Delivering an integrated data hub for per- and polyfluoroalkyl (PFAS) chemicals via the US-EPA CompTox Chemicals Dashboard
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There is increasing interest in the environmental impact of per- and polyfluoroalkyl substances (PFAS) chemicals and the aggregation of related data provides both agency and public access to support research. The US-EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a publicly accessible website providing access to data for ~900,000 chemical substances, including thousands of PFAS chemicals. The dashboard provides access to a wide array of experimental and predicted physicochemical properties, in vitro bioactivity and in vivo toxicity data, product use information and integrated linkages to a growing list of literature, toxicology, and analytical chemistry websites. The assembly of data has required hundreds of hours of manual curation and data checking to deliver a number of segregated lists of PFAS chemicals. Experimental data extracted from literature articles has allowed the optimization of QSAR models for the prediction of properties such as logP (octanol-water partition) and aqueous solubility. This presentation will provide an overview of the dashboard, the ongoing expansion of the PFAS chemical library, with associated categorization, and new physicochemical property and environmental fate and transport QSAR prediction models being developed for these chemicals. Our progress in the measurement and analysis of bioactivity data for PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.
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![Innovative Research for a Sustainable Futurewww.epa.gov/research
ORCID: 0000-0002-2668-4821
Antony Williams l williams.antony@epa.gov l 919-541-1033
Delivering an integrated data hub for per- and polyfluoroalkyl (PFAS)
chemicals via the US EPA CompTox Chemicals Dashboard
Antony Williams1, Chris Grulke1, Kamel Mansouri2, Grace Patlewicz1 and Ann Richard1
1U.S. Environmental Protection Agency, Office of Research and Development, National Center for Computational Toxicology, Research Triangle Park, NC
and 2Integrated Laboratory Systems, Research Triangle Park, NC.
ACS Fall 2019
San Diego, CA
August 25-29, 2019
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 poster provides 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
work 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.
The CompTox Chemicals Dashboard
Abstract
For records with chemical
structures experimental and
predicted physicochemical (logP,
water solubility etc.) and fate and
transport properties are provided.
These include OPERA models
reported by Mansouri et al. [1]
The landing page of the
dashboard is a simple text entry
box allowing a type-ahead
search for systematic, trade and
trivial names, CAS Registry
Numbers and InChI chemical
identifiers.Dashboard Entry Page
Chemical Record Page: PFOA
Chemical Properties Panel
Where possible, links are
provided to related Wikipedia
articles. Structure file formats are
available for download to the
desktop (SMILES and molfile)
and an executive summary
report regarding chemical toxicity
is provided.
Accessing PFAS Chemical Lists
Future Work
The dashboard provides access to ~20 individual PFAS chemical lists.
These include a list based on structural filters: (1) Formula must
contain 3 -1000 Fluorine atoms; 2) Structure must contain two
adjacent CF2 groups, either in a chain or in a ring system; 3) Fluorine
to Carbon ratio (#F/#C) = or > 0.5; 4) REMOVE charged species (e.g.,
bare anions), radicals, and deuterium- and C13-labeled chemicals
References
1. Mansouri et al. OPERA models for predicting physchem properties
and environmental fate endpoints, J. ChemInf. 10, 10 (2018)
2. PFAS Categories list on the CompTox Chemicals Dashboard
https://comptox.epa.gov/dashboard/chemical_lists/EPAPFASCAT
3. Patlewicz et al. A Chemical Category-Based Prioritization Approach
for Selecting 75 Per- and Polyfluoroalkyl Substances (PFAS) for
Tiered Toxicity and Toxicokinetic Testing. Environ Health Perspect.
2019 Jan;127(1):14501.
• In vitro toxicity and toxicokinetic measurements are underway for
~150 PFAS [3]. These will be released in the future on the
dashboard.
• Experimental property data are being harvested from literature and
online resources to include into the dashboard and OPERA models.
• Chemical categorization efforts continue in order to be
encompassing of more of the PFAS library.
List of chemical lists of PFAS
chemicals: 21 lists and growing
Structure-filtered list of PFAS
Problem Definition and Goals
Problem: There are many sources of PFAS data online to support
computational toxicology. However, curated datasets for the
thousands of known PFAS chemicals are not available in structured
formats,
Goals: Deliver online access to hundreds of thousands of chemicals
of interest to environmental science and computational toxicology.
Provide lists of PFAS substances via a simple to use web-based
interface. Deliver application to support diverse types of data
including experimental and predicted physicochemical properties, in
vivo hazard data and in vitro toxicity and toxicokinetic data. Make the
data available as downloadable data for reuse and repurposing in
other databases.
Toxicity Values Panel
Bioactivities: e.g. ToxCast Data
The Hazard tab provides access
to data assembled from a series
of public resources including EPA
data (i.e. IRIS and PPRTV
reports, ToxRef DB). Data can be
downloaded as TSV and Excel
files.
ToxCast Bioactivity data
measured over the past decade
are under the Bioassay Tab. Data
can be downloaded as Excel files.
New in vitro data are being
generated on a library of ~150
PFAS in collaboration with NTP.
Acknowledgements
The authors thank the chemical curation team for their rigorous work and
the software development team for the development of the dashboard.
A list of Markush Representations
associated with the selection of
chemicals for in vitro toxicity and
toxicokinetic screening is also
available [2,3].](https://image.slidesharecdn.com/posterdeliveringanintegrateddatahubforpfaschemicalsv1-190827061238/85/Delivering-an-integrated-data-hub-for-per-and-polyfluoroalkyl-PFAS-chemicals-via-the-US-EPA-CompTox-Chemicals-Dashboard-1-320.jpg)
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The CompTox Chemicals Dashboard (available at https://comptox.epa.gov/dashboard) is the latest in a suite of dashboards that have been delivered to the community by EPA’s National Center for Computational Toxicology. The dashboard delivers access to data for >875,000 chemicals and includes experimental and predicted physicochemical properties, hazard and exposure data, access to Toxcast/Tox21 bioactivity screening data and provides a link farm to dozens of other online resources. The dashboard delivers access to data with a variety of powerful search capabilities including searching by chemical identifier (e.g. CAS Number or Name), by commercial product type, or by mass or formula. Searches can be performed one chemical at a time or in batches of thousands. Whether you are a chemist, an analytical scientist or a toxicologist the dashboard is of value as it seamlessly integrates data from dozens of databases into a web-based user experience. Other integrated modules include real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed and almost 30 million publication abstracts. The data and functionality available via the dashboard can be of value in terms of decontamination by providing access to data to assist in detection (specifically via mass spectrometric detection), accessing literature and potential decontamination approaches associated with specific chemicals, and access to toxicity values for chemicals such as Military Exposure Guidelines. This presentation will provide an overview of the CompTox Chemicals Dashboard and how it has developed into an integrated data hub for environmental data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection AgencyPubChem and Big Data Chemistry
Presented at the Bioinformatics Seminar at the University of Arkansas, Little Rock on November 5, 2021.
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical database at the National Library of Medicine, National Institutes of Health. Arguably, PubChem is one of the largest chemical information resources in the public domain, with 111 million unique chemical structures, 1.39 million biological assays, and 292 million biological activity result outcomes. It also contains significant amounts of scientific research data and the inter-relationships between chemicals, proteins, genes, scientific literature, patents, and more. PubChem is a key resource for big data in chemistry and has been used in many studies for developing bioactivity and toxicity prediction models, discovering polypharmacologic (multi-target) ligands, and identifying new macromolecule targets of compounds (for drug-repurposing or off-target side effect prediction). It has also been used for cheminformatics education as well as chemical health and safety training. This presentation provides a high-level overview of PubChem’s data, tools, and services.
Adding complex expert knowledge into chemical database and transforming surfa...
Adding complex expert knowledge into chemical database and transforming surfa...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The increasing popularity of high mass accuracy non-target mass spectrometry methods has yielded extensive identification efforts based on chemical compound databases. Candidate structures are often retrieved with either exact mass or molecular formula from large resources such as PubChem, ChemSpider or the EPA CompTox Chemistry Dashboard. Additional data (e.g. fragmentation, physicochemical properties, reference and data source information) is then used to select potential candidates, depending on the experimental context. However, these strategies require the presence of substances of interest in these compound databases, which is often not the case as no database can be fully inclusive. A prominent example with clear data gaps are surfactants, used in many products in our daily lives, yet often absent as discrete structures in compound databases. Linear alkylbenzene sulfonates (LAS) are a common, high use and high priority surfactant class that have highly complex transformation behaviour in wastewater. Despite extensive reports in the environmental literature, few of the LAS and none of the related transformation products were reported in any compound databases during an investigation into Swiss wastewater effluents, despite these forming the most intense signals. The LAS surfactant class will be used to demonstrate how the coupling of environmental observations with high resolution mass spectrometry and detailed literature data (expert knowledge) on the transformation of these species can be used to progressively “fill the gaps” in compound databases. The LAS and their transformation products have been added to the CompTox Chemistry Dashboard (https://comptox.epa.gov/) using a combination of “representative structures” and “related structures” starting from the structural information contained in the literature. By adding this information into a centralized open resource, future environmental investigations can now profit from the expert knowledge previously scattered throughout the literature. Note: This abstract does not reflect US EPA policy.ICIC 2014 From SureChem to SureChEMBL
The patent literature has historically been complex and inaccessible to searches required for effective IP management and maintenance of a competitive position, particularly when it comes to chemical structure information. The availability of raw patent text feeds in a structured form have allowed the application of text-to-structure and image-to-structure conversion techniques. The problem then became one of applying this solution across massive data sets in an accurate and scalable manner to deliver a turnkey patent informatics system with automatically extracted, and searchable chemical structures. SureChem, an advanced cloud application, uses a tournament of methods to achieve higher coverage and accuracy than any single approach. This product was launched and licensed by a user community with a freemium business model. Latterly, user feedback and market shifts indicated a need to link biological data into patents too (sequences, genes, targets, diseases, etc). This created an opportunity to transition SureChem to EMBL-EBI, a public organisation with the remit of data dissemination and sharing, and deep experience of biodata, including the large ChEMBL database of Structure Activity Relationship Data. In 2014 SureChem became SureChEMBL. The presentation will review the development of SureChem, discuss the marketplace for patent informatics, and look ahead to future development plans for SureChEMBL.
PubChem as a resource for chemical information training
Presented at the 257th American Chemical Society (ACS) National Meeting in Orlando, FL (March 31, 2019). [CINF 13]
==== Abstract ====
Libraries at many large academic institutions provide chemical information training programs for students. However, these programs are based on commercial chemical information resources, which come with non-trivial subscription fees. These fees are often too expensive for small organizations, including many primarily undergraduate institutions (PUIs) and community colleges (CCs). It leads to disparity in access to chemical information as well as learning opportunities among students. This issue may be addressed at least in part by developing free online training programs based on public chemical databases, such as PubChem (https://pubchem.ncbi.nlm.nih.gov). PubChem has a great potential as an online resource for chemical education, but it also has important issues that students and teachers should keep in mind, such as data accuracy, data provenance, structure standardization, terminologies and so on. In this presentation, we will discuss various aspects of PubChem as a resource for chemical information training.
Environmental chemical information in PubChem
The slide was presented at the 257th ACS National Meeting, Spring, Orlando, 2019
ChemSpider Overview SLides August 2007
ChemSpider Overview SLides August 2007US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider is being built with the intention of being a chemical structure centric community for chemists. With over 16 million chemical structures as of August 2007, and with data deposition and curation mechanisms in place for text, structure and spectra ChemSpider intends to be a meeting place and collaborative environment for chemists to work together.Southan BIA 10-2474 Pharmacology 2017
These slides will be presented at the Pharmacology 2017 meeting in London during the following session:
Abstract Number: OB073
Abstract Title: Capturing new BIA 10-2474 molecular data in the IUPHAR/BPS Guide to PHARMACOLOGY
Date: Wednesday, December 13, 2017, 11:30 AM
Oral Session: Oral Communications: Mixed Tracks
Using open bioactivity data for developing machine-learning prediction models...
Presented at the 256th American Chemical Society (ACS) National Meeting in Boston, MA (August 22, 2018).
==== Abstract ====
The retinoid X receptor (RXR) is a nuclear hormone receptor that functions as a transcription factor with roles in development, cell differentiation, metabolism, and cell death. Chemicals that interfere the RXR signaling pathway may cause adverse effects on human health. In this study, open bioactivity data available at PubChem (https://pubchem.ncbi.nlm.nih.gov) were used to develop prediction models for chemical modulators of RXR-alpha, which is a subtype of RXR that plays a role in metabolic signaling pathways, dermal cysts, cardiac development, insulin sensitization, etc. The models were constructed from quantitative high-throughput screening (qHTS) data from the Tox21 project, using various supervised machine learning methods (including support vector machine, random forest, neural network, k-nearest neighbors, decision tree, and naïve Bayes). The performance of the models was evaluated with an external data set containing bioactivity data submitted by ChEMBL and the NCATS Chemical Genomics Center (NCGC). This study showcases how open data in the public domain can be used to develop prediction models for chemical toxicity.
Development of machine learning-based prediction models for chemical modulato...
Presented at the 2018 Research Festival at the National Institutes of Health (NIH) in Bethesda, MD (September 13, 2018).
==== Abstract ====
The retinoid X receptor (RXR) is a nuclear hormone receptor that functions as a transcription factor with roles in development, cell differentiation, metabolism, and cell death. Chemicals that interfere the RXR signaling pathway may cause adverse effects on human health. In this study, public-domain bioactivity data available in PubChem (https://pubchem.ncbi.nlm.nih.gov) were used to develop machine learning-based prediction models for chemical modulators of RXR-alpha, which is a subtype of RXR that plays a role in metabolic signaling pathways, dermal cysts, cardiac development, insulin sensitization, etc. The models were constructed from quantitative high-throughput screening (qHTS) data from the Tox21 project, using popular supervised machine learning methods (including support vector machine, random forest, neural network, k-nearest neighbors, decision tree, and naïve Bayes). The general applicability of the developed models was evaluated with external data sets from ChEMBL and the NCATS Chemical Genomics Center (NCGC). This study showcases how open data in the public domain can be used to develop prediction models for bioactivity of small molecules.
IUPHAR/BPS Guide to PHARMACOLOGY in 2017: new features and updates
Oral presentation slides to be presented at Pharmacology 2017, London, December 2017.
Guide to Malaria Pharmacology, GEMM 2019
IUPHAR/MMV Guide to Malaria Pharmacology slide set presented by Dr. Jane Armstrong at GEMM 2019, Edinburgh, UK.
Cheminformatics Online Chemistry Course (OLCC): A Community Effort to Introdu...
Presented at the American Chemical Society (ACS) Spring 2021 National Meeting (Virtual, April 16, 2021).
==== Abstract ====
Computer and informatics skills to handle an ever-increasing amount of chemical information are considered important for students pursuing STEM careers in the age of big data. However, many schools do not offer a cheminformatics course or alternative training opportunities. The Cheminformatics Online Chemistry Course (OLCC) is a community effort to introduce cheminformatics content into the undergraduate chemistry curriculum. It is a highly collaborative teaching project involving instructors at multiple schools as well as external cheminformatics experts recruited across sectors, including academia, government, and industry. Three Cheminformatics OLCCs were offered in the Fall 2015, Spring 2017, and Fall 2019 semesters. In each OLCC, the instructors at participating schools would meet face-to-face with the students, while external cheminformatics experts engaged through online discussions across campuses with both the instructors and students. All the material created in the course has been made available at the open education repositories of LibreTexts and CCCE websites for other institutions to adapt to their future needs. This presentation describes the instructional approaches of the Cheminformatics OLCC project and the lessons learned from this community effort. We also discuss future directions for this project as well as cheminformatics education in general, including pedagogy, resources, and course content.
Bringing it all together: A Web-based Database for Chemical and Biological Da...
Bringing it all together: A Web-based Database for Chemical and Biological Da...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The EPA Comptox Chemistry Dashboard is a web-based application providing access to a set of data resources provided by the National Center of Computational Toxicology. Sitting on a foundation of chemistry data for ~750,000 chemical substances the application integrates bioassay screening results, physicochemical and toxicological endpoints (both experimental and predicted) and consumer product and functional use data. By integrating a series of other EPA and public databases (e.g. ECOTOX, the EPA Substance Registry Service, EPA’s ChemView and PubChem), the dashboard provides a hub for connecting to other releases of value to environmental scientists and toxicologists. The underpinning architecture has been developed in a manner allowing for the release of the dashboard as a public resource, as well as for delivering applications used inside confidential business information environments. These applications are being assessed for potential applications to support risk decisions. This presentation will provide an overview of the dashboard focusing specifically on the most recent functionality supporting deeper integration to the ToxCast bioassay data and exposure data and predictions available via the dashboard. This abstract does not reflect U.S. EPA policy.PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...
PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases within the DSSTox project, and providing accurate linkages of data to chemical structures, exposure and hazard information. The data are made available via the EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard), a publicly accessible website providing access to data for ~880,000 chemical substances, the majority of these represented as chemical structures. The web application delivers a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data, as well as integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. In addition, several specific search types are in development to directly support the mass spectrometry non-targeted screening community, enabling cohesive workflows to support data generation for the detection and assessment of environmental exposures to chemicals contained within the database. The application provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders, including, for example, scientists interested in Per- & Polyfluoroalkyl Substances (PFAS). Added lists include those sourced from the European Union as well as developed in-house and now containing thousands of chemicals. A procured testing library of hundreds of PFAS chemicals annotated into chemical categories has been integrated into the dashboard with a number of resulting benefits: a searchable database of chemical properties, with hazard and exposure predictions, and links to the open literature. This presentation will provide an overview of the dashboard, the developing library of PFAS chemicals and associated categorization, and new physicochemical property and environmental fate and transport QSAR prediction models developed for these chemicals. The application of the dashboard to support mass spectrometry non-targeted analysis studies for the identification of PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.More Related Content
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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
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 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.Searching for chemical information using PubChem
Presented at the 257th American Chemical Society (ACS) National Meeting in Orlando, FL (April 1, 2019). [CHED 303]
==== Abstract ====
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical database, which provides information on a broad range of chemical entities, including small molecules, lipids, carbohydrates, and (chemically-modified) amino acid and nucleic acid sequences (including siRNA and miRNA). With three million unique users per month at peak, PubChem is ranked as one of the most visited chemistry websites in the world. A substantial number of PubChem users are between ages 18 and 24, who are likely to be undergraduate or graduate students at academic institutions. Therefore, PubChem has a great potential as an online resource for chemical education. In this talk, we will present “PubChem Search”, a new web interface that allows users to quickly find desired chemical information. This interface supports chemical name search as well as various types of chemical structure search, including identity/similarity search, superstructure/substructure search, and molecular search. Using PubChem Search, it is also possible to search for journal articles or patent documents that mention a given chemical. The hits returned from a search can be downloaded to local machines or further refined or analyzed in conjunction with other PubChem tools and services. In this presentation, we will demonstrate how the PubChem Search interface can be used to search beyond google for chemical information of interest.
PubChem and Its Applications for Drug Discovery
Presentation delivered at Lehigh University (Bethlehem, PA) on Friday, April 26, 2019.
This presentation provides a brief introduction to PubChem and discusses how to use PubChem for drug discovery. More detailed information on this topic can found in the following paper:
Getting the most out of PubChem for virtual screening.
Expert Opin Drug Discov. 2016 Aug 5; 11(9):843-55.
https://doi.org/10.1080/17460441.2016.1216967
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045798/
EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental C...
EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental C...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The CompTox Chemicals Dashboard (available at https://comptox.epa.gov/dashboard) is the latest in a suite of dashboards that have been delivered to the community by EPA’s National Center for Computational Toxicology. The dashboard delivers access to data for >875,000 chemicals and includes experimental and predicted physicochemical properties, hazard and exposure data, access to Toxcast/Tox21 bioactivity screening data and provides a link farm to dozens of other online resources. The dashboard delivers access to data with a variety of powerful search capabilities including searching by chemical identifier (e.g. CAS Number or Name), by commercial product type, or by mass or formula. Searches can be performed one chemical at a time or in batches of thousands. Whether you are a chemist, an analytical scientist or a toxicologist the dashboard is of value as it seamlessly integrates data from dozens of databases into a web-based user experience. Other integrated modules include real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed and almost 30 million publication abstracts. The data and functionality available via the dashboard can be of value in terms of decontamination by providing access to data to assist in detection (specifically via mass spectrometric detection), accessing literature and potential decontamination approaches associated with specific chemicals, and access to toxicity values for chemicals such as Military Exposure Guidelines. This presentation will provide an overview of the CompTox Chemicals Dashboard and how it has developed into an integrated data hub for environmental data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection AgencyPubChem and Big Data Chemistry
Presented at the Bioinformatics Seminar at the University of Arkansas, Little Rock on November 5, 2021.
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical database at the National Library of Medicine, National Institutes of Health. Arguably, PubChem is one of the largest chemical information resources in the public domain, with 111 million unique chemical structures, 1.39 million biological assays, and 292 million biological activity result outcomes. It also contains significant amounts of scientific research data and the inter-relationships between chemicals, proteins, genes, scientific literature, patents, and more. PubChem is a key resource for big data in chemistry and has been used in many studies for developing bioactivity and toxicity prediction models, discovering polypharmacologic (multi-target) ligands, and identifying new macromolecule targets of compounds (for drug-repurposing or off-target side effect prediction). It has also been used for cheminformatics education as well as chemical health and safety training. This presentation provides a high-level overview of PubChem’s data, tools, and services.
Adding complex expert knowledge into chemical database and transforming surfa...
Adding complex expert knowledge into chemical database and transforming surfa...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The increasing popularity of high mass accuracy non-target mass spectrometry methods has yielded extensive identification efforts based on chemical compound databases. Candidate structures are often retrieved with either exact mass or molecular formula from large resources such as PubChem, ChemSpider or the EPA CompTox Chemistry Dashboard. Additional data (e.g. fragmentation, physicochemical properties, reference and data source information) is then used to select potential candidates, depending on the experimental context. However, these strategies require the presence of substances of interest in these compound databases, which is often not the case as no database can be fully inclusive. A prominent example with clear data gaps are surfactants, used in many products in our daily lives, yet often absent as discrete structures in compound databases. Linear alkylbenzene sulfonates (LAS) are a common, high use and high priority surfactant class that have highly complex transformation behaviour in wastewater. Despite extensive reports in the environmental literature, few of the LAS and none of the related transformation products were reported in any compound databases during an investigation into Swiss wastewater effluents, despite these forming the most intense signals. The LAS surfactant class will be used to demonstrate how the coupling of environmental observations with high resolution mass spectrometry and detailed literature data (expert knowledge) on the transformation of these species can be used to progressively “fill the gaps” in compound databases. The LAS and their transformation products have been added to the CompTox Chemistry Dashboard (https://comptox.epa.gov/) using a combination of “representative structures” and “related structures” starting from the structural information contained in the literature. By adding this information into a centralized open resource, future environmental investigations can now profit from the expert knowledge previously scattered throughout the literature. Note: This abstract does not reflect US EPA policy.ICIC 2014 From SureChem to SureChEMBL
The patent literature has historically been complex and inaccessible to searches required for effective IP management and maintenance of a competitive position, particularly when it comes to chemical structure information. The availability of raw patent text feeds in a structured form have allowed the application of text-to-structure and image-to-structure conversion techniques. The problem then became one of applying this solution across massive data sets in an accurate and scalable manner to deliver a turnkey patent informatics system with automatically extracted, and searchable chemical structures. SureChem, an advanced cloud application, uses a tournament of methods to achieve higher coverage and accuracy than any single approach. This product was launched and licensed by a user community with a freemium business model. Latterly, user feedback and market shifts indicated a need to link biological data into patents too (sequences, genes, targets, diseases, etc). This created an opportunity to transition SureChem to EMBL-EBI, a public organisation with the remit of data dissemination and sharing, and deep experience of biodata, including the large ChEMBL database of Structure Activity Relationship Data. In 2014 SureChem became SureChEMBL. The presentation will review the development of SureChem, discuss the marketplace for patent informatics, and look ahead to future development plans for SureChEMBL.
PubChem as a resource for chemical information training
Presented at the 257th American Chemical Society (ACS) National Meeting in Orlando, FL (March 31, 2019). [CINF 13]
==== Abstract ====
Libraries at many large academic institutions provide chemical information training programs for students. However, these programs are based on commercial chemical information resources, which come with non-trivial subscription fees. These fees are often too expensive for small organizations, including many primarily undergraduate institutions (PUIs) and community colleges (CCs). It leads to disparity in access to chemical information as well as learning opportunities among students. This issue may be addressed at least in part by developing free online training programs based on public chemical databases, such as PubChem (https://pubchem.ncbi.nlm.nih.gov). PubChem has a great potential as an online resource for chemical education, but it also has important issues that students and teachers should keep in mind, such as data accuracy, data provenance, structure standardization, terminologies and so on. In this presentation, we will discuss various aspects of PubChem as a resource for chemical information training.
Environmental chemical information in PubChem
The slide was presented at the 257th ACS National Meeting, Spring, Orlando, 2019
ChemSpider Overview SLides August 2007
ChemSpider Overview SLides August 2007US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider is being built with the intention of being a chemical structure centric community for chemists. With over 16 million chemical structures as of August 2007, and with data deposition and curation mechanisms in place for text, structure and spectra ChemSpider intends to be a meeting place and collaborative environment for chemists to work together.Southan BIA 10-2474 Pharmacology 2017
These slides will be presented at the Pharmacology 2017 meeting in London during the following session:
Abstract Number: OB073
Abstract Title: Capturing new BIA 10-2474 molecular data in the IUPHAR/BPS Guide to PHARMACOLOGY
Date: Wednesday, December 13, 2017, 11:30 AM
Oral Session: Oral Communications: Mixed Tracks
Using open bioactivity data for developing machine-learning prediction models...
Presented at the 256th American Chemical Society (ACS) National Meeting in Boston, MA (August 22, 2018).
==== Abstract ====
The retinoid X receptor (RXR) is a nuclear hormone receptor that functions as a transcription factor with roles in development, cell differentiation, metabolism, and cell death. Chemicals that interfere the RXR signaling pathway may cause adverse effects on human health. In this study, open bioactivity data available at PubChem (https://pubchem.ncbi.nlm.nih.gov) were used to develop prediction models for chemical modulators of RXR-alpha, which is a subtype of RXR that plays a role in metabolic signaling pathways, dermal cysts, cardiac development, insulin sensitization, etc. The models were constructed from quantitative high-throughput screening (qHTS) data from the Tox21 project, using various supervised machine learning methods (including support vector machine, random forest, neural network, k-nearest neighbors, decision tree, and naïve Bayes). The performance of the models was evaluated with an external data set containing bioactivity data submitted by ChEMBL and the NCATS Chemical Genomics Center (NCGC). This study showcases how open data in the public domain can be used to develop prediction models for chemical toxicity.
Development of machine learning-based prediction models for chemical modulato...
Presented at the 2018 Research Festival at the National Institutes of Health (NIH) in Bethesda, MD (September 13, 2018).
==== Abstract ====
The retinoid X receptor (RXR) is a nuclear hormone receptor that functions as a transcription factor with roles in development, cell differentiation, metabolism, and cell death. Chemicals that interfere the RXR signaling pathway may cause adverse effects on human health. In this study, public-domain bioactivity data available in PubChem (https://pubchem.ncbi.nlm.nih.gov) were used to develop machine learning-based prediction models for chemical modulators of RXR-alpha, which is a subtype of RXR that plays a role in metabolic signaling pathways, dermal cysts, cardiac development, insulin sensitization, etc. The models were constructed from quantitative high-throughput screening (qHTS) data from the Tox21 project, using popular supervised machine learning methods (including support vector machine, random forest, neural network, k-nearest neighbors, decision tree, and naïve Bayes). The general applicability of the developed models was evaluated with external data sets from ChEMBL and the NCATS Chemical Genomics Center (NCGC). This study showcases how open data in the public domain can be used to develop prediction models for bioactivity of small molecules.
IUPHAR/BPS Guide to PHARMACOLOGY in 2017: new features and updates
Oral presentation slides to be presented at Pharmacology 2017, London, December 2017.
Guide to Malaria Pharmacology, GEMM 2019
IUPHAR/MMV Guide to Malaria Pharmacology slide set presented by Dr. Jane Armstrong at GEMM 2019, Edinburgh, UK.
Cheminformatics Online Chemistry Course (OLCC): A Community Effort to Introdu...
Presented at the American Chemical Society (ACS) Spring 2021 National Meeting (Virtual, April 16, 2021).
==== Abstract ====
Computer and informatics skills to handle an ever-increasing amount of chemical information are considered important for students pursuing STEM careers in the age of big data. However, many schools do not offer a cheminformatics course or alternative training opportunities. The Cheminformatics Online Chemistry Course (OLCC) is a community effort to introduce cheminformatics content into the undergraduate chemistry curriculum. It is a highly collaborative teaching project involving instructors at multiple schools as well as external cheminformatics experts recruited across sectors, including academia, government, and industry. Three Cheminformatics OLCCs were offered in the Fall 2015, Spring 2017, and Fall 2019 semesters. In each OLCC, the instructors at participating schools would meet face-to-face with the students, while external cheminformatics experts engaged through online discussions across campuses with both the instructors and students. All the material created in the course has been made available at the open education repositories of LibreTexts and CCCE websites for other institutions to adapt to their future needs. This presentation describes the instructional approaches of the Cheminformatics OLCC project and the lessons learned from this community effort. We also discuss future directions for this project as well as cheminformatics education in general, including pedagogy, resources, and course content.
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Bringing it all together: A Web-based Database for Chemical and Biological Da...
Bringing it all together: A Web-based Database for Chemical and Biological Da...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The EPA Comptox Chemistry Dashboard is a web-based application providing access to a set of data resources provided by the National Center of Computational Toxicology. Sitting on a foundation of chemistry data for ~750,000 chemical substances the application integrates bioassay screening results, physicochemical and toxicological endpoints (both experimental and predicted) and consumer product and functional use data. By integrating a series of other EPA and public databases (e.g. ECOTOX, the EPA Substance Registry Service, EPA’s ChemView and PubChem), the dashboard provides a hub for connecting to other releases of value to environmental scientists and toxicologists. The underpinning architecture has been developed in a manner allowing for the release of the dashboard as a public resource, as well as for delivering applications used inside confidential business information environments. These applications are being assessed for potential applications to support risk decisions. This presentation will provide an overview of the dashboard focusing specifically on the most recent functionality supporting deeper integration to the ToxCast bioassay data and exposure data and predictions available via the dashboard. This abstract does not reflect U.S. EPA policy.PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...
PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases within the DSSTox project, and providing accurate linkages of data to chemical structures, exposure and hazard information. The data are made available via the EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard), a publicly accessible website providing access to data for ~880,000 chemical substances, the majority of these represented as chemical structures. The web application delivers a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data, as well as integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. In addition, several specific search types are in development to directly support the mass spectrometry non-targeted screening community, enabling cohesive workflows to support data generation for the detection and assessment of environmental exposures to chemicals contained within the database. The application provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders, including, for example, scientists interested in Per- & Polyfluoroalkyl Substances (PFAS). Added lists include those sourced from the European Union as well as developed in-house and now containing thousands of chemicals. A procured testing library of hundreds of PFAS chemicals annotated into chemical categories has been integrated into the dashboard with a number of resulting benefits: a searchable database of chemical properties, with hazard and exposure predictions, and links to the open literature. This presentation will provide an overview of the dashboard, the developing library of PFAS chemicals and associated categorization, and new physicochemical property and environmental fate and transport QSAR prediction models developed for these chemicals. The application of the dashboard to support mass spectrometry non-targeted analysis studies for the identification of PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.The US-EPA CompTox Chemicals Dashboard – an information hub for over five tho...
The US-EPA CompTox Chemicals Dashboard – an information hub for over five tho...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a publicly accessible website providing access to data for ~770,000 chemical substances, the majority of these represented as chemical structures. The web application delivers a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data, product use information extracted from safety data sheets, and integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. The application provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders, including Per- & Polyfluoroalkyl Substances (PFAS) containing thousands of chemicals. A procured testing library of hundreds of PFAS chemicals annotated into chemical categories has been integrated into the dashboard with a number of resulting benefits: a searchable database of chemical properties, with hazard and exposure predictions, and links to the open literature. Several specific search types have been developed to directly support the mass spectrometry non-targeted screening community, enabling cohesive workflows to support data generation for the detection and assessment of environmental exposures to chemicals contained within DSSTox. This presentation will provide an overview of the dashboard, the ongoing expansion of the PFAS chemical library, with associated categorization, and new physicochemical property and environmental fate and transport QSAR prediction models developed for these chemicals. The application of the dashboard to support mass spectrometry non-targeted analysis studies for the identification of PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency. Targeted Lists of Chemicals to Support Non-Targeted Analysis via the US-EPA C...
Targeted Lists of Chemicals to Support Non-Targeted Analysis via the US-EPA C...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 US-EPA 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. A number of chemical lists (https://comptox.epa.gov/dashboard/chemical_lists) have also been developed to support specific applications including the identification of chemicals in human breath (i.e., the volatilome), chemicals in human media (e.g., blood, saliva), and in water. Other lists include PFAS (per- and polyfluoroalkyl substances) chemicals and toxins (e.g.. microcystins and cyanotoxins). Combining the synergies of a database containing ~900,000 chemicals with over 200 segregated chemical lists with dashboard search functionality into a comprehensive workflow provides a powerful tool to support NTA. This poster will review how the CompTox Chemicals Dashboard provides a freely available web-based application to support structure identification and NTA and how expansion of the types of data hosted in the database can support different targeted and non-targeted projects. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.The US-EPA CompTox Chemicals Dashboard – an online data integration hub suppo...
The US-EPA CompTox Chemicals Dashboard – an online data integration hub suppo...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 (e.g., to support breath research (the volatilome) 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 information for chemicals in hydraulic fracturing fluids using the ...
Accessing information for chemicals in hydraulic fracturing fluids using the ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases and providing accurate linkages of data to chemical structures, exposure and hazard information. The data are being made available via the EPA’s CompTox Chemistry Dashboard (https://comptox.epa.gov/dashboard), a publicly accessible website providing access to data for almost 760,000 chemical substances, the majority of these represented as chemical structures. The web application delivers a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data as well as integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. In addition, several specific search types are in development to directly support the mass spectroscopy non-targeted screening community, who are generating important data for detecting and assessing environmental exposures to chemicals contained within DSSTox. The application provides access to segregated lists of chemicals that are of specific interests to relevant stakeholders including, for example, scientists interested in algal toxins and hydraulic fracturing chemicals. This presentation will provide an overview of the challenges associated with the curation of data from EPA’s December 2016 Hydraulic Fracturing Drinking Water Assessment Report that represented chemicals reported to be used in hydraulic fracturing fluids and those found in produced water. The data have been integrated into the dashboard with a number of resulting benefits: a searchable database of chemical properties, with hazard and exposure predictions, and open literature. The application of the dashboard to support mass spectrometry non-targeted analysis studies will also be reviewed. This abstract does not reflect U.S. EPA policy.Cheminformatics Tools to Access Data for PFAS and Constituents of Fluorine-Fr...
Cheminformatics Tools to Access Data for PFAS and Constituents of Fluorine-Fr...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
A number of cheminformatics tools have been developed in recent years in the Computational Chemistry & Cheminformatics Branch (CCCB) of the Center for Computational Toxicology and Exposure. The DSSTox chemistry database underpins all cheminformatics tools and provides the foundation for multiple Dashboards including the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) and the proof-of-concept Cheminformatics Tools (https://www.epa.gov/chemical-research/cheminformatics). These applications provide access to property, hazard, exposure and safety data. This presentation will give an overview of available tools and how they may serve research applications regarding fluorine-free foams. Sourcing chemical hazard and safety data for PFAS chemicals via a US-EPA onli...
Sourcing chemical hazard and safety data for PFAS chemicals via a US-EPA onli...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
In recent years the Center for Computational Toxicology and Exposure at the US Environmental Protection Agency has delivered a number of valuable web-based applications which provide access to a myriad of data types for hundreds of thousands of chemicals. The data include property data, in vivo and in vitro hazard data, exposure data, and numerous other data types of interest to the scientific community. To date the preeminent application delivered by the center is the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) which presently delivers data for over 1.2 million chemicals. One aspect of delivering highly functional mature production software systems is the development of proof-of-concept applications to garner community interest in novel ways of interrogating and visualizing data. These tools include the Hazard Profile and Safety Profile modules which integrate publicly available data streams into a web-based interface delivering information regarding nine categories of GHS data (the Globally Harmonized System of Classification and Labeling of Chemicals), details regarding measures of accidental release (including cleanup and disposal), and firefighting measures. This presentation will provide an overview of publicly available proof-of-concept modules and new tools in development delivering access to chemistry-related data to a variety of stakeholders. Specific examples will be provided regarding how data for PFAS chemicals and those chemicals associated with AFFF mixtures can be sourced from the tools. Disclaimer: The views expressed in this article are those of the authors and do not necessarily represent the views or policies of the US EPA.The EPA Comptox Chemicals Dashboard as a Data Integration Hub for Environment...
The EPA Comptox Chemicals Dashboard as a Data Integration Hub for Environment...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This involves computational and data-driven approaches that integrate chemistry, exposure and biological data. The National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences, including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. The CompTox Chemicals Dashboard is a web-based application providing access to data associated with ~~875,000 chemical substances. New data are continuously added to the database on an ongoing basis, along with registration of new and emerging chemicals. This includes data extracted from the literature, identified by our analytical labs, and otherwise of interest to support specific research projects to the agency. By adding these data, with their associated chemical identifiers (names and CAS Registry Numbers), the dashboard uses linking approaches to allow for automated searching of PubMed, Google Scholar and an array of public databases. This presentation will provide an overview of the CompTox Chemicals Dashboard, how it has developed into an integrated data hub for environmental data, and how it can be used for the analysis of emerging chemicals in terms of sourcing related chemicals of interest, and deriving read-across as well as QSAR predictions in real time. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Comparison of lists of per- and polyfluoroalkyl substances (PFAS) based on di...
Comparison of lists of per- and polyfluoroalkyl substances (PFAS) based on di...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Per- and polyfluoroalkyl substances (PFAS) are a group of fluorinated substances that have generated increased public attention due to their potential health hazard and widespread presence in the environment. An attempt to define PFAS and establish standard categories was established in Buck et al. 2011. Since then, various groups, including the Organization for Economic Co-operation and Development and U.S. Environmental Protection Agency, have defined PFAS differently to serve their respective needs. The U.S. EPA’s CompTox Chemicals Dashboard is a public resource providing access to predicted or experimental data for ~900,000 chemical substances, the majority with defined structures, and with data types including hazard, bioactivity, property, and exposure data. With the increased attention given to PFAS, efforts have been dedicated to the assembly and curation of thousands of PFAS substances into the DSSTox database underlying the Dashboard. A set of more than 30 PFAS lists spanning EPA and international regulatory interests, as well as lists pertaining to research activities and analytical methods, are currently delivered via the Dashboard. Depending on the definition of what is deemed to be a PFAS, approximately 6,000 to upwards of 38,000 compounds currently in the Dashboard could be considered PFAS. We have defined an inventory of over 10,000 PFAS structures (the PFASSTRUC list) using a set of clearly defined structural filters that encompass current EPA programmatic interests. This list is serving as a benchmark for the community to apply cheminformatics approaches and better understand and survey the scope of PFAS chemistries of potential concern. PFASSTRUC was compared to several other structure-based definitions of PFAS to investigate what type of structures do and do not meet the definitions and thus what similar structures may be considered PFAS by some but not others. Such resources can help support the PFAS community to better frame the PFAS problem and aid in the development of categorization approaches for PFAS, as well as support the reporting of relevant data for the agency. Abstract does not reflect EPA policy. Accessing information for Per- & Polyfluoroalkyl Substances using the US EPA ...
Accessing information for Per- & Polyfluoroalkyl Substances using the US EPA ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases within the DSSTox project, and providing accurate linkages of data to chemical structures, exposure and hazard information. The data are made available via the EPA’s CompTox Chemistry Dashboard (https://comptox.epa.gov/dashboard), a publicly accessible website providing access to data for ~760,000 chemical substances, the majority of these represented as chemical structures. The web application delivers a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data, as well as integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. In addition, several specific search types are in development to directly support the mass spectrometry non-targeted screening community, enabling cohesive workflows to support data generation for the detection and assessment of environmental exposures to chemicals contained within DSSTox. The application provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders, including, for example, scientists interested in Per- & Polyfluoroalkyl Substances (PFAS). Added lists include those sourced from the European Union as well as developed in-house and now containing thousands of chemicals. A procured testing library of hundreds of PFAS chemicals annotated into chemical categories has been integrated into the dashboard with a number of resulting benefits: a searchable database of chemical properties, with hazard and exposure predictions, and links to the open literature. This presentation will provide an overview of the dashboard, the developing library of PFAS chemicals and associated categorization, and new physicochemical property and environmental fate and transport QSAR prediction models developed for these chemicals. The application of the dashboard to support mass spectrometry non-targeted analysis studies for the identification of PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Proof-of-Concept Publicly Accessible Data Dashboards from the US-EPA.pptx
Proof-of-Concept Publicly Accessible Data Dashboards from the US-EPA.pptxUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The US-EPA first delivered the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) to the community in 2016 and it has become one of the definitive online resources for sourcing chemical toxicity data. Used by thousands of scientists a day, the stability, uptime and data quality for such a production resource is critical. The assembly of increasingly diverse data types and approaches to interrogating and delivering such data is best investigated by the delivery of proof-of-concept applications for community feedback. This has been achieved by the delivery of the EPA Cheminformatics Modules (https://www.epa.gov/comptox-tools/cheminformatics).
Methods
The Cheminformatics Modules suite of tools is available to the community and delivers novel approaches for the hazard profiling of chemicals, QSAR batch prediction of physiochemical properties and toxicological endpoints, structure alerts based on structure and substructure, and profiling of chemicals using ToxPrint chemotypes using enrichment statistics associated with ToxCast in vitro bioactivity screening. These modules provide access to new capabilities not presently available to users of the Dashboard and enable new analyses for users interested in applications of computational toxicology data and resources.
Results
The Cheminformatics Modules have been used by multiple EPA regional offices, program offices and state offices to source data and perform analyses in terms of alternatives assessment for chlorinated solvents, aggregation of data related to chemicals of emerging concern (e.g., 6PPD and related phenylenediamines) and to support the development of state specific prioritization lists for chemicals. The modules are being used to provide access to data for emergency responders and onsite coordinators and is presently being expanded with safety data sourced from PubChem to provide GHS data, transportation details, and details regarding regulatory screening levels associated with federal and state specific guidelines. The ease of use of the modules has made the harvesting of data faster and easier for a breadth of general stakeholders as screening data for use in potential decision making.
Conclusions
The delivery of chemistry, toxicity, exposure and related data from the US-EPA’s Center for Computational Toxicology and Exposure to the community is facilitated using a number of web-based applications. Proof-of-concept tools provide a means by which to deliver novel search, visualization and data delivery approaches for testing and feedback prior to adding the capabilities into production-level tools.
This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.What is a PFAS?..and the challenges associated with defining them
What is a PFAS?..and the challenges associated with defining themUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at the XPAND2022 Annual Meeting for the Household & Commercial Products Association and focused on PFAS chemicals, the definition of what they are, how to categorize and classify them, and how data can be delivered via the CompTox Chemicals Dashboard 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
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.Structure identification approaches using the EPA CompTox Chemicals Dashboard...
Structure identification approaches using the EPA CompTox Chemicals Dashboard...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are utilized to identify emerging contaminants and chemical signatures of interest detected in various media. At the US Environmental Protection Agency the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is an open chemistry resource and web-based application containing data for ~900,000 substances and supports non-targeted and suspect screening analyses. Searching functionality includes identifier searches (e.g. systematic names, trade names and CAS Registry Numbers), mass and formula-based searches and prototype developments include combined substructure-mass/formula searches and searching experimental mass spectral data against predicted fragmentation spectra. A specific type of data mapping in the database uses “MS-Ready” structures, a way to process all registered substances to separate multi-component chemicals into their individual components, removal of stereochemical bonds and desalting and neutralization. This MS-Ready processing supports batch-searching using either mass or formulae to identify candidate chemicals and their mapped substances. A number of chemical lists (https://comptox.epa.gov/dashboard/chemical_lists) have also been developed to support the identification of chemicals related to agrochemistry, specifically pesticides (both active and inert constituents), insecticides and their metabolites and environmental breakdown products). This presentation will provide an overview of how the CompTox Chemicals Dashboard supports mass spectrometry based structure identification and non-targeted analysis of chemicals in agrochemistry. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...
The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
As part of our efforts to develop a public platform to provide access to predictive models we have attempted to disentangle the influence of the quality versus quantity of data available to develop and validate QSAR models. Using a thorough manual review of the data underlying the well-known EPI Suite software, we developed automated processes for the validation of the data using a KNIME workflow. This includes: approaches to validate different chemical structure representations (e.g. molfile and SMILES), identifiers (chemical names and registry numbers), and methods to standardize the data into QSAR-consumable formats for modeling. Our efforts to quantify and segregate data into various quality categories has allowed us to thoroughly investigate the resulting models developed from these data slices, as well as allowing us to examine whether or not efforts into the development of large high-quality datasets has the expected pay-off in terms of prediction performance. Machine-learning approaches have been applied to create a series of models that have been used to generate predicted physicochemical and environmental parameters for over 700,000 chemicals. These data are available online via the EPA’s iCSS Chemistry Dashboard. This abstract does not reflect U.S. EPA policy.Delivering chemical-associated data via EPA web applications
Delivering chemical-associated data via EPA web applicationsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at the conference: "Cheminformatics Resources of U.S. Governmental Organizations" and focuses on the CompTox Chemicals Dashboard and the sharing of our data https://www.fda.gov/news-events/fda-meetings-conferences-and-workshops/cheminformatics-resources-us-governmental-organizations-05092022#event-information US-EPA Chemicals Dashboard – an integrated data hub for environmental science
US-EPA Chemicals Dashboard – an integrated data hub for environmental scienceUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program utilizes computational and data-driven approaches that integrate chemistry, exposure and biological data to help characterize potential risks from chemical exposure. The National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences, including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. The CompTox Chemicals Dashboard website provides access to data associated with ~900,000 chemical substances. New data are added on an ongoing basis, including the registration of new and emerging chemicals, data extracted from the literature, chemicals studied in our labs, and data of interest to specific research projects at the EPA. Hazard and exposure data have been assembled from a large number of public databases and as a result the dashboard surfaces hundreds of thousands of data points. Other data includes experimental and predicted physicochemical property data, in vitro bioassay data and millions of chemical identifiers (names and CAS Registry Numbers) to facilitate searching. Other integrated modules include real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed. This presentation will provide an overview of the CompTox Chemicals Dashboard and how it has developed into an integrated data hub for environmental data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Web-based access to experimental and predicted data for environmental fate, t...
Web-based access to experimental and predicted data for environmental fate, t...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The EPA CompTox Chemistry Dashboard provides access to data associated with ~760,000 chemical substances. The available data includes experimental and predicted physicochemical properties, environmental fate and transport data, in vivo and in silico toxicity data, in vitro bioassay data, exposure data and a variety of other types of information. The data are under continuous expansion and curation and the experimental data have been used to develop QSAR and QSPR models. A number of these models are available via a web interface so that users can submit a chemical structure and predict properties in real time. The dashboard also provides access to pre-compiled chemical lists and categories, including pesticides, and chemicals detected in the environment via non-targeted mass spectrometry analysis. The data are searchable using chemical identifiers (systematic names, trade names, CAS Registry Numbers), by structure, mass and formula. Batch searches allow for data associated with thousands of chemicals to be obtained in a few seconds, with just a few button clicks, and downloaded to the desktop. This presentation will provide an overview of the Dashboard and its applications to accessing source data associated with agriculturally related chemicals. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.The EPA CompTox Chemistry Dashboard and Underpinning Software Architecture
The EPA CompTox Chemistry Dashboard and Underpinning Software Architecture US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The CompTox Chemistry Dashboard was developed by the Environmental Protection Agency’s National Center for Computational Toxicology. This dashboard has been architected in a manner that allows for the deployment of multiple “applications”, both as publicly available databases, and for deployment under the constraints of confidential business information (CBI). The public dashboard provide access to multiple types of data for ~750,000 chemicals. This includes, when available for a chemical substance, physicochemical parameters, toxicity and bioassay data, consumer use and analytical data. Fate, exposure, and hazard calculations can benefit from access to the data aggregation and curation efforts that underpin the public dashboard. Also, regulators can benefit from the integration of their own data within their closed infrastructure environments. This presentation will provide a review of the chemistry dashboard architecture and its present application providing access to data to the research and regulatory communities. We will also review present developments in the area of delivering an application programming interface, web services, and software components for integration into third party applications providing access to the data exposed via the dashboard. This abstract does not reflect U.S. EPA policy.Similar to Delivering an integrated data hub for per- and polyfluoroalkyl (PFAS) chemicals via the US-EPA CompTox Chemicals Dashboard (20)
Bringing it all together: A Web-based Database for Chemical and Biological Da...
Bringing it all together: A Web-based Database for Chemical and Biological Da...
PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...
PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...
The US-EPA CompTox Chemicals Dashboard – an information hub for over five tho...
The US-EPA CompTox Chemicals Dashboard – an information hub for over five tho...
Targeted Lists of Chemicals to Support Non-Targeted Analysis via the US-EPA C...
Targeted Lists of Chemicals to Support Non-Targeted Analysis via the US-EPA C...
The US-EPA CompTox Chemicals Dashboard – an online data integration hub suppo...
The US-EPA CompTox Chemicals Dashboard – an online data integration hub suppo...
Accessing information for chemicals in hydraulic fracturing fluids using the ...
Accessing information for chemicals in hydraulic fracturing fluids using the ...
Cheminformatics Tools to Access Data for PFAS and Constituents of Fluorine-Fr...
Cheminformatics Tools to Access Data for PFAS and Constituents of Fluorine-Fr...
Sourcing chemical hazard and safety data for PFAS chemicals via a US-EPA onli...
Sourcing chemical hazard and safety data for PFAS chemicals via a US-EPA onli...
The EPA Comptox Chemicals Dashboard as a Data Integration Hub for Environment...
The EPA Comptox Chemicals Dashboard as a Data Integration Hub for Environment...
Comparison of lists of per- and polyfluoroalkyl substances (PFAS) based on di...
Comparison of lists of per- and polyfluoroalkyl substances (PFAS) based on di...
Accessing information for Per- & Polyfluoroalkyl Substances using the US EPA ...
Accessing information for Per- & Polyfluoroalkyl Substances using the US EPA ...
Proof-of-Concept Publicly Accessible Data Dashboards from the US-EPA.pptx
Proof-of-Concept Publicly Accessible Data Dashboards from the US-EPA.pptx
What is a PFAS?..and the challenges associated with defining them
What is a PFAS?..and the challenges associated with defining them
An integrated data hub for per- and polyfluoroalkyl (PFAS) chemicals to suppo...
An integrated data hub for per- and polyfluoroalkyl (PFAS) chemicals to suppo...
Structure identification approaches using the EPA CompTox Chemicals Dashboard...
Structure identification approaches using the EPA CompTox Chemicals Dashboard...
The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...
The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...
Delivering chemical-associated data via EPA web applications
Delivering chemical-associated data via EPA web applications
US-EPA Chemicals Dashboard – an integrated data hub for environmental science
US-EPA Chemicals Dashboard – an integrated data hub for environmental science
Web-based access to experimental and predicted data for environmental fate, t...
Web-based access to experimental and predicted data for environmental fate, t...
The EPA CompTox Chemistry Dashboard and Underpinning Software Architecture
The EPA CompTox Chemistry Dashboard and Underpinning Software Architecture
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What is greenhouse gasses and how many gasses are there to affect the Earth.
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Salas, V. (2024) "John of St. Thomas (Poinsot) on the Science of Sacred Theol...
I Introduction
II Subalternation and Theology
III Theology and Dogmatic Declarations
IV The Mixed Principles of Theology
V Virtual Revelation: The Unity of Theology
VI Theology as a Natural Science
VII Theology’s Certitude
VIII Conclusion
Notes
Bibliography
All the contents are fully attributable to the author, Doctor Victor Salas. Should you wish to get this text republished, get in touch with the author or the editorial committee of the Studia Poinsotiana. Insofar as possible, we will be happy to broker your contact.
Toxic effects of heavy metals : Lead and Arsenic
Heavy metals are naturally occuring metallic chemical elements that have relatively high density, and are toxic at even low concentrations. All toxic metals are termed as heavy metals irrespective of their atomic mass and density, eg. arsenic, lead, mercury, cadmium, thallium, chromium, etc.
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THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.
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bordetella pertussis.................................ppt
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Breakthrough in Sustainable Energy Science
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...
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Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Deep Software Variability and Frictionless Reproducibility
Deep Software Variability and Frictionless ReproducibilityUniversity of Rennes, INSA Rennes, Inria/IRISA, CNRS
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
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Delivering an integrated data hub for per- and polyfluoroalkyl (PFAS) chemicals via the US-EPA CompTox Chemicals Dashboard
- 1. Innovative Research for a Sustainable Futurewww.epa.gov/research ORCID: 0000-0002-2668-4821 Antony Williams l williams.antony@epa.gov l 919-541-1033 Delivering an integrated data hub for per- and polyfluoroalkyl (PFAS) chemicals via the US EPA CompTox Chemicals Dashboard Antony Williams1, Chris Grulke1, Kamel Mansouri2, Grace Patlewicz1 and Ann Richard1 1U.S. Environmental Protection Agency, Office of Research and Development, National Center for Computational Toxicology, Research Triangle Park, NC and 2Integrated Laboratory Systems, Research Triangle Park, NC. ACS Fall 2019 San Diego, CA August 25-29, 2019 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 poster provides 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 work 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. The CompTox Chemicals Dashboard Abstract For records with chemical structures experimental and predicted physicochemical (logP, water solubility etc.) and fate and transport properties are provided. These include OPERA models reported by Mansouri et al. [1] The landing page of the dashboard is a simple text entry box allowing a type-ahead search for systematic, trade and trivial names, CAS Registry Numbers and InChI chemical identifiers.Dashboard Entry Page Chemical Record Page: PFOA Chemical Properties Panel Where possible, links are provided to related Wikipedia articles. Structure file formats are available for download to the desktop (SMILES and molfile) and an executive summary report regarding chemical toxicity is provided. Accessing PFAS Chemical Lists Future Work The dashboard provides access to ~20 individual PFAS chemical lists. These include a list based on structural filters: (1) Formula must contain 3 -1000 Fluorine atoms; 2) Structure must contain two adjacent CF2 groups, either in a chain or in a ring system; 3) Fluorine to Carbon ratio (#F/#C) = or > 0.5; 4) REMOVE charged species (e.g., bare anions), radicals, and deuterium- and C13-labeled chemicals References 1. Mansouri et al. OPERA models for predicting physchem properties and environmental fate endpoints, J. ChemInf. 10, 10 (2018) 2. PFAS Categories list on the CompTox Chemicals Dashboard https://comptox.epa.gov/dashboard/chemical_lists/EPAPFASCAT 3. Patlewicz et al. A Chemical Category-Based Prioritization Approach for Selecting 75 Per- and Polyfluoroalkyl Substances (PFAS) for Tiered Toxicity and Toxicokinetic Testing. Environ Health Perspect. 2019 Jan;127(1):14501. • In vitro toxicity and toxicokinetic measurements are underway for ~150 PFAS [3]. These will be released in the future on the dashboard. • Experimental property data are being harvested from literature and online resources to include into the dashboard and OPERA models. • Chemical categorization efforts continue in order to be encompassing of more of the PFAS library. List of chemical lists of PFAS chemicals: 21 lists and growing Structure-filtered list of PFAS Problem Definition and Goals Problem: There are many sources of PFAS data online to support computational toxicology. However, curated datasets for the thousands of known PFAS chemicals are not available in structured formats, Goals: Deliver online access to hundreds of thousands of chemicals of interest to environmental science and computational toxicology. Provide lists of PFAS substances via a simple to use web-based interface. Deliver application to support diverse types of data including experimental and predicted physicochemical properties, in vivo hazard data and in vitro toxicity and toxicokinetic data. Make the data available as downloadable data for reuse and repurposing in other databases. Toxicity Values Panel Bioactivities: e.g. ToxCast Data The Hazard tab provides access to data assembled from a series of public resources including EPA data (i.e. IRIS and PPRTV reports, ToxRef DB). Data can be downloaded as TSV and Excel files. ToxCast Bioactivity data measured over the past decade are under the Bioassay Tab. Data can be downloaded as Excel files. New in vitro data are being generated on a library of ~150 PFAS in collaboration with NTP. Acknowledgements The authors thank the chemical curation team for their rigorous work and the software development team for the development of the dashboard. A list of Markush Representations associated with the selection of chemicals for in vitro toxicity and toxicokinetic screening is also available [2,3].