How an Online Resource for Chemistry Can Change Our World
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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 chromatographers
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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 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
An overview of the types of searches available on ChemSpider for MS Spectrometrists and how MS scientists can derive value from the ChemSpider databaseChemspider For Mass Spectrometrists Public Version
Chemspider For Mass Spectrometrists Public VersionUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a presentation I gave to a group of students at Drexel University via webex and skype. This is the Powerpoint presentation component but it was intersected with a live demo of multiple online databases. The movie of the presentation is online at SciVee here: http://www.scivee.tv/node/14770Citizen Scientists and Their Contributions to Internet Based Chemistry
Citizen Scientists and Their Contributions to Internet Based ChemistryUS 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
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
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
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
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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 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
An overview of the types of searches available on ChemSpider for MS Spectrometrists and how MS scientists can derive value from the ChemSpider databaseChemspider For Mass Spectrometrists Public Version
Chemspider For Mass Spectrometrists Public VersionUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a presentation I gave to a group of students at Drexel University via webex and skype. This is the Powerpoint presentation component but it was intersected with a live demo of multiple online databases. The movie of the presentation is online at SciVee here: http://www.scivee.tv/node/14770Citizen Scientists and Their Contributions to Internet Based Chemistry
Citizen Scientists and Their Contributions to Internet Based ChemistryUS 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
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
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
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 "vendor presentation" that I gave in New Orleans on June 14th 2010. It is a very general presentation on ChemSpider relevant to the needs of librarians.ChemSpider Overview Presentation at Special Libraries Association
ChemSpider Overview Presentation at Special Libraries AssociationUS 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
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
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
Presentation given at the Federal Environment Symposium on March 28th 2022.
As part of its mission the Center for Computational Toxicology and Exposure (CCTE) delivers access to chemicals related data via online Dashboards. The CompTox Chemicals Dashboard (available at https://comptox.epa.gov/dashboard) provides access to >900,000 chemicals and associated data including experimental and predicted property data, in vivo hazard data, in vitro bioactivity data, exposure data, and various other data types. The application provides a set of flexible searches allowing for search, visualization and downloads of the data to the desktop for further interrogation. This presentation will provide an overview of the Dashboard and other proof-of-concept applications. For example, the Hazard Comparison Dashboard has a module which allows profiling of chemicals based on toxicity types (https://doi.org/10.1007/s10098-019-01795-w). This presentation will also introduce a number of proof-of-concept modules in development. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Accessing Environmental Chemistry Data via Data Dashboards
Accessing Environmental Chemistry Data via Data DashboardsUS 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
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
Online chemistry resources have expanded dramatically in the past few years with resources such as PubChem, ChEBI, Wikipedia, ChemSpider and many others offering rich resources to scientists seeking data and information. ChemSpider has become one of the primary chemistry portals delivering a heterogeneous mix of Open and Closed data. ChemSpider offers a structure-centric community for collaboration enabling the crowd-sourced deposition and validation of online chemistry data. ChemSpider has also been integrated into the ChemMantis system – CHEMistry Markup And Nomenclature Transformation Integrated System. This platform facilitates entity extraction of science related terms using both heuristics and highly curated dictionaries. The resulting documents are marked up to allow viewing of chemical structures linked out to over 200 different data sources via the ChemSpider database.How Internet Resources Are Providing a Collaborative Community for Chemistry
How Internet Resources Are Providing a Collaborative Community for Chemistry 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
The internet has revolutionized the sharing of data and information and in the domain of chemistry there are many resources available to help with our research. In recent years various online resources have been introduced that allow users to access information, properties and data associated with chemical entities. At a time when CAS has declared that they now have over 50 million unique chemical entities in the registry the number of chemical structures distributed across the internet also measures in the tens of millions. There are many tens of databases on the internet hosting chemical structures associated with data focused on the specific nature of the collection – metabolic pathways, spectral data collections, chemical vendor collections, biological assay data and crystal structures are examples. Unfortunately there has been no single way to search across all of these resources. ChemSpider has taken on the task of integrating the multiple online resources of information into a single database using the chemical structure as the primary key and retaining the link out and attribution to the original datasource. In this manner ChemSpider intends to become a structure-centric hub for the chemistry community. This talk will provide an overview of the ChemSpider platform, how it is being used as a crowdsourcing platform for community-based curation of the data and the future vision of ChemSpider as one of the pillars of the semantic web of chemistry.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
RSC|ChemSpider is one of the world’s largest online resources for chemistry related data and services. Developed with the intention of delivering access to structure-based chemistry data via the internet the ChemSpider platform hosts over 26 million unique chemical compounds aggregated from over 400 data sources and provides an environment for the community to both annotate and curate these existing data as well as deposit new data to the system. The search system delivers flexible querying capabilities together with links to external sites for publication and patent data. ChemSpider has spawned a number of projects include ChemSpider SyntheticPages for hosting openly peer-reviewed chemical synthesis articles. This presentation will review the present capabilities of the ChemSpider system providing direct examples of how to use the system to source high quality data of value to pharmaceutical companies. We will discuss some of the challenges associated with validating data quality, examine how ChemSpider is a part of the semantic web for chemistry and investigate approaches to using ChemSpider integrated to analytical instrumentation.Improving online chemistry one structure at a time
Improving online chemistry one structure at a timeUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The extraction of chemical entities from documents such as patents and publications has been pursued for a number of years. We wish to report on ChemMantis, an integrated system for chemistry-based entity extraction and document mark-up enabling access to the rich resource of online chemistry know as ChemSpider. We will discuss the development of the platform from its inception as a series of dictionaries to the integration of an entity extraction algorithm and its expansion to a public deposition and publishing platform for chemistry. Chemistry articles can now be deposited, marked-up and exposed to the public within a few minutes in many cases making it an ideal platform for communicating research and providing integrated access to data sources including PubChem, ChEBI, Wikipedia and Entrez.Building an integrated system for chemistry markup and online publishing inte...
Building an integrated system for chemistry markup and online publishing inte...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
RSC|ChemSpider is one of the world’s largest online resources for chemistry related data and services. Developed with the intention of delivering access to structure-based chemistry data via the internet the ChemSpider platform hosts over 26 million unique chemical compounds aggregated from over 400 data sources and provides an environment for the community to both annotate and curate these existing data as well as deposit new data to the system. The search system delivers flexible querying capabilities together with links to external sites for publication and patent data. This presentation will review the present capabilities of the ChemSpider system providing direct examples of how to use the system to source high quality data of value to chemists. We will discuss some of the challenges associated with validating data quality and examine how ChemSpider is a part of the new “semantic web for chemistry”. ChemSpider has also spawned a number of additional projects include ChemSpider SyntheticPages for hosting openly peer-reviewed chemical synthesis articles, Learn Chemistry Wiki for students learning chemistry and SpectraSchool for learning spectroscopy.Delivering Curated Chemistry to the World via Crowdsourced Deposition and Ann...
Delivering Curated Chemistry to the World via Crowdsourced Deposition and Ann...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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This is a "vendor presentation" that I gave in New Orleans on June 14th 2010. It is a very general presentation on ChemSpider relevant to the needs of librarians.ChemSpider Overview Presentation at Special Libraries Association
ChemSpider Overview Presentation at Special Libraries AssociationUS 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
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
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
Presentation given at the Federal Environment Symposium on March 28th 2022.
As part of its mission the Center for Computational Toxicology and Exposure (CCTE) delivers access to chemicals related data via online Dashboards. The CompTox Chemicals Dashboard (available at https://comptox.epa.gov/dashboard) provides access to >900,000 chemicals and associated data including experimental and predicted property data, in vivo hazard data, in vitro bioactivity data, exposure data, and various other data types. The application provides a set of flexible searches allowing for search, visualization and downloads of the data to the desktop for further interrogation. This presentation will provide an overview of the Dashboard and other proof-of-concept applications. For example, the Hazard Comparison Dashboard has a module which allows profiling of chemicals based on toxicity types (https://doi.org/10.1007/s10098-019-01795-w). This presentation will also introduce a number of proof-of-concept modules in development. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Accessing Environmental Chemistry Data via Data Dashboards
Accessing Environmental Chemistry Data via Data DashboardsUS 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
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
Online chemistry resources have expanded dramatically in the past few years with resources such as PubChem, ChEBI, Wikipedia, ChemSpider and many others offering rich resources to scientists seeking data and information. ChemSpider has become one of the primary chemistry portals delivering a heterogeneous mix of Open and Closed data. ChemSpider offers a structure-centric community for collaboration enabling the crowd-sourced deposition and validation of online chemistry data. ChemSpider has also been integrated into the ChemMantis system – CHEMistry Markup And Nomenclature Transformation Integrated System. This platform facilitates entity extraction of science related terms using both heuristics and highly curated dictionaries. The resulting documents are marked up to allow viewing of chemical structures linked out to over 200 different data sources via the ChemSpider database.How Internet Resources Are Providing a Collaborative Community for Chemistry
How Internet Resources Are Providing a Collaborative Community for Chemistry 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
The internet has revolutionized the sharing of data and information and in the domain of chemistry there are many resources available to help with our research. In recent years various online resources have been introduced that allow users to access information, properties and data associated with chemical entities. At a time when CAS has declared that they now have over 50 million unique chemical entities in the registry the number of chemical structures distributed across the internet also measures in the tens of millions. There are many tens of databases on the internet hosting chemical structures associated with data focused on the specific nature of the collection – metabolic pathways, spectral data collections, chemical vendor collections, biological assay data and crystal structures are examples. Unfortunately there has been no single way to search across all of these resources. ChemSpider has taken on the task of integrating the multiple online resources of information into a single database using the chemical structure as the primary key and retaining the link out and attribution to the original datasource. In this manner ChemSpider intends to become a structure-centric hub for the chemistry community. This talk will provide an overview of the ChemSpider platform, how it is being used as a crowdsourcing platform for community-based curation of the data and the future vision of ChemSpider as one of the pillars of the semantic web of chemistry.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
RSC|ChemSpider is one of the world’s largest online resources for chemistry related data and services. Developed with the intention of delivering access to structure-based chemistry data via the internet the ChemSpider platform hosts over 26 million unique chemical compounds aggregated from over 400 data sources and provides an environment for the community to both annotate and curate these existing data as well as deposit new data to the system. The search system delivers flexible querying capabilities together with links to external sites for publication and patent data. ChemSpider has spawned a number of projects include ChemSpider SyntheticPages for hosting openly peer-reviewed chemical synthesis articles. This presentation will review the present capabilities of the ChemSpider system providing direct examples of how to use the system to source high quality data of value to pharmaceutical companies. We will discuss some of the challenges associated with validating data quality, examine how ChemSpider is a part of the semantic web for chemistry and investigate approaches to using ChemSpider integrated to analytical instrumentation.Improving online chemistry one structure at a time
Improving online chemistry one structure at a timeUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The extraction of chemical entities from documents such as patents and publications has been pursued for a number of years. We wish to report on ChemMantis, an integrated system for chemistry-based entity extraction and document mark-up enabling access to the rich resource of online chemistry know as ChemSpider. We will discuss the development of the platform from its inception as a series of dictionaries to the integration of an entity extraction algorithm and its expansion to a public deposition and publishing platform for chemistry. Chemistry articles can now be deposited, marked-up and exposed to the public within a few minutes in many cases making it an ideal platform for communicating research and providing integrated access to data sources including PubChem, ChEBI, Wikipedia and Entrez.Building an integrated system for chemistry markup and online publishing inte...
Building an integrated system for chemistry markup and online publishing inte...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
RSC|ChemSpider is one of the world’s largest online resources for chemistry related data and services. Developed with the intention of delivering access to structure-based chemistry data via the internet the ChemSpider platform hosts over 26 million unique chemical compounds aggregated from over 400 data sources and provides an environment for the community to both annotate and curate these existing data as well as deposit new data to the system. The search system delivers flexible querying capabilities together with links to external sites for publication and patent data. This presentation will review the present capabilities of the ChemSpider system providing direct examples of how to use the system to source high quality data of value to chemists. We will discuss some of the challenges associated with validating data quality and examine how ChemSpider is a part of the new “semantic web for chemistry”. ChemSpider has also spawned a number of additional projects include ChemSpider SyntheticPages for hosting openly peer-reviewed chemical synthesis articles, Learn Chemistry Wiki for students learning chemistry and SpectraSchool for learning spectroscopy.Delivering Curated Chemistry to the World via Crowdsourced Deposition and Ann...
Delivering Curated Chemistry to the World via Crowdsourced Deposition and Ann...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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ChemSpider Overview Presentation at Special Libraries Association
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ChemSpider hosting linking and curating chemistry data for the community
ChemSpider – A Community Platform for Chemistry and Resources Supporting the ...
ChemSpider – A Community Platform for Chemistry and Resources Supporting the ...
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ChemSpider as a Foundation for Crowdsourcing and Collaborations in Open Chemi...
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Royal Society of Chemistry open source cheminformatics platforms and libraries
Royal Society of Chemistry open source cheminformatics platforms and libraries
Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry
Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry
Navigating the Complex Web of Chemistry Using ChemSpider
Navigating the Complex Web of Chemistry Using ChemSpider
Improving online chemistry one structure at a time
Improving online chemistry one structure at a time
Building an integrated system for chemistry markup and online publishing inte...
Building an integrated system for chemistry markup and online publishing inte...
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Delivering Curated Chemistry to the World via Crowdsourced Deposition and Ann...
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Similar a How an Online Resource for Chemistry Can Change Our World
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
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
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
ChemSpider – The Vision and Challenges Associated with Building a Free Online...
ChemSpider – The Vision and Challenges Associated with Building a Free Online...US 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
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
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
This is a general presentation about our efforts to build an internet based community for chemists using ChemSpider. A general overview of data quality online, crowdsourced deposition and curation and our progress to deliver a solution to the community for resourcing data.RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For ChemistsUS 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 of assays 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. The presentation will offer a perspective of what is available today, our experiences of building a public compound database to link together the internet and a suggested path forward for enabling even greater integration and connectivity for chemistry data for the masses to both use and participate in developing. How the web has weaved a web of interlinked chemistry data final
How the web has weaved a web of interlinked chemistry data finalUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a workshop I gave on "Online Public Compound Databases" at the BCCE in Dallas, Texas on August 3rd 2010. It is an overview of online resources, InChI, linking data, online data quality, searching and ChemSpider.Online Public Compound Databases
Online Public Compound DatabasesUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Connecting Chemistry Across the Internet Using ChemSpider
Connecting Chemistry Across the Internet 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
The ChemSpider database is an online resource containing >26 million chemicals sourced from over 400 data sources. As a result the database is a rich resource supporting the verification and elucidation of chemical structures and is utilized by mass spectrometrists around the world using the online user interface as well as the application programming interface. This presentation will provide an overview of how ChemSpider can be used for the purpose of structure identification and will include (1) direct interaction with the online interface; (2) integration to mass spectrometry vendor software; (3) applications to the identification of “known unknowns” and a comparison with the capabilities of CAS Scifinder and (4) the hosting of online mass spectral data. Structure verification and elucidation using the ChemSpider database
Structure verification and elucidation using the ChemSpider databaseUS 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
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How an Online Resource for Chemistry Can Change Our World
- 1. How an Online Chemistry Resource Could Change Our World Antony Williams Triangle Chromatography Discussion Group, Raleigh, NC, May 2009
- 8. “ Good Stuff” TotallySynthetic.com
- 9. PubChem
- 16. Link outs
- 17. Complex Data and Information
- 21. Search Database Based on Mass
- 23. 59 hits/1.3 seconds from 21.5 MILLION
- 27. Search based on Data Sources
- 29. Links out to KEGG Kyoto Encyclopedia of Genes and Genomes
- 34. Web Services
- 36. Test results
- 42. What is “wrong”?
- 43. Quality is a Major Issue- Search Butanol OLD EXAMPLE..now fixed
- 47. Does one stereocenter matter? Thalidomide
- 51. Structures on DailyMed Poor Representations
- 52. Incorrect Structures Scanning (?) Issues
- 55. Collaborative Knowledge Management for Chemists
- 57. Taxol on PubChem
- 63. Crowdsourcing
- 65. Multi-level Curation and Approval
- 67. On the fly conversion
- 69. Integrations Out to Other Sources
- 70. Reactions
- 71. ChemSpider Everywhere RSC Compounds
Notas del editor
- This is a list of some of the things an MS scientist might want to do and some of the queries we have already experienced