ChemSpider reactions – delivering a free community resource of chemical syntheses
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Presentation delivered by Colin Batchelor from the RSC eScience team at ACS New Orleans Spring Meeting April 2013. There are dozens of public compound databases now available online, some of these providing access to tens of millions of chemical compounds. However, very little effort has been put into the delivery of databases of chemical reactions with the majority of large resources being commercial in nature. In our five years of delivering chemical based data resources to the chemistry community one of the primary requests has been that chemists want to know how to synthesize many of the chemicals they are researching. This presentation will provide an overview of our concerted efforts to enhance access to freely available chemistry data and will discuss the ChemSpider Reactions as an integrating hub of content including data extracted from US patents, from RSC Journals and databases and from our micro-publishing platform ChemSpider Synthetic Pages (CSSP).
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Presentation delivered by Colin Batchelor from the RSC eScience team at ACS New Orleans Spring Meeting April 2013.
There are dozens of public compound databases now available online, some of these providing access to tens of millions of chemical compounds. However, very little effort has been put into the delivery of databases of chemical reactions with the majority of large resources being commercial in nature. In our five years of delivering chemical based data resources to the chemistry community one of the primary requests has been that chemists want to know how to synthesize many of the chemicals they are researching. This presentation will provide an overview of our concerted efforts to enhance access to freely available chemistry data and will discuss the ChemSpider Reactions as an integrating hub of content including data extracted from US patents, from RSC Journals and databases and from our micro-publishing platform ChemSpider Synthetic Pages (CSSP).ChemSpider reactions – delivering a free community resource of chemical synth...
ChemSpider reactions – delivering a free community resource of chemical synth...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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.Delivering The Benefits of Chemical-Biological Integration in Computational T...
Delivering The Benefits of Chemical-Biological Integration in Computational T...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Chemicals Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Chemicals Dashboard and its value to the community as an informational hub. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.EPA CompTox chemicals dashboard: An online resource for environmental chemists
EPA CompTox chemicals dashboard: An online resource for environmental chemists US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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.CompTox Chemicals Dashboard: Data and tools to support chemical and environme...
CompTox Chemicals Dashboard: Data and tools to support chemical and environme...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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 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
The internet has changed the way we access chemistry data as well as providing access to data that can quickly proliferate and becomes referenceable. Web access to chemical structures and their integration with biological data has become massively enabling with numbers for UniChem, PubChem and ChemSpider reaching 157, 97 and 71 million respectively (at the time of writing). A range of specialist databases small enough to be curated have stand-alone utility and synergies when integrated into the larger collections. These include DrugBank, BindingDB, ChEBI, and many others. Databases of any size have inherent quality challenges but at large scale various forms of “noise” accumulate to problematic levels. The unfortunate consequence is that “bigger gets worse”. This is particularly associated with large uncurated submissions from vendors and automated document extractions (even though these are high-value). Virtual enumerations and circularity between overlapping sources add to the problem. As a result of some of the noise in the larger databases the value becomes highly dependent on the specific applications. An example includes using the databases to support non-targeted analysis. This presentation covers examples of these noise and quality issues and suggests at least some options to ameliorate the problem. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency. Does bigger mean better in the world of chemistry databases?
Does bigger mean better in the world of chemistry databases? US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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.Structure Identification Using High Resolution Mass Spectrometry Data and the...
Structure Identification Using High Resolution Mass Spectrometry Data and the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Access to both experimental and predicted environmental fate and transport data is facilitated by the US-EPA CompTox Chemicals Dashboard. Providing access to various types of data associated with ~900,000 chemical substances, the dashboard is a web-based application supporting computational toxicology research in environmental chemistry. When experimental physicochemical and fate and transport data are not available, QSAR models developed using curated datasets are used for the prediction of properties. These include: bioaccumulation factors, bioconcentration factors, and biodegradation and fish biotransformation half-lives. For chemicals of interest that are not already registered in the dashboard real-time predictions based on structural inputs are available. This presentation will provide an overview of the dashboard with a focus on the availability of environmental fate and transport data, access to real time predictions, and our ongoing efforts to harvest and curate available experimental data from the literature and online databases. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.US-EPA CompTox Chemicals Dashboard providing access to experimental and predi...
US-EPA CompTox Chemicals Dashboard providing access to experimental and predi...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Recommended
Presentation delivered by Colin Batchelor from the RSC eScience team at ACS New Orleans Spring Meeting April 2013.
There are dozens of public compound databases now available online, some of these providing access to tens of millions of chemical compounds. However, very little effort has been put into the delivery of databases of chemical reactions with the majority of large resources being commercial in nature. In our five years of delivering chemical based data resources to the chemistry community one of the primary requests has been that chemists want to know how to synthesize many of the chemicals they are researching. This presentation will provide an overview of our concerted efforts to enhance access to freely available chemistry data and will discuss the ChemSpider Reactions as an integrating hub of content including data extracted from US patents, from RSC Journals and databases and from our micro-publishing platform ChemSpider Synthetic Pages (CSSP).ChemSpider reactions – delivering a free community resource of chemical synth...
ChemSpider reactions – delivering a free community resource of chemical synth...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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.Delivering The Benefits of Chemical-Biological Integration in Computational T...
Delivering The Benefits of Chemical-Biological Integration in Computational T...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Chemicals Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Chemicals Dashboard and its value to the community as an informational hub. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.EPA CompTox chemicals dashboard: An online resource for environmental chemists
EPA CompTox chemicals dashboard: An online resource for environmental chemists US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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.CompTox Chemicals Dashboard: Data and tools to support chemical and environme...
CompTox Chemicals Dashboard: Data and tools to support chemical and environme...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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 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
The internet has changed the way we access chemistry data as well as providing access to data that can quickly proliferate and becomes referenceable. Web access to chemical structures and their integration with biological data has become massively enabling with numbers for UniChem, PubChem and ChemSpider reaching 157, 97 and 71 million respectively (at the time of writing). A range of specialist databases small enough to be curated have stand-alone utility and synergies when integrated into the larger collections. These include DrugBank, BindingDB, ChEBI, and many others. Databases of any size have inherent quality challenges but at large scale various forms of “noise” accumulate to problematic levels. The unfortunate consequence is that “bigger gets worse”. This is particularly associated with large uncurated submissions from vendors and automated document extractions (even though these are high-value). Virtual enumerations and circularity between overlapping sources add to the problem. As a result of some of the noise in the larger databases the value becomes highly dependent on the specific applications. An example includes using the databases to support non-targeted analysis. This presentation covers examples of these noise and quality issues and suggests at least some options to ameliorate the problem. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency. Does bigger mean better in the world of chemistry databases?
Does bigger mean better in the world of chemistry databases? US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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.Structure Identification Using High Resolution Mass Spectrometry Data and the...
Structure Identification Using High Resolution Mass Spectrometry Data and the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Access to both experimental and predicted environmental fate and transport data is facilitated by the US-EPA CompTox Chemicals Dashboard. Providing access to various types of data associated with ~900,000 chemical substances, the dashboard is a web-based application supporting computational toxicology research in environmental chemistry. When experimental physicochemical and fate and transport data are not available, QSAR models developed using curated datasets are used for the prediction of properties. These include: bioaccumulation factors, bioconcentration factors, and biodegradation and fish biotransformation half-lives. For chemicals of interest that are not already registered in the dashboard real-time predictions based on structural inputs are available. This presentation will provide an overview of the dashboard with a focus on the availability of environmental fate and transport data, access to real time predictions, and our ongoing efforts to harvest and curate available experimental data from the literature and online databases. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.US-EPA CompTox Chemicals Dashboard providing access to experimental and predi...
US-EPA CompTox Chemicals Dashboard providing access to experimental and predi...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
In the domain of chemistry one of the greatest benefits to publishing research is that data can be shared. Unfortunately, the vast majority of chemical structure data associated with scientific publications remain locked up in document form, primarily in PDF files or trapped on webpages. Despite the explosive growth of online chemical databases and the overall maturity of cheminformatics platforms, many barriers stifle the exchange of chemical structures via publications. These challenges include incomplete support by accepted standards (especially InChI) for advanced stereochemistry, organometallic compounds and generic “Markush” representations, the difference between human-readable and computer-readable forms of data, and challenges with the computer representation of chemical structures. To address these obstacles to chemical structure sharing, US EPA National Center for Computational Toxicology scientists are using a combination of cheminformatics applications and online repositories to distribute chemical structure data associated with their publications. This presentation will describe how EPA-NCCT chemical structure data that is amenable to indexing and distribution are shared and highlight the benefit of open data sharing for modeling, data integration, and increasing research impact. This abstract does not reflect U.S. EPA policy.Sharing chemical structures with peer reviewed publications
Sharing chemical structures with peer reviewed publications US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Researchers at EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The goal of this research program is to quickly evaluate thousands of chemicals, but at a much reduced cost and shorter time frame relative to traditional approaches. The data generated by the Center includes characterization of thousands of chemicals across hundreds of high-throughput screening assays, consumer use and production information, pharmacokinetic properties, literature data, physical-chemical properties as well as the predictive computational modeling of toxicity and exposure. We have developed a number of databases and applications to deliver the data to the public, academic community, industry stakeholders, and regulators. This presentation will provide an overview of our work to develop an architecture that integrates diverse large-scale data from the chemical and biological domains, our approaches to disseminate these data, and the delivery of models supporting predictive computational toxicology. In particular, this presentation will review our new publicly-accessible CompTox Dashboard as the first application built on our newly developed architecture. This abstract does not reflect U.S. EPA policy. Delivering The Benefits of Chemical-Biological Integration in Computational T...
Delivering The Benefits of Chemical-Biological Integration in Computational T...US 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 2000 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 latest release 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.US-EPA CompTox Chemicals Dashboard – integrating chemistry and biology data t...
US-EPA CompTox Chemicals Dashboard – integrating chemistry and biology data t...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted analysis (NTA) uses high-resolution mass spectrometry to better understand the identity of a wide variety of chemicals present in environmental samples (and other matrices). However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. Analysis of the resultant mass spectrometry information relies on cheminformatics to identify and rank chemicals and the US EPA has developed functionality within the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) to address challenges related to this analysis. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will review how the CompTox Chemicals Dashboard via its flexible search capabilities, rich data for ~900,000 chemical substances, and visualization approaches within this open chemistry resource provides a freely available software tool to support structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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.The EPA iCSS Chemistry Dashboard to Support Compound Identification Using Hig...
The EPA iCSS Chemistry Dashboard to Support Compound Identification Using Hig...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation highlights known challenges with the production of high quality chemical databases and outline recent efforts made to address these challenges. Specific examples will be provided illustrating these challenges within the U.S. Environmental Protection Agency (EPA) Computational Toxicology Program. This includes consolidating EPA’s ACToR and DSSTox databases, augmenting computed properties and list search features, and introducing quality metrics to assess confidence in chemical structure assignments across hundreds of thousands of chemical substance records. The past decade has seen enormous investments in the generation and release of data from studies of chemicals and their toxicological effects. There is, however, commonly little concern given to provenance and, more generally, to the quality of the data. The presentation will emphasize the importance of rigorous data review procedures, progress in web-based public access to accurate chemical data sets for use in predictive modeling, and the benefits that these efforts will deliver to toxicologists to embrace the “Big Data” era.
This abstract does not necessarily represent the views of the U.S. Environmental Protection Agency.
The needs for chemistry standards, database tools and data curation at the ch...
The needs for chemistry standards, database tools and data curation at the ch...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Researchers at EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The goal of this research program is to quickly evaluate thousands of chemicals, but at a much reduced cost and shorter time frame relative to traditional approaches. The data generated by the Center includes characterization of thousands of chemicals across hundreds of high-throughput screening assays, consumer use and production information, pharmacokinetic properties, literature data, physical-chemical properties as well as the predictive computational modeling of toxicity and exposure. We have developed a number of databases and applications to deliver the data to the public, academic community, industry stakeholders, and regulators. This presentation will provide an overview of our work to develop an architecture that integrates diverse large-scale data from the chemical and biological domains, our approaches to disseminate these data, and the delivery of models supporting predictive computational toxicology. In particular, this presentation will review our new CompTox Chemistry Dashboard and the developing architecture to support real-time property and toxicity endpoint prediction. This abstract does not reflect U.S. EPA policy.New developments in delivering public access to data from the National Center...
New developments in delivering public access to data from the National Center...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Cheminformatics methods form an essential basis for providing analytical scientists with access to data, algorithms and workflows. There are an increasing number of free online databases (compound databases, spectral libraries, data repositories) and a rich collection of software approaches that can be used to support automated structure verification and elucidation, specifically for Nuclear Magnetic Resonance (NMR) and Mass Spectrometry (MS). This presentation will provide an overview of freely available data, tools, databases and approaches available to support chemical structure verification and elucidation and highlight some of the known issues regarding data quality and suggest approaches for resolving some of the issues. The importance of structure and spectral standards for data exchange will be discussed, especially with regard to how spectral data can be made openly available to the community via online tools and through scientific publishing. This work does not necessarily reflect U.S. EPA policy.Overview of open resources to support automated structure verification and e...
Overview of open resources to support automated structure verification and e...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
At RSC we are involved with a number of projects utilizing components of Advanced Chemistry Development software including nomenclature, physchem prediction and spectroscopy integration. This presentation was given at a small ACD/Labs user meeting in Loughborough, England in February 2013. An associated movie is available on YouTube here: http://youtu.be/2kAsyRU7lRgHow ACDLabs Software Tools are used by the Royal Society of Chemistry
How ACDLabs Software Tools are used by the Royal Society of ChemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The construction of QSAR models is critically dependent on the quality of available data. As part of our efforts to develop public platforms to provide access to predictive models, we have attempted to discriminate the influence of the quality versus quantity of data available to develop and validate QSAR models. We have focused our efforts on the widely used EPISuite software that was initially developed over two decades ago. Specific examples of quality issues for the EPISuite data include multiple records for the same chemical structure with different measured property values, inconsistency between the structure, chemical name and CAS registry number for single records, the inability to convert the SMILES strings into chemical structures, hypervalency in the chemical structures and the absence of stereochemistry for thousands of data records. Relative to the era of EPISuite development, modern cheminformatics tools allow for more advanced capabilities in terms of chemical structure representation and storage, as well as enabling automated data validation and standardization approaches to examine data quality. This presentation will review both our manual and automated approaches to examining key datasets related to the EPISuite training and test data. This includes approaches to validate between chemical structure representations (e.g. molfile and SMILES) and identifiers (chemical names and registry numbers), as well as approaches to standardize the data into QSAR-consumable formats for modeling. We have quantified and segregated the data into various quality categories to allow us to thoroughly investigate the resulting models that can be developed from these data slices and to examine to what extent efforts into the development of large high-quality datasets have the expected pay-off in terms of prediction performance. This abstract does not reflect U.S. EPA policy. The influence of data curation on QSAR Modeling – examining issues of qualit...
The influence of data curation on QSAR Modeling – examining issues of qualit...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry (RSC) is a major participant in providing access to chemistry related data via the web. As an internationally renowned society for the chemical sciences, a scientific publisher and the host of the ChemSpider database for the community, RSC continues to make dramatic strides in providing online access to data. ChemSpider provides access to over 30 million chemicals sourced from over 500 data suppliers and linked out to related information on the web. The platform is a crowdsourcing environment whereby members of the community can participate in validating and expanding the content of the database. With a set of application programming interfaces ChemSpider is used by various organizations and projects to serve up data for various purposes. These include structure identification for mass spectrometry instrument vendors, RSC databases such as the Marinlit natural products database and a European grant-based project from the Innovative Medicines Initiative fund. This presentation will provide an overview of various cheminformatics activities and projects that RSC is involved with to serve the medicinal chemistry community. This will include the Open PHACTS semantic web project, the PharmaSea project to identify new pharmaceutical leads from the ocean and the UK National Compound Collection to identify new lead compounds contained within PhD theses.Serving the medicinal chemistry community with Royal Society of Chemistry che...
Serving the medicinal chemistry community with Royal Society of Chemistry che...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Over the past five years the Royal Society of Chemistry has become world renowned for its public domain compound database that integrates chemical structures with online resources and available data. ChemSpider regularly serves over 50,000 users per day who are seeking chemistry related data. In parallel we have used ChemSpider and available software services to underpin a number of grant-based projects that we have been involved with: Open PHACTS – a semantic web project integrating chemistry and biology data, PharmaSea – seeking out new natural products from the ocean and the National Chemical Database Service for the United Kingdom. We are presently developing a new architecture that will offer broader scope in terms of the types of chemistry data that can be hosted. This presentation will provide an overview of our Cheminformatics activities at RSC, the development of a new architecture for a data repository that will underpin a global chemistry network, and the challenges ahead, as well as our activities in releasing software and data to the chemistry community. A chemistry data repository to serve them all
A chemistry data repository to serve them allUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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In the domain of chemistry one of the greatest benefits to publishing research is that data can be shared. Unfortunately, the vast majority of chemical structure data associated with scientific publications remain locked up in document form, primarily in PDF files or trapped on webpages. Despite the explosive growth of online chemical databases and the overall maturity of cheminformatics platforms, many barriers stifle the exchange of chemical structures via publications. These challenges include incomplete support by accepted standards (especially InChI) for advanced stereochemistry, organometallic compounds and generic “Markush” representations, the difference between human-readable and computer-readable forms of data, and challenges with the computer representation of chemical structures. To address these obstacles to chemical structure sharing, US EPA National Center for Computational Toxicology scientists are using a combination of cheminformatics applications and online repositories to distribute chemical structure data associated with their publications. This presentation will describe how EPA-NCCT chemical structure data that is amenable to indexing and distribution are shared and highlight the benefit of open data sharing for modeling, data integration, and increasing research impact. This abstract does not reflect U.S. EPA policy.Sharing chemical structures with peer reviewed publications
Sharing chemical structures with peer reviewed publications US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Researchers at EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The goal of this research program is to quickly evaluate thousands of chemicals, but at a much reduced cost and shorter time frame relative to traditional approaches. The data generated by the Center includes characterization of thousands of chemicals across hundreds of high-throughput screening assays, consumer use and production information, pharmacokinetic properties, literature data, physical-chemical properties as well as the predictive computational modeling of toxicity and exposure. We have developed a number of databases and applications to deliver the data to the public, academic community, industry stakeholders, and regulators. This presentation will provide an overview of our work to develop an architecture that integrates diverse large-scale data from the chemical and biological domains, our approaches to disseminate these data, and the delivery of models supporting predictive computational toxicology. In particular, this presentation will review our new publicly-accessible CompTox Dashboard as the first application built on our newly developed architecture. This abstract does not reflect U.S. EPA policy. Delivering The Benefits of Chemical-Biological Integration in Computational T...
Delivering The Benefits of Chemical-Biological Integration in Computational T...US 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 2000 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 latest release 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.US-EPA CompTox Chemicals Dashboard – integrating chemistry and biology data t...
US-EPA CompTox Chemicals Dashboard – integrating chemistry and biology data t...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted analysis (NTA) uses high-resolution mass spectrometry to better understand the identity of a wide variety of chemicals present in environmental samples (and other matrices). However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. Analysis of the resultant mass spectrometry information relies on cheminformatics to identify and rank chemicals and the US EPA has developed functionality within the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) to address challenges related to this analysis. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will review how the CompTox Chemicals Dashboard via its flexible search capabilities, rich data for ~900,000 chemical substances, and visualization approaches within this open chemistry resource provides a freely available software tool to support structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Non-targeted analysis supported by data and cheminformatics delivered via the...
Non-targeted analysis supported by data and cheminformatics delivered via the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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.The EPA iCSS Chemistry Dashboard to Support Compound Identification Using Hig...
The EPA iCSS Chemistry Dashboard to Support Compound Identification Using Hig...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation highlights known challenges with the production of high quality chemical databases and outline recent efforts made to address these challenges. Specific examples will be provided illustrating these challenges within the U.S. Environmental Protection Agency (EPA) Computational Toxicology Program. This includes consolidating EPA’s ACToR and DSSTox databases, augmenting computed properties and list search features, and introducing quality metrics to assess confidence in chemical structure assignments across hundreds of thousands of chemical substance records. The past decade has seen enormous investments in the generation and release of data from studies of chemicals and their toxicological effects. There is, however, commonly little concern given to provenance and, more generally, to the quality of the data. The presentation will emphasize the importance of rigorous data review procedures, progress in web-based public access to accurate chemical data sets for use in predictive modeling, and the benefits that these efforts will deliver to toxicologists to embrace the “Big Data” era.
This abstract does not necessarily represent the views of the U.S. Environmental Protection Agency.
The needs for chemistry standards, database tools and data curation at the ch...
The needs for chemistry standards, database tools and data curation at the ch...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Researchers at EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The goal of this research program is to quickly evaluate thousands of chemicals, but at a much reduced cost and shorter time frame relative to traditional approaches. The data generated by the Center includes characterization of thousands of chemicals across hundreds of high-throughput screening assays, consumer use and production information, pharmacokinetic properties, literature data, physical-chemical properties as well as the predictive computational modeling of toxicity and exposure. We have developed a number of databases and applications to deliver the data to the public, academic community, industry stakeholders, and regulators. This presentation will provide an overview of our work to develop an architecture that integrates diverse large-scale data from the chemical and biological domains, our approaches to disseminate these data, and the delivery of models supporting predictive computational toxicology. In particular, this presentation will review our new CompTox Chemistry Dashboard and the developing architecture to support real-time property and toxicity endpoint prediction. This abstract does not reflect U.S. EPA policy.New developments in delivering public access to data from the National Center...
New developments in delivering public access to data from the National Center...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Cheminformatics methods form an essential basis for providing analytical scientists with access to data, algorithms and workflows. There are an increasing number of free online databases (compound databases, spectral libraries, data repositories) and a rich collection of software approaches that can be used to support automated structure verification and elucidation, specifically for Nuclear Magnetic Resonance (NMR) and Mass Spectrometry (MS). This presentation will provide an overview of freely available data, tools, databases and approaches available to support chemical structure verification and elucidation and highlight some of the known issues regarding data quality and suggest approaches for resolving some of the issues. The importance of structure and spectral standards for data exchange will be discussed, especially with regard to how spectral data can be made openly available to the community via online tools and through scientific publishing. This work does not necessarily reflect U.S. EPA policy.Overview of open resources to support automated structure verification and e...
Overview of open resources to support automated structure verification and e...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
At RSC we are involved with a number of projects utilizing components of Advanced Chemistry Development software including nomenclature, physchem prediction and spectroscopy integration. This presentation was given at a small ACD/Labs user meeting in Loughborough, England in February 2013. An associated movie is available on YouTube here: http://youtu.be/2kAsyRU7lRgHow ACDLabs Software Tools are used by the Royal Society of Chemistry
How ACDLabs Software Tools are used by the Royal Society of ChemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The construction of QSAR models is critically dependent on the quality of available data. As part of our efforts to develop public platforms to provide access to predictive models, we have attempted to discriminate the influence of the quality versus quantity of data available to develop and validate QSAR models. We have focused our efforts on the widely used EPISuite software that was initially developed over two decades ago. Specific examples of quality issues for the EPISuite data include multiple records for the same chemical structure with different measured property values, inconsistency between the structure, chemical name and CAS registry number for single records, the inability to convert the SMILES strings into chemical structures, hypervalency in the chemical structures and the absence of stereochemistry for thousands of data records. Relative to the era of EPISuite development, modern cheminformatics tools allow for more advanced capabilities in terms of chemical structure representation and storage, as well as enabling automated data validation and standardization approaches to examine data quality. This presentation will review both our manual and automated approaches to examining key datasets related to the EPISuite training and test data. This includes approaches to validate between chemical structure representations (e.g. molfile and SMILES) and identifiers (chemical names and registry numbers), as well as approaches to standardize the data into QSAR-consumable formats for modeling. We have quantified and segregated the data into various quality categories to allow us to thoroughly investigate the resulting models that can be developed from these data slices and to examine to what extent efforts into the development of large high-quality datasets have the expected pay-off in terms of prediction performance. This abstract does not reflect U.S. EPA policy. The influence of data curation on QSAR Modeling – examining issues of qualit...
The influence of data curation on QSAR Modeling – examining issues of qualit...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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Similar to ChemSpider reactions – delivering a free community resource of chemical syntheses
The Royal Society of Chemistry (RSC) is a major participant in providing access to chemistry related data via the web. As an internationally renowned society for the chemical sciences, a scientific publisher and the host of the ChemSpider database for the community, RSC continues to make dramatic strides in providing online access to data. ChemSpider provides access to over 30 million chemicals sourced from over 500 data suppliers and linked out to related information on the web. The platform is a crowdsourcing environment whereby members of the community can participate in validating and expanding the content of the database. With a set of application programming interfaces ChemSpider is used by various organizations and projects to serve up data for various purposes. These include structure identification for mass spectrometry instrument vendors, RSC databases such as the Marinlit natural products database and a European grant-based project from the Innovative Medicines Initiative fund. This presentation will provide an overview of various cheminformatics activities and projects that RSC is involved with to serve the medicinal chemistry community. This will include the Open PHACTS semantic web project, the PharmaSea project to identify new pharmaceutical leads from the ocean and the UK National Compound Collection to identify new lead compounds contained within PhD theses.Serving the medicinal chemistry community with Royal Society of Chemistry che...
Serving the medicinal chemistry community with Royal Society of Chemistry che...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Over the past five years the Royal Society of Chemistry has become world renowned for its public domain compound database that integrates chemical structures with online resources and available data. ChemSpider regularly serves over 50,000 users per day who are seeking chemistry related data. In parallel we have used ChemSpider and available software services to underpin a number of grant-based projects that we have been involved with: Open PHACTS – a semantic web project integrating chemistry and biology data, PharmaSea – seeking out new natural products from the ocean and the National Chemical Database Service for the United Kingdom. We are presently developing a new architecture that will offer broader scope in terms of the types of chemistry data that can be hosted. This presentation will provide an overview of our Cheminformatics activities at RSC, the development of a new architecture for a data repository that will underpin a global chemistry network, and the challenges ahead, as well as our activities in releasing software and data to the chemistry community. A chemistry data repository to serve them all
A chemistry data repository to serve them allUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The internet has provided access to unprecedented quantities of data. In the domain of chemistry specifically over the past decade the web has become populated with tens of millions of chemical structures and related properties, both experimental and predicted, together with tens of thousands of spectra and syntheses. The data have, to a large extent, remained disparate and disconnected. In recent years with the wave of Web 2.0 participation any chemist can contribute to both the sharing and validation of chemistry-related data whether it be via Wikipedia, the online encyclopedia, or one of the multiple public compound databases. Toxicologists commonly wish to source data, either for reference purposes, to support the development of models or, when experimental data are not available, predicted data will suffice. This presentation will offer a perspective of the type and quality of chemistry data available today, our experiences of building the ChemSpider public compound database to link together chemistry on the internet and our efforts to both encourage and enable even greater integration and connectivity for chemistry data for the community. ChemSpider as an integration hub for interlinked chemistry data
ChemSpider as an integration hub for interlinked chemistry dataUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The phrase “Big Data” is generally used to describe a large volume of structured and/or unstructured data that cannot be processed using traditional database and software techniques. In the domain of chemistry the Royal Society of Chemistry certainly hosts large structured databases of chemistry data, for example ChemSpider, as well as unstructured content, in the form of our collection of scientific articles. Our research literature provides value to their readership and, at present, as an example of one of our databases, ChemSpider is accessed by many tens of thousands of scientists every day. But do these collections constitute “Big Data” or is it the potential which lies within the collections that can contribute to the Big Data movement. This presentation will discuss our activities to contribute both data, and service-based access to our data sets, to support grant-based projects such as the Innovative Medicines Initiative Open PHACTS project (to support drug discovery) and the PharmaSea initiative (to identify novel natural products from the ocean). We will also provide an overview of our activities to perform data mining of public patent collections and examine what can be done with the data. We are presently extracting physicochemical properties and textual forms of NMR spectra and, with the resulting data, are building predictive models (for melting points at present) and assembling a large NMR spectral database containing many hundreds of thousands of spectral-structure pairs. Our experiences to date have demonstrated that we are working at the edge of current algorithmic and computing capabilities for predictive model building, with over a quarter of a million melting points producing a matrix of over 200 billion descriptors. Our work to produce the NMR spectral database will necessitate batch processing of the data to examine consistency between the spectral-structure pairs and other forms of data validation. The intention is to take our experiences in this work applied to a public patents corpus and apply it to the RSC back file of publications to mine data and enable new paths to the discoverability of both data and the associated publications. Activities at the Royal Society of Chemistry to gather, extract and analyze b...
Activities at the Royal Society of Chemistry to gather, extract and analyze b...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Center for Computational Toxicology and Exposure (CCTE) is part of the Office of Research and Development at the US Environmental Protection Agency. As part of its mission the center delivers access to chemicals related data via web-based freely accessible online Dashboards to disseminate data generated within the center as well as harvested and integrated from open databases around the world. The CompTox Chemicals Dashboard (available at https://comptox.epa.gov/dashboard) provides access to >1.2 million chemicals and associated data including experimental and predicted property data, in vivo hazard data, in vitro bioactivity data, exposure data, and various other data types. The curation of the chemicals dataset has included the development of over 400 segregated lists of chemicals that represent specific research areas of interest including disinfectant by-products, per- and polyfluoroalkyl substances (PFAS), extractables and leachables, and chemicals of emerging concern. The chemicals collection, the associated data, the lists and searches for mass and formulae makes the Dashboard an ideal foundation technology to support our colleagues working in the field of mass spectrometry, especially in targeted and non-targeted analysis. This presentation will provide an overview of the Dashboard, its value to the community in terms of providing access to the integrated and highly curated data, and its utility to support researchers in the field of mass spectrometry. New proof-of-concept projects will also be introduced including the development of a cheminformatics enabled methods database. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Accessing Environmental Chemistry Data via Data Dashboards and Applications t...
Accessing Environmental Chemistry Data via Data Dashboards and Applications t...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
At a time when the data explosion has simply been redefined as “Big”, the hurdles associated with building a subject-specific data repository for chemistry are daunting. Combining a multitude of non-standard data formats for chemicals, related properties, reactions, spectra etc., together with the confusion of licensing and embargoing, and providing for data exchange and integration with services and platforms external to the repository, the challenge is significant. This all at a time when semantic technologies are touted as the fundamental technology to enhance integration and discoverability. Funding agencies are demanding change, especially a change towards access to open data to parallel their expectations around Open Access publishing. The Royal Society of Chemistry has been funded by the Engineering and Physical Science Research of the UK to deliver a “chemical database service” for UK scientists. This presentation will provide an overview of the challenges associated with this project and our progress in delivering a chemistry repository capable of handling the complex data types ssociated with chemistry. The benefits of such a repository in terms of providing data to develop prediction models to further enable scientific discovery will be discussed and the potential impact on the future of scientific publishing will also be examined. Big data challenges associated with building a national data repository for c...
Big data challenges associated with building a national data repository for c...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The US-EPA National Center for Computational Toxicity (NCCT) has been generating data and building software applications and web-based chemistry databases for over a decade. During this period the center has analyzed thousands of chemicals in hundreds of bioassays, has researched high-throughput physicochemical property measurements and investigated approaches for high throughput toxicokinetics. NCCT continues to expand the battery of assays and number of chemicals under examination and is now investigating the application of transcriptomics. In parallel to these experimental efforts, and to support our efforts to develop new approaches to prioritize chemicals based on potential human health risks, we aggregate and curate data streams of various types to support prediction models. Over the past few years some of the data have been delivered through prototype web-based “dashboards” for public consumption. The latest of these web applications, the CompTox Chemicals Dashboard, is an integrated access point to obtain information associated with 875,000 chemical substances and providing experimental and predicted data of various types. This includes physicochemical and fate and transport data, bioactivity data, exposure data and integrated literature searches. Real-time predictions and generalized read-across are possible and advanced search capabilities are available to support EPA-related projects including mass spectrometry non-targeted analysis. This presentation will provide an overview of the CompTox Chemicals Dashboard and the its role in delivering access to the outputs of NCCT. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Delivering web-based access to data and algorithms to support computational t...
Delivering web-based access to data and algorithms to support computational t...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Access to scientific information has changed in a manner that was likely never even imagined by the early pioneers of the internet. The quantities of data, the array of tools available to search and analyze, the devices and the shift in community participation continues to expand while the pace of change does not appear to be slowing. ChemSpider is one of the chemistry community’s primary online public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data tens of thousands of chemists every day and it serves as the foundation for many important international projects to integrate chemistry and biology data, facilitate drug discovery efforts and help to identify new chemicals from under the ocean. This presentation will provide an overview of the expanding reach of this eScience cheminformatics platform and the nature of the solutions that it helps to enable including structure validation, text mining and semantic markup, the National Chemical Database Service for the United Kingdom and the development of a chemistry data repository. We will also discuss the possibilities it offers in the domain of crowdsourcing and open data sharing. The future of scientific information and communication will be underpinned by these efforts, influenced by increasing participation from the scientific community and facilitated collaboration and ultimately accelerate scientific progress.eScience at the Royal Society of Chemistry and our current initiatives
eScience at the Royal Society of Chemistry and our current initiativesUS 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.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 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.
Dealing with the complex challenge of managing diverse chemistry data online
Dealing with the complex challenge of managing diverse chemistry data onlineUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Tens of thousands of chemicals are currently in commerce, and hundreds more are introduced every year. Because current chemical testing is resource intensive, only a small fraction of chemicals have been adequately evaluated for potential human health effects. New technologies and computational tools have shown promise for closing this knowledge gap. In the U.S. EPA’s ToxCast effort, the use of ~700 high-throughput in vitro assays has broadly characterized the biological activity and potential mechanisms of ~1,800 chemicals. Coupling the high-throughput in vitro assays with additional in vitro pharmacokinetic assays and in vitro-to-in vivo extrapolation modeling allows conversion of in vitro bioactive concentrations to estimates to an administered dose (mg/kg/day). High throughput exposure models are generating exposure estimates based on key aspects of chemical production, fate, transport, and personal use. The path for incorporating new approach methods and technologies for prioritization and assessment of chemical alternatives poses multiple scientific challenges. These challenges include sufficient coverage of toxicological mechanisms to meaningfully interpret negative test results, development of increasingly relevant test systems, computational modeling to integrate experimental data, characterizing uncertainty, and efficient validation of the test systems and computational models. The presentation will cover progress at the U.S. EPA in the development and application of these technologies and approaches in evaluating alternatives and systematically addressing each of these challenges. This abstract does not necessarily reflect U.S. EPA policy.Incorporating new technologies and High Throughput Screening in the design an...
Incorporating new technologies and High Throughput Screening in the design an...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was made to the University of North Carolina in Chapel Hill on 9/20/21. The presentation was a general introduction to cheminformatics prior to how to navigate the Dashboard.
• An introduction to the dashboard
• Substances vs structures
• Structure formats for data exchange and connectivity (SMILES, InChIs, molfiles)
• Identifiers – CASRN, chemical names, systematic names
• Data curation approaches: substance-structure ambiguity
• ChemReg: substance registration
• Data gathering for systematic reviews
• Curated lists
• Properties/Fate and Transport
• Access to Exposure Data
• Hazard data in the dashboard – ToxVal data (sourced from >40 databases, >50,000 chemicals, >900,000 data points)
• The Executive Summary of data
• Single chemical searches vs Batch searches
Introduction to Cheminformatics: Accessing data through the CompTox Chemicals...
Introduction to Cheminformatics: Accessing data through the CompTox Chemicals...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
At a time when the data explosion has simply been redefined as “Big”, the hurdles associated with building a subject-specific data repository for chemistry are daunting. Combining a multitude of non-standard data formats for chemicals, related properties, reactions, spectra etc., together with the confusion of licensing and embargoing, and providing for data exchange and integration with services and platforms external to the repository, the challenge is significant. This all at a time when semantic technologies are touted as the fundamental technology to enhance integration and discoverability. Funding agencies are demanding change, especially a change towards access to open data to parallel their expectations around Open Access publishing. The Royal Society of Chemistry has been funded by the Engineering and Physical Science Research of the UK to deliver a “chemical database service” for UK scientists. This presentation will provide an overview of the challenges associated with this project and our progress in delivering a chemistry repository capable of handling the complex data types associated with chemistry. The benefits of such a repository in terms of providing data to develop prediction models to further enable scientific discovery will be discussed and the potential impact on the future of scientific publishing will also be examined. The UK National Chemical Database Service – an integration of commercial and ...
The UK National Chemical Database Service – an integration of commercial and ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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Serving the medicinal chemistry community with Royal Society of Chemistry che...
Serving the medicinal chemistry community with Royal Society of Chemistry che...
ChemSpider as an integration hub for interlinked chemistry data
ChemSpider as an integration hub for interlinked chemistry data
ICIC 2013 Conference Proceedings Antony Williams Royal Society of Chemistry
ICIC 2013 Conference Proceedings Antony Williams Royal Society of Chemistry
Activities at the Royal Society of Chemistry to gather, extract and analyze b...
Activities at the Royal Society of Chemistry to gather, extract and analyze b...
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Accessing Environmental Chemistry Data via Data Dashboards and Applications t...
Big data challenges associated with building a national data repository for c...
Big data challenges associated with building a national data repository for c...
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ChemSpider – disseminating data and enabling an abundance of chemistry platforms
Delivering web-based access to data and algorithms to support computational t...
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eScience at the Royal Society of Chemistry and our current initiatives
eScience at the Royal Society of Chemistry and our current initiatives
Chemistry Validation and Standardization Platform v2.0
Chemistry Validation and Standardization Platform v2.0
US-EPA Chemicals Dashboard – an integrated data hub for environmental science
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ChemSpider reactions – delivering a free community resource of chemical syntheses
- 1. ChemSpider Reactions: Delivering a free community resource of chemical syntheses Valery Tkachenko, Colin Batchelor, Daniel Lowe, Ken Karapetyan, David Sharpe and Antony Williams ACS New Orleans April 2013
- 2. Overview • Motivation • The RSC and chemical reaction data • New sources of chemical reaction data • ChemSpider Reactions: bringing it all together • Experiments with reaction classification • The National Chemical Database Service
- 3. Who needs another reaction database? • Those who cannot afford to license access… • Those who would like to access data that is not abstracted • Those who might like to contribute data to a database • Anybody wanting to integrate their systems in and to pull data out.
- 4. RSC and chemical reaction data 1 Graphical abstracting journals: Methods in Organic Synthesis (monthly, 1990 to present) Catalysts and Catalysed Reactions (monthly, 2005 to present) These constitute a backfile of over 50000 novel reactions
- 5. RSC and chemical reaction data 2
- 6. RSC and chemical reaction data 3
- 7. New sources of reaction data Daniel Lowe’s PhD thesis (Cantab, 2012) was on extracting reactions from US patent data. We can apply this technology to the RSC Journal archive.
- 8. ChemSpider Reactions bringing it all together http://csr.dev.rsc-us.org/ WORK IN PROGRESS
- 9. Reaction classification 1 Project Prospect has text-mined RSC journal articles for named reactions and molecular processes, annotated according to Creative Commons-licensed ontologies: See http://rxno.googlecode.com/
- 10. Reaction classification 2 Classification of Daniel’s US Patent data
- 11. Reaction InChI To do for reactions what InChI has done for structures •Think online searching •Deduplication and linking http://www-rinchi.ch.cam.ac.uk/help.html
- 12. Reaction InChI Early work – RInChIs layered on to a few hundred thousand reactions •Not generated for a few 10s of thousands of reactions •Reaction deduplication results differ based on algorithm – GGA software versus RInChI •Under investigation
- 13. Other sources ChemSpider SyntheticPages •Electronic Lab Notebooks •University repositories Please send theses
- 14. What will ChemSpider Reactions serve? • Chemical Database Service • Linking back to original publications/supplementary data • Underpinning other tools e.g. retrosynthetic analysis (depends on data quality and mapping)
- 15. Chemical Database Service National Chemical Database Service for UK academics Integrates commercial databases and services Chemicals, analytical data, prediction algorithms Development of data repository
- 16. ARChem from SimBioSys 1 Synthesis planning tool which performs rule- and precedent-based retrosynthetic analysis back to commercially available starting materials.
- 17. ARChem from SimBiosys 2
- 18. ARChem from SimBioSys 3
- 19. But what about data quality? • Data validation and curation required • Encouraging participation with Rewards and RECOGNITION
- 20. Manual curation • Integrated commenting, curating and validation platform across ALL eScience and Publishing platforms • All integrated to a central RSC profile and feeding the alt-metrics tools
- 21. The other kind of RDF (made-up example) Chemical reactions are unusually well-suited to representation. (Donald Davidson’s event semantics) _:r1 a obo:RXNO_0000004 ; # Diels–Alder obo:has_participant_ceasing_to_exist _:m1 ; # a diene obo:has_participant_ceasing_to_exist _:m2 ; # an olefin obo:has_participant_starting_to_exist _:m3 . # a substituted cyclohexene _:m1 a <http://rdf.chemspider.com/233000> . _:m2 a <http://rdf.chemspider.com/233001> . _:m3 a <http://rdf.chemspider.com/233002> .