect screening analyses. Searching functionality includes identifier searches (e.g. systematic names, trade names and CAS Registry Numbers), mass and formula-based searches and prototype developments include combined substructure-mass/formula searches and searching experimental mass spectral data against predicted fragmentation spectra. A specific type of data mapping in the database uses “MS-Ready” structures, a way to process all registered substances to separate multi-component chemicals into their individual components, removal of stereochemical bonds and desalting and neutralization. This MS-Ready processing supports batch-searching using either mass or formulae to identify candidate chemicals and their mapped substances. A number of chemical lists (https://comptox.epa.gov/dashboard/chemical_lists) have also been developed to support the identification of chemicals related to agrochemistry, specifically pesticides (both active and inert constituents), insecticides and their metabolites and environmental breakdown products). This presentation will provide an overview of how the CompTox Chemicals Dashboard supports mass spectrometry based structure identification and non-targeted analysis of chemicals in agrochemistry. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Structure identification approaches using the EPA CompTox Chemicals Dashboard...
Structure identification approaches using the EPA CompTox Chemicals Dashboard...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The CompTox Chemicals Dashboard is an open chemistry resource and web-based application containing data for ~900,000 substances. While it pales in comparison to other online resources containing many tens of millions of chemical substances it represents two decades of effort to aggregate and curate chemical data to deliver access to physicochemical properties and environmental fate and transport data, in vitro and in vivo toxicity data and consumer product data for over 500,000 products. Associated with the chemical substance collections are specific lists based on chemical classes (e.g. polychlorinated biphenyls (PCBs)), usage categories (e.g. flame retardants, pesticides), specific environmental classes of interest (e.g. disinfectant by-products) and regulatory lists (e.g. TSCA, Toxics release inventory data). The underlying database expands daily as a result of the efforts of curators who continue to harvest data from peer-reviewed publications, regulatory documents and relevant online databases. The cheminformatics architecture allows for mapping between parent chemicals and related substances including metabolites and environmental degradants. The dashboard has become a valuable resource in the identification of chemical substances in the environment.
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are of increasing interest in chemical forensics for the identification of emerging contaminants and chemical signatures of interest. Our research using HRMS for non-targeted and suspect screening analyses utilizes Advanced Search capabilities including mass and formula-based searches. A specific type of data mapping in the underpinning database, using “MS-Ready” structures, has proven to be a valuable approach for structure identification that links structures that can be identified via HRMS with related substances in the form of salts, and other multi-component mixtures that are available in commerce. These MS-Ready structures have been used as an input set for computational MS-fragmentation to provide a database against which to search experimental data for spectral matching. This presentation will provide an overview of how CompTox Chemicals Dashboard, the underlying data, and how it supports structure identification and non-targeted analysis in chemical forensics. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.
What chemicals constitute the Exposome? Accessing data via the US EPA’s Comp...
What chemicals constitute the Exposome? Accessing data via the US EPA’s Comp...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation for Texas A&M Superfund Research Center virtual learning series, Big Data in Environmental Science and Toxicology. More details at https://superfund.tamu.edu/big-data-session-2-aug-18-2021/New Approach Methods - What is That?
New Approach Methods - What is That?US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program utilizes computational and data-driven approaches that integrate chemistry, exposure and biological data to help characterize potential risks from chemical exposure. The National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences, including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. The CompTox Chemicals Dashboard website provides access to data associated with ~900,000 chemical substances. New data are added on an ongoing basis, including the registration of new and emerging chemicals, data extracted from the literature, chemicals studied in our labs, and data of interest to specific research projects at the EPA. Hazard and exposure data have been assembled from a large number of public databases and as a result the dashboard surfaces hundreds of thousands of data points. Other data includes experimental and predicted physicochemical property data, in vitro bioassay data for over 4000 chemicals and 2000 assays, and millions of chemical identifiers (names and CAS Registry Numbers) to facilitate searching. Other integrated modules include an interactive read-across module, real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed. This presentation will provide an overview of the latest release of the CompTox Chemicals Dashboard and how it has developed into an integrated data hub for environmental data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.US-EPA CompTox Chemicals Dashboard – integrating chemistry and biology data t...
US-EPA CompTox Chemicals Dashboard – integrating chemistry and biology data t...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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This presentation highlights known challenges with the production of high quality chemical databases and outline recent efforts made to address these challenges. Specific examples will be provided illustrating these challenges within the U.S. Environmental Protection Agency (EPA) Computational Toxicology Program. This includes consolidating EPA’s ACToR and DSSTox databases, augmenting computed properties and list search features, and introducing quality metrics to assess confidence in chemical structure assignments across hundreds of thousands of chemical substance records. The past decade has seen enormous investments in the generation and release of data from studies of chemicals and their toxicological effects. There is, however, commonly little concern given to provenance and, more generally, to the quality of the data. The presentation will emphasize the importance of rigorous data review procedures, progress in web-based public access to accurate chemical data sets for use in predictive modeling, and the benefits that these efforts will deliver to toxicologists to embrace the “Big Data” era.
This abstract does not necessarily represent the views of the U.S. Environmental Protection Agency.
The needs for chemistry standards, database tools and data curation at the ch...
The needs for chemistry standards, database tools and data curation at the ch...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The development of QSAR models is critically dependent on the quality of available data. As part of our efforts to develop public platforms to provide access to predictive models, we have attempted to discriminate the influence of the quality versus quantity of data available to develop and validate QSAR models. We have focused our efforts on the widely used EPISuite software that was initially developed over two decades ago and, specifically, on the PHYSPROP dataset used to train the EPISuite prediction models. This presentation will review our approaches to examining key datasets, the delivery of curated data and the development of machine-learning models for thirteen separate property endpoints of interest to environmental science. We will also review how these data will be made freely accessible to the community via a new “chemistry dashboard”. This abstract does not reflect U.S. EPA policyAn examination of data quality on QSAR Modeling in regards to the environment...
An examination of data quality on QSAR Modeling in regards to the environment...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.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
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.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
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. 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
EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases and providing accurate linkages of data to chemical structures, exposure and hazard information. The data are being made available via the EPA’s CompTox Chemistry Dashboard (https://comptox.epa.gov/dashboard), a publicly accessible website providing access to data for almost 760,000 chemical substances, the majority of these represented as chemical structures. The web application delivers a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data as well as integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. In addition, several specific search types are in development to directly support the mass spectroscopy non-targeted screening community, who are generating important data for detecting and assessing environmental exposures to chemicals contained within DSSTox. The application provides access to segregated lists of chemicals that are of specific interests to relevant stakeholders including, for example, scientists interested in algal toxins and hydraulic fracturing chemicals. This presentation will provide an overview of the challenges associated with the curation of data from EPA’s December 2016 Hydraulic Fracturing Drinking Water Assessment Report that represented chemicals reported to be used in hydraulic fracturing fluids and those found in produced water. The data have been integrated into the dashboard with a number of resulting benefits: a searchable database of chemical properties, with hazard and exposure predictions, and open literature. The application of the dashboard to support mass spectrometry non-targeted analysis studies will also be reviewed. This abstract does not reflect U.S. EPA policy.Accessing information for chemicals in hydraulic fracturing fluids using the ...
Accessing information for chemicals in hydraulic fracturing fluids using the ...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.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
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.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
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.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
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.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
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.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
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.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
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.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
Non-targeted analysis (NTA) uses high-resolution mass spectrometry to better understand the identity of a wide variety of chemicals present in environmental samples (and other matrices). However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. Analysis of the resultant mass spectrometry information relies on cheminformatics to identify and rank chemicals and the US EPA has developed functionality within the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) to address challenges related to this analysis. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will review how the CompTox Chemicals Dashboard via its flexible search capabilities, rich data for ~900,000 chemical substances, and visualization approaches within this open chemistry resource provides a freely available software tool to support structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are utilized to identify emerging contaminants and chemical signatures of interest detected in various media. At the US Environmental Protection Agency the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is an open chemistry resource and web-based application containing data for ~900,000 substances and supports non-targeted and suspect screening analyses. Searching functionality includes identifier searches (e.g. systematic names, trade names and CAS Registry Numbers), mass and formula-based searches and prototype developments include combined substructure-mass/formula searches and searching experimental mass spectral data against predicted fragmentation spectra. A specific type of data mapping in the database uses “MS-Ready” structures, a way to process all registered substances to separate multi-component chemicals into their individual components, removal of stereochemical bonds and desalting and neutralization. This MS-Ready processing supports batch-searching using either mass or formulae to identify candidate chemicals and their mapped substances. A number of chemical lists (https://comptox.epa.gov/dashboard/chemical_lists) have also been developed to support the identification of chemicals related to agrochemistry, specifically pesticides (both active and inert constituents), insecticides and their metabolites and environmental breakdown products). This presentation will provide an overview of how the CompTox Chemicals Dashboard supports mass spectrometry based structure identification and non-targeted analysis of chemicals in agrochemistry. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Structure identification approaches using the EPA CompTox Chemicals Dashboard...
Structure identification approaches using the EPA CompTox Chemicals Dashboard...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The CompTox Chemicals Dashboard is an open chemistry resource and web-based application containing data for ~900,000 substances. While it pales in comparison to other online resources containing many tens of millions of chemical substances it represents two decades of effort to aggregate and curate chemical data to deliver access to physicochemical properties and environmental fate and transport data, in vitro and in vivo toxicity data and consumer product data for over 500,000 products. Associated with the chemical substance collections are specific lists based on chemical classes (e.g. polychlorinated biphenyls (PCBs)), usage categories (e.g. flame retardants, pesticides), specific environmental classes of interest (e.g. disinfectant by-products) and regulatory lists (e.g. TSCA, Toxics release inventory data). The underlying database expands daily as a result of the efforts of curators who continue to harvest data from peer-reviewed publications, regulatory documents and relevant online databases. The cheminformatics architecture allows for mapping between parent chemicals and related substances including metabolites and environmental degradants. The dashboard has become a valuable resource in the identification of chemical substances in the environment.
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are of increasing interest in chemical forensics for the identification of emerging contaminants and chemical signatures of interest. Our research using HRMS for non-targeted and suspect screening analyses utilizes Advanced Search capabilities including mass and formula-based searches. A specific type of data mapping in the underpinning database, using “MS-Ready” structures, has proven to be a valuable approach for structure identification that links structures that can be identified via HRMS with related substances in the form of salts, and other multi-component mixtures that are available in commerce. These MS-Ready structures have been used as an input set for computational MS-fragmentation to provide a database against which to search experimental data for spectral matching. This presentation will provide an overview of how CompTox Chemicals Dashboard, the underlying data, and how it supports structure identification and non-targeted analysis in chemical forensics. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.
What chemicals constitute the Exposome? Accessing data via the US EPA’s Comp...
What chemicals constitute the Exposome? Accessing data via the US EPA’s Comp...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program utilizes computational and data-driven approaches that integrate chemistry, exposure and biological data to help characterize potential risks from chemical exposure. The National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences, including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. The CompTox Chemicals Dashboard website provides access to data associated with ~900,000 chemical substances. New data are added on an ongoing basis, including the registration of new and emerging chemicals, data extracted from the literature, chemicals studied in our labs, and data of interest to specific research projects at the EPA. Hazard and exposure data have been assembled from a large number of public databases and as a result the dashboard surfaces hundreds of thousands of data points. Other data includes experimental and predicted physicochemical property data, in vitro bioassay data for over 4000 chemicals and 2000 assays, and millions of chemical identifiers (names and CAS Registry Numbers) to facilitate searching. Other integrated modules include an interactive read-across module, real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed. This presentation will provide an overview of the latest release of the CompTox Chemicals Dashboard and how it has developed into an integrated data hub for environmental data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.US-EPA CompTox Chemicals Dashboard – integrating chemistry and biology data t...
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How One Monkey on a Typewriter Made a Difference to Online ChemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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Similar to Structure Identification Using High Resolution Mass Spectrometry Data and the EPA’s Chemistry Dashboard
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...
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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.EPA’s CompTox Chemicals Dashboard, a tool with information on ~900,000 chemicals
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The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program utilizes computational and data-driven approaches that integrate chemistry, exposure and biological data to help characterize potential risks from chemical exposure. The National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences, including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. The CompTox Chemicals Dashboard website provides access to data associated with ~900,000 chemical substances. New data are added on an ongoing basis, including the registration of new and emerging chemicals, data extracted from the literature, chemicals studied in our labs, and data of interest to specific research projects at the EPA. Hazard and exposure data have been assembled from a large number of public databases and as a result the dashboard surfaces hundreds of thousands of data points. Other data includes experimental and predicted physicochemical property data, in vitro bioassay data for over 4000 chemicals and ~1500 assays, and millions of chemical identifiers (names and CAS Registry Numbers) to facilitate searching. Other integrated modules include an interactive read-across module, real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed. This presentation will provide an overview of the CompTox Chemicals Dashboard and how it has developed into an integrated data hub for environmental data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.US-EPA Chemicals Dashboard – an integrated data hub for environmental science
US-EPA Chemicals Dashboard – an integrated data hub for environmental scienceUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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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.The US-EPA CompTox Chemicals Dashboard – a key player in the domain of Open S...
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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.The US-EPA CompTox Chemicals Dashboard to support Non-Targeted Analysis
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US-EPA Chemicals Dashboard – an integrated data hub for environmental scienceUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Center for Computational Toxicology and Exposure (CCTE) is part of the Office of Research and Development at the US Environmental Protection Agency. As part of its mission the center delivers access to chemicals related data via web-based freely accessible online Dashboards to disseminate data generated within the center as well as harvested and integrated from open databases around the world. The CompTox Chemicals Dashboard (available at https://comptox.epa.gov/dashboard) provides access to >1.2 million 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 curation of the chemicals dataset has included the development of over 400 segregated lists of chemicals that represent specific research areas of interest including disinfectant by-products, per- and polyfluoroalkyl substances (PFAS), extractables and leachables, and chemicals of emerging concern. The chemicals collection, the associated data, the lists and searches for mass and formulae makes the Dashboard an ideal foundation technology to support our colleagues working in the field of mass spectrometry, especially in targeted and non-targeted analysis. This presentation will provide an overview of the Dashboard, its value to the community in terms of providing access to the integrated and highly curated data, and its utility to support researchers in the field of mass spectrometry. New proof-of-concept projects will also be introduced including the development of a cheminformatics enabled methods database. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Accessing Environmental Chemistry Data via Data Dashboards and Applications t...
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US-EPA Chemicals Dashboard – an integrated data hub for environmental scienceUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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 Cheminformatics Support for MS Supporting Exposomics
Cheminformatics Support for MS Supporting ExposomicsUS 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.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 US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a freely available web-based application providing access to data for ~900,000 chemical substances, the majority of these represented as chemical structures. The Dashboard also provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders and, in particular, a list of hundreds of disinfection by-product (DBP) chemicals reported in the literature and detected in the laboratory using mass spectrometric techniques. Many of these chemicals are explicit chemical structures whose structures have been confirmed using purchased or synthesized reference standards. However, some of these chemicals may be ambiguous in nature with no explicit positional isomers being possible to define but the formula and mass spec fragmentation sufficient to define a class of chemicals (e.g. dichlorophenol). Such chemicals may be represented with ambiguous chemical structure forms, so-called Markush structures, and mapped to the individual class members. Chemicals accessible via the Dashboard can include access to a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data, product use information extracted from safety data sheets, and integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. Since DBP chemicals are primarily identified using mass spectrometric techniques specific search types have been developed to directly support the non-targeted screening community, enabling cohesive workflows to support data generation for the detection and assessment of environmental exposures to chemicals contained within the database. This presentation will provide an overview of the Dashboard, the ongoing expansion of the DBP chemical list and specific functionality supporting identification of DBPs by mass spectrometry. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Web-based access to data for >600 disinfection by-products via the EPA CompTo...
Web-based access to data for >600 disinfection by-products via the EPA CompTo...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The EPA CompTox Chemistry Dashboard provides access to data associated with ~760,000 chemical substances. The available data includes 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. 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.Web-based access to experimental and predicted data for environmental fate, t...
Web-based access to experimental and predicted data for environmental fate, t...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation at: Digital design of molecules and formulations (https://www.soci.org/events/ai-and-digitalisation/digital-design-of-molecules-and-formulations). The Chemicals Dashboard is a free web-based application from the United States Environmental Protection Agency that provides various types of data for ~900,000 chemicals. These data include physicochemical properties, in vivo and in vitro toxicity data and information regarding the presence of chemicals in commercial products, including formulation data where available. The dashboard allows for sourcing of data associated with singleton chemicals or a batch mode for downloading data for thousands of chemicals at a time. This presentation will provide an overview of the Dashboard, the myriad of data sources underpinning the application and potential applications of the dashboard.US-EPA Chemicals Dashboard and Applications to Digital Design of Molecules
US-EPA Chemicals Dashboard and Applications to Digital Design of MoleculesUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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Structure Identification Using High Resolution Mass Spectrometry Data and the EPA’s Chemistry Dashboard
- 1. Structure Identification Using High Resolution Mass Spectrometry Data and the EPA Chemistry Dashboard Antony J. Williams†, Andrew McEachran, Jon Sobus, Chris Grulke, Jennifer Smith, Michelle Krzyzanowski, Jordan Foster and Jeff Edwards National Center for Computational Toxicology U.S. Environmental Protection Agency, RTP, NC August 21-25, 2016 ACS Fall Meeting, Philadelphia, PA 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 http://www.orcid.org/0000-0002-2668-4821 @ChemConnector on Twitter
- 2. Comparing Analysis Approaches • Targeted Analysis: - We know exactly what we’re looking for - 10s – 100s of chemicals • Suspect Screening Analysis (SSA): - We have chemicals of interest - 100s – 1,000s of chemicals • Non-Targeted Analysis (NTA): - We have no preconceived lists - 1,000s – 10,000s of chemicals - In dust, soil, food, air, water, products, plants, animals, and…us!!
- 3. General Goals of SSA/NTA - 1 Dust Sample - Negative Ionization Mode - 300 Extracted “Molecular Features” 1) Prioritize “Molecular Features” 2) Correctly assign formulas 3) Correctly assign structures 4) Determine chemical sources 5) Predict chemical concentrations C17H19NO3 12 µg/g (1) (2) (3) (4) (5) EXPOSURE
- 4. Non-targeted analysis challenges • 3000-5000 molecular features in a given sample • Current technologies can identify up to 5% • How can we improve identification??? – Simple workflows – Reliable formula prediction (Instrument) – Accurate ranking of likelihood (Databases)
- 5. The General Approach Analytical Instruments Comp. Tools & Workflows Databases
- 6. Previous Work with Suspect-Screening
- 7. We’re on the Right Path… • … but certainly room for improvement • ~thousands of molecular features (not unique) • 33 confirmed chemicals • State-of-the-art SSA yields <5% confirmed IDs • So what else is in these (and other) samples??
- 8. 2012: Definitive Study of Known- Unknowns using ChemSpider 7
- 9. 2012: Definitive Study of Known- Unknowns using ChemSpider 8
- 10. ChemSpider • http://www.chemspider.com • Grows daily with new depositors and annotations. Example Data Sources 9
- 12. Bisphenol A 11
- 15. Functional Use and Composition 14
- 17. National Environmental Methods Index 16
- 19. Formula Searching Formulae matching Bisphenol A 18
- 22. Download as SDF file 21
- 23. SDF file opened in ChemFolder 22
- 24. Rank-ordering all of those hits?? • With so many hits how do you rank order based on formulae? Or mass?? 23
- 26. Bisphenol A as an example ChemSpider: 1564 Structures 25
- 27. Bisphenol A as an example Dashboard: 215 Structures 26
- 28. A more pointed example…C15H15N3O2 6926 results 27
- 29. A more pointed example…C15H15N3O2 94 results 28
- 30. Particulate Matter Antibiotics used in animal production TYL= Tylosin MON= Monensin TC= Tetracycline OTC= Oxytetracycline CTC= Chlortetracycline McEachran AD, Blackwell BR, Hanson JD, Wooten KJ, Mayer GD, Cox SB, Smith PN. 2015. Antibiotics, bacteria, and antibiotic resistance genes: aerial transport from cattle feed yards via particulate matter. Environ Health Perspect 123:337-343; DOI:10.1289/EHP.1408555 Antibiotics in beef commercial feed
- 31. Mass-based Search Formula-based Search Agricultural Source # Compounds Dashboard ChemSpider Dashboard ChemSpider Wastewater land application1 34 1.3 1.8 1.1 1.1 Cattle Feedyard2 5 1.0 1.0 1.0 1.0 1McEachran AD, Shea D, Bodnar W, Nichols EG. 2016. Pharmaceutical Occurrence in groundwater and surface waters in forests land-applied with municipal wastewater. Environ Toxicol Chem 35: 898-905. DOI: 10.1002/etc.3216 2McEachran AD, Blackwell BR, Hanson JD, Wooten KJ, Mayer GD, Cox SB, Smith PN. 2015. Antibiotics, bacteria, and antibiotic resistance genes: aerial transport from cattle feed yards via particulate matter. Environ Health Perspect 123:337-343; DOI:10.1289/EHP.1408555 Mass-based Search Formula Based Search Dashboard ChemSpider Dashboard ChemSpider Tylosin 1/1 1/28 1/1 1/25 Monensin 1/1 1/39 1/1 1/24 Tetracycline 1/ 38 1/4008 1/11 1/355 Oxytetracycline 1/16 1/3271 1/3 1/110 Chlortetracycline 1/23 1/2545 1/3 1/77 Rank Position/Total # Results Mean Rank Position Rank-ordering Comparisons
- 32. Chemical Identification Dashboard vs ChemSpider Sorted by number of references (ChemSpider) or data sources (Dashboard) Monoisotopic Mass (+/- 0.005 amu) Search Position of compound sorted Source of List # of Compounds Search Tool Mean Position Median Position #1 #2 #3 #4 #5+ McEachran et al Wastewater 34 ChemSpider 1.8 1 28 5 0 0 1 Dashboard 1.3 1 31 2 0 0 1 Misc. NTA Compounds 13 ChemSpider 2 1 7 5 0 0 1 Dashboard 1.7 1 10 2 0 0 1 Bade et al (2016) 19 ChemSpider 2.1 1 11 2 5 0 1 Dashboard 1.6 1 12 3 3 1 0 Rager et al (2016) 24 ChemSpider 2.25 1 15 2 1 2 4 Dashboard 1.08 1 22 2 0 0 0
- 33. Dashboard vs ChemSpider Ranking Summary Mass-based Searching Formula Based Searching Dashboard ChemSpider Dashboard ChemSpider Cumulative Average Position 1.3 2.2 1.2 1.4 % in #1 Position 85% 70% 88% 80% 162 total individual chemicals in search
- 34. Functional Use to Sort Candidates 33 Anti-cancer Drug Microbiological Indicator Dye Textile/Product Dye
- 35. Future Work • Rank-ordering based on other criteria • Already testing QSARs to build retention time models for ranking • External links to methods: e.g. CDC NIOSH • Formula identification using isotope profiles 34
- 36. ToxCast Chemicals What impurities/ interaction products found? Engaging the MS Community
- 37. Conclusions • Our NTA research is focused on understanding our exposure to chemicals • New dashboard with focus on high-quality data – no large database will be perfect! • Specific searches/functionality are being developed with Non-targeted Analysis in mind • Dashboard outperforms ChemSpider, a community standard database, in ranking chemicals of environmental concern • Early work on new rank-ordering approaches show that we can improve things even further. 36
- 38. Acknowledgements EPA NCCT Chris Grulke Jeff Edwards Ann Richard Jordan Foster Jennifer Smith Andrew McEachran* Michelle Krzyzanowski EPA NERL Kathie Dionisio Katherine Phillips Jon Sobus Mark Strynar Elin Ulrich Seth Newton * = ORISE Participant
Editor's Notes
- For example- Rager was actually 33 confirmed; Bade was 25