Towards a gold standard: Regarding quality in public domain chemistry databases and approaches to improving the situation

Drug Discovery Today

Volumn 17, Issue 13-14, 2012, Pages 685-701

  Williams, Antony J ^a   Ekins, Sean ^b   Tkachenko, Valery ^a  

^a ROYAL SOCIETY OF CHEMISTRY   (United Kingdom)

^b Collaborations in Chemistry ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL COMPOUND; STEROID;

CHEMICAL STRUCTURE; ERROR; GOLD STANDARD; INFORMATION SCIENCE; MEDICAL LITERATURE; PROTEOMICS; QUALITY CONTROL; REFERENCE DATABASE; REVIEW; STEREOCHEMISTRY; VALIDATION STUDY;

DATABASES, CHEMICAL; DRUG DISCOVERY; INTERNET; PUBLIC SECTOR; QUALITY CONTROL; QUALITY IMPROVEMENT;

EID: 84863531180     PISSN: 13596446     EISSN: 18785832     Source Type: Journal    
DOI: 10.1016/j.drudis.2012.02.013     Document Type: Review

References (39)

1. L.M. Brzustowicz Molecular and statistical approaches to the detection and correction of errors in genotype databases Am. J. Hum. Genet. 53 1993 1137 1145 (Pubitemid 23313778)
2. E. Migliavacca MDB: a database system utilizing automatic construction of modules and STAR-derived universal language Bioinformatics 17 2001 1047 1052 (Pubitemid 33085611)
3. D. Fourches Trust, but verify: on the importance of chemical structure curation in cheminformatics and QSAR modeling research J. Chem. Inf. Model. 50 2010 1189 1204
4. T.I. Oprea, M. Olah, L. Ostopovici, R. Rad, and M. Mracec On the propagation of errors in the QSAR literature M. Ford, D. Livingstone, J. Dearden, H. Van de Waterbeemd, EuroQSAR 2002 - Designing drugs and crop protectants: Processes, problems and solutions 2003 Blackwell Publishing New York, NY 314 315
5. M.J. O'Neil The Merck Index: An Encyclopedia of Chemicals, Drugs, and Biologicals 14th edn 2006 Merck & Co.
6. F. Prinz Believe it or not: how much can we rely on published data on potential drug targets? Nat. Rev. Drug Discov. 10 2011 712
7. R.P. Sheridan, and J. Shpungin Calculating similarities between biological activities in the MDL drug data report database J. Chem. Inf. Comput. Sci. 44 2004 727 740
8. U. Wittig Classification of chemical compounds to support complex queries in a pathway database Comp. Funct. Genomics 5 2004 156 162 (Pubitemid 38744651)
9. D.L. Clarke Applying modern error theory to the problem of missed injuries in trauma World J. Surg. 32 2008 1176 1182
10. S.I. Goldberg Analysis of data errors in clinical research databases AMIA Annu. Symp. Proc. 2008 242 246
11. J.M. Finney An efficient record linkage scheme using graphical analysis for identifier error detection BMC Med. Inform. Decis. Mak. 11 2011 7
12. J.P. Ioannidis An epidemic of false claims. Competition and conflicts of interest distort too many medical findings Sci. Am. 304 2011 16
13. J.P. Ioannidis, and M.J. Khoury Improving validation practices in 'omics' research Science 334 2011 1230 1232
14. P.J. Castaldi An empirical assessment of validation practices for molecular classifiers Brief Bioinform. 12 2011 189 202
15. A.W. Bell A HUPO test sample study reveals common problems in mass spectrometry-based proteomics Nat. Methods 6 2009 423 430
16. J. Lamontagne Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome BMC Genomic 11 2010 300
17. C. Zhang Methods for labeling error detection in microarrays based on the effect of data perturbation on the regression model Bioinformatics 25 2009 2708 2714
18. E. Jeong Ontology-based instance data validation for high-quality curated biological pathways BMC Bioinform. 12 Suppl. 1 2011 S8
19. W.C. Wong More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology PLoS Comput. Biol. 6 2010 E1000867
20. A.M. Davis Limitations and lessons in the use of X-ray structural information in drug design Drug Discov. Today 13 2008 831 841
21. X. Fu Data governance in predictive toxicology: a review J. Cheminform. 3 2011 24
22. D.S. Wishart DrugBank: a knowledgebase for drugs, drug actions and drug targets Nucleic Acids Res. 36 Database issue 2008 D901 D906
23. A.J. Williams, and S. Ekins A quality alert and call for improved curation of public chemistry databases Drug Discov. Today 16 2011 747 750
24. A. Brazma Minimum information about a microarray experiment (MIAME)-toward standards for microarray data Nat. Genet. 29 2001 365 371 (Pubitemid 34326681)
25. R. Huang The NCGC pharmaceutical collection: a comprehensive resource of clinically approved drugs enabling repurposing and chemical genomics Sci. Transl. Med. 3 2011 80ps16
26. M. Baker Open-access chemistry databases evolving slowly but not surely Nat. Rev. Drug Discov. 5 2006 707 708 (Pubitemid 44323694)
27. K.M. Hettne Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining J. Cheminform. 2 2010 4
28. S. Ekins Collaborative Computational Technologies for Biomedical Research 2011 Wiley
29. G. Wohlgemuth The chemical translation service - a web-based tool to improve standardization of metabolomic reports Bioinformatics 26 2010 2647 2648
30. S. Ekins Pioneering use of the cloud for development of the collaborative drug discovery (cdd) database S. Ekins, Collaborative Computational Technologies for Biomedical Research Vols. 335-361 2011 Wiley and Sons
31. A.M. Richard DSSTox web site launch: Improving public access to databases for building structure-toxicity prediction models Preclinica 2 2006 103 108
32. R. Judson ACToR - aggregated computational toxicology resource Toxicol. Appl. Pharmacol. 233 2008 7 13
33. D.J. Dix The ToxCast program for prioritizing toxicity testing of environmental chemicals Toxicol. Sci. 95 2007 5 12 (Pubitemid 44942773)
34. Y. Wang PubChem: a public information system for analysing bioactivities of small molecules Nucleic Acids Res. 37 Web Server issue 2009 W623 W633
35. J.R. Kenseth, and S.J. Coldiron High-throughput characterization and quality control of small-molecule combinatorial libraries Curr. Opin. Chem. Biol. 8 2004 418 423 (Pubitemid 38996800)
36. C. Southan Quantitative assessment of the expanding complementarity between public and commercial databases of bioactive compounds J. Cheminform. 1 2009 10
37. A. Schuffenhauer An ontology for pharmaceutical ligands and its application for in silico screening and library design J. Chem. Inf. Comput. Sci. 42 2002 947 955 (Pubitemid 35355244)
38. X. Chen Toward automated biochemotype annotation for large compound libraries Mol. Divers 10 2006 495 509 (Pubitemid 46150642)
39. M. Olah WOMBAT: world of molecular bioactivity T.I. Oprea, Chemoinformatics in Drug Discovery 2005 Wiley 223 239