Our dire need to mandate data standards and expectations for scientific publishing
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The document discusses the need for mandating data standards and open sharing in scientific publishing. It notes the loss of data reproducibility due to a lack of standardized data formats. The author advocates that publishers should require authors to register chemical compounds, submit spectral data in standard digital formats rather than images, and make data openly available with metadata and provenance. Adopting standards like CVSP could help validate structures and spectra before publication. While mandates may not be preferred, open data standards are important for scientific progress and reproducibility.
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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
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.Investigating Impact Metrics for Performance for the US-EPA National Center f...
Investigating Impact Metrics for Performance for the US-EPA National Center f...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
At this time, and in a culture where online access is now an imperative, Wikipedia has become the definitive encyclopedia. In terms of its support for chemistry it is rich in many encyclopedic pages including named reactions, chemical and drug pages, articles about chemists, and many other forms of chemistry related information. Wikipedia is hosted on Mediawiki, an open source platform that can be utilized by anybody as the basis of their own hosted content collection. Mediawiki has been used as a collaborative environment by a number of chemists to create As a general contribution to the community Mediawiki has been used to create a number of resources that have become very popular with the chemistry community. These include VIPEr to support inorganic chemistry, ChemWiki as an online textbook and other educational resources and a Chemical Information Wikibook. Mediawiki has also been used by the author to host open source collections of data including scientists, scientific databases and mobile apps for science: the ScientistsDB, SciDBs and SciMobileApps wikis. This presentation will provide an overview of some of the chemistry resources that presently exist and celebrate the major contributions that Wikipedia and Mediawiki have made to the collaborative dissemination of chemistry. Value of the mediawiki platform for providing content to the chemistry community
Value of the mediawiki platform for providing content to the chemistry communityUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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. Open innovation contributions from RSC resulting from the Open Phacts project
Open innovation contributions from RSC resulting from the Open Phacts projectUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Many of us nowadays invest significant amounts of time in sharing our activities and opinions with friends and family via social networking tools. 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 future careers. We are being indexed and exposed on the internet via our publications, presentations and data. We also have many 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 will provide an overview of the various types of networking and collaborative sites available to scientists and ways to expose your scientific activities online. Many of these can ultimately contribute to the developing measures of you as a scientist as identified in the new world of alternative metrics. Participating offers a great opportunity to develop a scientific profile within the community and may ultimately be very beneficial, especially to scientists early in their career. Data integration and building a profile for yourself as an online scientist
Data integration and building a profile for yourself as an online scientistUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
With the flourishing environment of platforms for sharing data, establishing an online profile and engaging in scientific discourse through alternative modes of publishing and participation, there are numerous potential benefits. However, while many scientists invest significant amounts of time in sharing their activities and opinions with friends and family the majority do not make use of the new opportunities to participate in the developing social web of science, despite the potential impact and influence on future careers. We now have many new ways to contribute to science outside of the classical publishing model. These include the ability to annotate and curate data, to “publish” in new ways on blogs and micropublishing sites, and many of these activities can be as part of a growing crowdsourcing network. Our efforts in this area are already being indexed and exposed on the internet via our publications, presentations and data and increasingly we are being quantified. This presentation will provide an overview of the various types of networking and collaborative sites available to scientists and ways to expose their scientific activities online. Many of these can ultimately contribute to the developing metrics of a scientist as identified in the new world of alternative metrics. Participation offers a great opportunity to develop a scientific profile within the community and may ultimately be very beneficial, especially to scientists early in their career.The Benefits of Participation in the Social Web of Science
The Benefits of Participation in the Social Web of ScienceUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The structure elucidation of natural product structures from analytical data, specifically NMR and MS, remains a major challenge. With an enormous palette of NMR experiments to choose from, and supported by breakthrough technologies in hardware, the generation of high quality data to enable even the most complex of natural product structures to be determined is no longer the major hurdle. The challenge is in the analysis of the data. We are in a new era in terms of approaches to structure elucidation: one where computers, databases, and a synergy between scientists and algorithms can offer an accelerated path forward. Software tools are capable of digesting spectroscopic data to elucidate extremely complex natural products. Scientists can now elucidate chemical structures utilizing multinuclear chemical shift data, correlation data from an array of 2D NMR experiments and utilize existing data sets for the purpose of dereplication and computer-assisted structure elucidation. With the explosion of online data especially, in public databases such as PubChem and ChemSpider, many tens of millions of chemical structures are available to seed fragment databases to include in the elucidation process. This presentation will provide an overview of how cheminformatics and chemical databases have been brought together to assist in the identification of natural products. It will include an examination of the state-of-the-art developments in Computer-Assisted Structure Elucidation. Cheminformatics and the Structure Elucidation of Natural Products
Cheminformatics and the Structure Elucidation of Natural ProductsUS 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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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
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.Investigating Impact Metrics for Performance for the US-EPA National Center f...
Investigating Impact Metrics for Performance for the US-EPA National Center f...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
At this time, and in a culture where online access is now an imperative, Wikipedia has become the definitive encyclopedia. In terms of its support for chemistry it is rich in many encyclopedic pages including named reactions, chemical and drug pages, articles about chemists, and many other forms of chemistry related information. Wikipedia is hosted on Mediawiki, an open source platform that can be utilized by anybody as the basis of their own hosted content collection. Mediawiki has been used as a collaborative environment by a number of chemists to create As a general contribution to the community Mediawiki has been used to create a number of resources that have become very popular with the chemistry community. These include VIPEr to support inorganic chemistry, ChemWiki as an online textbook and other educational resources and a Chemical Information Wikibook. Mediawiki has also been used by the author to host open source collections of data including scientists, scientific databases and mobile apps for science: the ScientistsDB, SciDBs and SciMobileApps wikis. This presentation will provide an overview of some of the chemistry resources that presently exist and celebrate the major contributions that Wikipedia and Mediawiki have made to the collaborative dissemination of chemistry. Value of the mediawiki platform for providing content to the chemistry community
Value of the mediawiki platform for providing content to the chemistry communityUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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. Open innovation contributions from RSC resulting from the Open Phacts project
Open innovation contributions from RSC resulting from the Open Phacts projectUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Many of us nowadays invest significant amounts of time in sharing our activities and opinions with friends and family via social networking tools. 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 future careers. We are being indexed and exposed on the internet via our publications, presentations and data. We also have many 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 will provide an overview of the various types of networking and collaborative sites available to scientists and ways to expose your scientific activities online. Many of these can ultimately contribute to the developing measures of you as a scientist as identified in the new world of alternative metrics. Participating offers a great opportunity to develop a scientific profile within the community and may ultimately be very beneficial, especially to scientists early in their career. Data integration and building a profile for yourself as an online scientist
Data integration and building a profile for yourself as an online scientistUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
With the flourishing environment of platforms for sharing data, establishing an online profile and engaging in scientific discourse through alternative modes of publishing and participation, there are numerous potential benefits. However, while many scientists invest significant amounts of time in sharing their activities and opinions with friends and family the majority do not make use of the new opportunities to participate in the developing social web of science, despite the potential impact and influence on future careers. We now have many new ways to contribute to science outside of the classical publishing model. These include the ability to annotate and curate data, to “publish” in new ways on blogs and micropublishing sites, and many of these activities can be as part of a growing crowdsourcing network. Our efforts in this area are already being indexed and exposed on the internet via our publications, presentations and data and increasingly we are being quantified. This presentation will provide an overview of the various types of networking and collaborative sites available to scientists and ways to expose their scientific activities online. Many of these can ultimately contribute to the developing metrics of a scientist as identified in the new world of alternative metrics. Participation offers a great opportunity to develop a scientific profile within the community and may ultimately be very beneficial, especially to scientists early in their career.The Benefits of Participation in the Social Web of Science
The Benefits of Participation in the Social Web of ScienceUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The structure elucidation of natural product structures from analytical data, specifically NMR and MS, remains a major challenge. With an enormous palette of NMR experiments to choose from, and supported by breakthrough technologies in hardware, the generation of high quality data to enable even the most complex of natural product structures to be determined is no longer the major hurdle. The challenge is in the analysis of the data. We are in a new era in terms of approaches to structure elucidation: one where computers, databases, and a synergy between scientists and algorithms can offer an accelerated path forward. Software tools are capable of digesting spectroscopic data to elucidate extremely complex natural products. Scientists can now elucidate chemical structures utilizing multinuclear chemical shift data, correlation data from an array of 2D NMR experiments and utilize existing data sets for the purpose of dereplication and computer-assisted structure elucidation. With the explosion of online data especially, in public databases such as PubChem and ChemSpider, many tens of millions of chemical structures are available to seed fragment databases to include in the elucidation process. This presentation will provide an overview of how cheminformatics and chemical databases have been brought together to assist in the identification of natural products. It will include an examination of the state-of-the-art developments in Computer-Assisted Structure Elucidation. Cheminformatics and the Structure Elucidation of Natural Products
Cheminformatics and the Structure Elucidation of Natural ProductsUS 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
Many students spend enormous amounts of their time engaged with their computers, accepting of course that mobile devices are simply computers of a different form factor. Engaged with the social networks, utilizing computer platforms to source and share content of various forms, their contributions of “data” into what is the cloud, and in many cases a void, is enormous. What community and career benefit might result from those students spending some of their time contributing chemistry related data to the world? What challenges lie in the way of their participation and how might participating have a positive, or negative impact on their future career. The Royal Society of Chemistry hosts a number of chemistry data platforms to which students can actively contribute and for which their participation can be measured. Moreover the RSC’s micropublishing platform allows chemists to learn how to write up their scientific work, obtain review from their peers and chemistry professors in a non-threatening environment and produce an online published work in less than day that is both citable and available as a shared resource for the community. This presentation will demonstrate how to participate and encourage engagement from students early in their education. There are no longer any technology barriers to the sharing of the majority of chemistry related data.
Encouraging undergraduate students to participate as authors of scientific pu...
Encouraging undergraduate students to participate as authors of scientific pu...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
On Friday September 16th I was honored with the award for the North Carolina American Chemical Society Distinguished Speaker Award and got to review the past 20 years of my career. This was my short intro bio
"Antony Williams is a Ph.D. NMR spectroscopist and cheminformatician who has worked in academia, government, a Fortune 500 company, and two start-ups. He is co-founder of the free online chemical database ChemSpider, originally started as a hobby project and ultimately acquired by the Royal Society of Chemistry (in the UK) and now used by over 50,000 users per day. He is now a computational chemist at the Environmental Protection Agency in the National Center for Computational Toxicology and is focused on developing web applications to support data dissemination and progress efforts in allowing for faster and cheaper approaches to identify potential toxicological effects of chemicals. He has published >180 papers, >25 book chapters and a number of books. He is known as the ChemConnector on social networks. "How One Monkey on a Typewriter Made a Difference to Online Chemistry
How One Monkey on a Typewriter Made a Difference to Online ChemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry hosts a growing collection of online chemistry content. For much of our work the InChI identifier is an important component underpinning our projects. This enables the integration of chemical compounds with our archive of scientific publications, the delivery of a reaction database containing millions of reactions as well as a chemical validation and standardization platform developed to help improve the quality of structural representations on the internet. The InChI has been a fundamental part of each of our projects and has been pivotal in our support of international projects such as the Open PHACTS semantic web project integrating chemistry and biology data and the PharmaSea project focused on identifying novel chemical components from the ocean with the intention of identifying new antibiotics. This presentation will provide an overview of the importance of InChI in the development of many of our eScience platforms and how we have used it to provide integration across hundreds of websites and chemistry databases across the web. We will discuss how we are now expanding our efforts to develop a platform encompassing efforts in Open Source Drug Discovery and the support of data management for neglected diseases.How the InChI identifier is used to underpin our online chemistry databases a...
How the InChI identifier is used to underpin our online chemistry databases a...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
The Royal Society of Chemistry publishes many thousands of articles per year, the majority of these containing rich chemistry data that, in general, in limited in its value when isolated only to the HTML or PDF form of the articles commonly consumed by readers. RSC also has an archive of over 300,000 articles containing rich chemistry data especially in the form of chemicals, reactions, property data and analytical spectra. RSC is developing a platform integrating these various forms of chemistry data. The data will be aggregated both during the manuscript deposition process as well as the result of text-mining and extraction of data from across the RSC archive. This presentation will report on the development of the platform including our success in extracting compounds, reactions and spectral data from articles. We will also discuss our developing process for handling data at manuscript deposition and the integration and support of eLab Notebooks (ELNS) in terms of facilitating data deposition and sourcing data. Each of these processes is intended to ensure long-term access to research data with the intention of facilitating improved discovery. Royal society of chemistry activities to develop a data repository for chemis...
Royal society of chemistry activities to develop a data repository for chemis...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider is one of the chemistry community’s primary public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data to many tens of websites and software applications at this point. This presentation will provide an overview of the expanding reach of the ChemSpider platform and the nature of solutions that it helps to enable. We will also discuss some of the future directions for the project that are envisaged and how we intend to continue expanding the impact for the platform.ChemSpider – disseminating data and enabling an abundance of chemistry platforms
ChemSpider – disseminating data and enabling an abundance of chemistry platformsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Our access to scientific information has changed in ways that were hardly imagined even by the early pioneers of the internet. The immense quantities of data and the array of tools available to search and analyze online content 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 the ChemSpider platform and the nature of the solutions that it helps to enable. 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 Resources for the Chemistry Community from the Royal Society of Chem...
eScience Resources for the Chemistry Community from the Royal Society of Chem...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at the CLIR/DLF Postdoctoral Fellowship Summer Seminar at Bryn Mawr college in Pennsylvania on July 29th 2014. The intention was to communicate what we are doing in the fields of text and data mining in the domain of chemistry and specifically around mining the RSC archive publication and chemistry dissertations and theses. How would these experiences map over to the humanities?Data Mining Dissertations and Adventures and Experiences in the World of Chem...
Data Mining Dissertations and Adventures and Experiences in the World of Chem...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
Our access to scientific information has changed in ways that were hardly imagined even by the early pioneers of the internet. The immense quantities of data and the array of tools available to search and analyze online content continues to expand while the pace of change does not appear to be slowing. While scientists now have access to the enormous capacities and capability of the internet the vast majority of scientific communication continues to be through peer-reviewed scientific journals. The measure of a scientist’s contribution is primarily represented by their publication profile and the citations to their published works and offers an incomplete view of their activities. However, we are at the beginning of a new revolution where the ability to communicate offers the opportunity to embrace new forms of publishing and where scientific participation and influence will be measured in new ways. This presentation will provide an overview of our new generation of “openness” in which open source, open standards, open access and open data are proliferating. 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.The future of scientific information & communication
The future of scientific information & communicationUS 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
The Royal Society of Chemistry (RSC) is one of the world’s most prominent scientific societies and STM publishers. Our contributions to the scientific community include the delivery of a myriad of resources to support the chemistry community to access chemistry-related data, information and knowledge. This includes ChemSpider, a compound centric platform linking together over 30 million chemical compounds with internet-based resources. Using this compound database and its associated chemical identifiers as a basis the RSC is utilizing text and data mining approaches to data enable our published archive of scientific publications. This presentation will provide an overview of our technical approaches to text and data enable our archive of scientific articles, how we are developing an integrated database of chemical compounds, reactions, physical and analytical data and how it will be used to facilitate scientific discovery.The application of text and data mining to enhance the RSC publication archive
The application of text and data mining to enhance the RSC publication archiveUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry provides access to a number of databases hosting chemicals data, reactions, spectroscopy data and prediction services. These databases and services can be accessed via web services utilizing queries using standard data formats such as InChI and molfiles. Data can then be downloaded in standard structure and spectral formats allowing for reuse and repurposing. The ChemSpider database integrates to a number of projects external to RSC including Open PHACTS that integrates chemical and biological data. This project utilizes semantic web data standards including RDF. This presentation will provide an overview of how structure and spectral data standards have been critical in allowing us to integrate many open source tools, ease of integration to a myriad of services and underpin many of our future developments.The importance of standards for data exchange and interchange on the Royal So...
The importance of standards for data exchange and interchange on the Royal So...US 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
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
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
There are various online chemistry data that are free-to-access for the community. Many of these resources presently host millions of small molecule chemical compounds together with associated data and accessible via a number of search techniques. The challenges associated with providing a similar platform for “materials” are manifold but, if they could be addressed, would offer a valuable service to the materials community. This presentation will provide an overview of some of the challenges associated with data access and both closed and open identifiers (e.g. InChI), and how one particular online resource, ChemSpider, was built. The challenges faced to embrace the diverse world of materials informatics and online data access are manifold but it is possible that there is much to learn from some of the approaches taken with small molecules.Hosting Public Domain Chemicals Data Online for the Community – the Challenge...
Hosting Public Domain Chemicals Data Online for the Community – the Challenge...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
The Royal Society of Chemistry hosts large scale data collections and provides access to the data to the chemistry community. The largest RSC data set of wide scale interest to the community offers access to tens of millions of compounds. The host platform, ChemSpider, is limited as it is a structure centric hub only. A new architecture, the RSC data repository, has been developed that extends support to reactions, spectral data, crystallography data and related property data. It is also the architecture underlying a series of exemplar projects for managing data for a number of diverse laboratories. The adoption of data standards for the integration and distribution of data has been essential. Specific standards include molecular structure formats such as molfiles and InChIs, and spectral data formats such as JCAMP. This presentation will report on our development of the data repository, the importance of utilizing standards for data integration, the flexible nature of the architecture to deliver solutions for various laboratories and our efforts to develop new large data collections. This includes text-mining efforts to extract large spectrum-structure collections from large corpuses. Importance of data standards for large scale data integration in chemistry
Importance of data standards for large scale data integration in chemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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Many students spend enormous amounts of their time engaged with their computers, accepting of course that mobile devices are simply computers of a different form factor. Engaged with the social networks, utilizing computer platforms to source and share content of various forms, their contributions of “data” into what is the cloud, and in many cases a void, is enormous. What community and career benefit might result from those students spending some of their time contributing chemistry related data to the world? What challenges lie in the way of their participation and how might participating have a positive, or negative impact on their future career. The Royal Society of Chemistry hosts a number of chemistry data platforms to which students can actively contribute and for which their participation can be measured. Moreover the RSC’s micropublishing platform allows chemists to learn how to write up their scientific work, obtain review from their peers and chemistry professors in a non-threatening environment and produce an online published work in less than day that is both citable and available as a shared resource for the community. This presentation will demonstrate how to participate and encourage engagement from students early in their education. There are no longer any technology barriers to the sharing of the majority of chemistry related data.
Encouraging undergraduate students to participate as authors of scientific pu...
Encouraging undergraduate students to participate as authors of scientific pu...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
On Friday September 16th I was honored with the award for the North Carolina American Chemical Society Distinguished Speaker Award and got to review the past 20 years of my career. This was my short intro bio
"Antony Williams is a Ph.D. NMR spectroscopist and cheminformatician who has worked in academia, government, a Fortune 500 company, and two start-ups. He is co-founder of the free online chemical database ChemSpider, originally started as a hobby project and ultimately acquired by the Royal Society of Chemistry (in the UK) and now used by over 50,000 users per day. He is now a computational chemist at the Environmental Protection Agency in the National Center for Computational Toxicology and is focused on developing web applications to support data dissemination and progress efforts in allowing for faster and cheaper approaches to identify potential toxicological effects of chemicals. He has published >180 papers, >25 book chapters and a number of books. He is known as the ChemConnector on social networks. "How One Monkey on a Typewriter Made a Difference to Online Chemistry
How One Monkey on a Typewriter Made a Difference to Online ChemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry hosts a growing collection of online chemistry content. For much of our work the InChI identifier is an important component underpinning our projects. This enables the integration of chemical compounds with our archive of scientific publications, the delivery of a reaction database containing millions of reactions as well as a chemical validation and standardization platform developed to help improve the quality of structural representations on the internet. The InChI has been a fundamental part of each of our projects and has been pivotal in our support of international projects such as the Open PHACTS semantic web project integrating chemistry and biology data and the PharmaSea project focused on identifying novel chemical components from the ocean with the intention of identifying new antibiotics. This presentation will provide an overview of the importance of InChI in the development of many of our eScience platforms and how we have used it to provide integration across hundreds of websites and chemistry databases across the web. We will discuss how we are now expanding our efforts to develop a platform encompassing efforts in Open Source Drug Discovery and the support of data management for neglected diseases.How the InChI identifier is used to underpin our online chemistry databases a...
How the InChI identifier is used to underpin our online chemistry databases a...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
The Royal Society of Chemistry publishes many thousands of articles per year, the majority of these containing rich chemistry data that, in general, in limited in its value when isolated only to the HTML or PDF form of the articles commonly consumed by readers. RSC also has an archive of over 300,000 articles containing rich chemistry data especially in the form of chemicals, reactions, property data and analytical spectra. RSC is developing a platform integrating these various forms of chemistry data. The data will be aggregated both during the manuscript deposition process as well as the result of text-mining and extraction of data from across the RSC archive. This presentation will report on the development of the platform including our success in extracting compounds, reactions and spectral data from articles. We will also discuss our developing process for handling data at manuscript deposition and the integration and support of eLab Notebooks (ELNS) in terms of facilitating data deposition and sourcing data. Each of these processes is intended to ensure long-term access to research data with the intention of facilitating improved discovery. Royal society of chemistry activities to develop a data repository for chemis...
Royal society of chemistry activities to develop a data repository for chemis...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider is one of the chemistry community’s primary public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data to many tens of websites and software applications at this point. This presentation will provide an overview of the expanding reach of the ChemSpider platform and the nature of solutions that it helps to enable. We will also discuss some of the future directions for the project that are envisaged and how we intend to continue expanding the impact for the platform.ChemSpider – disseminating data and enabling an abundance of chemistry platforms
ChemSpider – disseminating data and enabling an abundance of chemistry platformsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Our access to scientific information has changed in ways that were hardly imagined even by the early pioneers of the internet. The immense quantities of data and the array of tools available to search and analyze online content 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 the ChemSpider platform and the nature of the solutions that it helps to enable. 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 Resources for the Chemistry Community from the Royal Society of Chem...
eScience Resources for the Chemistry Community from the Royal Society of Chem...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at the CLIR/DLF Postdoctoral Fellowship Summer Seminar at Bryn Mawr college in Pennsylvania on July 29th 2014. The intention was to communicate what we are doing in the fields of text and data mining in the domain of chemistry and specifically around mining the RSC archive publication and chemistry dissertations and theses. How would these experiences map over to the humanities?Data Mining Dissertations and Adventures and Experiences in the World of Chem...
Data Mining Dissertations and Adventures and Experiences in the World of Chem...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
Our access to scientific information has changed in ways that were hardly imagined even by the early pioneers of the internet. The immense quantities of data and the array of tools available to search and analyze online content continues to expand while the pace of change does not appear to be slowing. While scientists now have access to the enormous capacities and capability of the internet the vast majority of scientific communication continues to be through peer-reviewed scientific journals. The measure of a scientist’s contribution is primarily represented by their publication profile and the citations to their published works and offers an incomplete view of their activities. However, we are at the beginning of a new revolution where the ability to communicate offers the opportunity to embrace new forms of publishing and where scientific participation and influence will be measured in new ways. This presentation will provide an overview of our new generation of “openness” in which open source, open standards, open access and open data are proliferating. 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.The future of scientific information & communication
The future of scientific information & communicationUS 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
The Royal Society of Chemistry (RSC) is one of the world’s most prominent scientific societies and STM publishers. Our contributions to the scientific community include the delivery of a myriad of resources to support the chemistry community to access chemistry-related data, information and knowledge. This includes ChemSpider, a compound centric platform linking together over 30 million chemical compounds with internet-based resources. Using this compound database and its associated chemical identifiers as a basis the RSC is utilizing text and data mining approaches to data enable our published archive of scientific publications. This presentation will provide an overview of our technical approaches to text and data enable our archive of scientific articles, how we are developing an integrated database of chemical compounds, reactions, physical and analytical data and how it will be used to facilitate scientific discovery.The application of text and data mining to enhance the RSC publication archive
The application of text and data mining to enhance the RSC publication archiveUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry provides access to a number of databases hosting chemicals data, reactions, spectroscopy data and prediction services. These databases and services can be accessed via web services utilizing queries using standard data formats such as InChI and molfiles. Data can then be downloaded in standard structure and spectral formats allowing for reuse and repurposing. The ChemSpider database integrates to a number of projects external to RSC including Open PHACTS that integrates chemical and biological data. This project utilizes semantic web data standards including RDF. This presentation will provide an overview of how structure and spectral data standards have been critical in allowing us to integrate many open source tools, ease of integration to a myriad of services and underpin many of our future developments.The importance of standards for data exchange and interchange on the Royal So...
The importance of standards for data exchange and interchange on the Royal So...US 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
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
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
There are various online chemistry data that are free-to-access for the community. Many of these resources presently host millions of small molecule chemical compounds together with associated data and accessible via a number of search techniques. The challenges associated with providing a similar platform for “materials” are manifold but, if they could be addressed, would offer a valuable service to the materials community. This presentation will provide an overview of some of the challenges associated with data access and both closed and open identifiers (e.g. InChI), and how one particular online resource, ChemSpider, was built. The challenges faced to embrace the diverse world of materials informatics and online data access are manifold but it is possible that there is much to learn from some of the approaches taken with small molecules.Hosting Public Domain Chemicals Data Online for the Community – the Challenge...
Hosting Public Domain Chemicals Data Online for the Community – the Challenge...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
Mais procurados (20)
Encouraging undergraduate students to participate as authors of scientific pu...
Encouraging undergraduate students to participate as authors of scientific pu...
How One Monkey on a Typewriter Made a Difference to Online Chemistry
How One Monkey on a Typewriter Made a Difference to Online Chemistry
How the InChI identifier is used to underpin our online chemistry databases a...
How the InChI identifier is used to underpin our online chemistry databases a...
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...
Royal society of chemistry activities to develop a data repository for chemis...
Royal society of chemistry activities to develop a data repository for chemis...
ChemSpider – disseminating data and enabling an abundance of chemistry platforms
ChemSpider – disseminating data and enabling an abundance of chemistry platforms
eScience Resources for the Chemistry Community from the Royal Society of Chem...
eScience Resources for the Chemistry Community from the Royal Society of Chem...
Data Mining Dissertations and Adventures and Experiences in the World of Chem...
Data Mining Dissertations and Adventures and Experiences in the World of Chem...
eScience at the Royal Society of Chemistry and our current initiatives
eScience at the Royal Society of Chemistry and our current initiatives
The future of scientific information & communication
The future of scientific information & communication
The UK National Chemical Database Service – an integration of commercial and ...
The UK National Chemical Database Service – an integration of commercial and ...
The application of text and data mining to enhance the RSC publication archive
The application of text and data mining to enhance the RSC publication archive
The importance of standards for data exchange and interchange on the Royal So...
The importance of standards for data exchange and interchange on the Royal So...
ChemSpider as an integration hub for interlinked chemistry data
ChemSpider as an integration hub for interlinked chemistry data
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...
Big data challenges associated with building a national data repository for c...
Big data challenges associated with building a national data repository for c...
Overview of open resources to support automated structure verification and e...
Overview of open resources to support automated structure verification and e...
Hosting Public Domain Chemicals Data Online for the Community – the Challenge...
Hosting Public Domain Chemicals Data Online for the Community – the Challenge...
Sharing chemical structures with peer reviewed publications
Sharing chemical structures with peer reviewed publications
ICG-11 - genomic data projects around the world - nov 5 2016
ICG-11 - genomic data projects around the world - nov 5 2016
Semelhante a Our dire need to mandate data standards and expectations for scientific publishing
The Royal Society of Chemistry hosts large scale data collections and provides access to the data to the chemistry community. The largest RSC data set of wide scale interest to the community offers access to tens of millions of compounds. The host platform, ChemSpider, is limited as it is a structure centric hub only. A new architecture, the RSC data repository, has been developed that extends support to reactions, spectral data, crystallography data and related property data. It is also the architecture underlying a series of exemplar projects for managing data for a number of diverse laboratories. The adoption of data standards for the integration and distribution of data has been essential. Specific standards include molecular structure formats such as molfiles and InChIs, and spectral data formats such as JCAMP. This presentation will report on our development of the data repository, the importance of utilizing standards for data integration, the flexible nature of the architecture to deliver solutions for various laboratories and our efforts to develop new large data collections. This includes text-mining efforts to extract large spectrum-structure collections from large corpuses. Importance of data standards for large scale data integration in chemistry
Importance of data standards for large scale data integration in chemistryUS 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
The Royal Society of Chemistry hosts one of the worlds’ richest collections of online chemistry data that is free-to-access for the community. ChemSpider presently hosts over 30 million unique chemical compounds together with associated data and accessible via a number of search techniques. With almost 50,000 unique users per day from around the world the site offers scientists the ability to investigate the world of small molecules via property searches, analytical data and predictive models. The challenges associated with providing a similar platform for “materials” are manifold but, if they could be addressed, would offer a valuable service to the materials community. This presentation will provide an overview of how ChemSpider was built, our efforts to expand the capabilities to a more encompassing data repository and some of the challenges faced to embrace the diverse world of materials informatics and online data access.Hosting public domain chemicals data online for the community – the challenge...
Hosting public domain chemicals data online for the community – the challenge...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Science has evolved from the isolated individual tinkering in the lab, through the era of the “gentleman scientist” with his or her assistant(s), to group-based then expansive collaboration and now to an opportunity to collaborate with the world. With the advent of the internet the opportunity for crowd-sourced contribution and large-scale collaboration has exploded and, as a result, scientific discovery has been further enabled. The contributions of enormous open data sets, liberal licensing policies and innovative technologies for mining and linking these data has given rise to platforms that are beginning to deliver on the promise of semantic technologies and nanopublications, facilitated by the unprecedented computational resources available today, especially the increasing capabilities of handheld devices. The speaker will provide an overview of his experiences in developing a crowdsourced platform for chemists allowing for data deposition, annotation and validation. The challenges of mapping chemical and pharmacological data, especially in regards to data quality, will be discussed. The promise of distributed participation in data analysis is already in place.Facilitating Scientific Discovery through Crowdsourcing and Distributed Parti...
Facilitating Scientific Discovery through Crowdsourcing and Distributed Parti...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Jean-Claude Bradley had an incredible passion for providing open science tools and data to the community. He had boundless energy, no shortage of ideas and ran so many projects in parallel that it was often difficult to keep up. But at RSC we tried. We provided access to our data, our application programming interfaces and lots of our out-of-hours time to help turn his vision into reality. As a result we helped in the delivery of the SpectralGame to help people learn about NMR and we supported the integration of our services into GoogleDocs underpinning the management and curation of physicochemical property data. We tweaked a number of our services based on JC’s input and as a result we have ended up with a suite of capabilities that serve many of our existing efforts to integrate to electronic lab notebooks and support the ongoing shift towards Open Chemistry. JC was very much ahead of his time….and we were glad to have supported his work. This presentation will give a snapshot of some of the work we did to support his vision. Providing support for JC Bradleys vision of open science using RSC cheminform...
Providing support for JC Bradleys vision of open science using RSC cheminform...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given as a part of the Microsoft eScience panel discussion in Sao Paulo, Brazil. The panel discussion was in regards to Going Native, a reference to a quote from Jim Gray along the lines of “in order to really understand the computing needs of a scientist you have to go native”. Jim himself did this, immersing himself in astronomy to build what would become the WorldWide Telescope. Bridging the gap between experimental scientists and the computing that underpins their discoveries is an ongoing challenge for eScience. The panel explored what it means to go native and gave examples of where they have seen this work well and shared lesson’s learned from working in this way.Delivering on the promise of a chemistry data repository for the world
Delivering on the promise of a chemistry data repository for the worldUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry hosts one of the largest online chemistry databases containing almost 30 million unique chemical structures. The database, ChemSpider, provides the underpinning for a series of eScience projects allowing for the integration of chemical compounds with our archive of scientific publications, the delivery of a reaction database containing millions of reactions as well as a chemical validation and standardization platform developed to help improve the quality of structural representations on the internet. The InChI has been a fundamental part of each of our projects and has been pivotal in our support of international projects such as the Open PHACTS semantic web project integrating chemistry and biology data and the PharmaSea project focused on identifying novel chemical components from the ocean with the intention of identifying new antibiotics. This presentation will provide an overview of the importance of InChI in the development of many of our eScience platforms and how we have used it specifically in the ChemSpider project to provide integration across hundreds of websites and chemistry databases across the web. We will discuss how we are now expanding our efforts to develop a Global Chemistry Network encompassing efforts in Open Source Drug Discovery and the support of data management for neglected diseases.The importance of the InChI identifier as a foundation technology for eScienc...
The importance of the InChI identifier as a foundation technology for eScienc...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
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Our dire need to mandate data standards and expectations for scientific publishing
- 1. Our dire need to mandate data standards and expectations for scientific publishing Antony Williams ACS Denver, March 2015
- 2. Reproducibility, Reporting, Sharing & Plagiarism • I will present from the point of view of: • Losing way too much of my own data! • Someone who actively wants to share data • My involvement with a chemistry database • As a reviewer of publications • As an author of scientific publications • ..and as a replacement speaker…
- 3. Consider a shift to Openness
- 4. Times have really changed… Open Access funder mandates…
- 6. The world of Open Data is here
- 7. What technical solutions tho’? • Despite the push for Open Data the funders are not really pushing solutions yet • Institutional repositories are commonplace • (Partial) solutions are becoming available
- 10. RSC ChemSpider
- 11. So what do I do… • VP Strategic Development for RSC • Manage the cheminformatics team • Interested in Open Drug Discovery, Open Data management, Cheminformatics standards • But originally an NMR spectroscopist with a focus on structure elucidation - very interested in “CASE”, study of natural products
- 12. Some NMR…in this CASE…
- 13. Some NMR…
- 14. Studying DOZENS of compounds • NO access to raw data files – in binary or even standard file formats for processing • Figures are close to USELESS for 2D NMR – representative not accurate shifts • Tabulated shifts are in PDF files and needed transcribing – where are CSV files??? • TORTUROUS WORK!!!!
- 15. …I (co-)author many articles…
- 16. My favorite part of writing! What.. NO STANDARD???
- 17. In researcher mode… • I want to access and use data • I want to: • Download molecules • Download tables • Download spectra • Download figures • Then reprocess, replot, repurpose
- 18. Community Norms • Some wonderful community norms and mandates! • Deposit crystal structures in CSD • Deposit Proteins in PDB • Deposit gene sequences in Genbank • Increasingly deposit bioassay data in Pubchem
- 19. What of general chemistry? • We publish into locked down files and then “abstract” the data! • Could publishers help drive a community norm for: • Chemical compound registration • Spectral data • Property data • What else?
- 22. Could we at least improve quality of compounds? • Maybe forcing compound registration ahead of time won’t work (would need a business model etc.) • But what can be done to help correct the many issues we see with structures? • Examples?
- 28. EXPERTS must get it right?!
- 29. What about a validated dictionary?
- 33. CVSP: Validate and Standardize
- 34. CVSP Rules Sets
- 35. CVSP Filtering of DrugBank
- 36. CVSP Filtering of DrugBank
- 37. CVSP is Open to Anyone!
- 38. What if… • CVSP was used to check and process all ChemDraw, Molfiles, SDF files before submitting to publishers or databases? • Publishers used the CVSP API to check their data? • All the rules were openly available for adoption
- 39. A Talk from Yesterday… http://www.slideshare.net/AntonyWilliams/
- 40. Spectral Data
- 41. ChemSpider ID 24528095 H1 NMR
- 42. ChemSpider ID 24528095 C13 NMR
- 43. ChemSpider ID 24528095 HHCOSY
- 44. ESI – Text Spectra
- 45. We want to find text spectra? • We can find and index text spectra:13C NMR (CDCl3, 100 MHz): δ = 14.12 (CH3), 30.11 (CH, benzylic methane), 30.77 (CH, benzylic methane), 66.12 (CH2), 68.49 (CH2), 117.72, 118.19, 120.29, 122.67, 123.37, 125.69, 125.84, 129.03, 130.00, 130.53 (ArCH), 99.42, 123.60, 134.69, 139.23, 147.21, 147.61, 149.41, 152.62, 154.88 (ArC) • What would be better are spectral figures – and include assignments where possible!
- 46. 1H NMR (CDCl3, 400 MHz): δ = 2.57 (m, 4H, Me, C(5a)H), 4.24 (d, 1H, J = 4.8 Hz, C(11b)H), 4.35 (t, 1H, Jb = 10.8 Hz, C(6)H), 4.47 (m, 2H, C(5)H), 4.57 (dd, 1H, J = 2.8 Hz, C(6)H), 6.95 (d, 1H, J = 8.4 Hz, ArH), 7.18–7.94 (m, 11H, ArH)
- 47. Developing Proof-of-Concept • Extract from 1976-2014 USPTO applications *unknown – starts off with NMR: peak list (no nucleus) H 975543 C 56536 unknown 44306 F 9429 P 3241 B 91 Si 62 Sn 22 Se 11 N 8
- 48. ESI Data also contains figures
- 49. “Where is the real data please?” FIGURE DATA
- 50. Extraction is the WRONG WAY • We should NOT mine data out – digital form! • Structures should be submitted “correctly” • Spectra should be digital spectral formats, not images • ESI should be RICH and interactive • Data should be open, available, with meta data and provenance
- 51. We can solve for Authors here Will it be used though??? YES!
- 52. Supplementary Info Data now..
- 53. The challenges of analytical data • Vendors produce complex proprietary data formats and standard formats are required (JCAMP, NetCDF, AniML) • ChemSpider already hosts thousands of JCAMP spectra • Support of “assigned spectra” in place • Data validation approaches understood • There are a myriad of analytical data types…
- 54. Analytical data
- 55. Data Mining – it’s mine, mine!
- 56. Related… Published this week
- 57. It’s Dangerous to Mandate • Scientists prefer guidelines rather than rules • It can be more work to meet mandates • Mandates may discourage submissions to journals • But what’s good for science? • Will the Open Data movement shift things? • Will the latest generation share more?
- 58. Reproducibility, Reporting, Sharing & Plagiarism • If publishers demanded it of me… • I would lose less of my own data! • I would actively be sharing data • As a reviewer of publications..enables me • As an author of scientific publications..makes the publications better I believe • ..and I did my best as a replacement speaker…
- 59. It’s a long road ahead…
- 60. Thank you Email: williamsa@rsc.org ORCID: 0000-0002-2668-4821 Twitter: @ChemConnector Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams