The ChemSpider database is a free online resource containing information for over 28 million unique chemicals. The platform has been used as the foundation of a number of other resources including ChemSpider SyntheticPages (CSSP), an online “micro-publishing” site serving chemists interested in chemical syntheses. Synthetic chemists are encouraged to publish the details of their experiments in order to communicate the details of their work. Using a template-based entry form, multimedia support including interactive display of spectral data, CSSP provides an environment for students to develop their writing skills in terms of reporting science. The articles are reviewed by the CSSP editorial board, made up of university professors, as well as then being peer-reviewed by the incorporation of public commentary. Each micro-publication includes a digital object identifier (DOI) making the CSSP contribution a citable object on a CV. This presentation will provide an overview of the ChemSpider SyntheticPages platform and demonstrate how chemists can actively expose their work to the community-at-large and can use the ChemSpider platform to access data that could be of value in everyday lab work. We will also discuss our view of a future platform for managing personal, institutional and public chemistry in a shared environment.

1. ChemSpider SyntheticPages –
the Benefits of Publishing
Chemical Syntheses Online

2. If it was not just about me…

3. If it was not just about me…
 We might have a community
built encyclopedia
 I might know where the best
restaurants are
 I might get good advice on
books to read
 I might know which movies
to watch
 I might know which plumber
to call
 Data might just be Open

4. If it was not just about me…
 We might have a community
built encyclopedia
 I might know where the best
restaurants are
 I might get good advice on
books to read
 I might know which movies
to watch
 I might know which plumber
to call
 Data might just be Open

5. ChemSpider SyntheticPages
 Many syntheses are not published but are of value
 A database of synthesis procedures built for the
community, by the community.
 Peer-reviewed by the community
 Each contribution DOI’ed. Develop online scientific
reputation at a time of “micro-publications”
 Integrates semantic mark-up and visualization tools

6. ChemSpider SyntheticPages
http://cssp.chemspider.com

8. ChemSpider SyntheticPages

9. Submission process
 Register as a user
 Use the Submit button and fill in the fields…

10. Submission Process
 Submissions reviewed by editorial board
 Published as is or comments sent to author
 Online Peer Review process – engage chemists
in ongoing discussions and feedback loop
 Data supported include web movies, images, live
spectra etc.

11. Recent Submissions

12. Semantic Markup: Project Prospect

13. Entity-Extraction, Mark-up, Annotate

14. Success Depends on Dictionaries
Link to a Structure or the Right Structure?

15. Name-Structure Pairs

16. Semantic Linking of Structures
 What would you want
to link off a structure?
 Chemical suppliers
 Other publications
 Analytical Data
 Related Reactions
 Wikipedia
 Patents
 “Everything”

17. 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

18. Answer Questions with ChemSpider
 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?

19. I want to know about “Vincristine”

20. I want to know about “Vincristine”
If all algorithms work then
everything on the page is
correct by default except
the name!

21. Vincristine: Identifiers and Properties

22. Vincristine: Identifiers and Properties

23. Vincristine: Vendors and Sources

24. Vincristine: Patents

25. Vincristine: Articles

26. Searches: The INTERNET
All ChemSpider and Internet searches are “simply algorithms”
but synonym searching is based on an assertion

27. InChIs

28. Validated Names for Searching…

31. Interactive Data

33. Most Accessed

34. Is it working?
 Show of hands…
 How many of you know CSSP?
 Have any of you submitted to CSSP?
 Low submissions but some dedicated authors

35. Popular Authors

36. Is it working?
 Show of hands…
 How many of you know CSSP?
 Have any of you submitted to CSSP?
 Low submissions but some dedicated authors
 What reasons are there you would not publish?
 Time
 Approval from supervisor
 Need to keep the science quiet
 Publishing on CSSP prevents future publishing?

37. How will it improve?
Participation
and
contribution

38. The Social Network
 Career-wise NOT having a personal presence
online will be a detriment
 Self-marketing
 Establishing a profile
 Getting on the record
 Collaborative Science
 Demonstrating a skill set
 Measured using alternative metrics
 Contributing to the public peer review process

39. Social Networking Tools
 A growing number of social networking tools:
 Facebook
 Twitter
 Linked-In
 Flickr
 YouTube
 Blogs
 Communities
 Collaborative environments

40. Chemistry Social Networking
 Methods of sharing MY chemistry online include:
 Wikis or blogs
 Slideshare for presentations
 YouTube for videos
 Flickr, Wikimedia etc. for images
 PubChem for assay data
 NMRShiftDB for NMR assignments
 GoogleDocs for data

41. Drivers in the Social Network
 Anonymity is a choice in the social networks
 Anonymity in peer-review will likely become less
important and may be generational
 I may want acknowledgment if…
 I share my data
 I review a paper
 I share my expertise

42. The Alt-Metrics Manifesto
 http://altmetrics.org/manifesto/

43. Enabled by ORCID…

44. The Joint Responsibility of Authors

45. What is my ImpactStory?

46. ImpactStory

47. The Linked Network

48. Imperial College
 Data repository activities initiated with Imperial
 Storage of research data from electronic lab
notebook
 Chemicals
 Reactions
 Analytical data – spectra
 Experimental data points
 Open Data with CC licenses of NC-SA

49. Feeding ELN Data into ChemSpider
 Integrate e-Notebooks into ChemSpider
 IDBS e-Workbook plug-in allows direct
deposition of chemical structures
 Can be extended to more ELN content
 Spectra
 Reactions
 Properties etc.
 Integration Video http://tinyurl.com/9xnprqr

50. Feeding ELN Data into ChemSpider

51. What is already in testing…
 ChemSpider Google
 Searching Google Scholar, Google Books and
Google Patents by chemical structure
 ChemSpider reactions – alpha version
 300,000 reactions extracted from US patents
 ChemSpider SyntheticPages container
 Container for future RSC Archive reactions
 Accepting Electronic Lab Notebook depositions
 Successful AND Failed Reactions

52. Work in Progress – 300k Reactions

53. Data Enabling the RSC Archive
 An archive going back to 1841. Project underway
to “data enable” the archive:
 Extract chemistry – chemicals, reactions,
experimental data points, complex data
 Semantic enriching of the articles for interactive
viewing and crowdsourced annotation/curation
 Dramatically enables the type of queries
possible across the archive

54. EPSRC National Chemical Database
 RSC is preferred bidder for the EPSRC national
chemical database tender – presently completing
legal documentation etc.
 Will deliver federated access to a series of
commercial databases plus data repository –
personal, group and institutional
 Citable data objects for papers, supplementary
info, non-published work

55. A model for data segregation
Integrate to Institutional repositories
Access to Theses and Dissertations

56. Model Building with Community Data
 Community data can be the basis of model
building
 Consume data from available databases, RSC
archive, new publications and build predictive
algorithms for the community
 Accept research data from the community and
include into predictions

57. An Open Data-Centric Chemistry Hub
Internet Data
Small organic molecules Commercial Software
Undefined materials Pre-competitive Data
Organometallics Open Science
Nanomaterials Open Data
Polymers Publishers
Minerals Educators
Particle bound Open Databases
Links to Biologicals Chemical Vendors

58. Benefits of Publishing
Chemical Syntheses Online
 Not all syntheses will be “published”
 Publishing is changing and has many forms
 Online exposure develops reputation,
benefits the community, engages discussion
and collaboration. Peer review in the open.
 CSSP offers a platform for exposure, linking
to ChemSpider, interactive visualization and
is a feed to ChemSpider reactions
 ELNs are a natural feed to the CSSP micro-
publishing platform

59. Acknowledgments
 RSC|ChemSpider team
 CSSP Editorial Team
 All data source providers
 Curators and annotators
 Service providers:
 ACD/Labs
 OpenEye
 GGA Software Services
 Many others….

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