Building an integrated system for chemistry markup and online publishing integrated to online chemistry resources
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The extraction of chemical entities from documents such as patents and publications has been pursued for a number of years. We wish to report on ChemMantis, an integrated system for chemistry-based entity extraction and document mark-up enabling access to the rich resource of online chemistry know as ChemSpider. We will discuss the development of the platform from its inception as a series of dictionaries to the integration of an entity extraction algorithm and its expansion to a public deposition and publishing platform for chemistry. Chemistry articles can now be deposited, marked-up and exposed to the public within a few minutes in many cases making it an ideal platform for communicating research and providing integrated access to data sources including PubChem, ChEBI, Wikipedia and Entrez.
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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
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This is a "vendor presentation" that I gave in New Orleans on June 14th 2010. It is a very general presentation on ChemSpider relevant to the needs of librarians.ChemSpider Overview Presentation at Special Libraries Association
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Text Mining for Chemistry and Building a Public Platform for Document Markup
The identification of chemical names in documents has provided platforms to enable structure-based searching of patents and mark-up chemistry publications. A natural extension is the ability to make chemistry articles, blog pages, wiki pages and other documents searchable by the extracted chemical structures. The ChemSpider database is built on a database of over 21 million unique chemical entities from close to 200 data sources and provides a rich resource of information for chemists. We will report on our efforts to integrate chemical name extraction with the ChemSpider platform to enable structure searching of Open Access chemistry articles, and online chemistry materials. We will unveil our online document markup platform for chemists to make both their open- and closed-access publications searchable by the language of chemistry – the structure.
Text Mining for Chemistry and Building a Public Platform for Document Markup
Text Mining for Chemistry and Building a Public Platform for Document MarkupUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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Connecting Chemistry Across the Internet Using ChemSpider
Connecting Chemistry Across the Internet Using ChemSpiderUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
There is an increasing availability of free and open access resources for scientists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 200 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. This presentation will provide an overview of the ChemSpider platform and how it is fast becoming the centralized hub for resourcing information about chemical entities. Navigating the Complex Web of Chemistry Using ChemSpider
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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.
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Crawling Across the Web of Chemistry Using ChemSpider US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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ChemSpider Overview Presentation at Special Libraries AssociationUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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The identification of chemical names in documents has provided platforms to enable structure-based searching of patents and mark-up chemistry publications. A natural extension is the ability to make chemistry articles, blog pages, wiki pages and other documents searchable by the extracted chemical structures. The ChemSpider database is built on a database of over 21 million unique chemical entities from close to 200 data sources and provides a rich resource of information for chemists. We will report on our efforts to integrate chemical name extraction with the ChemSpider platform to enable structure searching of Open Access chemistry articles, and online chemistry materials. We will unveil our online document markup platform for chemists to make both their open- and closed-access publications searchable by the language of chemistry – the structure.
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Taming The Wild West Of Internet Based Chemistry You Can HelpUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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The ChemSpider database is an online resource containing >26 million chemicals sourced from over 400 data sources. As a result the database is a rich resource supporting the verification and elucidation of chemical structures and is utilized by mass spectrometrists around the world using the online user interface as well as the application programming interface. This presentation will provide an overview of how ChemSpider can be used for the purpose of structure identification and will include (1) direct interaction with the online interface; (2) integration to mass spectrometry vendor software; (3) applications to the identification of “known unknowns” and a comparison with the capabilities of CAS Scifinder and (4) the hosting of online mass spectral data. Structure verification and elucidation using the ChemSpider database
Structure verification and elucidation using the ChemSpider databaseUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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
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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
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At RSC we are involved with a number of projects utilizing components of Advanced Chemistry Development software including nomenclature, physchem prediction and spectroscopy integration. This presentation was given at a small ACD/Labs user meeting in Loughborough, England in February 2013. An associated movie is available on YouTube here: http://youtu.be/2kAsyRU7lRgHow ACDLabs Software Tools are used by the Royal Society of Chemistry
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Sharing chemical structures with peer reviewed publications US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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The ChemSpider database is an online resource containing >26 million chemicals sourced from over 400 data sources. As a result the database is a rich resource supporting the verification and elucidation of chemical structures and is utilized by mass spectrometrists around the world using the online user interface as well as the application programming interface. This presentation will provide an overview of how ChemSpider can be used for the purpose of structure identification and will include (1) direct interaction with the online interface; (2) integration to mass spectrometry vendor software; (3) applications to the identification of “known unknowns” and a comparison with the capabilities of CAS Scifinder and (4) the hosting of online mass spectral data. Structure verification and elucidation using the ChemSpider database
Structure verification and elucidation using the ChemSpider databaseUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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
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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
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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
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
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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.
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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.
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ChemSpider is being built with the intention of being a chemical structure centric community for chemists. With over 16 million chemical structures as of August 2007, and with data deposition and curation mechanisms in place for text, structure and spectra ChemSpider intends to be a meeting place and collaborative environment for chemists to work together.ChemSpider Overview SLides August 2007
ChemSpider Overview SLides August 2007US 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 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
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 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 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
ChemSpider – The Vision and Challenges Associated with Building a Free Online...
ChemSpider – The Vision and Challenges Associated with Building a Free Online...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The increasing availability of free and open access resources for scientists on the internet presents us with a revolution in data availability. The Royal Society of Chemistry hosts ChemSpider, a free access website for chemists built with the intention of building community for chemists (http://www.chemspider.com/).
ChemSpider is an aggregator of chemistry related information, at present over 20 million unique chemical entities linked out to over 300 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. It is also a public deposition platform where chemists can deposit their own data including novel structures, analytical data, synthesis procedures and host data associated with the growing activities associated with Open Notebook Science.
This presentation will examine chemistry on the internet, the dubious quality of what is available and how the ChemSpider crowdsourced curation platform is fast becoming one of the centralized hubs for resourcing information about chemical entities.
We will also review our efforts to provide free resources for synthesis procedures, spectral data and structure-based searching of the chemistry literature and how chemists can contribute directly to each of these projects.
RSC ChemSpider -- Managing and Integrating Chemistry on the Internet to Build...
RSC ChemSpider -- Managing and Integrating Chemistry on the Internet to Build...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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
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 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
With an intention to provide a free internet resource of chemistry related data for the community, ChemSpider provides an online database of chemical compounds, reaction syntheses and related data. Members of the community can contribute to the database via the deposition of chemical structures, synthesis procedures and analytical data. Data are also aggregated from many other depositors, at present over 400 data sources. The aggregation of data associated with over 25 million chemical compounds does not come without data quality issues. By engaging the community to curate the data the quality continues to improve on a daily basis. The presentation will provide an overview of our ongoing efforts to expand and curate the database. Using a combination of game-based and recognition systems as well as our dependence on societal giveaway by the community ChemSpider continues its path to become a high quality resource and foundation for the semantic web for chemistry.How Community Crowdsourcing and Social Networking is Helping to Build a Quali...
How Community Crowdsourcing and Social Networking is Helping to Build a Quali...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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Building an integrated system for chemistry markup and online publishing integrated to online chemistry resources
- 1. Building an integrated system for chemistry markup and online publishing integrated to online chemistry resources
- 4. Reflect
- 7. And linked to STITCH…
- 8. Success Depends on Dictionaries
- 9. Concept Web Alliance, Knewco, Others
- 12. Nature Chemistry Compound Pages
- 13. Project Prospect
- 18. Manual Curation is Necessary
- 23. Species – linked to Wikipedia
- 32. Org Prep Daily (Blog)
- 33. Molbank (Open Access Journal)
- 38. Online Journals and Live Data
- 41. Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog