The Royal Society of Chemistry hosts an increasing number of chemistry related databases and have utilized SQL-based technologies for our development platforms in general. In recent years the interest in noSQL databases has exploded as the associated technologies have developed and have shown great promise in terms of enhanced performance. We have collaborated with GGA Software Services to implement their noSQL technologies and have integrated it into the compound repository presently being developed as part of the underpinning architecture for compound data management at the RSC. This presentation will provide an overview of the reasons why we have integrated a noSQL solution, quantitative analysis of the benefits of inclusion and our thoughts regarding further approaches to optimize search performance for the chemical compound repository.

1. Experiences and adventures with noSQL
and its applications to cheminformatics
data
Valery Tkachenko, Antony Williams, Ken Karapetyan,
Alexey Pshenichnov, Mikhail Rybalkin
ACS, 248th National Meeting
San Francisco, CA
August 14th
2014

2. Chemistry research

3. Standard designs

6. Scientific article
Compounds
Reaction
Analytical Data
Text and References

7. Compounds model

8. Reaction datamodel

9. Analytical Data Model

10. Research Knowledge Model

11. RSC Databases
RSC Compounds
RSC Reactions
RSC Spectra
RSC Crystals
RSC Polymers
RSC Materials
RSC Assays
RSC Algorithms
RSC Models
…and on…

12. Compounds domain

13. Reactions domain

14. Reactions domain

15. Analytical data domain

16. Crystallography domain

17. APIs, endpoints and widgets

19. Technical view - unification

20. Chemistry Validation and Standardization
Platform

21. Input pipeline

22. Output pipeline

25. Scaling approaches

26. Federated linked system

27. Federated repositories
• Privacy
• Security
• Authenticity
• Safety
• Deployment
• Access
• Etc

28. SQL database issues
• Scalability

29. noSQL cartridge performance
Query Bingo Standalone Module Bingo for SQL Server
Time Difference (how
standalone version
works faster)# Smiles Hits
Time (sec)
Hits Time (sec)
First 10000 hits All
1C(CN)C(F)F 53684 4.51 14.91 53684 55.56 40.65
2[SiH](C)(C)C[SiH2]C 2740 7.59 7.59 2740 26.99 19.41
3C1(=O)CCCC1C 57397 7.69 25.86 57397 39.59 13.73
4C1CCCC=1N=C 1652 6.21 6.21 1652 27.62 21.40
5C(OCC)/C=CC 672278 1.75 77.88 672278 94.25 16.37
6C1N(C=NC1)CC 21986 11.92 14.50 21986 43.16 28.66
7C1(C)=CCC(C)=C1 8982 7.16 7.16 8982 10.11 2.95
8P(=O)(O)CCCC 28403 7.34 9.25 28403 12.18 2.93
9C1(I)=CN=CC=C1 3012 8.36 8.36 3012 9.18 0.82
10C1(CC)=CC=CO1 291005 1.48 24.67 291005 39.79 15.13
11SC1N=CC=CC=1 130485 2.08 17.92 130485 24.09 6.17
12C1N=NSC=1Cl 2348 5.61 5.61 2348 8.33 2.72
13C(/C1CC1)=NN 4769 7.82 7.82 4769 11.43 3.62
14N1=CC=CN=C1 1166342 0.82 70.29 1166342 141.77 71.48
15C1=NON=C1C 15718 7.30 7.79 15718 34.17 26.38
16C(CCC)CC 6541041 0.46 421.05 6541041 664.98 243.94
17C1(=NN=CN1)C 864513 1.08 56.80 864513 137.24 80.45
18[Cr](=O)O[Cr]([O-])=O 127 3.36 3.36 127 6.94 3.58
19[BH2-]1[NH2+]C=CCN1 1 2.36 2.36 1 6.70 4.35
20P(O)(OC)CC 37364 4.09 7.22 37364 9.95 2.72
21C(CN)S(=O)=O 301168 2.99 29.10 301168 41.71 12.61
22C(C)COC=O 1236803 0.82 123.43 1236803 149.82 26.39
23N1(NNCN1)C 122 4.68 4.68 122 8.13 3.45
24C(=C)/C=NC=N 23916 9.93 12.21 23916 18.50 6.29
25CNCCOC 4503264 0.62 262.43 4503264 441.03 178.60
26C(CO)CCS 148233 11.49 128.54 148233 34.09 -94.45
27C1(S)C=CNC=1 35624 7.49 10.81 35624 23.02 12.21
28S([O-])(=O)(=O)CC 17442 7.79 9.11 17442 15.67 6.56
29P(OPN)(N)N 75 4.73 4.73 75 15.05 10.32

30. Thank you
Email: tkachenkov@rsc.org
Slides: http://www.slideshare.net/valerytkachenko16