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.

1. Contributions to the World of
eScience from the Royal
Society of Chemistry
Antony Williams
University of North Florida
November 14th 2013

2. We Have …Too Much Data!!!

3. The World of Online
Chemistry
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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

4. e-Science and Primary Data
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How much data generated in a lab, that COULD go
public, is lost forever?
Public Domain reference databases of value?
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Syntheses
Properties
Spectra
CIFs
Images
Much of chemistry is chemical structure-based –
where and how could we host these data?

5. RSC’s ChemSpider

6. ChemSpider
• >29 million unique chemicals from >500
data sources
• Focus on improving data quality,
enhancing functionality, integrating and
enabling

7. Crowdsourced “Annotations”
• Users can add
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Descriptions/Syntheses/Commentaries
Links to PubMed articles
Links to articles via DOIs
Add spectral data
Add Crystallographic Information Files
Add photos
Add MP3 files
Add Videos

8. Spectra

9. Chemistry Data online are
messy
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We have inherited errors
All public compound databases have errors
“Incorrect” structures – assertions, timelines etc
“Incorrect” names associated with structures
Properties
Links
Publications
ENORMOUS CHALLENGE

10. Crowdsourced Curation
• Crowd-sourced curation: identify/tag
errors, edit names, synonyms, identify
records to deprecate

11. Search “Vitamin H”

12. “Curate” Identifiers

13. “Curate” Identifiers

14. “Curate” Identifiers

15. Validated Name-Structure
Dictionaries
• Chemical name dictionaries are used
for:
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Text-mining (publications, patents)
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Linking to other databases – think Biology!
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Used to index PubMed and link to Google Patents
When structures are not available drug names link
Searching the web
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Names link to structures link to InChIs

16. I want to know about
“Vincristine”

17. Vincristine: Identifiers and
Properties

18. Vincristine: Vendors and
Sources
Linked by Structure

19. Vincristine: Patents
Linked by Name

20. Vincristine: Articles
Linked by Name

21. Semantic Mark-up of Articles

22. Linking Names to Structures

23. The InChI Identifier

24. InChIStrings Hash to
InChIKeys

25. Vancomycin – Search the
Internet

26. Vancomycin
Search Molecular
SKELETON
Search Full Molecule

27. Full Skeleton Search: 104
Hits

28. Full Molecule Search: 4 Hits

29. Publications - a summary of
work
• Scientific publications are a summary of
work
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Is all work reported?
How much science is lost to pruning?
What of value sits in notebooks and is lost?
• How much data is lost?
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How many compounds never reported?
How many syntheses fail or succeed?
How many characterization measurements?

30. What if we could capture it all?
Digitally Enhancing the RSC Archive

31. Start with data in publications

32. Turn “Figures” Into Data

33. ChemSpider Reactions
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Starting with data from CSSP, MOS and CCR
Will cover reactions extracted from:
• Patents
• RSC journal articles and ESI

34. About Me…as a Chemist
• I’ve performed a few dozen chemical
syntheses
• I’ve run thousands of analytical spectra
• I’ve generated thousands of NMR
assignments
• I’ve probably published <5% of all work
• Most of it has been lost
• But things can be different today….
• But it still needs to be associated with me…

35. Micropublishing Syntheses

36. ChemSpider SyntheticPages

37. Visibility Means Discoverability
• Does a Social Profile matter?
• You are visible, when you share your skills,
experience and research activities by:
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Establishing a public profile
Getting on the record
Collaborative Science
Demonstrating a skill set
Measured using “alternative metrics”
Contributing to the public peer review
process

38. Scientists are “Quantified”
• Scientists are quantified
• Stats are gathered and analyzed
• Employers can find them, tenure will
depend on them, and these already
happen without your participation
• Scientists Impact Factors, H-index and
many other variants.

39. How you can be Quantified…

40. ResearchGate

41. The Alt-Metrics Manifesto
• http://altmetrics.org/manifesto/

43. AltMetrics via Plum Analytics

44. Usage, Citations, Social
Media, Etc

45. Detailed Usage Statistics

46. Your Profile as a Scientist
• If you are an active scientist – i.e. already
published, active researcher, generator of
data, early, mid- or late career there is
lots to do!
• If you are a junior scientist the benefits of
investing time now will provide a strong
foundation for your future!
• So what do I do??

47. Branding: I am
ChemConnector

48. Enabled by
• Persistent unique digital identifier
• Integrates to workflows such as
manuscript and grant submission
• Supports automated linkages with your
professional activities

49. An Online Profile
• Methods of sharing science online include:
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Wikis or blogs
Slideshare for presentations
YouTube for videos
Flickr, Wikimedia etc. for images
ChemSpider for chemistry
GoogleDocs for data
Google Scholar Citations for citations
Microsoft Academic Scholar for papers

50. LinkedIn
http://www.linkedin.com/in/AntonyWilliams

51. My Career Captured…

52. And “Endorsements”

53. Are you sharing your slides
online?
• Slideshare to host, expose and share your
presentations, publications, posters and
videos (subject to copyright you might have
transferred!)
http://www.slideshare.net/
• Register for an account and retain your
branding! Keep your online brand consistent

54. Upload and Add Details
• Edit title, add tags, add “abstract”, choose
category
• Select checkbox for allow/disallow file
download

55. SlideShare

56. Social Media Tools Feed
Each Other
• Plugins and connectors integrate your
activities across the social media platforms
• Expose your Tweeting and your Slideshare
presentations directly on LinkedIn.
• Plug-ins allow your tweets and presentations
to be automagically displayed on LinkedIn

57. From Slideshare Into the
Network

58. Add Applications to LinkedIn

59. Places to Share Videos
• There are other sites for you to share
your videos online as a scientist
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YouTube
SciVee
Vimeo
Slideshare

60. Share/Manage Your
Publications
• Where do you “manage your publications”?
• Share your “activities” with the community
• My publications/slides/videos are my CV on
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My Blog
On LinkedIn
On SlideShare
On Researchgate
On Academia.edu

61. Academia.edu

62. Academia.edu

63. And Mendeley
http://www.mendeley.com/profiles/antony-williams/

64. My Google Scholar Profile

65. My Co-author Graph on
MAS..

66. Share Science!!! Not Just
Yourself
• Become a community contributor to science
• Share your expertise in the new world of
openness
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Share your code
Share your data and your model
Share your Figures
Contribute to Wikis – Wikipedia and others
Become an Open Notebook Scientist

67. The Power of Blogs & Social
Media

68. The Power of Blogs & Social
Media

69. The Power of Blogs & Social
Media

71. And into the AltMetrics World

72. And into the AltMetrics World

73. Social Networking for
Scientists
• The representation of YOU on the web is
going to become increasingly important…
• Engagement and participation is a
choice…
• Consider the value to both you and to
your community regarding contribution
• Open Data, Curations, Annotations etc.

74. Conclusions
• Online chemistry has exploded…
• Each of you has the opportunity to contribute
• Contributions will ultimately be credited to
you and your scientific career
• Imagine starting to build your online
presence early and how it can benefit you
• There is no time that is too early to start
actively building profile/reputation

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