The EPA iCSS Chemistry Dashboard to Support Compound Identification Using High Resolution Mass Spectrometry Data
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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.
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The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Chemicals Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Chemicals Dashboard and its value to the community as an informational hub. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.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
This document discusses adding complex expert knowledge about surfactants to chemical databases to aid in the identification of unknown compounds from wastewater samples. It describes how over 60% of peaks detected by high resolution mass spectrometry in wastewater samples are unknown. Literature data on surfactant properties and spectra were compiled and added to databases to support the identification of homologous series and complex mixtures present. A list of surfactants was developed and incorporated into toxicity databases to enable in silico modeling and computational mass spectrometry approaches to aid non-target screening. International collaboration is helping to establish a global exchange of suspect lists to support the identification of unknown contaminants.What chemicals constitute the Exposome? Accessing data via the US EPA’s Comp...
What chemicals constitute the Exposome? Accessing data via the US EPA’s Comp...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The CompTox Chemicals Dashboard is an open chemistry resource and web-based application containing data for ~900,000 substances. While it pales in comparison to other online resources containing many tens of millions of chemical substances it represents two decades of effort to aggregate and curate chemical data to deliver access to physicochemical properties and environmental fate and transport data, in vitro and in vivo toxicity data and consumer product data for over 500,000 products. Associated with the chemical substance collections are specific lists based on chemical classes (e.g. polychlorinated biphenyls (PCBs)), usage categories (e.g. flame retardants, pesticides), specific environmental classes of interest (e.g. disinfectant by-products) and regulatory lists (e.g. TSCA, Toxics release inventory data). The underlying database expands daily as a result of the efforts of curators who continue to harvest data from peer-reviewed publications, regulatory documents and relevant online databases. The cheminformatics architecture allows for mapping between parent chemicals and related substances including metabolites and environmental degradants. The dashboard has become a valuable resource in the identification of chemical substances in the environment.
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are of increasing interest in chemical forensics for the identification of emerging contaminants and chemical signatures of interest. Our research using HRMS for non-targeted and suspect screening analyses utilizes Advanced Search capabilities including mass and formula-based searches. A specific type of data mapping in the underpinning database, using “MS-Ready” structures, has proven to be a valuable approach for structure identification that links structures that can be identified via HRMS with related substances in the form of salts, and other multi-component mixtures that are available in commerce. These MS-Ready structures have been used as an input set for computational MS-fragmentation to provide a database against which to search experimental data for spectral matching. This presentation will provide an overview of how CompTox Chemicals Dashboard, the underlying data, and how it supports structure identification and non-targeted analysis in chemical forensics. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.
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 document discusses how the EPA's CompTox Chemicals Dashboard can be used to support mass spectrometry analyses for structure identification. The Dashboard contains data on over 800,000 chemicals including properties, lists, and links to other resources. It allows searching by formula, structure, and mass to find related chemicals. Candidate structures can be ranked using metadata. Predicted mass spectra from over 800,000 structures may also be accessible. The Dashboard integrates data to help identify unknown chemicals detected by mass spectrometry.Open PHACTS Chemistry Platform Update and Learnings
Open PHACTS Chemistry Platform Update and Learnings US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was a webinar update to the Open PHACTS community regarding the release of the OPen PHACTS open source components of the Chemical Registration System and, more specifically, the Chemical validation and Standardization Platform. The need for a community set of rules was driven home with the Chemical validation and Standardization Platform potentially being an example platform for the rules. 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
I do not have enough information to answer that question. The dashboard contains lists of chemicals from various sources, but does not state the number of chemicals in the Toxics Release Inventory list specifically.New Approach Methods - What is That?
New Approach Methods - What is That?US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation for Texas A&M Superfund Research Center virtual learning series, Big Data in Environmental Science and Toxicology. More details at https://superfund.tamu.edu/big-data-session-2-aug-18-2021/Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted analysis (NTA) uses high-resolution mass spectrometry to better understand the identity of a wide variety of chemicals present in environmental samples (and other matrices). However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. Analysis of the resultant mass spectrometry information relies on cheminformatics to identify and rank chemicals and the US EPA has developed functionality within the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) to address challenges related to this analysis. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will review how the CompTox Chemicals Dashboard via its flexible search capabilities, rich data for ~900,000 chemical substances, and visualization approaches within this open chemistry resource provides a freely available software tool to support structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.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 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.How One Monkey on a Typewriter Made a Difference to Online Chemistry
How One Monkey on a Typewriter Made a Difference to Online ChemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
On Friday September 16th I was honored with the award for the North Carolina American Chemical Society Distinguished Speaker Award and got to review the past 20 years of my career. This was my short intro bio
"Antony Williams is a Ph.D. NMR spectroscopist and cheminformatician who has worked in academia, government, a Fortune 500 company, and two start-ups. He is co-founder of the free online chemical database ChemSpider, originally started as a hobby project and ultimately acquired by the Royal Society of Chemistry (in the UK) and now used by over 50,000 users per day. He is now a computational chemist at the Environmental Protection Agency in the National Center for Computational Toxicology and is focused on developing web applications to support data dissemination and progress efforts in allowing for faster and cheaper approaches to identify potential toxicological effects of chemicals. He has published >180 papers, >25 book chapters and a number of books. He is known as the ChemConnector on social networks. "More Related Content
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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 by Mass Spectrometry Non-Targeted Analysis using the...
Structure identification by Mass Spectrometry Non-Targeted Analysis using the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Identification of unknowns in mass spectrometry based non-targeted analyses (NTA) requires the integration of complementary pieces of data to arrive at a confident, consensus structure. Researchers use chemical reference databases, spectral matching, fragment prediction tools, retention time prediction tools, and a variety of other data to arrive at tentative, probable, and confirmed, if possible, identifications. With the diverse, robust data contained within the US EPA’s CompTox Chemistry Dashboard (https://comptox.epa.gov), the goal of this research is to identify and implement a harmonized identification tool and workflow using previously generated chemistry data. Data has been compiled from product use, functional use prediction models, environmental media occurrence prediction models, and PubMed references, among other sources. We will report on our development of a visualization tool whereby users can visualize the relative contribution of identification-based metrics on a list of candidate structures and observe the greatest likelihood of occurrence. These data and visualization tools support NTA identification via the Dashboard and demonstrate an open, accessible tool for all users of HRMS data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Chemical identification of unknowns in high resolution mass spectrometry usin...
Chemical identification of unknowns in high resolution mass spectrometry usin...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted and suspect screening studies using high resolution mass spectrometry (HRMS) have revolutionized the detection of chemicals in complex matrices. However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. The US EPA has developed functionality within the CompTox Chemicals Dashboard (https://comptox.epa.gov) to address challenges related to data processing and analysis in HRMS. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will introduce the tools and combined workflow, including visualization and access via the CompTox Chemicals Dashboard. These tools, data, and visualization approaches within an open chemistry resource provides a publicly available software tool to support structure identification and non-targeted analyses. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.An 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
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 policyThe 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
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.
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
The document describes the EPA's CompTox Chemistry Dashboard, which provides access to data on over 760,000 chemicals. It focuses on how the Dashboard can be used to access information on chemicals used in hydraulic fracturing. Key features include searching for chemicals by name or formula, viewing associated property and hazard data, and links to other resources. The process of curating chemical lists from sources like EPA's hydraulic fracturing study involves mapping names to CAS numbers and structures through iterative checking. This allows accessing additional screening data, exposure information, and integrating identifiers to support searches.Using the US EPA’s CompTox Chemistry Dashboard for structure identification a...
Using the US EPA’s CompTox Chemistry Dashboard for structure identification a...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are advancing the identification of emerging contaminants in environmental matrices, improving the means by which exposure analyses can be conducted. However, confidence in structure identification of unknowns in NTA presents challenges to analytical chemists. Structure identification requires integration of complementary data types such as reference databases, fragmentation prediction tools, and retention time prediction models. The goal of this research is to optimize and implement structure identification functionality within the US EPA’s CompTox Chemistry Dashboard, an open chemistry resource and web application containing data for ~760,000 substances. Rank-ordering the number of sources associated with chemical records within the Dashboard (Data Source Ranking) improves the identification of unknowns by bringing the most likely candidate structures to the top of a search results list. Database searching has been further optimized with the generation of MS-Ready Structures. MS-Ready structures are de-salted, stripped of stereochemistry, and mixture separated to replicate the form of a chemical observed via HRMS. Functionality to conduct batch searching of molecular formulae and monoisotopic masses was designed and released to improve searching efforts. Finally, a scoring-based identification scheme was developed, optimized, and surfaced via the Dashboard using multiple data streams contained within the database underlying the Dashboard. The scoring-based identification scheme improved the identification of unknowns over previous efforts using data source ranking alone. Combining these steps within an open chemistry resource provides a freely available software tool for structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for ...
US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Chemical risk assessment is both time-consuming and difficult because it requires the assembly of data for chemicals generally distributed across multiple sources. The US EPA CompTox Chemistry Dashboard is a publicly accessible web-based application providing access to various data streams on ~760,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, consumer product and functional use information and a myriad of related data of value to environmental scientists and toxicologists. At this stage of development, the public dashboard provides access to almost 20 predicted physicochemical and environmental fate and transport endpoints with full transparency in terms of model performance. Experimental and predicted human and ecological toxicity data are also available, as are in vitro to in vivo extrapolation dosimetry predictions and predicted exposure and functional use. In parallel to the CompTox Chemistry Dashboard we are developing RapidTox, a web-based application that enables a rapid, flexible and transparent prioritization process for sets of chemicals using several previously used workflows focused on scoring of traditional risk metrics and the inclusion of alternative hazard and exposure estimates. This presentation will give an overview of the CompTox Chemistry Dashboard, RapidTox, our approaches to building transparent and open prediction models, and our efforts to provide access to real time predictions. This abstract does not necessarily represent U.S. EPA policy.Development of a Tool for Systematic Integration of Traditional and New Appro...
Development of a Tool for Systematic Integration of Traditional and New Appro...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Multiple regulatory bodies (EPA, ECHA, Health Canada) are currently tasked with prioritizing chemicals for data collection and risk assessments. These prioritization efforts are in response to regulatory mandates to identify chemicals for further assessment. We have developed a web-based application that enables a rapid, flexible and transparent prioritization process. The tool includes multiple data streams related to human and ecological hazard, exposure, and physicochemical properties (persistence and bioaccumulation). For human hazard, the data streams include quantitative points of departure (PODs) that are compiled from multiple sources such as EPA ToxRefDB, ECHA, COSMOS; estimated PODs from high-throughput in vitro screening assays and computational models; and qualitative measurements and predictions of specific endpoints (e.g., genotoxicity, endocrine activity). For ecological hazard, quantitative PODs are taken from the EPA ECOTOX database. Exposure information includes production volume, quantitative predictions using the EPA ExpoCast and SHEDS models, biomonitoring data, and qualitative information such as media occurrence, use profiles and likelihood of consumer and childhood exposures. The use of the tool is illustrated by prioritizing chemicals related to TSCA and the Safer Choice Ingredient List. The underpinning data streams for this application are already available in the EPA CompTox Chemistry Dashboard and have been repurposed to deliver this application. This is in keeping with our overarching software development methodology of providing multiple “building blocks” in the form of databases, web services and visualization components to deliver fit-for purpose applications to the relevant audiences. This abstract does not necessarily represent U.S. EPA policy.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
The National Center for Computational Toxicology at the EPA has developed the CompTox Chemistry Dashboard to provide public access to toxicity and chemical property data. The dashboard integrates data from high-throughput screening, predicted properties, chemical hazard assessments, literature searches, and exposure information for over 760,000 chemicals. It allows users to search for chemicals individually or in batches, access detailed chemical pages, view predicted and experimental properties, and download open data. The dashboard is meant to be an integration hub that makes NCCT's data and models more accessible and reusable to other scientists.CompTox Chemicals Dashboard: Data and tools to support chemical and environme...
CompTox Chemicals Dashboard: Data and tools to support chemical and environme...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Information and data on chemicals is used by scientists to evaluate potential health and ecological risks due to environmental exposures. EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov) helps evaluate the safety of chemicals by providing public access to a variety of information on over 760,000 chemicals. Within the Dashboard, users can access chemical structures, chemistry information, toxicity data, hazard data, exposure information, and additional links to relevant websites and applications. These data are compiled from sources including EPA’s computational toxicology research databases, from public domain databases and with collaborators across the world. Chemical lists have been added that provide access to various classes of chemicals and project-based datasets are under constant development. Specific functionality has been delivered within the Dashboard to support mass spectrometry including “MS-ready forms” of chemical substances that would be detectable by mass spectrometry. Workflows have been developed to assist in candidate identification and have now been proven with multiple published studies. An integration path between the dashboard and MetFrag has also been established to provide users the significant benefits resulting from the marriage between the two applications. The datasets underpinning the dashboard are freely available (https://comptox.epa.gov/dashboard/downloads) for integration into third party databases. This presentation will provide an overview of the available data types and functionality of the dashboard prior to examining how it is developing to support mass spectrometry based analyses within the agency and for the community in general. This will include a review of our research efforts to enhance the dashboard using in silico MS/MS fragmentation prediction for spectral matching. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.EPA CompTox chemicals dashboard: An online resource for environmental chemists
EPA CompTox chemicals dashboard: An online resource for environmental chemists US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Chemicals Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Chemicals Dashboard and its value to the community as an informational hub. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.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
This document discusses adding complex expert knowledge about surfactants to chemical databases to aid in the identification of unknown compounds from wastewater samples. It describes how over 60% of peaks detected by high resolution mass spectrometry in wastewater samples are unknown. Literature data on surfactant properties and spectra were compiled and added to databases to support the identification of homologous series and complex mixtures present. A list of surfactants was developed and incorporated into toxicity databases to enable in silico modeling and computational mass spectrometry approaches to aid non-target screening. International collaboration is helping to establish a global exchange of suspect lists to support the identification of unknown contaminants.What chemicals constitute the Exposome? Accessing data via the US EPA’s Comp...
What chemicals constitute the Exposome? Accessing data via the US EPA’s Comp...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The CompTox Chemicals Dashboard is an open chemistry resource and web-based application containing data for ~900,000 substances. While it pales in comparison to other online resources containing many tens of millions of chemical substances it represents two decades of effort to aggregate and curate chemical data to deliver access to physicochemical properties and environmental fate and transport data, in vitro and in vivo toxicity data and consumer product data for over 500,000 products. Associated with the chemical substance collections are specific lists based on chemical classes (e.g. polychlorinated biphenyls (PCBs)), usage categories (e.g. flame retardants, pesticides), specific environmental classes of interest (e.g. disinfectant by-products) and regulatory lists (e.g. TSCA, Toxics release inventory data). The underlying database expands daily as a result of the efforts of curators who continue to harvest data from peer-reviewed publications, regulatory documents and relevant online databases. The cheminformatics architecture allows for mapping between parent chemicals and related substances including metabolites and environmental degradants. The dashboard has become a valuable resource in the identification of chemical substances in the environment.
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are of increasing interest in chemical forensics for the identification of emerging contaminants and chemical signatures of interest. Our research using HRMS for non-targeted and suspect screening analyses utilizes Advanced Search capabilities including mass and formula-based searches. A specific type of data mapping in the underpinning database, using “MS-Ready” structures, has proven to be a valuable approach for structure identification that links structures that can be identified via HRMS with related substances in the form of salts, and other multi-component mixtures that are available in commerce. These MS-Ready structures have been used as an input set for computational MS-fragmentation to provide a database against which to search experimental data for spectral matching. This presentation will provide an overview of how CompTox Chemicals Dashboard, the underlying data, and how it supports structure identification and non-targeted analysis in chemical forensics. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.
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 document discusses how the EPA's CompTox Chemicals Dashboard can be used to support mass spectrometry analyses for structure identification. The Dashboard contains data on over 800,000 chemicals including properties, lists, and links to other resources. It allows searching by formula, structure, and mass to find related chemicals. Candidate structures can be ranked using metadata. Predicted mass spectra from over 800,000 structures may also be accessible. The Dashboard integrates data to help identify unknown chemicals detected by mass spectrometry.Open PHACTS Chemistry Platform Update and Learnings
Open PHACTS Chemistry Platform Update and Learnings US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was a webinar update to the Open PHACTS community regarding the release of the OPen PHACTS open source components of the Chemical Registration System and, more specifically, the Chemical validation and Standardization Platform. The need for a community set of rules was driven home with the Chemical validation and Standardization Platform potentially being an example platform for the rules. 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
I do not have enough information to answer that question. The dashboard contains lists of chemicals from various sources, but does not state the number of chemicals in the Toxics Release Inventory list specifically.New Approach Methods - What is That?
New Approach Methods - What is That?US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation for Texas A&M Superfund Research Center virtual learning series, Big Data in Environmental Science and Toxicology. More details at https://superfund.tamu.edu/big-data-session-2-aug-18-2021/Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted analysis (NTA) uses high-resolution mass spectrometry to better understand the identity of a wide variety of chemicals present in environmental samples (and other matrices). However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. Analysis of the resultant mass spectrometry information relies on cheminformatics to identify and rank chemicals and the US EPA has developed functionality within the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) to address challenges related to this analysis. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will review how the CompTox Chemicals Dashboard via its flexible search capabilities, rich data for ~900,000 chemical substances, and visualization approaches within this open chemistry resource provides a freely available software tool to support structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.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 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.What's hot (20)
Structure Identification Using High Resolution Mass Spectrometry Data and the...
Structure Identification Using High Resolution Mass Spectrometry Data and the...
Structure identification by Mass Spectrometry Non-Targeted Analysis using the...
Structure identification by Mass Spectrometry Non-Targeted Analysis using the...
Chemical identification of unknowns in high resolution mass spectrometry usin...
Chemical identification of unknowns in high resolution mass spectrometry usin...
An 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...
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...
Accessing information for chemicals in hydraulic fracturing fluids using the ...
Accessing information for chemicals in hydraulic fracturing fluids using the ...
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 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 ...
Development of a Tool for Systematic Integration of Traditional and New Appro...
Development of a Tool for Systematic Integration of Traditional and New Appro...
New developments in delivering public access to data from the National Center...
New developments in delivering public access to data from the National Center...
CompTox Chemicals Dashboard: Data and tools to support chemical and environme...
CompTox Chemicals Dashboard: Data and tools to support chemical and environme...
EPA CompTox chemicals dashboard: An online resource for environmental chemists
EPA CompTox chemicals dashboard: An online resource for environmental chemists
Adding complex expert knowledge into chemical database and transforming surfa...
Adding complex expert knowledge into chemical database and transforming surfa...
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...
Structure identification approaches using the EPA CompTox Chemicals Dashboard...
Structure identification approaches using the EPA CompTox Chemicals Dashboard...
Open PHACTS Chemistry Platform Update and Learnings
Open PHACTS Chemistry Platform Update and Learnings
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...
Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...
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...
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How One Monkey on a Typewriter Made a Difference to Online Chemistry
How One Monkey on a Typewriter Made a Difference to Online ChemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
On Friday September 16th I was honored with the award for the North Carolina American Chemical Society Distinguished Speaker Award and got to review the past 20 years of my career. This was my short intro bio
"Antony Williams is a Ph.D. NMR spectroscopist and cheminformatician who has worked in academia, government, a Fortune 500 company, and two start-ups. He is co-founder of the free online chemical database ChemSpider, originally started as a hobby project and ultimately acquired by the Royal Society of Chemistry (in the UK) and now used by over 50,000 users per day. He is now a computational chemist at the Environmental Protection Agency in the National Center for Computational Toxicology and is focused on developing web applications to support data dissemination and progress efforts in allowing for faster and cheaper approaches to identify potential toxicological effects of chemicals. He has published >180 papers, >25 book chapters and a number of books. He is known as the ChemConnector on social networks. "Using Ecological Momentary Assessment to Examine Post-food Consumption Affect...
We used smartphone app to prompt brief electronic surveys to assess a sample of mothers' eating behaviors and feelings randomly throughout their daily lives.
Simple Springshare Mashups: Cross-Platform Strategies for Repurposing Digital...
Simple Springshare Mashups: Cross-Platform Strategies for Repurposing Digital...Georgia Libraries Conference (formerly Ga COMO).
The document discusses how a library shares development and maintenance of technical and public services. It describes how the library maintains databases, ebooks, print books, and websites. Content developed on template guides can be mapped to FAQ posts on multiple platforms for discoverability. Newspaper boxes created on a template guide were copied and pasted into corresponding FAQ posts to dynamically map the content. Link assets were then mapped from the template guide to a newspapers guide to centrally manage all newspaper content from a single page.From Data Availability to Information Accessibility: The WellWiki Project
This slides accompanied a talk I gave on January 27, 2016, at Startup Edmonton's "Lunchalytics" speaker series. The event was held in the Mercer Warehouse, 10359 104 Street Northwest, Edmonton, Alberta, Canada.
NSF Data Management Requirements 101
The National Science Foundation (NSF) provides over $7 billion annually to fund basic research through competitive grants. The NSF requires all grant proposals to include a Data Management Plan that describes how research data will be managed and shared. In 2015, the NSF published a Public Access Plan outlining new, more extensive requirements for researchers to share both published works and original research data. These include depositing data in repositories and making it publicly available with appropriate metadata. Directorates may provide additional guidance for specific research communities. The plan aims to maximize access to and reuse of research funded by the NSF.
SMS Berlin 2016 Cultural Perspectives on Strategic Management
Strategic Management Society 2016 Conference
Berlin, Germany
Sunday, September 18
Session 253 - Cultural Perspectives on Strategic Management
Track J
Session Chair
Joel Gehman, University of Alberta
Krsto Pandza, University of Leeds
Session Panelists
Shahzad Ansari, University of Cambridge
Rodolphe Durand, HEC-Paris
Candace Jones, University of Edinburgh Business School
Michael Lounsbury, University of Alberta
Richard Whittington, University of Oxford
This session aims to spark conversations between scholars at the intersection of strategic management and organization theory. In particular, we hope the event will generate awareness of, stimulate interest in, and set direction for research at the SM-OT interface. Especially, the panelists will address potential connections between perennial strategy topics such as resources, capabilities, innovation, competition, governance, nonmarket strategy and strategy process and practice and topics of central interest to organization theory such as institutional logics, organizational forms, legitimacy, creativity, framing and categories. Panellist will identify the most promising questions that could benefit from integrating strategy and organizational theory concepts as well as discussing possible challenges of such a theoretical bricolage.
Investigating Impact Metrics for Performance for the US-EPA National Center f...
Investigating Impact Metrics for Performance for the US-EPA National Center f...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The National Center for Computational Toxicology at the EPA investigates impact metrics to measure the performance and value of its work. NCCT's key products include scientific publications, research data, software tools, collaborations, training, and scientific leadership. NCCT is exploring alternative metrics like downloads, views, citations, reuse, and social media mentions to better quantify the impact of these products beyond traditional bibliometric measures. An integrated website is being developed to aggregate these alternative metrics for NCCT's work across multiple platforms to demonstrate its large scientific impact.Social Media Tools for Scientists and Building an Online Profile
Social Media Tools for Scientists and Building an Online ProfileUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Despite the availability of many platforms for scientists to connect and share with their peers in the scientific community the majority do not make use of these tools, despite their promise and potential impact and influence on our careers. We are already being indexed and exposed on the internet via our publications, presentations and data and new “AltMetric scores” are being assigned to scientific publications as measures of popularity and, supposedly, of impact. We now have even more ways to contribute to science, to annotate and curate data, to “publish” in new ways, and many of these activities are as part of a growing crowdsourcing network. This presentation provides an overview of the various types of networking and collaborative sites available to scientists and ways to expose your scientific activities online. It will discuss the new world of AltMetrics that is in an explosive growth curve and will help you understand how to influence and leverage some of these new measures. Participating online, whether it be simply for career advancement or for wider exposure of your research, there are now a series of web applications that can provide a great opportunity to develop a scientific profile within the community.A Bird in the Hand: Leveraging ILL Requests to Improve Electronic Resource A...
A Bird in the Hand: Leveraging ILL Requests to Improve Electronic Resource A...Georgia Libraries Conference (formerly Ga COMO).
Presenter(s): Jeffrey Mortimore, Jessica Garner, Jermaine Bryant, Jessica Williams.
Interlibrary Loan (ILL) requests reveal a lot about our collections, from development needs to access issues. This session focuses on how ILL and Technical Services personnel at Georgia Southern University are using ILL request information to troubleshoot and improve electronic resource access across our collections.
Shaping Expectations: Defining and Refining the Role of Technical Services in...
From trial to implementation, technical services staff play an important role in shaping awareness of, and expectations for, new resources. Internally, technical services staff provide information and instruction to public services staff. Externally, they influence how new resources are integrated into the library website and other platforms. With appropriate “message control,” technical services staff can positively influence awareness of new resources while keeping everyone’s expectations in check.
During fall 2015, technical services staff at Georgia Southern University adopted a protocol for new resource rollouts that explicitly times and structures internal and external communications to ensure that all library staff are ready to support new resources as they go live. This protocol focuses on providing appropriate lead-time notifications to public services staff and “training the trainers” first, prior to releasing any external communications. Furthermore, this protocol integrates with activities of the library’s promotion committee, supporting smooth transition to public services promotion of new resources.
During this session, presenters will discuss this protocol in detail, with special emphasis on timing of internal and external communications, the importance of providing sufficient staff training and support materials early on, and the importance of maintaining objectivity and accuracy in all rollout communications and assets. Presenters will share protocol planning tools and worksheets, describe how these are integrated into implementation workflows, and engage participants in discussion about the role of technical services in new resource rollouts.
Presenters:
Jeff Mortimore & Debra Skinner
Zach S. Henderson Library
Georgia Southern University
Building an Online Profile Using Social Networking and Amplification Tools fo...
Building an Online Profile Using Social Networking and Amplification Tools fo...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Many of us nowadays invest significant amounts of time in sharing our activities and opinions with friends and family via social networking tools such as Facebook, Twitter or other related websites. However, despite the availability of many platforms for scientists to connect and share with their peers in the scientific community the majority do not make use of these tools, despite their promise and potential impact and influence on our careers. We are already being indexed and exposed on the internet via our publications, presentations and data and new “AltMetric scores” are being assigned to scientific publications as measures of popularity and, supposedly, of impact. We now have even more ways to contribute to science, to annotate and curate data, to “publish” in new ways, and many of these activities are as part of a growing crowdsourcing network. This presentation provides an overview of the various types of networking and collaborative sites available to scientists and ways to expose your scientific activities online. It will discuss the new world of AltMetrics that is in an explosive growth curve and will help you understand how to influence and leverage some of these new measures. Participating online, whether it be simply for career advancement or for wider exposure of your research, there are now a series of web applications that can provide a great opportunity to develop a scientific profile within the community.Web Preservation, or Managing your Organisation’s Online Presence After the O...
Slides for talk on "Web Preservation, or Managing your Organisation’s Online Presence After the Organisation Ceases to Exist" given by Brian Kelly, UK Web Focus at the IRMS 2016 conference in Brighton on 17 May 2016.
See http://ukwebfocus.com/events/irms-2016-web-preservation
Going Concerns: A Perspective from the Nexus of Business, Culture and Instit...
These slides accompany a talk I gave on November 4, 2015, at the University of Alberta, in Edmonton, Canada, as part of the Office of the Vice President of Research Social Sciences and Humanities Research Council "Open Minds" event.
For a video of my talk, see: https://youtu.be/3lI5mUWCHZ8
Abstract
Climate change, water scarcity, urban poverty, hydraulic fracturing, social license. For organizations, especially businesses, the rapid emergence and escalation of such cultural concerns can pose significant strategic and technological challenges. For their part, governments also may be pressed to adapt and respond to cultural concerns through policy and regulation. There also can be interactive effects, with changes in one sphere cascading into another. I consider such concerns in the context of unconventional oil and gas development, and provide a brief overview WellWiki.org. I conclude by highlighting the importance of such research for helping us to articulate potential trajectories for living.
2016 davis-plantbio
The document discusses the challenges and opportunities that will arise from the exponential growth of biological data in the coming years. It outlines four key areas: 1) Research approaches will need to effectively analyze infinite amounts of data. 2) Software and decentralized infrastructure will be needed to process the data. 3) Open science and reproducible research practices are important for data-driven biology. 4) Training the next generation of biologists in data analysis skills will be a major challenge. The document advocates for open source tools, reproducible research methods, and expanded training programs to help biology take advantage of the coming data deluge.
2016 bergen-sars
This document outlines a 12-step program for biology to adapt to the era of data-intensive science. It summarizes the author's background and research interests. It then discusses the rapid growth of biological data from techniques like DNA sequencing. It introduces the concept of digital normalization as a way to efficiently process large transcriptome datasets. Finally, it outlines some proposed steps for the field, including investing in computational training, a focus on biological questions, and moving to continuous data updating models.
2016 davis-biotech
- Biology is generating vast amounts of data from techniques like DNA sequencing that is growing exponentially. However, biology is unprepared to effectively analyze and utilize this "big data".
- There are few researchers trained in both data analysis and biology. Data is often not shared between researchers, and the current publishing system discourages open sharing of knowledge. Most computational research also lacks reproducibility.
- The presenter advocates for open science, data sharing, and improved training for the next generation of researchers in both biology and data analysis skills to help address these challenges and better leverage the growing stores of biological data.
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How One Monkey on a Typewriter Made a Difference to Online Chemistry
How One Monkey on a Typewriter Made a Difference to Online Chemistry
Using Ecological Momentary Assessment to Examine Post-food Consumption Affect...
Using Ecological Momentary Assessment to Examine Post-food Consumption Affect...
Simple Springshare Mashups: Cross-Platform Strategies for Repurposing Digital...
Simple Springshare Mashups: Cross-Platform Strategies for Repurposing Digital...
From Data Availability to Information Accessibility: The WellWiki Project
From Data Availability to Information Accessibility: The WellWiki Project
SMS Berlin 2016 Cultural Perspectives on Strategic Management
SMS Berlin 2016 Cultural Perspectives on Strategic Management
Investigating Impact Metrics for Performance for the US-EPA National Center f...
Investigating Impact Metrics for Performance for the US-EPA National Center f...
Social Media Tools for Scientists and Building an Online Profile
Social Media Tools for Scientists and Building an Online Profile
A Bird in the Hand: Leveraging ILL Requests to Improve Electronic Resource A...
A Bird in the Hand: Leveraging ILL Requests to Improve Electronic Resource A...
Shaping Expectations: Defining and Refining the Role of Technical Services in...
Shaping Expectations: Defining and Refining the Role of Technical Services in...
Building an Online Profile Using Social Networking and Amplification Tools fo...
Building an Online Profile Using Social Networking and Amplification Tools fo...
Web Preservation, or Managing your Organisation’s Online Presence After the O...
Web Preservation, or Managing your Organisation’s Online Presence After the O...
Going Concerns: A Perspective from the Nexus of Business, Culture and Instit...
Going Concerns: A Perspective from the Nexus of Business, Culture and Instit...
Similar to The EPA iCSS Chemistry Dashboard to Support Compound Identification Using High Resolution Mass Spectrometry Data
Structure identification using high resolution mass spectrometry data and the...
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.
Accessing Environmental Chemistry Data via Data Dashboards and Applications t...
Accessing Environmental Chemistry Data via Data Dashboards and Applications t...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The document summarizes a presentation about accessing environmental chemistry data through data dashboards and applications to mass spectrometry non-targeted analysis. It introduces the CompTox Chemicals Dashboard, which provides data on over 1.2 million chemicals. It describes how the dashboard supports mass spectrometry analysis and efforts to build databases of analytical methods and experimental spectra to help with identification. Sources of data and ongoing work to curate additional documents and spectra are also summarized.Integrating Mass Spectrometry Non-Targeted Analysis and Computational Chemis...
Integrating Mass Spectrometry Non-Targeted Analysis and Computational Chemis...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at the XPAND2022 Annual Meeting for the Household & Commercial Products Association and focused non-targeted analysis mass spectrometry and applications of the CompTox Chemicals Dashboard.Cheminformatics Support for MS Supporting Exposomics
Cheminformatics Support for MS Supporting ExposomicsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
A presentation given at the 5th Metabolomics of North America webinar on September 8th 2023. Provides an overview of the cheminformatics support provided by the DSSTox database, CompTox Chemicals Dashboard and multiple other web-based applications in development TRIANGLE AREA MASS SPECTOMETRY MEETING: Structure Identification Approaches U...
TRIANGLE AREA MASS SPECTOMETRY MEETING: Structure Identification Approaches U...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at a TRIANGLE AREA MASS SPECTOMETRY meeting on 01/29/2019 in Research Triangle Park, North Carolina to provide a general overview of the CompTox Chemicals Dashboard to an audience of mass spectrometrists and people interested in the capabilities of the dashboard for chemical forensics, structure identification etc.Cheminformatics tools and chemistry data underpinning mass spectrometry analy...
Cheminformatics tools and chemistry data underpinning mass spectrometry analy...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Mass spectrometry analyses at the US-EPA, especially non-targeted analysis studies, are highly dependent on the cheminformatics efforts which have been underway within the agency for almost a decade. These research efforts have resulted in a rich data infrastructure based on the DSSTox database, data integration approaches based on a structure standardization approach to produce “MS-ready” structures, and a number of supporting data types to facilitate ranking of non-targeted analysis candidates. This presentation will provide an overview of all tools in development and the integrated nature of the applications based on the underlying chemistry data. This includes the development of the underlying chemistry database of >1.2 million chemical substances (DSSTox), approaches to structure standardization to facilitate structure-substance mapping, development of a spectral database of >150,000 spectra for >25,000 chemicals, a database of >3000 analytical methods, prediction models for LCMS amenability, and an application for the profiling of toxicity hazards for batches of chemical substances. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.The US-EPA CompTox Chemicals Dashboard to support Non-Targeted Analysis
The US-EPA CompTox Chemicals Dashboard to support Non-Targeted AnalysisUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at the ASMS Sanibel Conference "Unraveling the Exposome" and provided a general overview of the dashboard and how it integrates to many of the projects that we support but with a special focus on list generation, mass and formula searching based on MS-Ready structures and some of the prototypes that we have been developing to support non-targeted analysis.Progress in Using Big Data in Chemical Toxicity Research at the National Cent...
Progress in Using Big Data in Chemical Toxicity Research at the National Cent...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at Proctor and Gamble in Mason, OH, in June 2017 in a symposium regarding "Big Data: Perspectives from Diverse Fields on How to Extract, Filter and Manipulate Large Data Sets to Answer Scientific Questions"Data delivery from the US-EPA Center for Computational Toxicology and Exposur...
Data delivery from the US-EPA Center for Computational Toxicology and Exposur...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
In recent years, the growth of scientific data and the increasing need for data sharing and collaboration in the field of environmental chemistry has led to the creation of various software and databases that facilitate research and development into the safety and toxicity of chemicals. The US-EPA Center for Computational Toxicology and Exposure has been developing software and databases that have served the chemistry community for many years. Several web-based software applications have been developed at the US-EPA and made available to the community to provide access to information regarding mycotoxins. This includes related structures, experimental and predicted properties, hazard data and mass spectrometry analytical data and methods. While the primary software application from the Center is the CompTox Chemicals Dashboard almost a dozen proof-of-concept applications have been built serving various capabilities. The publicly accessible Cheminformatics Modules (https://www.epa.gov/chemical-research/cheminformatics) provides access to modules to allow for hazard comparison for sets of chemicals, structure-substructure-similarity searching and batch QSAR prediction of both physicochemical and toxicity endpoints. This presentation will provide an overview of all tools in development that provide access to mycotoxin related data and the integrated nature of the applications based on the underlying chemistry data set. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.The US-EPA CompTox Chemicals Dashboard – a key player in the domain of Open S...
The US-EPA CompTox Chemicals Dashboard – a key player in the domain of Open S...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are advancing the identification of emerging contaminants in environmental matrices, improving the means by which exposure analyses can be conducted. However, confidence in structure identification of unknowns in NTA presents challenges to analytical chemists. Structure identification requires integration of complementary data types such as reference databases (either commercial or open databases), fragmentation prediction tools, and retention time prediction models. One goal of our research is to optimize and implement structure identification functionality within the US EPA’s CompTox Chemicals Dashboard, an open chemistry resource and web application containing data for ~900,000 substances. Database searching using mass or formula-based inputs has been optimized for structure identification using “MS-Ready Structures”: de-salted, stripped of stereochemistry, and mixture separated to replicate the form of a chemical observed via HRMS. Functionality to conduct batch searching of molecular formulae and monoisotopic masses has also been implemented. While the increasing number of free online databases are of value to support chemical structure verification and elucidation there are known issues regarding data quality and careful data curation is a very necessary part of the development of these resources. This presentation will provide an overview of our latest enhancements to the dashboard to support mass spectrometry, incorporation of specific datasets (i.e. to support breath research and household dust analysis) and the value of metadata and predicted fragmentation spectral matching to support structure identification. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Accessing Environmental Chemistry Data via Data Dashboards
Accessing Environmental Chemistry Data via Data Dashboards US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
As part of its mission the Center for Computational Toxicology and Exposure (CCTE) delivers access to chemicals related data via online Dashboards. The CompTox Chemicals Dashboard (available at https://comptox.epa.gov/dashboard) provides access to >900,000 chemicals and associated data including experimental and predicted property data, in vivo hazard data, in vitro bioactivity data, exposure data, and various other data types. The application provides a set of flexible searches allowing for search, visualization and downloads of the data to the desktop for further interrogation. This presentation will provide an overview of the Dashboard and other proof-of-concept applications that are now publicly available (https://www.epa.gov/chemical-research/cheminformatics). For example, the Hazard Comparison module (shown in the figure below) allows profiling of chemicals based on toxicity types (https://doi.org/10.1007/s10098-019-01795-w). This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted analysis (NTA) uses high-resolution mass spectrometry to better understand the identity of a wide variety of chemicals present in environmental samples (and other matrices). However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. Analysis of the resultant mass spectrometry information relies on cheminformatics to identify and rank chemicals and the US EPA has developed functionality within the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) to address challenges related to this analysis. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will review how the CompTox Chemicals Dashboard via its flexible search capabilities, rich data for ~875,000 chemical substances, and visualization approaches within this open chemistry resource provides a freely available software tool to support structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.US-EPA Chemicals Dashboard – an integrated data hub for environmental science
US-EPA Chemicals Dashboard – an integrated data hub for environmental scienceUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program utilizes computational and data-driven approaches that integrate chemistry, exposure and biological data to help characterize potential risks from chemical exposure. The National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences, including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. The CompTox Chemicals Dashboard website provides access to data associated with ~900,000 chemical substances. New data are added on an ongoing basis, including the registration of new and emerging chemicals, data extracted from the literature, chemicals studied in our labs, and data of interest to specific research projects at the EPA. Hazard and exposure data have been assembled from a large number of public databases and as a result the dashboard surfaces hundreds of thousands of data points. Other data includes experimental and predicted physicochemical property data, in vitro bioassay data for over 4000 chemicals and ~1500 assays, and millions of chemical identifiers (names and CAS Registry Numbers) to facilitate searching. Other integrated modules include an interactive read-across module, real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed. This presentation will provide an overview of the CompTox Chemicals Dashboard and how it has developed into an integrated data hub for environmental data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Delivering access to chemistry and bioassay data from the National Center for...
Delivering access to chemistry and bioassay data from the National Center for...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 software architecture. This abstract does not reflect U.S. EPA policy.US-EPA Chemicals Dashboard – an integrated data hub for environmental science
US-EPA Chemicals Dashboard – an integrated data hub for environmental scienceUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The US-EPA Chemicals Dashboard is a web-based database and integrated data hub containing information on over 875,000 chemical substances. It includes experimental and predicted physicochemical properties, in vivo toxicity data, in vitro bioactivity screening results, and links to external resources. Key features include search capabilities, chemical profiles with summarized toxicity information, modules for literature searching and read-across, and batch searching and downloading of data for multiple chemicals. The goal is to provide a transparent, integrated resource to support computational toxicology and exposure science. Ongoing efforts focus on expanding the breadth of data and ensuring data quality through expert curation.US-EPA Chemicals Dashboard and Applications to Digital Design of Molecules
US-EPA Chemicals Dashboard and Applications to Digital Design of MoleculesUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Presentation at: Digital design of molecules and formulations (https://www.soci.org/events/ai-and-digitalisation/digital-design-of-molecules-and-formulations). The Chemicals Dashboard is a free web-based application from the United States Environmental Protection Agency that provides various types of data for ~900,000 chemicals. These data include physicochemical properties, in vivo and in vitro toxicity data and information regarding the presence of chemicals in commercial products, including formulation data where available. The dashboard allows for sourcing of data associated with singleton chemicals or a batch mode for downloading data for thousands of chemicals at a time. This presentation will provide an overview of the Dashboard, the myriad of data sources underpinning the application and potential applications of the dashboard.Delivering web-based access to data and algorithms to support computational t...
Delivering web-based access to data and algorithms to support computational t...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The US-EPA National Center for Computational Toxicity (NCCT) has been generating data and building software applications and web-based chemistry databases for over a decade. During this period the center has analyzed thousands of chemicals in hundreds of bioassays, has researched high-throughput physicochemical property measurements and investigated approaches for high throughput toxicokinetics. NCCT continues to expand the battery of assays and number of chemicals under examination and is now investigating the application of transcriptomics. In parallel to these experimental efforts, and to support our efforts to develop new approaches to prioritize chemicals based on potential human health risks, we aggregate and curate data streams of various types to support prediction models. Over the past few years some of the data have been delivered through prototype web-based “dashboards” for public consumption. The latest of these web applications, the CompTox Chemicals Dashboard, is an integrated access point to obtain information associated with 875,000 chemical substances and providing experimental and predicted data of various types. This includes physicochemical and fate and transport data, bioactivity data, exposure data and integrated literature searches. Real-time predictions and generalized read-across are possible and advanced search capabilities are available to support EPA-related projects including mass spectrometry non-targeted analysis. This presentation will provide an overview of the CompTox Chemicals Dashboard and the its role in delivering access to the outputs of NCCT. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Using Cheminformatics Approaches to Develop a Structure Searchable Database o...
Using Cheminformatics Approaches to Develop a Structure Searchable Database o...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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Consensus ranking and fragmentation prediction for identification of unknowns...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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- 1. The EPA iCSS Chemistry Dashboard to Support Compound Identification Using High Resolution Mass Spectrometry Data 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 http://www.orcid.org/0000-0002-2668-4821 The views expressed in this presentation are those of the author and do not necessarily reflect the views or policies of the U.S. EPA
- 2. Who is NCCT? • National Center for Computational Toxicology – part of EPA’s Office of Research and Development • Research driven by EPA’s Chemical Safety for Sustainability Research Program – Develop new approaches to evaluate the safety of chemicals – Integrate advances in biology, biotechnology, chemistry, exposure science and computer science • Goal - To identify chemical exposures that may disrupt biological processes and cause adverse outcomes. 1
- 3. Our Dashboard Applications • Some of our Web-based Applications 2
- 4. Introducing Our Latest Dashboard https://comptox.epa.gov 3 • >720,000 chemicals • >10 years assembling data
- 8. Functional Use and Composition 7
- 11. Monoisotopic Mass Search 10 Found 344 results for '215.096 ± 0.005 amu'
- 13. Formula Search 12 Found 8 results for 'C8H14ClN5'
- 14. Formula Searching Formulae matching Bisphenol A 13
- 17. Download as SDF file 16
- 18. SDF file downloaded to desktop 17
- 19. Rank-Ordering of “Known-Unknowns” using ChemSpider 18
- 21. Does the Dashboard Add Value? • Remember: – Focus on high quality data and curation – Data sources include EPA data sources and a focus on environmental chemistry • No “dilution” by chemical vendors 20
- 23. Bisphenol A as an example ChemSpider: 1564 Structures 22
- 24. Bisphenol A as an example Dashboard: 215 Structures 23
- 25. 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
- 26. 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% • Selected peer-reviewed publications • 162 total individual chemicals in search
- 27. ChemSpider 6926 Results!!! 26 Tacedinaline Methyl Red C.I Disperse Yellow 3
- 28. Using Functional Use to Sort Candidates 27 Anti-cancer Drug Microbiological Indicator Dye Textile/Product Dye
- 29. Same top hits – different ranking 90 hits only versus 6926 hits 28 18 17 4Tacedinaline Methyl Red C.I Disperse Yellow 3
- 30. Dashboard: External Links to Analytical Methods 29
- 31. National Environmental Methods Index 30
- 34. Google Chemical Searches Enhanced with Query Terms 33
- 35. Non-Targeted Analysis Research - 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) What is contained in house dust, waste streams etc???
- 36. Previous Work with Suspect-Screening The dashboard is being enhanced to support Non-targeted Analysis
- 37. Future Work • Presently researching rank-ordering based on other criteria – Pubmed • Additional links to methods – CDC NIOSH • Links to Mass Spec databases – Thermo’s mzCloud, Massbank. Metlin etc. • Consider predicting metabolites and degradants • Searching based on “MS-ready” structures 36
- 38. “MS Ready” structures • Many compounds are salts – searches should be on the “neutral form” • Need to search for adducts (+Na, +K, +NH4), decarboxylation, loss of water etc. 37
- 39. Conclusions • Dashboard support for MS is focused on NTA research – related to chemical exposure • Dashboard outperforms ChemSpider for ranking chemicals of environmental concern • New searches developed with Non-targeted Analysis in mind - new rank-ordering approaches in development 38
- 40. Acknowledgements EPA NCCT Chris Grulke Jeff Edwards Ann Richard Jordan Foster Jennifer Smith Andrew McEachran* Michelle Krzyzanowski EPA NERL Jon Sobus * = ORISE Participant
Editor's Notes
- For example- Rager was actually 33 confirmed; Bade was 25