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. The Expansive Reach of
ChemSpider as a Resource for
the Chemistry Community
Antony Williams
University of Oregon, April 24th
2013

2. 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

3. We Have …Too Much Data!!!

4. e-Science and Primary Data
• How much data generated in a lab, that COULD go public, is
lost forever?

5. TotallySynthetic.com

6. e-Science and Primary Data
• How much data generated in a lab, that COULD go public, is
lost forever?
• Public Domain reference databases of value?
– Syntheses
– Properties
– Spectra
– CIFs
– Images

7. Collaborative Knowledge Management

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

9. RSC’s ChemSpider

10. Crowdsourced “Annotations”
• Users can add
– 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

12. Spectra

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

14. The Structure of Vitamin K?

15. MeSH
• A lipid cofactor that is required for normal blood clotting.
Several forms of vitamin K have been identified:
VITAMIN K 1 (phytomenadione) derived from plants,
VITAMIN K 2 (menaquinone) from bacteria, and synthetic
naphthoquinone provitamins, VITAMIN K 3 (menadione).
Vitamin K 3 provitamins, after being alkylated in vivo,
exhibit the antifibrinolytic activity of vitamin K. Green
leafy vegetables, liver, cheese, butter, and egg yolk are
good sources of vitamin K

16. The Structure of Vitamin K1?

17. What is the Structure of Vitamin
K1?

18. CAS’s Common Chemistry

19. Wikipedia

24. “2-methyl-3-(3,7,11,15-tetramethylhexadec-2-
enyl)naphthalene-1,4-dione”
• Variants of systematic names on PubChem
– 2-methyl-3-[(E,7R,11R)-3,7,11,15-tetramethyl
– 2-methyl-3-[(E,7S,11R)-3,7,11,15-tetramethyl
– 2-methyl-3-[(E,7R,11S)-3,7,11,15-tetramethyl
– 2-methyl-3-[(E,7S,11S)-3,7,11,15-tetramethyl
– 2-methyl-3-[(E,11S)-3,7,11,15-tetramethyl
– 2-methyl-3-[(E)-3,7,11,15-tetramethyl
– 2-methyl-3-(3,7,11,15-tetramethyl
– 2-methyl-3-[(E)-3,7,11,15-tetramethyl

25. Question Everything online: www.dhmo.org

26. It’s all on Wikipedia…

27. Chemistry on The Internet Is Messy

28. It’s Methane…

29. What’s Methane?

30. What’s Methane?

31. What ELSE is Methane???

32. With Great Fanfare…

33. NPC Browser http://tripod.nih.gov/npc/

34. NPC Browser http://tripod.nih.gov/npc/

36. Public Domain Databases
• Our databases are a mess…
• Non-curated databases are proliferating errors
• We source and deposit data between databases
• Original sources of errors hard to determine
• Curation is time-consuming and challenging

37. Stop Whining – Fix it

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

39. Search “Vitamin H”

40. “Curate” Identifiers

41. “Curate” Identifiers

42. “Curate” Identifiers

43. Standards : Structure Standardization

44. Standards : Structure Standardization

45. Standards : Structure Standardization

46. The InChI Identifier

47. Multiple Layers

48. InChIStrings Hash to InChIKeys

49. Vancomycin – Search the Internet

50. Vancomycin
Search Molecular
SKELETON
Search Full Molecule

51. Full Skeleton Search: 104 Hits

52. Full Molecule Search: 4 Hits

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

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

55. Vincristine: Identifiers and
Properties

56. Vincristine: Vendors and Sources
Linked by Structure

57. Vincristine: Patents
Linked by Name

58. Vincristine: Articles
Linked by Name

59. ChemSpider Resources for Chemistry

60. Micropublishing Syntheses

61. ChemSpider SyntheticPages

62. Olympicene

63. So you Want a Profile???

66. Interactive Data

68. PharmaSea
• Dereplication via ChemSpider
• Segregation of natural products datasets
• Analytical data algorithms & integration
– Mass spec searching – predicted fragmentation
– NMR feature searching – NMR prediction
– Computer-assisted structure elucidation

69. It is so difficult to navigate…
What’s the
structure?
What’s the
structure?
Are they in
our file?
Are they in
our file?
What’s
similar?
What’s
similar?
What’s the
target?
What’s the
target?Pharmacology
data?
Pharmacology
data?
Known
Pathways?
Known
Pathways?
Working On
Now?
Working On
Now?Connections to
disease?
Connections to
disease?
Expressed in
right cell type?
Expressed in
right cell type?
Competitors?Competitors?
IP?IP?

70. • 3-year Innovative Medicines Initiative project
• Integrating chemistry and biology data using semantic
web technologies
• Open source code, open data and open standards
• Academics, Pharma companies, Publishers….

71. ChemSpider Contributions
• The host of the chemistry services
– Supplier of “standardized” chemical data files
– Chemistry searching (structure, substructure etc)
– Provider of data in RDF format
– Curator and data quality checking
• Now building the Open PHACTS chemical
registration system

72. ChemSpider Contributions
• Supplier of chemistry UI components
• “Quality Police” for data checking
• Chemical Validation and Standardization Platform
• Nanopublications from RSC publications

73. Integrate to instruments and software
• Integration to analytical instrumentation vendors
already in place
– Agilent, Bruker, Thermo, Waters
• Also, Cheminformatics vendors link to ChemSpider
– Accelrys, ACD/Labs, ChemAxon, iChemLabs, and…

74. Natural Products Updates
• Names hard, Structures
“Obvious”
• New content based on
monthly updates of the
database
• Click through to the Natural
Products Updates entry

75. National Chemical Database Service

76. Chemical Database
Service
• National Chemical Database Service
for UK Academics
• Integrating Commercial Databases
and Services
• Chemicals, analytical data,
prediction algorithms
• Development of data repository

77. Publications - a summary of work
• Scientific publications are a summary of work
– 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?
– How many compounds never reported?
– How many syntheses fail or succeed?
– How many characterization measurements?

78. Community Repository for Data
• Funding agencies encourage sharing of data
• Increasing availability of “Open Data”
• Institutional repositories no specific domain
support
• Develop a community repository for chemistry
data – private, public, embargoed
• Provides data to develop models/algorithms

79. Community Repository for Data
• Automated depositions of data
• DOI’ed data objects for citation purposes
• A database of reference data, but validated by
the community
• National services feeding the repository –
crystallography, mass spectrometry
• Integrate to blogging tools for chemistry
• Integrate to Electronic Lab Notebooks as feeds

80. Model Building with Community Data
• Community data as a basis of model building
– Consume data from available databases, community
data, new publications and build predictive
algorithms for the community
– How many algorithms are reported and lost? How
much repeat work is done in the domain of
algorithmic development?

81. Pulling Data from our Archive
• Our contribution to the world of chemistry data
• DERA – digitally enabling the RSC archive
– Text mining
• Find chemicals, reactions, analytical data, properties
– Algorithmic checking
• Validate algorithmically what we can - robots
– “Web 2.0 interfaces” for curating and validating

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

83. Data Validation and Curation Required
Encouraging Participation with
Rewards and RECOGNITION

84. Manual Curation
• Integrated commenting, curating and validation
platform across ALL eScience and publishing
platforms
• All integrated to a central RSC profile and
feeding the AltMetrics tools

85. Structure Review

86. Maybe Hybrid Man-Machine

87. Where we are now…

88. Rewards and Recognition
Congratulations! Your 1st CSSP article
has been published. Philosopher Lao
Tzu said “A journey of a thousand
miles begins with a single step”. In the
same way we hope that this will be
the first of many submissions that you
make to CSSP.
The First Step badge is
awarded when a user
submits (& has published)
their 1st
CSSP article.

89. Future Recognition in AltMetrics?
ChemSpider

90. Internet Data
The Future
Commercial Software
Pre-competitive Data
Open Science
Open Data
Publishers
Educators
Open Databases
Chemical Vendors
Small organic molecules
Undefined materials
Organometallics
Nanomaterials
Polymers
Minerals
Particle bound
Links to Biologicals

91. The Future of Chemistry on the Web?
• Public compound databases federate & build a
linked environment of validated data!
• Data validation needs are not ignored
• Publishers layer on information to make
publications discoverable
• Public-Private databases can be linked
• Open Data proliferate
• The “Semantic Web” in action

92. Acknowledgments
• Valery Tkachenko and the eScience team
• Our data providers, depositors, collaborators
and curators
• Software providers – OpenEye, ChemDoodle,
ACD/Labs, GGA Software, Open Source (Jmol,
JSpecView, OpenBabel)

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