ChemSpider and How The Wisdom Of The Crowds Can Improve The Quality Of Chemistry On The Internet

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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 articles

Technology Education

ChemSpider: How the Wisdom of the Crowd Can Improve the Quality of Chemistry on the Internet

Overview ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Linked Data on the Web Taken from: Rafael Sidis’ Blog

Where Would You look? What Do You Trust?

Lots of “Public Compound” Databases ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Connecting Chemistry on the Web ,[object Object],[object Object],[object Object]

Antony Williams vs Identifiers Passport ID Dad, Tony, others SSN Green Card License 5 email addresses ChemSpiderman (blog, Twitter account, Facebook, Friendfeed) OpenID … .

Aspirin names and synonyms ,[object Object],[object Object],[object Object]

Vancomycin ,[object Object],[object Object]

What is ChemSpider? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Link off a structure in ChemSpider ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Answering Questions for Chemists ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Chemistry on the Internet ,[object Object],[object Object]

Question Everything online: www.dhmo.org

Vancomycin Search Molecular SKELETON Search Full Molecule

Wikipedia, C&E News, PubChem ,[object Object]

Feedback from Steve Ritter ,[object Object],[object Object]

Assertion and Chemical Entities ,[object Object],[object Object],[object Object]

Crowd-sourcing Chemistry Curation ,[object Object]

Multi-level Curation and Approval Building a Structure Centric Community for Chemists

The Intention ,[object Object],[object Object],[object Object],[object Object]

Does it Matter? ,[object Object],[object Object],[object Object],[object Object]

The Process ,[object Object],[object Object],[object Object],[object Object],[object Object]

One Name – Multiple Structures NO Stereo Full Stereo Partial Stereo Partial Stereo

How bad can it get??? And who is right????

Name-Structure Pairs ,[object Object],[object Object],[object Object],[object Object]

ChemMantis ,[object Object],[object Object],[object Object]

Semantic Linking of Structures ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Dictionaries are Easily Enhanced ,[object Object],[object Object],[object Object],[object Object]

Where To From Here? ,[object Object],[object Object],[object Object]

If We Had Our Way… ,[object Object],[object Object],[object Object],[object Object]

ChemSpider Everywhere Crowdsourced Curation of Spectra

ChemSpider Everywhere ChemMobi Building a Structure Centric Community for Chemists

Linking to Resources ,[object Object],[object Object]

Conclusions ,[object Object],[object Object],[object Object],[object Object],[object Object]

Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams

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Connecting Chemists to the Internet Through ChemSpider

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

There is an increasing availability of free and open access resources for chemists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. It was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. There are tens if not hundreds of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the fact that there were a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness was lacking in many regards. The intention with ChemSpider was to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data, experimental properties and linking to other valuable resources. It has grown into a resource containing over 21 million unique chemical structures from over 200 data sources. ChemSpider has enabled real time curation of the data, association of analytical data with chemical structures, real-time deposition of single or batch chemical structures (including with activity data) and transaction-based predictions of physicochemical data. The social community aspects of the system demonstrate the potential of this approach. Curation of the data continues daily and thousands of edits and depositions by members of the community have dramatically improved the quality of the data relative to other public resources for chemistry. This presentation will provide an overview of the history of ChemSpider, the present capabilities of the platform and how it can become one of the primary foundations of the semantic web for chemistry. It will also discuss some of the present projects underway since the acquisition of ChemSpider by the Royal Society of Chemistry.

ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd So...

US 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

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. 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

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

Whitney Symposium Lecture June 2008

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

Building A Community Resource For The Life Sciences

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

ChemSpider Presentation At University Of Toronto

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

Taming The Wild West Of Internet Based Chemistry You Can Help

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

ChemSpider – The Vision and Challenges Associated with Building a Free Online...

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

The Great Promise of Online Data for Chemistry and the Life Sciences

US 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...

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...

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

The Internet is the world’s publicly accessible container for a myriad of resources containing chemistry related data. Whether it be collections of millions of chemical compounds with their associated properties, interactive displays for analytical data, access to publications and patents or tapping into the increasing availability of online computational engines, the web has became the primary enabling technology to source information and data. Scientists collectively applaud and utilize the availability of such resources and an increasing proportion of the community are willing to support these resources by contributing both their data and skills to help curate and validate information on the web. This “crowdsourcing” has started to contribute large amounts of data to the commons and serves has a valuable platform for reference and, potentially, discovery. ChemSpider is one of the chemistry community’s primary online resources and allows scientists to search across 25 million unique chemical compounds linked out to over 400 original data sources and has become a central hub for searching for chemistry-related data. The platform however offers much more to the community and has become a central repository for analytical data, specifically spectra, is a host for community-authored chemical syntheses and facilitates data curation and annotation by any of its users. This presentation will provide an overview of the ChemSpider platform in terms of available data and its efforts to act as a public repository and clearing ground for data curation. We will discuss how such a platform, when coupled with game-based approaches, facilitates both teaching and data validation and will discuss whether public domain resources such as ChemSpider will ultimately become authorities for chemistry.

ChemSpider hosting linking and curating chemistry data for the community

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

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...

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

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

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

Laboratories around the world continue to generate immense amounts of data that are non-proprietary and of value to the community. If available these data could dramatically reduce costs by minimizing rework and ultimately facilitating faster research. High quality reference data collections of chemical compound dictionaries, properties and spectra have been generated over many decades. With the advent of social networking tools and platforms such as Wikipedia, the community has an opportunity to contribute. The ChemSpider platform hosted by the Royal Society of Chemistry is a compound centric database with associated data. Already populated with almost 25 million unique compounds the community can deposit and host their own data, and curate and annotate existing data including those generated in Open Notebook Science Efforts. This presentation will provide an overview of progress to date and outline the vision of this community platform for chemistry and ensuring the longevity of chemistry reference data.

Hosting a compound centric community resource for chemistry data

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

ChemSpider was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. There are many tens of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the diversity of databases available online their inherent quality, accuracy and completeness is lacking in many regards. ChemSpider was established to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data and experimental properties. ChemSpider has now grown into a database of 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...

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

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