Navigating an Internet of Chemistry via ChemSpider
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This is a presentation I gave via the BigBlueButton system to students and faculty at the University of Arkansas, Little Rock, regarding searching the internet for Chemistry.
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This is a short presentation given to chemistry students at Drexel University as a remote presentation. This was for the class of Jean-Claude Bradley.ChemSpider and Traveling the Internet via Chemical Structures Cheminformatics...
ChemSpider and Traveling the Internet via Chemical Structures Cheminformatics...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry hosts one of the worlds’ richest collections of online chemistry data that is free-to-access for the community. ChemSpider presently hosts over 30 million unique chemical compounds together with associated data and accessible via a number of search techniques. With almost 50,000 unique users per day from around the world the site offers scientists the ability to investigate the world of small molecules via property searches, analytical data and predictive models. The challenges associated with providing a similar platform for “materials” are manifold but, if they could be addressed, would offer a valuable service to the materials community. This presentation will provide an overview of how ChemSpider was built, our efforts to expand the capabilities to a more encompassing data repository and some of the challenges faced to embrace the diverse world of materials informatics and online data access.Hosting public domain chemicals data online for the community – the challenge...
Hosting public domain chemicals data online for the community – the challenge...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a presentation given to a group of students at the UNC Eshelman School of Pharmacy.
As chemists many of us want to resource information that is high quality, accurate and addresses our query. With the increasing proliferation of online chemistry resources it is very common for us to turn to these resources to source data. However, are resources such as Wikipedia, PubChem and the plethora of databases delivering information for metabolism, medicinal chemistry and synthetic chemistry trustworthy? Which of these resources, if any, should be treated as authorities? What is the most integrated approach to resource chemistry related data online? What approaches can be taken to validate the data that is available and how can individual scientists participate in helping to improve the content and quality of chemistry related data on the web.
Antony Williams is ChemSpiderman. He started the ChemSpider database (www.chemspider.com) as a hobby to deliver a free platform for the community to source chemistry related data. Within three years the system was acquired by the Royal Society of Chemistry and now serves up close to 25 million chemical structures linked to over 400 data sources across the internet and offers individual scientists the opportunity to host and share their data with the community and to participate in data curation and annotation. Tony will share his experiences of building this chemistry database with a focus on data validation and curation and sourcing high quality data. During the presentation he will discuss ways to check chemical structure representations before submission to public systems for searching and provide an overview of chemical identifiers such as SMILES strings and the International Chemical Identifier (InChI) allows for the interlinking of resources. Attendees can expect to leave the session with a deeper understanding of utilizing the internet to resource chemistry related data.
Chemicals, Chemical Identifiers and Navigating Through Databases
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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
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
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
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
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This is a short presentation given to chemistry students at Drexel University as a remote presentation. This was for the class of Jean-Claude Bradley.ChemSpider and Traveling the Internet via Chemical Structures Cheminformatics...
ChemSpider and Traveling the Internet via Chemical Structures Cheminformatics...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry hosts one of the worlds’ richest collections of online chemistry data that is free-to-access for the community. ChemSpider presently hosts over 30 million unique chemical compounds together with associated data and accessible via a number of search techniques. With almost 50,000 unique users per day from around the world the site offers scientists the ability to investigate the world of small molecules via property searches, analytical data and predictive models. The challenges associated with providing a similar platform for “materials” are manifold but, if they could be addressed, would offer a valuable service to the materials community. This presentation will provide an overview of how ChemSpider was built, our efforts to expand the capabilities to a more encompassing data repository and some of the challenges faced to embrace the diverse world of materials informatics and online data access.Hosting public domain chemicals data online for the community – the challenge...
Hosting public domain chemicals data online for the community – the challenge...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a presentation given to a group of students at the UNC Eshelman School of Pharmacy.
As chemists many of us want to resource information that is high quality, accurate and addresses our query. With the increasing proliferation of online chemistry resources it is very common for us to turn to these resources to source data. However, are resources such as Wikipedia, PubChem and the plethora of databases delivering information for metabolism, medicinal chemistry and synthetic chemistry trustworthy? Which of these resources, if any, should be treated as authorities? What is the most integrated approach to resource chemistry related data online? What approaches can be taken to validate the data that is available and how can individual scientists participate in helping to improve the content and quality of chemistry related data on the web.
Antony Williams is ChemSpiderman. He started the ChemSpider database (www.chemspider.com) as a hobby to deliver a free platform for the community to source chemistry related data. Within three years the system was acquired by the Royal Society of Chemistry and now serves up close to 25 million chemical structures linked to over 400 data sources across the internet and offers individual scientists the opportunity to host and share their data with the community and to participate in data curation and annotation. Tony will share his experiences of building this chemistry database with a focus on data validation and curation and sourcing high quality data. During the presentation he will discuss ways to check chemical structure representations before submission to public systems for searching and provide an overview of chemical identifiers such as SMILES strings and the International Chemical Identifier (InChI) allows for the interlinking of resources. Attendees can expect to leave the session with a deeper understanding of utilizing the internet to resource chemistry related data.
Chemicals, Chemical Identifiers and Navigating Through Databases
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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
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
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
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
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
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
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.
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ChemSpider – A Community Platform for Chemistry and Resources Supporting the ...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
With an intention to provide a high quality free internet resource of chemistry related data for the community, ChemSpider has aggregated almost 25 million compounds linked out to over 400 data sources and provided a platform for the community to both deposit and curate data. This experiment in crowdsourcing for chemistry has now been running for over three years. This presentation will review a number of aspects of the project including (a) the level of community participation in depositing and curating data; (b) the nature of data and content supplied by the community; (c) how ChemSpider is used by the community; (d) using game-based systems to assist in data curation; (e) algorithmic-based approaches to data validation and filtering; and (f) sharing data curation efforts with other online databases. ChemSpider - Does Community Engagement work to Build a Quality Online Resourc...
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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
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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
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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
The ChemSpider database is a resource hosted by the Royal Society of Chemistry. With over 28 million unique chemicals on the database linked out to over 400 data sources the platform provides access to experimental and predicted data (properties, spectra etc.), links to publications, patents and a myriad of other resources. The ChemSpider database has been used as the foundation of a number of other resources for chemists including ChemSpider SyntheticPages, the Learn Chemistry Wiki and the Spectral Game. This presentation will provide an overview of ChemSpider and discuss how chemists can both derive value from and contribute to the content available from the database and its related resources. We will also discuss our view of future platform for managing personal, institutional and public chemistry in a shared environment.RSC ChemSpider is the online chemistry database where community contributions...
RSC ChemSpider is the online chemistry database where community contributions...US 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 ...
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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...
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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
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 is a presentation I gave at the Nature Publishing group offices in London UK. It covers general information about ChemSPider and our efforts with ChemMantis.A Presentation at Nature Publishing Group Crowdsourcing, Collaborations and T...
A Presentation at Nature Publishing Group Crowdsourcing, Collaborations and T...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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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
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
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.
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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
With an intention to provide a high quality free internet resource of chemistry related data for the community, ChemSpider has aggregated almost 25 million compounds linked out to over 400 data sources and provided a platform for the community to both deposit and curate data. This experiment in crowdsourcing for chemistry has now been running for over three years. This presentation will review a number of aspects of the project including (a) the level of community participation in depositing and curating data; (b) the nature of data and content supplied by the community; (c) how ChemSpider is used by the community; (d) using game-based systems to assist in data curation; (e) algorithmic-based approaches to data validation and filtering; and (f) sharing data curation efforts with other online databases. ChemSpider - Does Community Engagement work to Build a Quality Online Resourc...
ChemSpider - Does Community Engagement work to Build a Quality Online Resourc...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
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
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
The ChemSpider database is a resource hosted by the Royal Society of Chemistry. With over 28 million unique chemicals on the database linked out to over 400 data sources the platform provides access to experimental and predicted data (properties, spectra etc.), links to publications, patents and a myriad of other resources. The ChemSpider database has been used as the foundation of a number of other resources for chemists including ChemSpider SyntheticPages, the Learn Chemistry Wiki and the Spectral Game. This presentation will provide an overview of ChemSpider and discuss how chemists can both derive value from and contribute to the content available from the database and its related resources. We will also discuss our view of future platform for managing personal, institutional and public chemistry in a shared environment.RSC ChemSpider is the online chemistry database where community contributions...
RSC ChemSpider is the online chemistry database where community contributions...US 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 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
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
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 is a presentation I gave at the Nature Publishing group offices in London UK. It covers general information about ChemSPider and our efforts with ChemMantis.A Presentation at Nature Publishing Group Crowdsourcing, Collaborations and T...
A Presentation at Nature Publishing Group Crowdsourcing, Collaborations and T...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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Navigating an Internet of Chemistry via ChemSpider
- 1. Navigating an Internet of Chemistry via ChemSpider Antony Williams University of Arkansas, Little Rock, October 2011 UALR Chemistry Seminar Guest Lecture
- 4. Representative Flavors of Chemistry
- 8. Stereo
- 13. Multiple Layers
- 14. Tautomers – “Mobile H Perception”
- 15. Stereo
- 17. Checking for Stereochemistry Use your drawing package!
- 23. InChIStrings Hash to InChIKeys
- 24. Vancomycin
- 25. Vancomycin Search Molecular SKELETON Search Full Molecule
- 29. I want to know about “Vincristine”
- 30. Vincristine: Identifiers and Properties
- 31. Vincristine: Identifiers and Properties
- 32. Vincristine: Vendors and Sources
- 35. Vancomycin Search Molecular SKELETON Search Full Molecule
- 36. Full Skeleton Search: 104 Hits
- 37. Full Molecule Search: 4 Hits
- 39. What’s said on the web is true…
- 40. What’s said on the web is true…
- 47. Spectra
- 51. Thank you Email: williamsa@rsc.org Twitter: ChemConnector Blog: www.chemspider.com/blog Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams