Chemical databases: Curation or integration by user-defined equivalence?

Drug Discovery Today: Technologies

Volumn 14, Issue , 2015, Pages 17-24

  Hersey, Anne ^a   Chambers, Jon ^a   Bellis, Louisa ^a   Patricia Bento A ^a   Gaulton, Anna ^a   Overington, John P ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHEMICAL DATABASE; CHEMICAL STRUCTURE; COMMERCIAL PHENOMENA; COMPUTER PROGRAM; DATA BASE; INFORMATION PROCESSING; MOLECULAR LIBRARY; STANDARDIZATION; DRUG DEVELOPMENT; SOFTWARE;

DATABASES, CHEMICAL; DRUG DISCOVERY; MOLECULAR STRUCTURE; SOFTWARE;

EID: 84951907857     PISSN: None     EISSN: 17406749     Source Type: Journal    
DOI: 10.1016/j.ddtec.2015.01.005     Document Type: Review

References (28)

1. A.J. Williams, L. Harland, P. Groth, S. Pettifer, C. Chichester, E.L. Willighagen, and et al. Open PHACTS: semantic interoperability for drug discovery Drug Discov Today 17 21-22 2012 1188 1198
2. H.E. Pence, and Williams A. ChemSpider. An online chemical information resource J Chem Educ 87 11 2010 1123 1124
3. A.J. Williams, S. Ekins, and V. Tkachenko Towards a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation Drug Discov Today 17 13-14 2012 685 701
4. P. Tiikkainen, L. Bellis, Y. Light, and L. Franke Estimating error rates in bioactivity databases J Chem Inf Model 53 10 2013 2499 2505
5. D. Fourches, E. Muratov, and A. Tropsha Trust but verify on the importance of chemical structure curation in cheminformatics and QSAR modeling research J Chem Inf Model 50 2010 1189 1204
6. R. Huang, N. Southall, Y. Wang, A. Yasgar, P. Shinn, A. Jadhav, and et al. The NCGC Pharmaceutical Collection: a comprehensive resource of clinically approved drugs enabling repurposing and chemical genomics Sci Transl Med 3 80 2011 ps16
7. USP dictionary of USAN and international drug names 2010 2010 United States Pharmacopeial
8. A. Hersey, S. Senger, and J.P. Overington Open data for drug discovery: learning from the biological community Future Med Chem 4 15 2012 1865 1867
9. A. Dalby, J.G. Nourse, W.D. Hounshell, A.K.I. Gushurst, D.L. Grier, B.A. Leland, and et al. Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited J Chem Inf Comput Sci 32 3 1992 244 255
10. United States Adopted Names. http://www.ama-assn.org/ama/pub/physician-resources/medical-science/united-states-adopted-names-council.page.
11. S. Heller, A. McNaught, S. Stein, D. Tchekhovskoi, and I. Pletnev InChI - the worldwide chemical structure identifier standard J Cheminform 5 2013 7
12. InChI FAQs from the InChI Trust. http://www.inchi-trust.org/fileadmin/user-upload/html/inchifaq/inchi-faq.html.
13. Food and Drug Administration Substance Registration System Standard Operating Procedure Version 5c. http://www.fda.gov/downloads/ForIndustry/DataStandards/SubstanceRegistrationSystem-UniqueIngredientIdentifierUNII/ucm127743.pdf.
14. E. Bolton, Y. Wang, P.A. Thiessen, and S.H. Bryant PubChem: integrated platform of small molecules and biological activities Annual reports in computational chemistry vol. 4 2008 Elsevier 217 240 [chapter 12]
15. Karapetyan K, Batchelor C, Sharpe D, Tkachenko, Williams AJ. The Chemical Validation and Standardization Platform (CVSP). Large-scale automated validation of chemical structure datasets in preparation (private communication from AJ Williams, submitted to Journal of Cheminformatics).
16. ChemAxon Standardiser. https://docs.chemaxon.com/display/standardizer/Home.
17. Biovia (formerly Accelrys) Cheshire. http://accelrys.com/products/pdf/cheshire.pdf.
18. Perspectives in drug discovery and design: tautomers and tautomerism Y.C. Martin J Comput Aided Mol Des 24 6-7 2010
19. W.A. Warr Tautomerism in chemical information management systems J Comput Aided Mol Des 24 6-7 2010 497 520
20. J. Hastings, P. de Matos, A. Dekker, M. Ennis, B. Harsha, N. Kale, and et al. The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013 Nucleic Acids Res 41 Database Issue 2013 D456 D463
21. C.A. Lipinski, N.K. Litterman, C. Southan, A.J. Williams, A.M. Clark, and S. Ekins Parallel worlds of public and commercial bioactive chemistry data J Med Chem 2014 [Dec 4 Epub ahead of print]
22. M. Sitzmann, W. Ihlenfeldt, and M.C. Nicklaus Tautomerism in large databases J Comput Aided Mol Des 24 2010 521 551
23. J. Chambers, M. Davies, A. Gaulton, A. Hersey, S. Velankar, R. Petryszak, and et al. UniChem: a unified chemical structure cross-referencing and identifier tracking system J Cheminform 5 2013 3
24. J. Chambers, M. Davies, A. Gaulton, G. Papadatos, A. Hersey, and J.P. Overington UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers J Cheminform 6 2014 43
25. A. Gaulton, L.J. Bellis, A. Patrícia Bento, J. Chambers, M. Davies, A. Hersey, and et al. ChEMBL: a large-scale bioactivity database for drug discovery Nucleic Acids Res 40 Database Issue 2012 D1100 D1107
26. C. Knox, V. Law, T. Jewison, P. Liu, S. Ly, A. Frolkis, and et al. DrugBank 3.0: a comprehensive resource for 'omics' research on drugs Nucleic Acids Res 39 Database Issue 2011 D1035 D1041
27. J.J. Irwin, T. Sterling, M.M. Mysinger, E.S. Bolstad, and R.G. Coleman ZINC: a free tool to discover chemistry for biology J Chem Inf Model 52 7 2012 1757 1768
28. A. Gutmanas, Y. Alhroub, G.M. Battle, J.M. Berrisford, E. Bochet, M.J. Conroy, and et al. PDBe: protein data bank in Europe Nucleic Acids Res 42 Database Issue 2014 D285 D291