RSC ChemSpider for students

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

This document discusses ChemSpider, a free online chemistry database containing over 28 million chemical records aggregated from over 400 sources. ChemSpider aims to be a central hub for chemists to find information on chemicals, spectra, properties and related data. It also allows users to deposit and curate new data. The document provides examples of common chemistry questions that can be answered using ChemSpider and demonstrates how to search for information on specific chemicals like Vincristine. It highlights ChemSpider's ability to link spectra data and discusses efforts to crowdsource curation of chemical identifier data.

Technology Education

ChemSpider – The Free Chemistry
Database for the Community

Antony Williams
Duke University, September 17th 2012

The World of Online Chemistry
 Property databases
 Compound aggregators
 Screening assay results
 Scientific publications
 Encyclopedic articles (Wikipedia)
 Metabolic pathway databases
 ADME/Tox data – eTOX for example
 Blogs/Wikis and Open Notebook Science
 Contributing Open Source code to projects

ChemSpider
 The Free Chemical Database

 A central hub for chemists to source information
 >28 million unique chemical records
 Aggregated from >400 data sources
 Chemicals, spectra, CIF files, movies, images,
podcasts, links to patents, publications,
predictions

 A central hub for chemists to deposit & curate data

We Want to Answer Questions
 Questions a chemist might ask…
 What is the melting point of n-heptanol?
 What is the chemical structure of Xanax?
 Chemically, what is phenolphthalein?
 What are the stereocenters of cholesterol?
 Where can I find publications about xylene?
 What are the different trade names for Ketoconazole?
 What is the NMR spectrum of Aspirin?
 What are the safety handling issues for Thymol Blue?

Sources of Spectra
 Sourced from online sources with permission

 Private collections

 The MAJORITY deposited by ChemSpider users

Data Uploading – YOU HELP
 Locate the structure of interest and deposit
spectrum

Vancomycin

Search Molecular Search Full Molecule
SKELETON

www.SpectralGame.com
http://www.jcheminf.com/content/1/1/9

Conclusions
 ChemSpider is a FREE resource for the community
 Grows daily with new data – do you have any to
share?
 Concerned about data quality! YOU SHOULD BE!
 Crowdsourced and algorithmic curation is working
 API is available to access data – any informatics
people want access??

 If you want hands on training I can come and give it

Thank you

Email: williamsa@rsc.org
Twitter: ChemConnector
Blog: www.chemspider.com/blog
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams

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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. 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.

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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.

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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.

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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.

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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.

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RSC ChemSpider for students

1. ChemSpider – The Free Chemistry Database for the Community Antony Williams Duke University, September 17th 2012

2. We Have …Too Much Data!!!

3. The World of Online Chemistry  Property databases  Compound aggregators  Screening assay results  Scientific publications  Encyclopedic articles (Wikipedia)  Metabolic pathway databases  ADME/Tox data – eTOX for example  Blogs/Wikis and Open Notebook Science  Contributing Open Source code to projects

4. ChemSpider  The Free Chemical Database  A central hub for chemists to source information  >28 million unique chemical records  Aggregated from >400 data sources  Chemicals, spectra, CIF files, movies, images, podcasts, links to patents, publications, predictions  A central hub for chemists to deposit & curate data

5. We Want to Answer Questions  Questions a chemist might ask…  What is the melting point of n-heptanol?  What is the chemical structure of Xanax?  Chemically, what is phenolphthalein?  What are the stereocenters of cholesterol?  Where can I find publications about xylene?  What are the different trade names for Ketoconazole?  What is the NMR spectrum of Aspirin?  What are the safety handling issues for Thymol Blue?

6. I want to know about “Vincristine”

7. Vincristine: Identifiers and Properties

8. Vincristine: Vendors and Sources

9. Vincristine: Patents

10. Vincristine: Articles

11. ChemSpider : Spectra Linked

12. Sources of Spectra  Sourced from online sources with permission  Private collections  The MAJORITY deposited by ChemSpider users

13. Data Uploading – YOU HELP  Locate the structure of interest and deposit spectrum

14. Multiple Spectra for One Structure

15. ChemSpider ID 24528095 H1 NMR

16. ChemSpider ID 24528095 C13 NMR

17. ChemSpider ID 24528095 HHCOSY

18. Spectra Linked

19. CURATION Search “Vitamin H”

20. “Curate” Identifiers

21. “Curate” Identifiers

22. “Curate” Identifiers

23. The InChI Identifier

24. Multiple Layers

25. InChIStrings Hash to InChIKeys

26. Vancomycin – Search the Internet

27. Vancomycin Search Molecular Search Full Molecule SKELETON

28. Searches: The INTERNET

29. Validated Names for Searching…

30. And InChIs…

31. ChemSpider Interface

32.

33. www.SpectralGame.com http://www.jcheminf.com/content/1/1/9

34. Spectral Game

35. Increasing Complexity

36. Structure Database Lookup

37. ChemSpider SyntheticPages

38. ChemSpider Everywhere : ChemMobi

39. SpectralGame in the hand

40. ChemSpider Resources for Chemistry

41. Conclusions  ChemSpider is a FREE resource for the community  Grows daily with new data – do you have any to share?  Concerned about data quality! YOU SHOULD BE!  Crowdsourced and algorithmic curation is working  API is available to access data – any informatics people want access??  If you want hands on training I can come and give it

42. Thank you Email: williamsa@rsc.org Twitter: ChemConnector Blog: www.chemspider.com/blog Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams

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