experiences and adventures with no sql and its applications to cheminformatics data
TRANSCRIPT
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
Chemistry research
Standard designs
Scientific article
Compounds
Reaction
Analytical Data
Text and References
Compounds model
Reaction datamodel
Analytical Data Model
Research Knowledge Model
RSC Databases
RSC CompoundsRSC ReactionsRSC SpectraRSC CrystalsRSC PolymersRSC MaterialsRSC AssaysRSC AlgorithmsRSC Models…and on…
Compounds domain
Reactions domain
Reactions domain
Analytical data domain
Crystallography domain
APIs, endpoints and widgets
Technical view - unification
Chemistry Validation and Standardization Platform
Input pipeline
Output pipeline
Scaling approaches
Federated linked system
Federated repositories
• Privacy
• Security• Authenticity• Safety• Deployment• Access• Etc
SQL database issues
• Scalability
noSQL cartridge performanceQuery 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 40.652 [SiH](C)(C)C[SiH2]C 2740 7.59 7.59 2740 26.99 19.413C1(=O)CCCC1C 57397 7.69 25.86 57397 39.59 13.734C1CCCC=1N=C 1652 6.21 6.21 1652 27.62 21.405C(OCC)/C=C\C 672278 1.75 77.88 672278 94.25 16.376C1N(C=NC1)CC 21986 11.92 14.50 21986 43.16 28.667C1(C)=CCC(C)=C1 8982 7.16 7.16 8982 10.11 2.958P(=O)(O)CCCC 28403 7.34 9.25 28403 12.18 2.939C1(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 15.1311SC1N=CC=CC=1 130485 2.08 17.92 130485 24.09 6.1712C1N=NSC=1Cl 2348 5.61 5.61 2348 8.33 2.7213C(/C1CC1)=N\N 4769 7.82 7.82 4769 11.43 3.6214N1=CC=CN=C1 1166342 0.82 70.29 1166342 141.77 71.4815C1=NON=C1C 15718 7.30 7.79 15718 34.17 26.3816C(CCC)CC 6541041 0.46 421.05 6541041 664.98 243.9417C1(=NN=CN1)C 864513 1.08 56.80 864513 137.24 80.4518 [Cr](=O)O[Cr]([O-])=O 127 3.36 3.36 127 6.94 3.5819 [BH2-]1[NH2+]C=CCN1 1 2.36 2.36 1 6.70 4.3520P(O)(OC)CC 37364 4.09 7.22 37364 9.95 2.7221C(CN)S(=O)=O 301168 2.99 29.10 301168 41.71 12.6122C(C)COC=O 1236803 0.82 123.43 1236803 149.82 26.3923N1(NNCN1)C 122 4.68 4.68 122 8.13 3.4524C(=C)/C=N\C=N 23916 9.93 12.21 23916 18.50 6.2925CNCCOC 4503264 0.62 262.43 4503264 441.03 178.6026C(CO)CCS 148233 11.49 128.54 148233 34.09 -94.4527C1(S)C=CNC=1 35624 7.49 10.81 35624 23.02 12.2128S([O-])(=O)(=O)CC 17442 7.79 9.11 17442 15.67 6.5629P(OPN)(N)N 75 4.73 4.73 75 15.05 10.32
