Building A Community Resource For The Life Sciences
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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.
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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
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
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
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
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
There is an increasing availability of free and open access resources for chemists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. It was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge.
There are tens if not hundreds of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the fact that there were a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness was lacking in many regards. The intention with ChemSpider was to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data, experimental properties and linking to other valuable resources. It has grown into a resource containing over 21 million unique chemical structures from over 200 data sources.
ChemSpider has enabled real time curation of the data, association of analytical data with chemical structures, real-time deposition of single or batch chemical structures (including with activity data) and transaction-based predictions of physicochemical data. The social community aspects of the system demonstrate the potential of this approach. Curation of the data continues daily and thousands of edits and depositions by members of the community have dramatically improved the quality of the data relative to other public resources for chemistry.
This presentation will provide an overview of the history of ChemSpider, the present capabilities of the platform and how it can become one of the primary foundations of the semantic web for chemistry. It will also discuss some of the present projects underway since the acquisition of ChemSpider by the Royal Society of Chemistry.
ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd So...
ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd So...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The internet 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
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
Recommandé
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
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
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
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
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
There is an increasing availability of free and open access resources for chemists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. It was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge.
There are tens if not hundreds of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the fact that there were a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness was lacking in many regards. The intention with ChemSpider was to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data, experimental properties and linking to other valuable resources. It has grown into a resource containing over 21 million unique chemical structures from over 200 data sources.
ChemSpider has enabled real time curation of the data, association of analytical data with chemical structures, real-time deposition of single or batch chemical structures (including with activity data) and transaction-based predictions of physicochemical data. The social community aspects of the system demonstrate the potential of this approach. Curation of the data continues daily and thousands of edits and depositions by members of the community have dramatically improved the quality of the data relative to other public resources for chemistry.
This presentation will provide an overview of the history of ChemSpider, the present capabilities of the platform and how it can become one of the primary foundations of the semantic web for chemistry. It will also discuss some of the present projects underway since the acquisition of ChemSpider by the Royal Society of Chemistry.
ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd So...
ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd So...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The internet 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
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
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
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 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 is one of the internet’s primary resources for chemists. ChemSpider is a structure-centric platform and hosts over 26 million unique chemical entities sourced from over 400 different data sources and delivers information including commercial availability, associated publications, patents, analytical data, experimental and predicted properties. ChemSpider serves a rather unique role to the community in that any chemist has the ability to deposit, curate and annotate data. In this manner they can contribute their skills, and data, to any chemist using the system. A number of parallel projects have been developed from the initial platform including ChemSpider SyntheticPages, a community generated database of reaction syntheses, and the Learn Chemistry wiki, an educational wiki for secondary school students.
This presentation will provide an overview of the project in terms of our success in engaging scientists to contribute to crowdsouring chemistry. We will also discuss some of our plans to encourage future participation and engagement in this and related projects.
Crowdsourcing Chemistry for the Community – 5 Years of Experiences
Crowdsourcing Chemistry for the Community – 5 Years of ExperiencesUS 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
ChemSpider is a structure centric database hosted by the Royal Society of Chemistry and integrating over 25 million chemical compounds to over 400 internet-based resources including many public domain databases, Wikipedia, chemical vendors, patents, publications and other web-based services. The intention is for ChemSpider to become one of the primary online hubs for chemists to source chemistry related data. During the development of the ChemSpider database we have utilized numerous approaches to standardizing, curating and validating the data supplied to us for hosting and integration. This presentation will provide an overview of our initial development of the ChemSpider database and provide an overview of our present processes and procedures for handling incoming data depositions. We will also discuss how crowdsourcing can help to expand, curate and validate the data on the ChemSpider database.ChemSpider – A Crowdsourcing Environment for Hosting and Validating Chemistry...
ChemSpider – A Crowdsourcing Environment for Hosting and Validating Chemistry...US 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
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
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
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
This is the presentation I gave at OpenSciNY 2010. It was a great gathering of Librarians and people interested in Open Science. Sharing the stage with Beth Brown Jean-Claude Bradley and Heather Joseph was, as usual, a good opportunity to discuss how openness and online data sharing is changing the way we access and share data. We live in interesting and exciting times.ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Comm...
ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Comm...US 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
Our access to scientific information has changed in ways that were hardly imagined even by the early pioneers of the internet. The immense quantities of data and the array of tools available to search and analyze online content continues to expand while the pace of change does not appear to be slowing. ChemSpider is one of the chemistry community’s primary online public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data tens of thousands of chemists every day and it serves as the foundation for many important international projects to integrate chemistry and biology data, facilitate drug discovery efforts and help to identify new chemicals from under the ocean. This presentation will provide an overview of the expanding reach of the ChemSpider platform and the nature of the solutions that it helps to enable. We will also discuss the possibilities it offers in the domain of crowdsourcing and open data sharing. The future of scientific information and communication will be underpinned by these efforts, influenced by increasing participation from the scientific community and facilitated collaboration and ultimately accelerate scientific progress.The expansive reach of ChemSpider as a resource for the chemistry community
The expansive reach of ChemSpider as a resource for the chemistry communityUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Access to scientific information has changed in a manner that was likely never even imagined by the early pioneers of the internet. The quantities of data, the array of tools available to search and analyze, the devices and the shift in community participation continues to expand while the pace of change does not appear to be slowing. ChemSpider is one of the chemistry community’s primary online public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data tens of thousands of chemists every day and it serves as the foundation for many important international projects to integrate chemistry and biology data, facilitate drug discovery efforts and help to identify new chemicals from under the ocean. This presentation will provide an overview of the expanding reach of this eScience cheminformatics platform and the nature of the solutions that it helps to enable including structure validation, text mining and semantic markup, the National Chemical Database Service for the United Kingdom and the development of a chemistry data repository. We will also discuss the possibilities it offers in the domain of crowdsourcing and open data sharing. The future of scientific information and communication will be underpinned by these efforts, influenced by increasing participation from the scientific community and facilitated collaboration and ultimately accelerate scientific progress.eScience at the Royal Society of Chemistry and our current initiatives
eScience at the Royal Society of Chemistry and our current initiativesUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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
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
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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
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 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 is one of the internet’s primary resources for chemists. ChemSpider is a structure-centric platform and hosts over 26 million unique chemical entities sourced from over 400 different data sources and delivers information including commercial availability, associated publications, patents, analytical data, experimental and predicted properties. ChemSpider serves a rather unique role to the community in that any chemist has the ability to deposit, curate and annotate data. In this manner they can contribute their skills, and data, to any chemist using the system. A number of parallel projects have been developed from the initial platform including ChemSpider SyntheticPages, a community generated database of reaction syntheses, and the Learn Chemistry wiki, an educational wiki for secondary school students.
This presentation will provide an overview of the project in terms of our success in engaging scientists to contribute to crowdsouring chemistry. We will also discuss some of our plans to encourage future participation and engagement in this and related projects.
Crowdsourcing Chemistry for the Community – 5 Years of Experiences
Crowdsourcing Chemistry for the Community – 5 Years of ExperiencesUS 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
ChemSpider is a structure centric database hosted by the Royal Society of Chemistry and integrating over 25 million chemical compounds to over 400 internet-based resources including many public domain databases, Wikipedia, chemical vendors, patents, publications and other web-based services. The intention is for ChemSpider to become one of the primary online hubs for chemists to source chemistry related data. During the development of the ChemSpider database we have utilized numerous approaches to standardizing, curating and validating the data supplied to us for hosting and integration. This presentation will provide an overview of our initial development of the ChemSpider database and provide an overview of our present processes and procedures for handling incoming data depositions. We will also discuss how crowdsourcing can help to expand, curate and validate the data on the ChemSpider database.ChemSpider – A Crowdsourcing Environment for Hosting and Validating Chemistry...
ChemSpider – A Crowdsourcing Environment for Hosting and Validating Chemistry...US 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
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
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
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
This is the presentation I gave at OpenSciNY 2010. It was a great gathering of Librarians and people interested in Open Science. Sharing the stage with Beth Brown Jean-Claude Bradley and Heather Joseph was, as usual, a good opportunity to discuss how openness and online data sharing is changing the way we access and share data. We live in interesting and exciting times.ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Comm...
ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Comm...US 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
Our access to scientific information has changed in ways that were hardly imagined even by the early pioneers of the internet. The immense quantities of data and the array of tools available to search and analyze online content continues to expand while the pace of change does not appear to be slowing. ChemSpider is one of the chemistry community’s primary online public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data tens of thousands of chemists every day and it serves as the foundation for many important international projects to integrate chemistry and biology data, facilitate drug discovery efforts and help to identify new chemicals from under the ocean. This presentation will provide an overview of the expanding reach of the ChemSpider platform and the nature of the solutions that it helps to enable. We will also discuss the possibilities it offers in the domain of crowdsourcing and open data sharing. The future of scientific information and communication will be underpinned by these efforts, influenced by increasing participation from the scientific community and facilitated collaboration and ultimately accelerate scientific progress.The expansive reach of ChemSpider as a resource for the chemistry community
The expansive reach of ChemSpider as a resource for the chemistry communityUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Access to scientific information has changed in a manner that was likely never even imagined by the early pioneers of the internet. The quantities of data, the array of tools available to search and analyze, the devices and the shift in community participation continues to expand while the pace of change does not appear to be slowing. ChemSpider is one of the chemistry community’s primary online public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data tens of thousands of chemists every day and it serves as the foundation for many important international projects to integrate chemistry and biology data, facilitate drug discovery efforts and help to identify new chemicals from under the ocean. This presentation will provide an overview of the expanding reach of this eScience cheminformatics platform and the nature of the solutions that it helps to enable including structure validation, text mining and semantic markup, the National Chemical Database Service for the United Kingdom and the development of a chemistry data repository. We will also discuss the possibilities it offers in the domain of crowdsourcing and open data sharing. The future of scientific information and communication will be underpinned by these efforts, influenced by increasing participation from the scientific community and facilitated collaboration and ultimately accelerate scientific progress.eScience at the Royal Society of Chemistry and our current initiatives
eScience at the Royal Society of Chemistry and our current initiativesUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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
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
Tendances (20)
ChemSpider 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 ...
Connecting Chemists to the Internet Through ChemSpider
Connecting Chemists to the Internet Through ChemSpider
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
ChemSpider hosting linking and curating chemistry data for the community
ChemSpider hosting linking and curating chemistry data for the community
Crowdsourcing Chemistry for the Community – 5 Years of Experiences
Crowdsourcing Chemistry for the Community – 5 Years of Experiences
Why Chemistry and the Web Will Benefit from a ChemSpider
Why Chemistry and the Web Will Benefit from a ChemSpider
ChemSpider – A Crowdsourcing Environment for Hosting and Validating Chemistry...
ChemSpider – A Crowdsourcing Environment for Hosting and Validating Chemistry...
RSC ChemSpider is the online chemistry database where community contributions...
RSC ChemSpider is the online chemistry database where community contributions...
ChemSpider - Does Community Engagement work to Build a Quality Online Resourc...
ChemSpider - Does Community Engagement work to Build a Quality Online Resourc...
Navigating the Complex Web of Chemistry Using ChemSpider
Navigating the Complex Web of Chemistry Using ChemSpider
ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Comm...
ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Comm...
How Internet Resources Are Providing a Collaborative Community for Chemistry
How Internet Resources Are Providing a Collaborative Community for Chemistry
The expansive reach of ChemSpider as a resource for the chemistry community
The expansive reach of ChemSpider as a resource for the chemistry community
eScience at the Royal Society of Chemistry and our current initiatives
eScience at the Royal Society of Chemistry and our current initiatives
ChemSpider – A Platform to Gather, Host and Integrate Structure Based Data Ac...
ChemSpider – A Platform to Gather, Host and Integrate Structure Based Data Ac...
ChemSpider – The Vision and Challenges Associated with Building a Free Online...
ChemSpider – The Vision and Challenges Associated with Building a Free Online...
En vedette
En vedette (7)
Similaire à Building A Community Resource For The Life Sciences
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
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 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
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 ability to query across a chemistry publishers content using chemical structure searching can dramatically enhance discoverability. RSC has been applying a number of procedures to integrate RSC’s ChemSpider community resource with our published content and databases. These include: 1) entity extraction procedures 2) chemical name conversion procedures using software algorithms and curated dictionaries 3) semantic markup and 4) a crowdsourced curation processes. This presentation will provide an overview of the processes we have utilized in order to provide structure-based integration to RSC content. We will discuss our ongoing efforts to extend the approaches to the mining of data from the rich supplementary information sections of many RSC publications. Our intention is to provide access to synthesis procedures and analytical data and further enrich the ChemSpider database for the benefit of the chemistry community. Enhancing Discoverability Across Royal Society Of Chemistry Content By Integr...
Enhancing Discoverability Across Royal Society Of Chemistry Content By Integr...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
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
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
Scientists commonly find themselves in a state of overwhelm in regards to the availability of information accessible to them. The distribution of resources now includes the entire space of the worldwide web, access to primary databases such as CAS and, commonly, a plethora of internally developed systems. While the web has provided improved access to chemistry-related information there has not been an online central resource allowing integrated chemical structure-searching of chemistry databases, chemistry articles, patents and web pages such as blogs and wikis. ChemSpider has built a structure centric community for chemists by providing free access to an online database and collaboration tool for chemists. The online database offers an environment for curating the data on ChemSpider as well as the deposition of chemical structures, analytical data and associated information and provides a significant knowledge base and resource for chemists working in different domains. An overview of present and future capabilities is given.Chemspider Presentation at the ACS Meeting in New orleans
Chemspider Presentation at the ACS Meeting in New orleansUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The 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 presentation given at the Triangle Chromatography Discussion Group with a focus on Mass Spectrometry and associated web services and what is possible for chromatographersHow an Online Resource for Chemistry Can Change Our World
How an Online Resource for Chemistry Can Change Our WorldUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Laboratories around the world continue to generate immense amounts of data that are non-proprietary and of value to the community. If available these data could dramatically reduce costs by minimizing rework and ultimately facilitating faster research. High quality reference data collections of chemical compound dictionaries, properties and spectra have been generated over many decades. With the advent of social networking tools and platforms such as Wikipedia, the community has an opportunity to contribute. The ChemSpider platform hosted by the Royal Society of Chemistry is a compound centric database with associated data. Already populated with almost 25 million unique compounds the community can deposit and host their own data, and curate and annotate existing data including those generated in Open Notebook Science Efforts. This presentation will provide an overview of progress to date and outline the vision of this community platform for chemistry and ensuring the longevity of chemistry reference data. Hosting a compound centric community resource for chemistry data
Hosting a compound centric community resource for chemistry dataUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a presentation I gave at the Library of Congress as part of a NFAIS/FLICC/CENDI meeting as outlined here: http://www.chemspider.com/blog/making-the-web-work-for-science-presentation-at-the-library-of-congress.html
The presentation provides an overview of some of the challenges the publishers face moving forward, how they are responding to it, how InChI is an enabling technology, how quality is important.Qualifying Online Information Resources for Chemists
Qualifying Online Information Resources for ChemistsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at the EBI Meeting in Cambridge on October 11th 2011 regarding Chemical Registration and Standardization.ChemSpider – An Online Database and Registration System Linking the Web
ChemSpider – An Online Database and Registration System Linking the WebUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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Navigating the Complex Web of Chemistry Using ChemSpider
Navigating the Complex Web of Chemistry Using ChemSpider
Taming The Wild West Of Internet Based Chemistry You Can Help
Taming The Wild West Of Internet Based Chemistry You Can Help
Crawling Across the Web of Chemistry Using ChemSpider
Crawling Across the Web of Chemistry Using ChemSpider
ChemSpider Overview Presentation at Special Libraries Association
ChemSpider Overview Presentation at Special Libraries Association
Enhancing Discoverability Across Royal Society Of Chemistry Content By Integr...
Enhancing Discoverability Across Royal Society Of Chemistry Content By Integr...
Chemspider hosting linking and curating chemistry data for the community
Chemspider hosting linking and curating chemistry data for the community
ChemSpider as a Foundation for Crowdsourcing and Collaborations in Open Chemi...
ChemSpider as a Foundation for Crowdsourcing and Collaborations in Open Chemi...
Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry
Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry
Citizen Scientists and Their Contributions to Internet Based Chemistry
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Chemspider Presentation at the ACS Meeting in New orleans
Chemspider Presentation at the ACS Meeting in New orleans
How the web has weaved a web of interlinked chemistry data final
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How an Online Resource for Chemistry Can Change Our World
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Hosting a compound centric community resource for chemistry data
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Qualifying Online Information Resources for Chemists
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ChemSpider – An Online Database and Registration System Linking the Web
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Building A Community Resource For The Life Sciences
- 1. Building A Community Platform to Support Chemistry and the Life Sciences
- 2. Where Would You look? What Do You Trust?
- 7. The Final Search Strategy
- 8. All Those Names, One Structure A problem to solve…
- 11. Where Would You look? What Do You Trust?
- 12. Structural Data for LifeSciences DailyMed
- 14. Incorrect Structures
- 15. Ugh…
- 16. Drugs are REALLY Messy
- 18. The EXPERTS must get it right?!
- 27. Search “OEA”
- 28. Search OEA
- 31. Search OEA
- 32. Search OEA
- 33. Google Books
- 34. Google Scholar
- 35. Linked Patents for OEA
- 37. Google Patents
- 39. RSC Journals
- 40. RSC Databases
- 44. Multiple Layers
- 45. InChIStrings Hash to InChIKeys
- 46. Link the Internet with InChIKeys! Taken from: Rafael Sidis’ Blog
- 47. Vancomycin – Search the Internet
- 48. Vancomycin Search Molecular SKELETON Search Full Molecule
- 49. Full Molecule Search: 4 Hits
- 50. Full Skeleton Search: 104 Hits
- 54. Vancomycin
- 55. Vancomycin on ChemSpider 1 compound – 3 days
- 56. InChIKeys Make the internet searchable by adding InChIKeys Publishers add InChIKeys to papers now…
- 57. InChIKeys Make the internet searchable by adding InChIKeys Publishers add InChIKeys to papers now… is what???
- 59. InChI Resolver to DOIs Structure Search the Web
- 62. Multi-level Curation and Approval Building a Structure Centric Community for Chemists
- 63. Semantic Markup: Project Prospect
- 66. Org Prep Daily (Blog)
- 71. Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams