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Category Archives: Division of Chemical Information

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.

 

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!

 

 

PRESENTATION: Building an Online Profile Using Social Networking and Amplification Tools for Scientists

This presentation was given as a 2 hour hands-on training course at the Frontier Building in the Research Triangle Park in NC funded by an Industry Award Grant from the ACS and matching financial support from the Research Triangle Institute.

Abstract “Many of us nowadays invest significant amounts of time in sharing our activities and opinions with friends and family via social networking tools such as Facebook, Twitter or other related websites. However, despite the availability of many platforms for scientists to connect and share with their peers in the scientific community the majority do not make use of these tools, despite their promise and potential impact and influence on our careers. We are already being indexed and exposed on the internet via our publications, presentations and data and new “AltMetric scores” are being assigned to scientific publications as measures of popularity and, supposedly, of impact. We now have even more ways to contribute to science, to annotate and curate data, to “publish” in new ways, and many of these activities are as part of a growing crowdsourcing network. This presentation provides an overview of the various types of networking and collaborative sites available to scientists and ways to expose your scientific activities online. It will discuss the new world of AltMetrics that is in an explosive growth curve and will help you understand how to influence and leverage some of these new measures. Participating online, whether it be simply for career advancement or for wider exposure of your research, there are now a series of web applications that can provide a great opportunity to develop a scientific profile within the community.”

 

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

Presentation given at ACS Meeting in Philadelphia in August 2016

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.

THis work is relevant to the article: “Linking high resolution mass spectrometry data with exposure and toxicity forecasts to advance high-throughput environmental monitoring” DOI: http://dx.doi.org/10.1016/j.envint.2015.12.008
 

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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Our dire need to mandate data standards and expectations for scientific publishing

This is a presentation that I delivered at the ACS Division of Chemical Information meeting regarding “Reproducibility, Reporting, Sharing & Plagiarism” at ACS Denver on 23rd March 2015.

I took the opportunity to remove my hat that has me be the VP of Strategic Development at RSC, and a member of the cheminformatics group that built ChemSpider and works on other RSC projects related to it. Instead I presented on how a LACK OF MANDATES from publishers on me in terms of submission of data accompanying articles I am involved with writing is actually weakening my scientific record as data is not getting shared in the most useful forms possible to the benefit of the community. I think there would be benefits for publishers to start pushing me for MORE data, in fairly general standards, and allowing me (and others) to download the data in the form of molecules (and collections), spectral data, CSV files etc.

 

 

Using an online database of chemical compounds for the purpose of structure identification #ACSsanfran

Using an online database of chemical compounds for the purpose of structure identification

Online databases can be used for the purposes of structure identification. The Royal Society of Chemistry provides access to an online database containing tens of millions of compounds and this has been shown to be a very effective platform for the development of tools for structure identification. Since in many cases an unknown to an investigator is known in the chemical literature or reference database, these “known unknowns” are commonly available now on aggregated internet resources. The identification of these types of compounds in commercial, environmental, forensic, and natural product samples can be identified by searching against these large aggregated databases querying by either elemental composition or monoisotopic mass. Searching by elemental composition is the preferred approach as it is often difficult to determine a unique elemental composition for compounds with molecular weights greater than 600 Da. In these cases, searching by the monoisotopic mass is advantageous. In either case, the search results can be refined by appropriate filtering to identify the compounds. We will report on integrated filtering and search approaches on our aggregated compound database for the purpose of structure identification and review our progress in using the platform for natural product dereplication purposes.

 

Open innovation and chemistry data management contributions from the Royal Society of Chemistry resulting from the Open PHACTS project at #ACSsanfran

This is my presentation on Thursday 14th August at the ACS Meeting in San Francisco

Open innovation and chemistry data management contributions from the Royal Society of Chemistry resulting from the Open PHACTS project

The Royal Society of Chemistry was pleased to contribute to the Open PHACTS project, a 3 year project funded by the Innovative Medicines Initiative fund from the European Union. For three years we developed our existing platforms, created new and innovative widgets and data platforms to handle chemistry data, extended existing chemistry ontologies and embraced the semantic web open standards. As a result RSC served as the centralized chemistry data hub for the project. With the conclusion of the Open PHACTS project we will report on our experiences resulting from our participation in the project and provide an overview of what tools, capabilities and data have been released into the community as a result of our participation and how this may influence future projects. This will include the Open PHACTS open chemistry data dump including the chemistry related data in chemistry and semantic web consumable formats as well as some of the resulting chemistry software released to the community. The Open PHACTS project resulted in significant contributions to the chemistry community as well as the supporting pharmaceutical companies and biomedical community.

 

Accessing 3D Printable Chemical Structures Online at #ACSsanfran

This presentation was given by Vincent Scalfani and covers the work we have done to provide access to 3D printable chemical structures online…

Accessing 3D Printable Chemical Structures Online

We have been exploring routes to create 3D printable chemical structure files (.WRL and .STL). These digital 3D files can be generated directly from crystallographic information files (.CIF) using a variety of software packages such as Jmol. After proper conversion to the .STL (or .WRL) file format, the chemical structures can be fabricated into tangible plastic models using 3D printers. This technique can theoretically be used for any molecular or solid structure. Researchers and educators are no longer limited to building models via traditional piecewise plastic model kits. As such, 3D printed molecular models have tremendous value for teaching and research. As the number of available 3D printable structures continues to grow, there is a need for a robust chemical database to store these files. This presentation will discuss our efforts to incorporate 3D printable chemical structures within the Royal Society of Chemistry’s online compound database.

 

 

Dealing with the Complex Challenge of Managing Diverse Chemistry Data Online to Enable Chemistry Across the World #ACSsanfran

This is my third presentation today at the ACS meeting in San Francisco on 11th August 2014

Dealing with the Complex Challenge of Managing Diverse Chemistry Data Online to Enable Chemistry Across the World

The Royal Society of Chemistry has provided access to data associated with millions of chemical compounds via our ChemSpider database for over 5 years. During this period the richness and complexity of the data has continued to expand dramatically and the original vision for providing an integrated hub for structure-centric data has been delivered across the world to hundreds of thousands of users. With an intention of expanding the reach to cover more diverse aspects of chemistry-related data including compounds, reactions and analytical data, to name just a few data-types, we are in the process of implementing a new architecture to build a Chemistry Data Repository. The data repository will manage the challenges of associated metadata, the various levels of required security (private, shared and public) and exposing the data as appropriate using semantic web technologies. Ultimately this platform will become the host for all chemicals, reactions and analytical data contained within RSC publications and specifically supplementary information. This presentation will report on how our efforts to manage chemistry related data has impacted chemists and projects across the world and will review specifically our contributions to projects involving natural products for collaborators in Brazil and China, for the Open Source Drug Discovery project in India, and our collaborations with scientists in Russia.

 

 
 
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