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Category Archives: EPA Presentations

Presentations at the Spring ACS Meeting in Orlando, April 2019

I am giving a number of presentations at the ACS meeting in Orlando in April 2019. If you are interested in coming to listen and maybe chat after please see the list below.

1) PAPER ID: 3080890 
PAPER TITLE: Consensus ranking and fragmentation prediction for identification of unknowns in high resolution mass spectrometry (final paper number: AGFD 10)


DIVISION: Division of Agricultural and Food Chemistry
SESSION: Recent Advances in Food Fraud & Authenticity Analysis
SESSION TIME: 8:30 AM – 10:55 AM

PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Sunday, March, 31, 2019 from 9:25 AM – 9:50 AM
ROOM & LOCATION: Florida Ballroom B  – Hyatt Regency Orlando 

Title: Consensus ranking and fragmentation prediction for identification of unknowns in high resolution mass spectrometry

Antony J. Williams1, Andrew McEachran2, Tommy Cathey3, Tom Transue3, Jon Sobus4

High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are advancing the identification of emerging contaminants in environmental and agricultural matrices.  However, confidence in structure identification of unknowns in NTA presents challenges to analytical chemists.  Structure identification requires integration of complementary data types such as reference databases, fragmentation prediction tools, and retention time prediction models.  The goal of this research is to optimize and implement structure identification functionality within the US EPA’s CompTox Chemicals Dashboard, an open chemistry resource and web application containing data for ~760,000 substances.  Rank-ordering the number of sources associated with chemical records within the Dashboard (Data Source Ranking) improves the identification of unknowns by bringing the most likely candidate structures to the top of a search results list.  Incorporating additional data streams contained within the database underlying the Dashboard further enhances identifications.  Integrating tandem mass spectrometry data into NTA workflows enables spectral match scores and increases confidence in structural assignments.  We have generated and stored predicted MS/MS fragmentation spectra for the entirety of the Chemistry Dashboard using the in silico prediction tool CFM-ID.  Predicted fragments incorporated into the identification workflow were used as both a scoring term and as a candidate threshold cutoff.  Combining these steps within an open chemistry resource provides a freely available software tool for structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

2) PAPER ID: 3081133 
PAPER TITLE: Applications of the US EPA’s CompTox chemicals dashboard to support structure identification and chemical forensics using mass spectrometry (final paper number: ANYL 320)


DIVISION: Division of Analytical Chemistry
SESSION: Frontiers in Forensic Mass Spectrometry
SESSION TIME: 8:00 AM – 12:10 PM

PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Tuesday, April, 02, 2019 from 11:40 AM – 12:10 PM
ROOM & LOCATION: Plaza International Ballroom K  – Hyatt Regency Orlando

Title: Applications of the US EPA’s CompTox Chemicals Dashboard to support structure identification and chemical forensics using mass spectrometry

Antony J. Williams, Andrew D. McEachran, Jon R. Sobus and Emma Schymanski

High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are of increasing interest in chemical forensics for the identification of emerging contaminants and chemical signatures of interest. At the US Environmental Protection Agency, our research using HRMS for non-targeted and suspect screening analyses utilizes databases and cheminformatics approaches that are applicable to chemical forensics. The CompTox Chemicals Dashboard is an open chemistry resource and web-based application containing data for ~760,000 substances. Basic functionality for searching through the data is provided through identifier searches, such as systematic name, trade names and CAS Registry Numbers. Advanced Search capabilities supporting mass spectrometry include mass and formula-based searches, combined substructure-mass searches and searching experimental mass spectral data against predicted fragmentation spectra. A specific type of data mapping in the underpinning database, using “MS-Ready” structures, has proven to be a valuable approach for structure identification that links structures that can be identified via HRMS with related substances in the form of salts, and other multi-component mixtures that are available in commerce. This presentation will provide an overview of the CompTox Chemicals Dashboard and demonstrate its utility for supporting structure identification and NTA in chemical forensics. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

3) PAPER ID: 3084559 
PAPER TITLE: Antony Williams, the ChemConnector: A career path through a diverse series of roles and responsibilities (final paper number: CINF 25)

DIVISION: Division of Chemical Information
SESSION: Careers in Chemical Information
SESSION TIME: 1:30 PM – 4:25 PM

PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Sunday, March, 31, 2019 from 3:05 PM – 3:25 PM
ROOM & LOCATION: West Hall B4 – Theater 11  – Orange County Convention Center

Antony Williams, the ChemConnector – a career path through a diverse series of roles and responsibilities

Authors: Antony Williams

Antony Williams is a Computational Chemist at the US Environmental Protection Agency in the National Center for Computational Toxicology. He has been involved in cheminformatics and the dissemination of chemical information for over twenty-five years. He has worked for a Fortune 500 company (Eastman Kodak), in two successful start-ups (ACD/Labs and ChemSpider), for the Royal Society of Chemistry (in publishing) and, now, at the EPA. Throughout his career path he has experienced multiple diverse work cultures and focused his efforts on understanding the needs of his employers and the often unrecognized needs of a larger community. Antony will provide a short overview of his career path and discuss the various decisions that helped motivate his change in career from professional spectroscopist to website host and innovator, to working for one of the world’s foremost scientific societies and now for one of the most impactful government organizations in the world. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

4) PAPER ID: 3084590 
PAPER TITLE: US-EPA CompTox chemicals dashboard: A web-based data integration hub for environmental chemistry data (final paper number: CINF 43)


DIVISION: Division of Chemical Information
SESSION: Web-Based Chemoinformatics Platforms
SESSION TIME: 8:00 AM – 11:50 AM

PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Monday, April, 01, 2019 from 11:20 AM – 11:50 AM
ROOM & LOCATION: West Hall B4 – Theater 10  – Orange County Convention Center

The EPA Comptox Chemicals Dashboard as a Data Integration Hub for Environmental Chemistry Data

Authors: Antony Williams, Andrew McEachran, Imran Shah, Richard Judson, John Wambaugh, Nancy Baker, George Helman, Chris Grulke, Kamel Mansouri, Grace Patlewicz, Ann Richard and Jeff Edwards.

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 ~760,000 chemical substances. New data are continuously added to the database on an ongoing basis, along with registration of new and emerging chemicals. This includes data extracted from the literature, identified by our analytical labs, and otherwise of interest to support specific research projects to the agency. By adding these data, with their associated chemical identifiers (names and CAS Registry Numbers), the dashboard uses linking approaches to allow for automated searching of PubMed, Google Scholar and an array of public databases. This presentation will provide an overview of the 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.

5) PAPER ID: 3084575 
PAPER TITLE: EPA CompTox chemicals dashboard: An online resource for environmental chemists (final paper number: CINF 94)


DIVISION: Division of Chemical Information
SESSION: Applications of Cheminformatics to Environmental Science
SESSION TIME: 8:00 AM – 12:00 PM

PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Wednesday, April, 03, 2019 from 8:25 AM – 8:45 AM

ROOM & LOCATION: West Hall B4 – Theater 10  – Orange County Convention Center 

EPA CompTox Chemicals Dashboard – an online resource for environmental chemists

Authors: Antony Williams, Chris Grulke, Jennifer Smith, Kamel Mansouri, Andrew McEachran, Kathie Dionisio, Katherine Phillips, Grace Patlewicz, Jeremy Fitzpatrick, Nancy Baker, Todd Martin, Ann Richard and Jeff Edwards

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Chemicals Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Chemicals Dashboard and its value to the community as an informational hub. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

6) PAPER ID: 3095464 
PAPER TITLE: Cheminformatics approaches to support chemical identification delivered via the EPA CompTox Chemicals Dashboard (final paper number: ENVR 173)


DIVISION: Division of Environmental Chemistry
SESSION: Accurate Mass/High Resolution Mass Spectrometry for Environmental Monitoring & Remediation
SESSION TIME: 1:00 PM – 4:10 PM

PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Monday, April, 01, 2019 from 1:25 PM – 1:45 PM
ROOM & LOCATION: Valencia Ballroom B-D – Theater 8  – Orange County Convention Center

Cheminformatics approaches to support chemical identification delivered via the EPA CompTox Chemicals Dashboard

Antony J. Williams, Andrew McEachran, Chris M. Grulke, Elin M. Ulrich and Jon R. Sobus

The identification of chemicals in environment media depends on the application of analytical methods, the primary approach being one of the multiple mass spectrometry techniques. Cheminformatics solutions are critical to supporting the chemical identification process. This includes the assembly of large chemical substance databases, prioritization ranking of potential candidate search hits, and search approaches that support both targeted and non-targeted screening approaches. The US Environmental Protection Agency CompTox Chemicals Dashboard is a web-based application providing access to data for over 760,000 chemical substances. This includes access to physicochemical property, environmental fate and transport data, both human and ecological toxicity data, information regarding chemicals contained in products in commerce, and in vitro bioactivity data. Searches are allowed based on chemical identifiers, product and use, genes and assays associated with the EPA ToxCast assays and, specific to supporting mass spectrometry, searches based on masses and formulae. These searches make use of a novel “MS-Ready structures” approach collapsing chemicals related as mixtures, salts, stereoforms and isotopomers. The dashboard supports both singleton or batch searching by accurate mass/chemical formula, supported by MS-ready structures, and utilizes rich meta data to facilitate candidate ranking and the prioritization of chemicals of concern based on toxicity and exposure data. The dashboard also hosts tens of chemical lists that have been assembled from public databases, many supporting non-targeted analysis and mass spectrometry databases.

This presentation will provide an overview of the dashboard and will review our latest research into structure identification by searching experimental mass spectrometry data against predicted fragmentation spectra for LC-MS (positive and negative ion mode) and GC-MS (EI), a total of 3 million predicted spectra. We will also provide an overview of our progress supporting structure and substructure searching, using mass and formula-based filtering, and report on the latest applications of the dashboard to support structure identification projects of interest to the EPA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

7) PAPER ID: 3084594 
PAPER TITLE: US-EPA comptox chemicals dashboard: an information hub for over five thousand per- & polyfluoroalkyl chemical substances (final paper number: ENVR 217)


DIVISION: Division of Environmental Chemistry
SESSION: Per- & Polyfluoroalkyl Substances in the Environment: From Legacy To Emerging Contaminants
SESSION TIME: 8:30 AM – 12:00 PM

PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Tuesday, April, 02, 2019 from 10:10 AM – 10:30 AM
ROOM & LOCATION: Valencia Ballroom B-D – Theater 10  – Orange County Convention Center

Title: The US-EPA CompTox Chemicals Dashboard – an information hub for over five thousand per- & polyfluoroalkyl chemical substances

Authors: Antony Williams, Chris Grulke, Grace Patlewicz and Ann Richard

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.

8) PAPER ID: 3084611 
PAPER TITLE: CompTox chemicals dashboard: Data and tools to support chemical and environmental risk assessment and the ENTACT project (final paper number: ENVR 648)


DIVISION: Division of Environmental Chemistry
SESSION: True Positives in EPA’S Non-Targeted Analysis Collaborative Trial (ENTACT)
SESSION TIME: 1:30 PM – 5:00 PM

PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Wednesday, April, 03, 2019 from 2:15 PM – 2:35 PM
ROOM & LOCATION: Valencia Ballroom B-D – Theater 13  – Orange County Convention Center

Title: The CompTox Chemicals Dashboard: Data and Tools to Support Chemical and Environmental Risk Assessment and the ENTACT project

Authors and affiliations: Antony J. Williams1, Christopher M. Grulke1, Andrew D. McEachran2, Emma L. Schymanski3,4, Jon Sobus5, Elin Ulrich5, Ann M. Richard1, Jeremy Dunne1 and Jeff Edwards1

1 EPA, National Center for Computational Toxicology, RTP, NC, USA

2 ORISE Fellow, Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA

3 Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, 6, avenue du Swing, L-4367 Belvaux, Luxembourg

4 EPA, National Exposure Research Laboratory, RTP, NC, USA

Information and data on chemicals is used by scientists to evaluate potential health and ecological risks due to environmental exposures. EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov) helps evaluate the safety of chemicals by providing public access to a variety of information on over 760,000 chemicals. Within the Dashboard, users can access chemical structures, chemistry information, toxicity data, hazard data, exposure information, and additional links to relevant websites and applications. These data are compiled from sources including EPA’s computational toxicology research databases, from public domain databases and with collaborators across the world. Chemical lists have been added that provide access to various classes of chemicals and project-based datasets are under constant development. Specific functionality has been delivered within the Dashboard to support mass spectrometry including “MS-ready forms” of chemical substances that would be detectable by mass spectrometry. Workflows have been developed to assist in candidate identification and have now been proven with multiple published studies. An integration path between the dashboard and MetFrag has also been established to provide users the significant benefits resulting from the marriage between the two applications. The datasets underpinning the dashboard are freely available (https://comptox.epa.gov/dashboard/downloads) for integration into third party databases. This presentation will provide an overview of the available data types and functionality of the dashboard prior to examining how it is developing to support mass spectrometry based analyses within the agency and for the community in general. This will include a review of our research efforts to enhance the dashboard using in silico MS/MS fragmentation prediction for spectral matching. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

 

Predicting organ toxicity using in vitro bioactivity data and chemical structure

I get to work with some great scientists in my job. I am getting to work on projects that a couple of years ago were way out of my depth. Let’s be honest, I have no formal training as a toxicologist and my training is formally as an analytical scientist, then cheminformatician, then into publishing and informatics and now in the National Center for Computational Toxicology. I didn’t realize that the trial by fire would be so stimulating and fun but working at EPA is great. So many people make flippant comments about working for the government, leaving early, etc. We work HARD and are productive and, for me at least, I feel we are doing important work and making real contributions. The latest paper I am involved with is “Predicting organ toxicity using in vitro bioactivity data and chemical structure” (http://dx.doi.org/10.1021/acs.chemrestox.7b00084). The abstract is listed below…

“Animal testing alone cannot practically evaluate the health hazard posed by tens of thousands of environmental chemicals. Computational approaches making use of high-throughput experimental data may provide more efficient means to predict chemical toxicity. Here, we use a supervised machine learning strategy to systematically investigate the relative importance of study type, machine learning algorithm, and type of descriptor on predicting in vivo repeat-dose toxicity at the organ-level. A total of 985 compounds were represented using chemical structural descriptors, ToxPrint chemotype descriptors, and bioactivity descriptors from ToxCast in vitro high-throughput screening assays. Using ToxRefDB, a total of 35 target organ outcomes were identified that contained at least 100 chemicals (50 positive and 50 negative). Supervised machine learning was performed using Naïve Bayes, k-nearest neighbor, random forest, classification and regression trees, and support vector classification approaches. Model performance was assessed based on F1 scores using five-fold cross-validation with balanced bootstrap replicates. Fixed effects modeling showed the variance in F1 scores was explained mostly by target organ outcome, followed by descriptor type, machine learning algorithm, and interactions between these three factors. A combination of bioactivity and chemical structure or chemotype descriptors were the most predictive. Model performance improved with more chemicals (up to a maximum of 24%) and these gains were correlated (ρ= 0.92) with the number of chemicals. Overall, the results demonstrate that a combination of bioactivity and chemical descriptors can accurately predict a range of target organ toxicity outcomes in repeat-dose studies, but specific experimental and methodologic improvements may increase predictivity.”

 
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Posted by on August 6, 2017 in EPA Presentations

 

Comparing the EPA CompTox Dashboard with ChemSpider for MS-based Structure Identification

It’s almost ten years, this April, since ChemSpider was released to the public at the 233rd ACS meeting in Chicago. For two years, prior to being acquired by RSC in May 2009, we worked very closely with a number of mass spectrometry vendors including Waters (Micromass), Thermo and Agilent. I always considered that the work that we did with ChemSpider could be highly valued by the mass spectrometry community. This was especially true after we published the work for the identification of known unknowns with James Little (http://link.springer.com/article/10.1007/s13361-011-0265-y)  Certainly ChemSpider has become highly recognized, and used, by an increasing number of mass spectrometry vendors (through the ChemSpider Web Services).

A few months ago Andrew McEachran joined our team as a postdoc. Combining my experience with bringing ChemSpider to bear for the purpose of structure identification, his mass spectrometry skills and experience, and our tremendous development team to the development of the CompTox Chemistry Dashboard, we were able to make some further advances in the “identification known unknowns”. Our efforts were recently reported in this publication “Identifying known unknowns using the US EPA’s CompTox Chemistry Dashboard” (http://link.springer.com/article/10.1007%2Fs00216-016-0139-z). Readers are pointed to the summary tables in the article (results) demonstrating the improved performance of the CompTox Chemistry Dashboard based on high quality data sources and new approaches to rank ordering results based on formula and mass searching.

We recently rolled out new functionality and “MS-Ready structure batch-based searching” to offer even greater support for MS-structure identification . We will report on further extensions to this work at the Spring ACS Meeting.

 
The AltMetrics for the Article are shown below

 

Spring ACS Meeting San Francisco, April 2017

The Spring ACS Meeting is coming, and it’s coming quickly. Every time the New Year starts I think I have a long time before I have to assemble posters and write talks for the ACS Meeting. When I worked at the RSC it was easier in some ways as NO ONE reviewed them, no one gave comments on them and there was no clearance process involved. Mostly I was writing the talks on the flight out to the ACS or, more commonly, was writing them the evening before or morning of the presentations. There have been days when I got up in the morning at 4am to write two talks on the day I presented. Quite exhausting but at least I got to show the latest and greatest capabilities.

As an employee at the EPA there are different expectations especially in regards to the clearance process where the presentations are reviewed and signed off, pushed through our internal repository and, post-presentation, released to the community via Science Inventory. Some, not all, of the presentations and papers I have been involved with since joining EPA, are here.

I will be going to the ACS meeting with a number of colleagues and chairing a session on Thursday, all day, with Chris Grulke for the Division of Environmental Chemistry. I will be presenting a number of posters and presentations as listed below. A number of my colleagues will also be presenting. Andrew McEachran, a recent postdoc with the center will be presenting on a lot of the work that has been done in terms of the use of the Chemistry Dashboard to facilitate structure identification. The recent publication “Identifying known unknowns using the US EPA’s CompTox Chemistry Dashboard” (http://link.springer.com/article/10.1007%2Fs00216-016-0139-z) reported on a comparison of the dashboard versus ChemSpider. Since then we have rolled out a lot of new functionality to support structure identification and Andrew will report on that.

PAPER ID: 2624963
PAPER TITLE: Twenty five years in cheminformatics: A career path through a diverse series of roles and responsibilities

DIVISION: Division of Chemical Information
SESSION: Careers in Chemical Information
PRESENTATION FORMAT: Oral
DAY & HALF DAY OF PRESENTATION: Sunday, April, 02, 2017 – AM

PAPER ID: 2616719
PAPER TITLE: Evaluating suspect screening and non-targeted analysis approaches using a collaborative research trial at the US EPA

DIVISION: Division of Analytical Chemistry
SESSION: Analytical Division Poster Session
PRESENTATION FORMAT: Poster
DAY & HALF DAY OF PRESENTATION: Sunday, April, 02, 2017 – EVE

PAPER ID: 2624980
PAPER TITLE: EPA CompTox chemistry dashboard: An online resource for environmental chemists

DIVISION: Division of Chemical Health and Safety
SESSION: Information Flow in Environmental Health & Safety
PRESENTATION FORMAT: Oral
DAY & HALF DAY OF PRESENTATION: Tuesday, April, 04, 2017 – PM
PAPER ID: 2624984
PAPER TITLE: Delivering an informational hub for data at the National Center for Computational Toxicology

DIVISION: Division of Environmental Chemistry
SESSION: Applications of Cheminformatics & Computational Chemistry in Environmental Health
PRESENTATION FORMAT: Poster
DAY & HALF DAY OF PRESENTATION: Wednesday, April, 05, 2017 – EVE

Looking forward to seeing you at ACS!

 

 

The EPA Online Prediction Physicochemical Prediction Platform to Support Environmental Scientists

This poster was presented at the American Chemical Society in Philadelphia in August 2016 at the Sci-Mix gathering and at the ENVR section on Wednesday.

SESSION: Sci-Mix
SESSION TIME:
August 22, 2016 from 8:00 PM to 10:00 PM

and

SESSION TIME: Wednesday, August, 24, 2016, 6:00 PM – 8:00 PM
ROOM & LOCATION:
Hall D – Pennsylvania Convention Center

Poster Title: The EPA Online Prediction Physicochemical Prediction Platform to Support Environmental Scientists

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.

 

Investigating Impact Metrics for Performance for the US-EPA National Center for Computational Toxicology

This presentation was presented at the American Chemical Society in Philadelphia in August 2016

DAY & TIME OF PRESENTATION: Sunday, August, 21, 2016 from 4:10 PM – 4:30 PM
ROOM & LOCATION: Room 112B – Pennsylvania Convention Center

Title: Investigating Impact Metrics for Performance for the US-EPA National Center for Computational Toxicology

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. We have delivered public access to terabytes of open data, as well to a large number of publicly accessible databases and applications, to support the research efforts for a large community of scientists. Many of our contributions to science are summarily described in research papers but  to date we have not optimized our contributions to  inform altmetrics statistics associated with our work. Critically missing from altmetrics is access to our numerous software applications and web service accesses, as well as the growing importance of our experimental data and models (e.g ToxCast, ExpoCast, DSSTox and others) to the scientific and regulatory communities.  This presentation will provide an overview of our efforts to more fully understand, and quantify, our impact on the environmental sciences using a combination of our measurement approaches and available altmetrics tools. This abstract does not reflect U.S. EPA policy.

 

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Structure Identification Using High Resolution Mass Spectrometry Data and the EPA’s Chemistry Dashboard

This presentation was presented at the American Chemical Society in Philadelphia in August 2016

DAY & TIME OF PRESENTATION: Sunday, August, 21, 2016 from 1:10 PM – 1:35 PM
ROOM & LOCATION: Room 105A – Pennsylvania Convention Center

Title: Structure Identification Using High Resolution Mass Spectrometry Data and the EPA’s Chemistry Dashboard

The iCSS Chemistry Dashboard is a publicly accessible dashboard provided by the National Center for Computation Toxicology at the US-EPA. It serves a number of purposes, including providing a chemistry database underpinning many of our public-facing projects (e.g. ToxCast and ExpoCast). The available data and searches provide a valuable path to structure identification using mass spectrometry as the source data. With an underlying database of over 720,000 chemicals, the dashboard has already been used to assist in identifying chemicals present in house dust. However, it can also be applied to many other purposes, e.g., the identification of agrochemicals in waste streams. This presentation will provide a review of the EPA’s platform and underlying algorithms used for the purpose of compound identification using high-resolution mass spectrometry data. We will also discuss progress towards a high-throughput non-targeted analysis platform for use by the mass spectrometry community.  This abstract does not reflect U.S. EPA policy.

 

 

Presentations and Posters at #ACSPhiladelphia August 2016

I will be delivering five presentations and a poster (twice) at the ACS Meeting in Philadelphia this week. These presentations will introduce the latest version of our CompTox Dashboard, renamed from the iCSS Chemistry Dashboard because now we are offering way more than just a large set of chemical structures! I look forward to introducing attendees to the latest and greatest.

DAY & TIME OF PRESENTATION: Sunday, August, 21, 2016 from 1:10 PM – 1:35 PM
ROOM & LOCATION: Room 105A – Pennsylvania Convention Center

Title: Structure Identification Using High Resolution Mass Spectrometry Data and the EPA’s Chemistry Dashboard

The iCSS Chemistry Dashboard is a publicly accessible dashboard provided by the National Center for Computation Toxicology at the US-EPA. It serves a number of purposes, including providing a chemistry database underpinning many of our public-facing projects (e.g. ToxCast and ExpoCast). The available data and searches provide a valuable path to structure identification using mass spectrometry as the source data. With an underlying database of over 720,000 chemicals, the dashboard has already been used to assist in identifying chemicals present in house dust. However, it can also be applied to many other purposes, e.g., the identification of agrochemicals in waste streams. This presentation will provide a review of the EPA’s platform and underlying algorithms used for the purpose of compound identification using high-resolution mass spectrometry data. We will also discuss progress towards a high-throughput non-targeted analysis platform for use by the mass spectrometry community.  This abstract does not reflect U.S. EPA policy.

 

DAY & TIME OF PRESENTATION: Sunday, August, 21, 2016 from 4:10 PM – 4:30 PM
ROOM & LOCATION: Room 112B – Pennsylvania Convention Center

Title: Investigating Impact Metrics for Performance for the US-EPA National Center for Computational Toxicology

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. We have delivered public access to terabytes of open data, as well to a large number of publicly accessible databases and applications, to support the research efforts for a large community of scientists. Many of our contributions to science are summarily described in research papers but  to date we have not optimized our contributions to  inform altmetrics statistics associated with our work. Critically missing from altmetrics is access to our numerous software applications and web service accesses, as well as the growing importance of our experimental data and models (e.g ToxCast, ExpoCast, DSSTox and others) to the scientific and regulatory communities.  This presentation will provide an overview of our efforts to more fully understand, and quantify, our impact on the environmental sciences using a combination of our measurement approaches and available altmetrics tools. This abstract does not reflect U.S. EPA policy.

DAY & TIME OF PRESENTATION: Wednesday, August, 24, 2016 from 9:40 AM – 10:00 AM
ROOM & LOCATION:
Juniper’s Ballroom – Philadelphia Downtown Courtyard by Marriott

Title: Delivering The Benefits of Chemical-Biological Integration in Computational Toxicology at the EPA

Abstract: Researchers at the EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The intention of this research program is to quickly evaluate thousands of chemicals for potential risk but with much reduced cost relative to historical approaches. This work involves computational and data driven approaches including high-throughput screening, modeling, text-mining and the integration of chemistry, exposure and biological data. We have developed a number of databases and applications that are delivering on the vision of developing a deeper understanding of chemicals and their effects on exposure and biological processes that are supporting a large community of scientists in their research efforts. This presentation will provide an overview of our work to bring together diverse large scale data from the chemical and biological domains, our approaches to integrate and disseminate these data, and the delivery of models supporting computational toxicology. This abstract does not reflect U.S. EPA policy.

 

DAY & TIME OF PRESENTATION: Wednesday, August, 24, 2016 from 11:10 AM – 11:40 AM
ROOM & LOCATION: Ormandy East – DoubleTree by Hilton Hotel Philadelphia Center City

Title: Data Aggregation, Curation and Modeling Approaches to Deliver Prediction Models to Support Computational Toxicology at the EPA

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program develops and utilizes QSAR modeling approaches across a broad range of applications. In terms of physical chemistry we have a particular interest in the prediction of basic physicochemical parameters such as logP, aqueous solubility, vapor pressure and other parameters to invoke in our exposure models or for the purpose of modeling environmental toxicity. We are also interested in the development of models related to environmental fate. As a result of our efforts we have assembled and curated data sets for various physicochemical properties and, utilizing modern machine-learning modeling approaches, have developed a number of high performing models that we are now delivering to the public. Our website, the iCSS Chemistry Dashboard, provides access to data predicted for over 700,000 chemical compounds. The original training data are available for review and the details of prediction for each endpoint include the domain of applicability as well as a measure of performance accuracy.  This presentation will provide an overview of the existing aggregated data, our approaches to data curation and our progress towards an interactive environment for prediction of physicochemical and environmental fate parameters. The utilization of these parameters to support read-across approaches will also be discussed. This abstract does not reflect U.S. EPA policy.

 

DAY & TIME OF PRESENTATION: Thursday, August, 25, 2016 from 3:00 PM – 3:20 PM
ROOM & LOCATION:: Room 104A – Pennsylvania Convention Center

Title: The EPA iCSS Chemistry Dashboard to Support Compound Identification Using High Resolution Mass Spectrometry Data

There is a growing need for rapid chemical screening and prioritization to inform regulatory decision-making on thousands of chemicals in the environment. We have previously used high-resolution mass spectrometry to examine household vacuum dust samples using liquid chromatography time-of-flight mass spectrometry (LC-TOF/MS). Using a combination of exact mass, isotope distribution, and isotope spacing, molecular features were matched with a list of chemical formulas from the EPA’s Distributed Structure-Searchable Toxicity (DSSTox) database. This has further developed our understanding of how openly available chemical databases, together with the appropriate searches, could be used for the purpose of compound identification. We report here on the utility of the EPA’s iCSS Chemistry Dashboard for the purpose of compound identification using searches against a database of over 720,000 chemicals. We also examine the benefits of QSAR prediction for the purpose of retention time prediction to allow for alignment of both chromatographic and mass spectral properties. This abstract does not reflect U.S. EPA policy.

 

SESSION: Sci-Mix
SESSION TIME:
August 22, 2016 from 8:00 PM to 10:00 PM

and

SESSION TIME: Wednesday, August, 24, 2016, 6:00 PM – 8:00 PM
ROOM & LOCATION:
Hall D – Pennsylvania Convention Center

Poster Title: The EPA Online Prediction Physicochemical Prediction Platform to Support Environmental Scientists

As part of our efforts to develop a public platform to provide access to predictive models we have attempted to disentangle the influence of the quality versus quantity of data available to develop and validate QSAR models.  Using a thorough manual review of the data underlying the well-known EPI Suite software, we developed automated processes for the validation of the data using a KNIME workflow. This includes: approaches to validate different chemical structure representations (e.g. molfile and SMILES), identifiers (chemical names and registry numbers), and methods to standardize the data into QSAR-consumable formats for modeling. Our efforts to quantify and segregate data into various quality categories has allowed us to thoroughly investigate the resulting models developed from these data slices, as well as allowing us to examine whether or not efforts into the development of large high-quality datasets has the expected pay-off in terms of prediction performance. Machine-learning approaches have been applied to create a series of models that have been used to generate predicted physicochemical and environmental parameters for over 700,000 chemicals. These data are available online via the EPA’s iCSS Chemistry Dashboard. This abstract does not reflect U.S. EPA policy.

 

 

The needs for chemistry standards, database tools and data curation at the chemical-biology interface

This presentation was given at the Society of Laboratory Automation and Screening in San Diego, California on January 25th 2016.

The needs for chemistry standards, database tools and data curation at the chemical-biology interface

This presentation will highlight known challenges with the production of high quality chemical databases and outline recent efforts made to address these challenges.  Specific examples will be provided illustrating these challenges within the U.S. Environmental Protection Agency (EPA) Computational Toxicology Program. This includes consolidating EPA’s ACToR and DSSTox databases, augmenting computed properties and list search features, and introducing quality metrics to assess confidence in chemical structure assignments across hundreds of thousands of chemical substance records.  The past decade has seen enormous investments in the generation and release of data from studies of chemicals and their toxicological effects.  There is, however, commonly little concern given to provenance and, more generally, to the quality of the data.  The presentation will emphasize the importance of rigorous data review procedures, progress in web-based public access to accurate chemical data sets for use in predictive modeling, and the benefits that these efforts will deliver to toxicologists to embrace the “Big Data” era.

This abstract does not necessarily represent the views of the U.S. Environmental Protection Agency

The presentation is available from the EPA’s Science Inventory site as a PDF file here.

 
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Posted by on January 28, 2016 in EPA Presentations

 

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