Environmental Sciences Rev 1 Science Teachers
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This document provides an overview and links to environmental science and toxicology resources available through the TOXNET system developed by the National Library of Medicine (NLM). It summarizes the six main TOXNET databases that contain information on toxic chemicals, hazardous substances, carcinogenicity studies, and toxic releases. It also provides instructions on how to search within the individual databases or across all databases to find toxicity, risk, and exposure information.
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![Environmental Sciences Resources Mary Markland Southeast Clinical Campus Librarian UND School of Medicine and Health Sciences 701-293-4173 [email_address] March 29, 2008 This project has been funded in whole or in part with federal funds from the National Library of Medicine,National Institutes of Health, under Contract No. NO1-LM-6-3505.](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)
Recommandé
There is increasing interest in the environmental impact of per- and polyfluoroalkyl substances (PFAS) chemicals and the aggregation of related data provides both agency and public access to support research. The US-EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a publicly accessible website providing access to data for ~875,000 chemical substances, including thousands of PFAS chemicals. The dashboard provides access to a wide array of experimental and predicted physicochemical properties, in vitro bioactivity and in vivo toxicity data, product use information and integrated linkages to a growing list of literature, toxicology, and analytical chemistry websites. The assembly of data has required hundreds of hours of manual curation and data checking to deliver a number of segregated lists of PFAS chemicals. Experimental data extracted from literature articles has allowed the optimization of QSAR models for the prediction of properties such as logP (octanol-water partition) and aqueous solubility. This presentation will provide an overview of the dashboard, the ongoing expansion of the PFAS chemical library, with associated categorization, and new physicochemical property and environmental fate and transport QSAR prediction models being developed for these chemicals. Our progress in the measurement and analysis of bioactivity data for PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.An integrated data hub for per- and polyfluoroalkyl (PFAS) chemicals to suppo...
An integrated data hub for per- and polyfluoroalkyl (PFAS) chemicals to suppo...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted screening, targeted screening and suspect screening, as well as “Known Unknowns” and “Unknown Unknowns” are now common terms in the field of water analysis. While data processing can be highly automated, the identification of chemicals from extracted masses, formulae or fragmentation utilizes reference spectral libraries or identification and ranking of tentative candidate lists from large structure libraries. The US-EPA CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) provides access to data for ~875,000 substances, searchable by mass and formula and then ranked using associated meta-data. Cheminformatics approaches are also utilized to provide mapped relationships between individual substances and their “MS-Ready” (desalted, non-stereospecific) forms. This presentation will review how the freely available Dashboard application can be utilized to support structure identification using mass spectrometry and our efforts to enhance the application using computational spectral fragmentation and access to predicted data such as relative retention time index values and computed collision cross section values to support ion mobility spectrometry. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.US-EPA CompTox Chemicals Dashboard as a web-based data resource to help ident...
US-EPA CompTox Chemicals Dashboard as a web-based data resource to help ident...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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
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
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
Recommandé
There is increasing interest in the environmental impact of per- and polyfluoroalkyl substances (PFAS) chemicals and the aggregation of related data provides both agency and public access to support research. The US-EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a publicly accessible website providing access to data for ~875,000 chemical substances, including thousands of PFAS chemicals. The dashboard provides access to a wide array of experimental and predicted physicochemical properties, in vitro bioactivity and in vivo toxicity data, product use information and integrated linkages to a growing list of literature, toxicology, and analytical chemistry websites. The assembly of data has required hundreds of hours of manual curation and data checking to deliver a number of segregated lists of PFAS chemicals. Experimental data extracted from literature articles has allowed the optimization of QSAR models for the prediction of properties such as logP (octanol-water partition) and aqueous solubility. This presentation will provide an overview of the dashboard, the ongoing expansion of the PFAS chemical library, with associated categorization, and new physicochemical property and environmental fate and transport QSAR prediction models being developed for these chemicals. Our progress in the measurement and analysis of bioactivity data for PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.An integrated data hub for per- and polyfluoroalkyl (PFAS) chemicals to suppo...
An integrated data hub for per- and polyfluoroalkyl (PFAS) chemicals to suppo...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted screening, targeted screening and suspect screening, as well as “Known Unknowns” and “Unknown Unknowns” are now common terms in the field of water analysis. While data processing can be highly automated, the identification of chemicals from extracted masses, formulae or fragmentation utilizes reference spectral libraries or identification and ranking of tentative candidate lists from large structure libraries. The US-EPA CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) provides access to data for ~875,000 substances, searchable by mass and formula and then ranked using associated meta-data. Cheminformatics approaches are also utilized to provide mapped relationships between individual substances and their “MS-Ready” (desalted, non-stereospecific) forms. This presentation will review how the freely available Dashboard application can be utilized to support structure identification using mass spectrometry and our efforts to enhance the application using computational spectral fragmentation and access to predicted data such as relative retention time index values and computed collision cross section values to support ion mobility spectrometry. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.US-EPA CompTox Chemicals Dashboard as a web-based data resource to help ident...
US-EPA CompTox Chemicals Dashboard as a web-based data resource to help ident...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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
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
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
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. A new web application, the CompTox Chemistry Dashboard provides access to data associated with ~720,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists.
The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identification based on non-targeted analysis studies using mass spectrometry. Chemical identification using both mass and formula-based searching utilizes rank-ordering of results via functional use statistics, thereby providing a solution to help prioritize chemicals for further review when detected in environmental media.
This presentation will provide an overview of the CompTox Dashboard, its capabilities for delivering data to the environmental toxicology community and how the architecture provides a foundation for the development of additional applications to support chemical risk assessment. This abstract does not reflect U.S. EPA policy.
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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
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
Non-targeted analysis (NTA) uses high-resolution mass spectrometry to better understand the identity of a wide variety of chemicals present in environmental samples (and other matrices). However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. Analysis of the resultant mass spectrometry information relies on cheminformatics to identify and rank chemicals and the US EPA has developed functionality within the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) to address challenges related to this analysis. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will review how the CompTox Chemicals Dashboard via its flexible search capabilities, rich data for ~875,000 chemical substances, and visualization approaches within this open chemistry resource provides a freely available software tool to support structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases within the DSSTox project, and providing accurate linkages of data to chemical structures, exposure and hazard information. The data are made available via the EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard), a publicly accessible website providing access to data for ~880,000 chemical substances, the majority of these represented as chemical structures. The web application delivers a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data, as well as integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. In addition, several specific search types are in development to directly support the mass spectrometry non-targeted screening community, enabling cohesive workflows to support data generation for the detection and assessment of environmental exposures to chemicals contained within the database. The application provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders, including, for example, scientists interested in Per- & Polyfluoroalkyl Substances (PFAS). Added lists include those sourced from the European Union as well as developed in-house and now containing thousands of chemicals. A procured testing library of hundreds of PFAS chemicals annotated into chemical categories has been integrated into the dashboard with a number of resulting benefits: a searchable database of chemical properties, with hazard and exposure predictions, and links to the open literature. This presentation will provide an overview of the dashboard, the developing library of PFAS chemicals and associated categorization, and new physicochemical property and environmental fate and transport QSAR prediction models developed for these chemicals. The application of the dashboard to support mass spectrometry non-targeted analysis studies for the identification of PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...
PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...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
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
EPA’s CompTox Chemicals Dashboard, a tool with information on ~900,000 chemicalsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation for Texas A&M Superfund Research Center virtual learning series, Big Data in Environmental Science and Toxicology. More details at https://superfund.tamu.edu/big-data-session-1-july-14-2021/How to place your research questions or results into the context of the "Lega...
How to place your research questions or results into the context of the "Lega...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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
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
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The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. A new web application, the CompTox Chemistry Dashboard provides access to data associated with ~720,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists.
The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identification based on non-targeted analysis studies using mass spectrometry. Chemical identification using both mass and formula-based searching utilizes rank-ordering of results via functional use statistics, thereby providing a solution to help prioritize chemicals for further review when detected in environmental media.
This presentation will provide an overview of the CompTox Dashboard, its capabilities for delivering data to the environmental toxicology community and how the architecture provides a foundation for the development of additional applications to support chemical risk assessment. This abstract does not reflect U.S. EPA policy.
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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
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
Non-targeted analysis (NTA) uses high-resolution mass spectrometry to better understand the identity of a wide variety of chemicals present in environmental samples (and other matrices). However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. Analysis of the resultant mass spectrometry information relies on cheminformatics to identify and rank chemicals and the US EPA has developed functionality within the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) to address challenges related to this analysis. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will review how the CompTox Chemicals Dashboard via its flexible search capabilities, rich data for ~875,000 chemical substances, and visualization approaches within this open chemistry resource provides a freely available software tool to support structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases within the DSSTox project, and providing accurate linkages of data to chemical structures, exposure and hazard information. The data are made available via the EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard), a publicly accessible website providing access to data for ~880,000 chemical substances, the majority of these represented as chemical structures. The web application delivers a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data, as well as integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. In addition, several specific search types are in development to directly support the mass spectrometry non-targeted screening community, enabling cohesive workflows to support data generation for the detection and assessment of environmental exposures to chemicals contained within the database. The application provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders, including, for example, scientists interested in Per- & Polyfluoroalkyl Substances (PFAS). Added lists include those sourced from the European Union as well as developed in-house and now containing thousands of chemicals. A procured testing library of hundreds of PFAS chemicals annotated into chemical categories has been integrated into the dashboard with a number of resulting benefits: a searchable database of chemical properties, with hazard and exposure predictions, and links to the open literature. This presentation will provide an overview of the dashboard, the developing library of PFAS chemicals and associated categorization, and new physicochemical property and environmental fate and transport QSAR prediction models developed for these chemicals. The application of the dashboard to support mass spectrometry non-targeted analysis studies for the identification of PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...
PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...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
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
EPA’s CompTox Chemicals Dashboard, a tool with information on ~900,000 chemicalsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation for Texas A&M Superfund Research Center virtual learning series, Big Data in Environmental Science and Toxicology. More details at https://superfund.tamu.edu/big-data-session-1-july-14-2021/How to place your research questions or results into the context of the "Lega...
How to place your research questions or results into the context of the "Lega...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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
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
Tendances (20)
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...
Chemical identification of unknowns in high resolution mass spectrometry usin...
Chemical identification of unknowns in high resolution mass spectrometry usin...
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 ...
Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...
PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...
PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...
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...
EPA’s CompTox Chemicals Dashboard, a tool with information on ~900,000 chemicals
EPA’s CompTox Chemicals Dashboard, a tool with information on ~900,000 chemicals
How to place your research questions or results into the context of the "Lega...
How to place your research questions or results into the context of the "Lega...
Adding complex expert knowledge into chemical database and transforming surfa...
Adding complex expert knowledge into chemical database and transforming surfa...
Harding_ImmunopharmacologyWorkshop_Pharmacology2019
Harding_ImmunopharmacologyWorkshop_Pharmacology2019
Diagnostic criteria and clinical guidelines standardization to automate case ...
Diagnostic criteria and clinical guidelines standardization to automate case ...
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ترجمة معتمدة لسفارة تايلاند بالقاهرة ترجمة معتمدة لقنصلية تايلاند
ترجمة معتمدة لسفارة تايلاند بالقاهرة ترجمة معتمدة لقنصلية تايلاند
Getting back to work after a long weekend or holiday
Getting back to work after a long weekend or holiday
Satta Matka, Kalyan Matka, Matka Result, Fix Matka Number, Matka
Satta Matka, Kalyan Matka, Matka Result, Fix Matka Number, Matka
Libro da colorare sulla sicurezza. Scarica su www.giochiecolori.it
Libro da colorare sulla sicurezza. Scarica su www.giochiecolori.it
How should a company respond to a competitor's price change
How should a company respond to a competitor's price change
Similaire à Environmental Sciences Rev 1 Science Teachers
The biomedical research community is providing large-scale data sources to enable knowledge discovery from the data alone, or from novel scientific experiments in combination with the existing knowledge.
Increasingly semantic Web technologies are being developed and used including ontologies, triple stores and combinations thereof.
The amount of data is constantly increasing as well as the complexity of data.
Since the data sources are publicly available, the amount of content can be derived giving an overview on the accessible content but also on the state of the data representation in comparison to the existing content.
For a better understanding of the existing data resources, i.e.\ judgments on the distribution of data triples across concepts, data types and primary providers, we have performed a comprehensive analysis which delivers an overview on the accessible content for semantic Web solutions.
It can be derived that the information related to genes, proteins and chemical entities form the center, whereas the content related to diseases and pathways forms a smaller portion.
Further data relates to dietary content and specific questions such as cancer prevention and toxicological effects of drugs.Quantifying the content of biomedical semantic resources as a core for drug d...
Quantifying the content of biomedical semantic resources as a core for drug d...Syed Muhammad Ali Hasnain
This is a presentation given at the Opal Events meeting ""Drug Discovery Partnerships: Filling the Pipeline". I was speaking in a session with Jean-Claude Bradley regarding "Pre-competitive Collaboration: Sharing Data to Increase Predictability". This presentation discussed some of the work we are doing on Open PHACTS. My thanks especially to Carole Goble, Lee Harland and Sean Ekins for their comments. Online Resources to Support Open Drug Discovery Systems
Online Resources to Support Open Drug Discovery SystemsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Neglected infectious diseases such as tuberculosis (TB) and malaria kill millions of people annually and the oral drugs used are subject to resistance requiring the urgent development of new therapeutics. Several groups, including pharmaceutical companies, have made large sets of antimalarial screening hit compounds and the associated bioassay data available for the community to learn from and potentially optimize. We have examined both intrinsic and predicted molecular properties across these datasets and compared them with large libraries of compounds screened against Mycobacterium tuberculosis in order to identify any obvious patterns, trends or relationships. One set of antimalarial hits provided by GlaxoSmithKline appears less optimal for lead optimization compared with two other sets of screening hits we examined. Active compounds against both diseases were identified to have larger molecular weight ([similar]350–400) and logP values of [similar]4.0, values that are, in general, distinct from the less active compounds. The antimalarial hits were also filtered with computational rules to identify potentially undesirable substructures. We were surprised that approximately 75–85% of these compounds failed one of the sets of filters that we applied during this work. The level of filter failure was much higher than for FDA approved drugs or a subset of antimalarial drugs. Both antimalarial and antituberculosis drug discovery should likely use simple available approaches to ensure that the hits derived from large scale screening are worth optimizing and do not clearly represent reactive compounds with a higher probability of toxicity in vivo.Meta analysis of molecular property patterns and filtering of public datasets...
Meta analysis of molecular property patterns and filtering of public datasets...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Similaire à Environmental Sciences Rev 1 Science Teachers (20)
Collaborative Drug Discovery: A Platform For Transforming Neglected Disease R...
Collaborative Drug Discovery: A Platform For Transforming Neglected Disease R...
Hepatotoxicity related to antidepressive psychopharmacotherapy: implications ...
Hepatotoxicity related to antidepressive psychopharmacotherapy: implications ...
Quantifying the content of biomedical semantic resources as a core for drug d...
Quantifying the content of biomedical semantic resources as a core for drug d...
Toxic Chemicals and Children’s Health in North America
Toxic Chemicals and Children’s Health in North America
Online Resources to Support Open Drug Discovery Systems
Online Resources to Support Open Drug Discovery Systems
Information Resources for Environmental Health Research and Practice
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Meta analysis of molecular property patterns and filtering of public datasets...
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Environmental Sciences Rev 1 Science Teachers
- 2. Environmental Sciences Resources Mary Markland Southeast Clinical Campus Librarian UND School of Medicine and Health Sciences 701-293-4173 [email_address] March 29, 2008 This project has been funded in whole or in part with federal funds from the National Library of Medicine,National Institutes of Health, under Contract No. NO1-LM-6-3505.
- 16. TOXNET: Toxicology & Environmental Information http://toxnet.nlm.nih.gov/
- 21. Search will be conducted only in the chosen database
- 28. Or, search all TOXNET databases for information:
- 29. Results are hyperlinked. Click a link to see results from that database:
- 31. TOXNET’s 2 Literature Files
- 34. Using TOXLINE
- 36. Click here to access this record in PubMed Search terms appear in red Terms in blue are hyperlinks. Click to retrieve more records with those terms.
- 39. Searching TRI Search by chemical name or CAS Specify release amount and type Select a year or years Search by facility name Search by location Search by SIC code
- 40. Searching for North Dakota
- 44. Haz-Map