1. Dealing with the complex challenge of managing diverse chemistry data online
Antony Williams, Valery Tkachenko, Alexey Pshenichnov and Ken Karapetyan
ACS San Francisco
August 2014

3. CAS Counter http://www.cas.org/content/counter

4. 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…

5. Think about chemistry a mo’
If we imagine that permission exists… (i.e. forget IP, chemical and pharma companies etc…think students…)
How many syntheses are performed
How many spectra are run
How many properties are measured
How many compounds are made
How many, how much, how big??.....
Let’s go manage it all!!

7. Consider a shift to Openness

8. Open Access funder mandates…
Times have changed…
Open Access funder mandates…

9. Publishers are responding

10. The world of Open Data is here

11. Open Data are everywhere
Is Openness and Social Sharing changing the world?
The cultural experiments in Open Data and exchange are almost daily
Mobile platforms enhance participation
And then what of Chemistry Data???

12. An Experiment - ChemSpider
ChemSpider allowed the community to participate in linking the internet of chemistry & crowdsourcing of data
Successful experiment in terms of building a central hub for integrated web search
More people are “users” than “contributors”
Yet basic feedback and game-play helps

13. An Experiment - CSSP

14. An EPSRC Call
“…the identification of the need for a UK national service for the provision of a searchable, electronic chemical database for the UK academic research community.”

15. National Chemical Database Service

16. We set a vision…
Manage “all” of the chemistry data associated with chemical substances – PUBLISHED and UNPUBLISHED
Based on user selected licensing the data to be downloadable, reusable, interactive
Build a platform that enables the scientist
Data storage, validation, standardization and curation
Collaborative data sharing
Provide data platform that can enable and enhance publishing of scientific papers

17. Data Repository Registration of chemical compounds
Deposition of chemical syntheses
Addition of analytical data
Integration to electronic notebooks
Rewards and recognition for data sharing
Document processing
Hosting of data as private, embargoed or public

18. Development of Data Repository
Data repository should not just be a data dump – should not be a “big disk”
Searchable, integrated, segregated repository of data types
Data access including private, shared embargoed and public
Delivery of derived models from data

19. New Repository Architecture doi: 10.1007/s10822-014-9784-5

20. New Repository Architecture

21. Input data pipeline

22. Compounds

23. Reactions

24. Analytical data

25. Crystallography data

26. For Deposition of Data Quality of data at source
ensuring chemicals are correct - VALIDATION
reactions map and balance as appropriate – VALIDATION and STANDARDIZATION
file format handling for analytical data types – binary file formats are proprietary - STANDARDIZATION
valid interpretation of data – VALIDATION and ANNOTATION

27. Input data pipeline

28. Depositions Gateway User Interface

29. Deposition of Data

30. Validate and Standardize

31. CVSP Filtering

32. CVSP Filtering of DrugBank

33. ChEMBL (1.3 million records)
11,020 records with 4 bonds and zero charge, e.g. CHEMBL or CHEMBL501973
271 records with hypervalent oxygen (e.g. , CHEMBL ), carbon (e.g ), boron, chlorine, iodine or phosphine
6,177 records where direction of bond makes no sense, e.g. CHEMBL12760 and CHEMBL34704

35. Depositions User Interface

36. The challenges of analytical data
Vendors produce complex proprietary data formats and standard formats are required (JCAMP, NetCDF, AniML)
ChemSpider already hosts thousands of JCAMP spectra
Support of “assigned spectra” in place
Data validation approaches understood
There are a myriad of analytical data types…

37. ChemSpider ID H1 NMR

38. ChemSpider ID C13 NMR

39. ChemSpider ID HHCOSY

40. ChemSpider ID HSQC

41. ChemSpider ID HMBC

42. Managing Assignments?

43. Depositions User Interface

44. Depositions from ELNs
Development work integrating chemistry into the Southampton Labtrove notebook
Stoichiometry table development
Analytical data integration
“ChemTrove” rolled out to a small test group in January

48. Document deposition/processing

49. Experimental data checker

50. User Interface Approach

53. User Interface Approach

55. Display Widgets

56. Work in Progress

57. Work in Progress

58. User Interface Approach

60. A Compounds Repository Interface

61. A Reactions/Document Interface

63. The PharmaSea Website

64. The Open PHACTS community ecosystem

65. Open Source Drug Discovery India

66. What can drive participation?
What can drive scientists to participate and contribute?
Ensuring provenance of their data for reuse
Mandates from funding agencies
Improved systems to ease contribution
Additional contributions to science
Improved publishing processes
Recognition for contributions

67. Scientists are Increasingly Quantified…

68. AltMetrics as Scientist Impact

69. AltMetrics

71. Detailed Usage Statistics

72. Rewards and Recognition
The First Step badge is awarded when a user submits (& has published) their 1st CSSP article.
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.

74. AltMetrics Feeds
For our data repository ensure contribution of data will feed out to the AltMetrics platforms
Every data point, every data download, use and reuse will be associated with the scientist
Data will be DOI’ed (presently under review)
Services provided will allow for AltMetrics use

75. What do we have in place?
We are testing an early form of the data repository on our data – ChemSpider and our archive of publications
Working with collaborators to define needs
Testing and enhancing deposition systems
Chemical validation & standardization platform
Analytical data handling formats
And lots in development…

76. The Challenges Ahead Chemistry is NOT just nicely defined structures!
Materials, minerals, attached to beads, polymers, ambiguous materials
Domain-specific measurements
File format standards are limited in application
Encouraging scientists to free up their data
AltMetrics, open data mandates, systems
The data explosion continues

77. But it’s not easy of course
Not everything we would like around data handling is there for sure
Many systems, tools, platforms are already available but we don’t know about them or even if we did contributing us “more work”
“What’s in it for me?”, “It’s my data”, “It’s too much work”, “What credit do I get?”

78. And yes…we know…

79. Thank you
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