How a Structure-Centric Community for Chemists Can Benefit Drug Discovery - Virtual Screening Experiments Utilizing a Publicly Accessible Ligand Database, QSAR Modeling Tools and a Virtual Docking Software Package
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ChemSpider is an online database of over 20 million chemical structures assembled from almost a hundred data sources including chemical and screening library vendors, publicly accessible databases and resources, commercial databases and Open Access literature articles. Such a public resource provides a rich source of ligands for the purpose of virtual screening experiments. These can take many forms. This work will present results from two specific types of studies: 1) Quantitative Structure Activity Relationship (QSAR) based analyses and 2) In-silico docking into protein receptor sites. We will review results from the application of both approaches to a number of specific examples using the software outlined below. The QSAR analyses utilize the ChemModLab environment which is a free, web-based toolbox for fitting and assessing quantitative structure-activity relationships. Its elements include a cheminformatics front end to supply molecular descriptors, a set of statistical methods for fitting models, and methods for validating the resulting model. Five molecular descriptor sets are used with 16 math modeling methods to give a total of 80 QSAR models. The input is a file of compounds and a text file for biological activity. The in-silico docking experiments are conducted using a combination QSAR/Docking approach using the SimBioSys eHITS and Lasso software programs. The docking procedure allows for the screening of a complete molecular database to obtain the correct binding poses and estimated binding affinities. The ligand based screening tool utilizes a novel conformation independent 3D QSAR descriptor, ideally suited for scaffold hopping.
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Scientists commonly find themselves in a state of overwhelm in regards to the availability of information accessible to them. The distribution of resources now includes the entire space of the worldwide web, access to primary databases such as CAS and, commonly, a plethora of internally developed systems. While the web has provided improved access to chemistry-related information there has not been an online central resource allowing integrated chemical structure-searching of chemistry databases, chemistry articles, patents and web pages such as blogs and wikis. ChemSpider has built a structure centric community for chemists by providing free access to an online database and collaboration tool for chemists. The online database offers an environment for curating the data on ChemSpider as well as the deposition of chemical structures, analytical data and associated information and provides a significant knowledge base and resource for chemists working in different domains. An overview of present and future capabilities is given.Chemspider Presentation at the ACS Meeting in New orleans
Chemspider Presentation at the ACS Meeting in New orleansUS 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
This was a presentation I gave to an audience at Nature Publishing Group in New York on May 7th 2009. It's a long presentation and over an hour in length. Not much new here relative to other presentations...just a knitting together of many of the others on here.
There is an increasing availability of free and open access resources for scientists to use on the internet. Coupled with an increasing number of Open Source software programs we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 190 separate data sources, ChemSpider has taken on the task of both robotically and manually integrating and curating publicly available data sources. ChemSpider has also provided an environment for users to deposit, curate and annotate chemistry-related information. This has allowed the community to enhance ChemSpider by adding analytical data, associating synthetic pathways and publications and connecting to social networking resources. I will discuss how ChemSpider is fast becoming the premier curated platform and centralized hub for resourcing information about chemical entities and how the platform provides the foundation data for services allowing the analysis of analytical data and collaborative science.ChemSpider as a Foundation for Crowdsourcing and Collaborations in Open Chemi...
ChemSpider as a Foundation for Crowdsourcing and Collaborations in Open Chemi...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry provides open access to data associated with tens of millions of chemical compounds. 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 delivering 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 the challenges of managing “Big Data” for chemists around the world and providing access to tools for structure dereplication, spectral database searching and the crowdsourcing of the worlds’ largest spectral database.Dealing with the complex challenge of managing diverse analytical chemistry d...
Dealing with the complex challenge of managing diverse analytical chemistry d...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. There are many tens of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the diversity of databases available online their inherent quality, accuracy and completeness is lacking in many regards. ChemSpider was established to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data and experimental properties. ChemSpider has now grown into a database of over 20 million chemical substances integrated with over 300 disparate data sources, many of these directly supporting the Life Sciences. This presentation will provide an overview of our efforts to improve the quality of data online, to provide a foundation for the semantic web for chemistry and to provide access to a set online tools and services to support access to these data. I will also discuss how ChemSpider is being used to enhance Semantic Publishing in Chemistry at RSC.
ChemSpider – A Community Platform for Chemistry and Resources Supporting the ...
ChemSpider – A Community Platform for Chemistry and Resources Supporting the ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Laboratories around the world continue to generate immense amounts of data that are non-proprietary and of value to the community. If available these data could dramatically reduce costs by minimizing rework and ultimately facilitating faster research. High quality reference data collections of chemical compound dictionaries, properties and spectra have been generated over many decades. With the advent of social networking tools and platforms such as Wikipedia, the community has an opportunity to contribute. The ChemSpider platform hosted by the Royal Society of Chemistry is a compound centric database with associated data. Already populated with almost 25 million unique compounds the community can deposit and host their own data, and curate and annotate existing data including those generated in Open Notebook Science Efforts. This presentation will provide an overview of progress to date and outline the vision of this community platform for chemistry and ensuring the longevity of chemistry reference data. Hosting a compound centric community resource for chemistry data
Hosting a compound centric community resource for chemistry dataUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The internet now offers access to a myriad of online resources that can be of value to chemists working in the Life Sciences. While finding information online is, in many cases, a simple search away, the accuracy and validity of the associated data and information should be questioned. As more databases and resources are introduced online, and commonly not integrated to other resources, a scientist must perform multiple searches and then undertake the task of meshing and merging data. ChemSpider is a freely accessible online database that has taken on the challenge of meshing together distributed resources across the internet to provide a structure-based hub. It is a crowdsourcing environment hosting over 26 million unique compounds linked out to over 400 data sources. With well defined programming interfaces for integration ChemSpider has been integrated to many commercial and open software packages and is presently serving as the chemistry foundation for the IMI Open PHACTS project.
Integrating and curating internet based chemistry resources to serve life sci...
Integrating and curating internet based chemistry resources to serve life sci...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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Scientists commonly find themselves in a state of overwhelm in regards to the availability of information accessible to them. The distribution of resources now includes the entire space of the worldwide web, access to primary databases such as CAS and, commonly, a plethora of internally developed systems. While the web has provided improved access to chemistry-related information there has not been an online central resource allowing integrated chemical structure-searching of chemistry databases, chemistry articles, patents and web pages such as blogs and wikis. ChemSpider has built a structure centric community for chemists by providing free access to an online database and collaboration tool for chemists. The online database offers an environment for curating the data on ChemSpider as well as the deposition of chemical structures, analytical data and associated information and provides a significant knowledge base and resource for chemists working in different domains. An overview of present and future capabilities is given.Chemspider Presentation at the ACS Meeting in New orleans
Chemspider Presentation at the ACS Meeting in New orleansUS 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
This was a presentation I gave to an audience at Nature Publishing Group in New York on May 7th 2009. It's a long presentation and over an hour in length. Not much new here relative to other presentations...just a knitting together of many of the others on here.
There is an increasing availability of free and open access resources for scientists to use on the internet. Coupled with an increasing number of Open Source software programs we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 190 separate data sources, ChemSpider has taken on the task of both robotically and manually integrating and curating publicly available data sources. ChemSpider has also provided an environment for users to deposit, curate and annotate chemistry-related information. This has allowed the community to enhance ChemSpider by adding analytical data, associating synthetic pathways and publications and connecting to social networking resources. I will discuss how ChemSpider is fast becoming the premier curated platform and centralized hub for resourcing information about chemical entities and how the platform provides the foundation data for services allowing the analysis of analytical data and collaborative science.ChemSpider as a Foundation for Crowdsourcing and Collaborations in Open Chemi...
ChemSpider as a Foundation for Crowdsourcing and Collaborations in Open Chemi...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry provides open access to data associated with tens of millions of chemical compounds. 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 delivering 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 the challenges of managing “Big Data” for chemists around the world and providing access to tools for structure dereplication, spectral database searching and the crowdsourcing of the worlds’ largest spectral database.Dealing with the complex challenge of managing diverse analytical chemistry d...
Dealing with the complex challenge of managing diverse analytical chemistry d...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. There are many tens of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the diversity of databases available online their inherent quality, accuracy and completeness is lacking in many regards. ChemSpider was established to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data and experimental properties. ChemSpider has now grown into a database of over 20 million chemical substances integrated with over 300 disparate data sources, many of these directly supporting the Life Sciences. This presentation will provide an overview of our efforts to improve the quality of data online, to provide a foundation for the semantic web for chemistry and to provide access to a set online tools and services to support access to these data. I will also discuss how ChemSpider is being used to enhance Semantic Publishing in Chemistry at RSC.
ChemSpider – A Community Platform for Chemistry and Resources Supporting the ...
ChemSpider – A Community Platform for Chemistry and Resources Supporting the ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Laboratories around the world continue to generate immense amounts of data that are non-proprietary and of value to the community. If available these data could dramatically reduce costs by minimizing rework and ultimately facilitating faster research. High quality reference data collections of chemical compound dictionaries, properties and spectra have been generated over many decades. With the advent of social networking tools and platforms such as Wikipedia, the community has an opportunity to contribute. The ChemSpider platform hosted by the Royal Society of Chemistry is a compound centric database with associated data. Already populated with almost 25 million unique compounds the community can deposit and host their own data, and curate and annotate existing data including those generated in Open Notebook Science Efforts. This presentation will provide an overview of progress to date and outline the vision of this community platform for chemistry and ensuring the longevity of chemistry reference data. Hosting a compound centric community resource for chemistry data
Hosting a compound centric community resource for chemistry dataUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The internet now offers access to a myriad of online resources that can be of value to chemists working in the Life Sciences. While finding information online is, in many cases, a simple search away, the accuracy and validity of the associated data and information should be questioned. As more databases and resources are introduced online, and commonly not integrated to other resources, a scientist must perform multiple searches and then undertake the task of meshing and merging data. ChemSpider is a freely accessible online database that has taken on the challenge of meshing together distributed resources across the internet to provide a structure-based hub. It is a crowdsourcing environment hosting over 26 million unique compounds linked out to over 400 data sources. With well defined programming interfaces for integration ChemSpider has been integrated to many commercial and open software packages and is presently serving as the chemistry foundation for the IMI Open PHACTS project.
Integrating and curating internet based chemistry resources to serve life sci...
Integrating and curating internet based chemistry resources to serve life sci...US 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
The increasing availability of free and open access resources for scientists on the internet presents us with a revolution in data availability. The Royal Society of Chemistry hosts ChemSpider, a free access website for chemists built with the intention of building community for chemists (http://www.chemspider.com/).
ChemSpider is an aggregator of chemistry related information, at present over 20 million unique chemical entities linked out to over 300 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. It is also a public deposition platform where chemists can deposit their own data including novel structures, analytical data, synthesis procedures and host data associated with the growing activities associated with Open Notebook Science.
This presentation will examine chemistry on the internet, the dubious quality of what is available and how the ChemSpider crowdsourced curation platform is fast becoming one of the centralized hubs for resourcing information about chemical entities.
We will also review our efforts to provide free resources for synthesis procedures, spectral data and structure-based searching of the chemistry literature and how chemists can contribute directly to each of these projects.
RSC ChemSpider -- Managing and Integrating Chemistry on the Internet to Build...
RSC ChemSpider -- Managing and Integrating Chemistry on the Internet to Build...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
A Talk delivered at both UNC Chapel Hill and Drexel University
There is an increasing availability of free and open access resources for scientists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. However, freedom costs and in many cases the cost is quality. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 150 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. This presentation will provide an overview of the issue of quality in many chemistry-related databases, approaches to cleaning up the data and how a curated platform can become the centralized hub for resourcing information about chemical entities. This includes experimental and predicted properties, analytical data, publications, suppliers and integrated databases. I will detail three efforts :1) the curation of chemistry on Wikipedia 2) an examination of structure integrity on the FDA Daily Med website, a web site of medication content and labeling as found in medication package inserts 3) recognizing chemical names in documents and providing a platform for structure-based searching of Open Access chemistry literature.Crowdsourcing, Collaborations And Text Mining In A World Of Open Chemistry
Crowdsourcing, Collaborations And Text Mining In A World Of Open ChemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider is a free access website for chemists built with the vision of providing a structure centric community for chemists. Vision is great…execution is better. ChemSpider is now one of the internet’s primary portals for chemistry offering access to over 23 million unique chemical structures from over 200 data sources and expanding daily. Even though there are tens if not hundreds of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. there has been no single way to search across them. Despite the fact that there are a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness remains lacking in many regards. With ChemSpider we have provided a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data, experimental properties and linking to other valuable resources.
This presentation will provide an overview of ChemSpider and its value to chemists as a search tool, as a public repository of information and how it can become one of the primary foundations of internet-based chemistry. I will also discuss the vision for ChemSpider and some of the exciting goals we are setting for the system moving forward.Why Chemistry and the Web Will Benefit from a ChemSpider
Why Chemistry and the Web Will Benefit from a ChemSpiderUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are advancing the identification of emerging contaminants in environmental and agricultural matrices. However, confidence in structure identification of unknowns in NTA presents challenges to analytical chemists. Structure identification requires integration of complementary data types such as reference databases, fragmentation prediction tools, and retention time prediction models. The goal of this research is to optimize and implement structure identification functionality within the US EPA’s CompTox Chemicals Dashboard, an open chemistry resource and web application containing data for ~760,000 substances. Rank-ordering the number of sources associated with chemical records within the Dashboard (Data Source Ranking) improves the identification of unknowns by bringing the most likely candidate structures to the top of a search results list. Incorporating additional data streams contained within the database underlying the Dashboard further enhances identifications. Integrating tandem mass spectrometry data into NTA workflows enables spectral match scores and increases confidence in structural assignments. We have generated and stored predicted MS/MS fragmentation spectra for the entirety of the Chemistry Dashboard using the in silico prediction tool CFM-ID. Predicted fragments incorporated into the identification workflow were used as both a scoring term and as a candidate threshold cutoff. Combining these steps within an open chemistry resource provides a freely available software tool for structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Consensus ranking and fragmentation prediction for identification of unknowns...
Consensus ranking and fragmentation prediction for identification of unknowns...US 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
The internet continues to offer increased access to chemistry data that may be of value to scientists interested in populating systems containing reference toxicology data as well as to provide data for the development of predictive models. This presentation will give an overview of some of the various sources of data available via the internet, provide an overview of some of the challenges associated with gathering high-quality data and discuss methods by which to mesh together disparate data sources.Sourcing high quality online data resources for computational toxicology
Sourcing high quality online data resources for computational toxicologyUS 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 original abstract for the talk is below BUT the talk changed based on a big interest in InChI and the possibilities to use in a Semantic Web for Chemistry
The increasing availability of free and open access resources for scientists on the internet presents us with a revolution in data availability. However, freedom costs and in many cases the cost is quality. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 150 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. This presentation will provide an overview of how a curated platform can become the centralized hub for resourcing information about chemical entities. We will also present ChemMantis, an entity extraction platform for extracting chemical names and scientific terms in documents and providing a platform for structure-based searching of Open Access chemistry literature.Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry
Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry 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
Presentation "Effective Embedding of Information and
Knowledge about Group Activity
into the Discussion Process". Author: Santi Caballé for the journey "Análisis del comportamiento de los estudiantes de la UOC"Effective Embedding of Information and Knowledge about Group Activity into th...
Effective Embedding of Information and Knowledge about Group Activity into th...UNESCO Chair in Education & Technology for Social Change
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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
The increasing availability of free and open access resources for scientists on the internet presents us with a revolution in data availability. The Royal Society of Chemistry hosts ChemSpider, a free access website for chemists built with the intention of building community for chemists (http://www.chemspider.com/).
ChemSpider is an aggregator of chemistry related information, at present over 20 million unique chemical entities linked out to over 300 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. It is also a public deposition platform where chemists can deposit their own data including novel structures, analytical data, synthesis procedures and host data associated with the growing activities associated with Open Notebook Science.
This presentation will examine chemistry on the internet, the dubious quality of what is available and how the ChemSpider crowdsourced curation platform is fast becoming one of the centralized hubs for resourcing information about chemical entities.
We will also review our efforts to provide free resources for synthesis procedures, spectral data and structure-based searching of the chemistry literature and how chemists can contribute directly to each of these projects.
RSC ChemSpider -- Managing and Integrating Chemistry on the Internet to Build...
RSC ChemSpider -- Managing and Integrating Chemistry on the Internet to Build...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
A Talk delivered at both UNC Chapel Hill and Drexel University
There is an increasing availability of free and open access resources for scientists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. However, freedom costs and in many cases the cost is quality. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 150 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. This presentation will provide an overview of the issue of quality in many chemistry-related databases, approaches to cleaning up the data and how a curated platform can become the centralized hub for resourcing information about chemical entities. This includes experimental and predicted properties, analytical data, publications, suppliers and integrated databases. I will detail three efforts :1) the curation of chemistry on Wikipedia 2) an examination of structure integrity on the FDA Daily Med website, a web site of medication content and labeling as found in medication package inserts 3) recognizing chemical names in documents and providing a platform for structure-based searching of Open Access chemistry literature.Crowdsourcing, Collaborations And Text Mining In A World Of Open Chemistry
Crowdsourcing, Collaborations And Text Mining In A World Of Open ChemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider is a free access website for chemists built with the vision of providing a structure centric community for chemists. Vision is great…execution is better. ChemSpider is now one of the internet’s primary portals for chemistry offering access to over 23 million unique chemical structures from over 200 data sources and expanding daily. Even though there are tens if not hundreds of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. there has been no single way to search across them. Despite the fact that there are a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness remains lacking in many regards. With ChemSpider we have provided a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data, experimental properties and linking to other valuable resources.
This presentation will provide an overview of ChemSpider and its value to chemists as a search tool, as a public repository of information and how it can become one of the primary foundations of internet-based chemistry. I will also discuss the vision for ChemSpider and some of the exciting goals we are setting for the system moving forward.Why Chemistry and the Web Will Benefit from a ChemSpider
Why Chemistry and the Web Will Benefit from a ChemSpiderUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are advancing the identification of emerging contaminants in environmental and agricultural matrices. However, confidence in structure identification of unknowns in NTA presents challenges to analytical chemists. Structure identification requires integration of complementary data types such as reference databases, fragmentation prediction tools, and retention time prediction models. The goal of this research is to optimize and implement structure identification functionality within the US EPA’s CompTox Chemicals Dashboard, an open chemistry resource and web application containing data for ~760,000 substances. Rank-ordering the number of sources associated with chemical records within the Dashboard (Data Source Ranking) improves the identification of unknowns by bringing the most likely candidate structures to the top of a search results list. Incorporating additional data streams contained within the database underlying the Dashboard further enhances identifications. Integrating tandem mass spectrometry data into NTA workflows enables spectral match scores and increases confidence in structural assignments. We have generated and stored predicted MS/MS fragmentation spectra for the entirety of the Chemistry Dashboard using the in silico prediction tool CFM-ID. Predicted fragments incorporated into the identification workflow were used as both a scoring term and as a candidate threshold cutoff. Combining these steps within an open chemistry resource provides a freely available software tool for structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Consensus ranking and fragmentation prediction for identification of unknowns...
Consensus ranking and fragmentation prediction for identification of unknowns...US 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
The internet continues to offer increased access to chemistry data that may be of value to scientists interested in populating systems containing reference toxicology data as well as to provide data for the development of predictive models. This presentation will give an overview of some of the various sources of data available via the internet, provide an overview of some of the challenges associated with gathering high-quality data and discuss methods by which to mesh together disparate data sources.Sourcing high quality online data resources for computational toxicology
Sourcing high quality online data resources for computational toxicologyUS 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 original abstract for the talk is below BUT the talk changed based on a big interest in InChI and the possibilities to use in a Semantic Web for Chemistry
The increasing availability of free and open access resources for scientists on the internet presents us with a revolution in data availability. However, freedom costs and in many cases the cost is quality. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 150 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. This presentation will provide an overview of how a curated platform can become the centralized hub for resourcing information about chemical entities. We will also present ChemMantis, an entity extraction platform for extracting chemical names and scientific terms in documents and providing a platform for structure-based searching of Open Access chemistry literature.Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry
Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry 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
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Current advances to bridge the usability-expressivity gap in biomedical seman...
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Clustering the royal society of chemistry chemical repository to enable enhan...
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Acs collaborative computational technologies for biomedical research an enabl...
Data integration and building a profile for yourself as an online scientist
Data integration and building a profile for yourself as an online scientist
RSC ChemSpider -- Managing and Integrating Chemistry on the Internet to Build...
RSC ChemSpider -- Managing and Integrating Chemistry on the Internet to Build...
Crowdsourcing, Collaborations And Text Mining In A World Of Open Chemistry
Crowdsourcing, Collaborations And Text Mining In A World Of Open Chemistry
ICIC 2017: Freeware and public databases: Towards a Wiki Drug Discovery?
ICIC 2017: Freeware and public databases: Towards a Wiki Drug Discovery?
Why Chemistry and the Web Will Benefit from a ChemSpider
Why Chemistry and the Web Will Benefit from a ChemSpider
Consensus ranking and fragmentation prediction for identification of unknowns...
Consensus ranking and fragmentation prediction for identification of unknowns...
Building linked data large-scale chemistry platform - challenges, lessons and...
Building linked data large-scale chemistry platform - challenges, lessons and...
eScience Resources for the Chemistry Community from the Royal Society of Chem...
eScience Resources for the Chemistry Community from the Royal Society of Chem...
Sourcing high quality online data resources for computational toxicology
Sourcing high quality online data resources for computational toxicology
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Serving the medicinal chemistry community with Royal Society of Chemistry che...
Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry
Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry
eScience at the Royal Society of Chemistry and our current initiatives
eScience at the Royal Society of Chemistry and our current initiatives
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Ähnlich wie How a Structure-Centric Community for Chemists Can Benefit Drug Discovery - Virtual Screening Experiments Utilizing a Publicly Accessible Ligand Database, QSAR Modeling Tools and a Virtual Docking Software Package
ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. It was developed to index available sources of chemical structures and their associated data into a single searchable repository and making it available to everybody, at no charge. While there are a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness is severely lacking. ChemSpider has provided a platform so that the chemistry community could contribute to improving the quality of data online and expanding the information to include data such as reaction syntheses, analytical data, experimental properties and linkages to other valuable resources. It has grown into a resource containing over 21 million unique chemical structures from over 200 data sources.
This presentation will provide an overview of ChemSpider and its value to chemists as a search tool, as a public repository of information and how it can become one of the primary foundations of internet-based chemistry. I will also discuss the vision for ChemSpider and some of the lofty goals we are setting for the system moving forward.
Crawling Across the Web of Chemistry Using ChemSpider
Crawling Across the Web of Chemistry Using ChemSpider US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
These are the slides I will be giving here at the Science Commons Symposium Pacific Northwest at the Microsoft Campus here in Redmond in about 5 minutes timeRSC ChemSpider Science Commons Symposium Pacific Northwest #scspn
RSC ChemSpider Science Commons Symposium Pacific Northwest #scspnUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
I am an adjunct prof at University of North Carolina Chapel Hill so when I stopped by yesterday for a business meeting I was informed that I had been lined up to give a talk to the students at 1pm. I had 20 minutes to prepare and assembled a mish-mash of information that might be of value to Citizen Chemists, those who might want to contribute to chemistry on the internetTaming The Wild West Of Internet Based Chemistry You Can Help
Taming The Wild West Of Internet Based Chemistry You Can HelpUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a presentation I gave at the FDA on December 1st 2009 in Wahington DC as part of a symposium involving PubChem, ChemIDPLus, PillBox, DailyMed and other related systems. The focus was, as usual, on the quality of data online and how to clean up the information and with a specific focus on the quality of data on the FDA's DailyMed and our efforts to apply semantic markup to the DailyMed articlesChemSpider and How The Wisdom Of The Crowds Can Improve The Quality Of ...
ChemSpider and How The Wisdom Of The Crowds Can Improve The Quality Of ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This slide deck was used for an overview training at RSC, Burlington House in March 2010.Connecting Chemists To The Internet Training at Burlington House 2010
Connecting Chemists To The Internet Training at Burlington House 2010US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The presentation of ChemSpider was to a groub of science librarians, specifically chemistry librarians, and was meant to provide an overview of the platform and answer the question posed: What is the difference between ChemSpider, CAS Scifinder and Reaxys. ChemSpider Presentation At University Of Toronto
ChemSpider Presentation At University Of TorontoUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a presentation given to the Royal Society General Assembly in Birmingham on November 20th 2009. This covers the present status and future vision for ChemSpiderConnecting Chemists to the Internet Through ChemSpider
Connecting Chemists to the Internet Through ChemSpiderUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider is an online database of over 20 million chemical structures assembled from well over a hundred data sources including chemical and screening library vendors, publicly accessible databases and resources, commercial databases and Open Access literature articles. Such a public resource provides a rich source of ligands for the purpose of virtual screening experiments. These can take many forms. This work will present results from two specific types of studies: 1) Quantitative Structure Activity Relationship (QSAR) based analyses and 2) In-silico docking into protein receptor sites. We will review results from the application of both approaches to a number of specific examples. QSAR analyses utilizing the ChemModLab environment for assessing quantitative structure-activity relationships will and screening using a molecular surface descriptor model.Can a Free Access Structure-Centric Community for Chemists Benefit Drug Disco...
Can a Free Access Structure-Centric Community for Chemists Benefit Drug Disco...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
There is an increasing availability of free and open access resources for chemists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. It was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge.
There are tens if not hundreds of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the fact that there were a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness was lacking in many regards. The intention with ChemSpider was to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data, experimental properties and linking to other valuable resources. It has grown into a resource containing over 21 million unique chemical structures from over 200 data sources.
ChemSpider has enabled real time curation of the data, association of analytical data with chemical structures, real-time deposition of single or batch chemical structures (including with activity data) and transaction-based predictions of physicochemical data. The social community aspects of the system demonstrate the potential of this approach. Curation of the data continues daily and thousands of edits and depositions by members of the community have dramatically improved the quality of the data relative to other public resources for chemistry.
This presentation will provide an overview of the history of ChemSpider, the present capabilities of the platform and how it can become one of the primary foundations of the semantic web for chemistry. It will also discuss some of the present projects underway since the acquisition of ChemSpider by the Royal Society of Chemistry.
ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd So...
ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd So...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Internet is the world’s publicly accessible container for a myriad of resources containing chemistry related data. Whether it be collections of millions of chemical compounds with their associated properties, interactive displays for analytical data, access to publications and patents or tapping into the increasing availability of online computational engines, the web has became the primary enabling technology to source information and data. Scientists collectively applaud and utilize the availability of such resources and an increasing proportion of the community are willing to support these resources by contributing both their data and skills to help curate and validate information on the web. This “crowdsourcing” has started to contribute large amounts of data to the commons and serves has a valuable platform for reference and, potentially, discovery.
ChemSpider is one of the chemistry community’s primary online resources and allows scientists to search across 25 million unique chemical compounds linked out to over 400 original data sources and has become a central hub for searching for chemistry-related data. The platform however offers much more to the community and has become a central repository for analytical data, specifically spectra, is a host for community-authored chemical syntheses and facilitates data curation and annotation by any of its users. This presentation will provide an overview of the ChemSpider platform in terms of available data and its efforts to act as a public repository and clearing ground for data curation. We will discuss how such a platform, when coupled with game-based approaches, facilitates both teaching and data validation and will discuss whether public domain resources such as ChemSpider will ultimately become authorities for chemistry.
ChemSpider hosting linking and curating chemistry data for the community
ChemSpider hosting linking and curating chemistry data for the communityUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program utilizes computational and data-driven approaches that integrate chemistry, exposure and biological data to help characterize potential risks from chemical exposure. The National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences, including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. The CompTox Chemicals Dashboard website provides access to data associated with ~900,000 chemical substances. New data are added on an ongoing basis, including the registration of new and emerging chemicals, data extracted from the literature, chemicals studied in our labs, and data of interest to specific research projects at the EPA. Hazard and exposure data have been assembled from a large number of public databases and as a result the dashboard surfaces hundreds of thousands of data points. Other data includes experimental and predicted physicochemical property data, in vitro bioassay data and millions of chemical identifiers (names and CAS Registry Numbers) to facilitate searching. Other integrated modules include real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed. This presentation will provide an overview of the CompTox Chemicals Dashboard and how it has developed into an integrated data hub for environmental data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.US-EPA Chemicals Dashboard – an integrated data hub for environmental science
US-EPA Chemicals Dashboard – an integrated data hub for environmental scienceUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a presentation given in Track 4, Open Access and Cheminformatics, at the Bio-IT Meeting in Boston on April 21st 2010. It is a general overview of ChemSpider activities to link together the internet for chemists and validate and curate data. We won the Bio-IT Best Practices Community Service Award that evening also.Building A Community Resource For The Life Sciences
Building A Community Resource For The Life SciencesUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation provides an overview to chemical vendors (and to some extent to other depositors) of the value of putting their chemical compound collections online at ChemSPider. This is a no cost service for the community - no costs to the user or to the chemical vendor.The Benefits to Chemical Vendors of Putting their data on ChemSpider
The Benefits to Chemical Vendors of Putting their data on ChemSpiderUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a presentation given at the Triangle Chromatography Discussion Group with a focus on Mass Spectrometry and associated web services and what is possible for chromatographersHow an Online Resource for Chemistry Can Change Our World
How an Online Resource for Chemistry Can Change Our WorldUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
There is an increasing availability of free and open access resources for scientists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 200 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. This presentation will provide an overview of the ChemSpider platform and how it is fast becoming the centralized hub for resourcing information about chemical entities. Navigating the Complex Web of Chemistry Using ChemSpider
Navigating the Complex Web of Chemistry Using ChemSpiderUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. There are many tens of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the diversity of databases available online their inherent quality, accuracy and completeness is lacking in many regards. ChemSpider was established to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data and experimental properties. ChemSpider has now grown into a database of well over 20 million chemical substances integrated with over 300 disparate data sources, many of these directly supporting the Life Sciences. This presentation will provide an overview of our efforts to improve the quality of data online, to provide a foundation for the semantic web for chemistry and to provide access to a set online tools and services to support access to these data. I will also discuss how ChemSpider is being used to enhance Semantic Publishing in Chemistry at RSC. ChemSpider – A Platform to Gather, Host and Integrate Structure Based Data Ac...
ChemSpider – A Platform to Gather, Host and Integrate Structure Based Data Ac...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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Crawling Across the Web of Chemistry Using ChemSpider
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RSC ChemSpider Science Commons Symposium Pacific Northwest #scspn
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Taming The Wild West Of Internet Based Chemistry You Can Help
ChemSpider and How The Wisdom Of The Crowds Can Improve The Quality Of ...
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Connecting Chemists To The Internet Training at Burlington House 2010
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Connecting Chemists to the Internet Through ChemSpider
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Can a Free Access Structure-Centric Community for Chemists Benefit Drug Disco...
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ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd So...
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ChemSpider hosting linking and curating chemistry data for the community
US-EPA Chemicals Dashboard – an integrated data hub for environmental science
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Building A Community Resource For The Life Sciences
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How an Online Resource for Chemistry Can Change Our World
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Navigating the Complex Web of Chemistry Using ChemSpider
Navigating the Complex Web of Chemistry Using ChemSpider
ChemSpider – A Platform to Gather, Host and Integrate Structure Based Data Ac...
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How a Structure-Centric Community for Chemists Can Benefit Drug Discovery - Virtual Screening Experiments Utilizing a Publicly Accessible Ligand Database, QSAR Modeling Tools and a Virtual Docking Software Package
- 9. Search Open Access Journals – ChemSpider
- 10. Search PubMed – ChemSpider
- 12. Quality is a Major Issue
- 14. Multi-level Curation and Approval
- 19. LASSO Descriptors on ChemSpider
- 21. LASSO Searching Method 2
- 26. General Trends?
- 27. ChemModLab + ChemSpider ECCR at North Carolina State Statistical Analysis Statistical Model Selected Compounds Initial Compounds Active Compounds Screen Compounds Collection
- 30. Results 2M commercial compounds taken from ChemSpider. Batches of 50k compounds processed. 42 batches on 12 processors takes about 12 minutes. Top 1000 predicted compounds selected Best model was Random Forest
- 31. PowerMV, 1000 predicted actives
- 32. Similarity Set 1
- 33. Similarity Set 2