The ToxBank data warehouse: Supporting the replacement of in vivo repeated dose systemic toxicity testing

Molecular Informatics

Volumn 32, Issue 1, 2013, Pages 47-63

  Kohonen, Pekka ^a   Benfenati, Emilio ^b   Bower, David ^c   Ceder, Rebecca ^a   Crump, Michael ^c   Cross, Kevin ^c   Grafström, Roland C ^a   Healy, Lyn ^d   Helma, Christoph ^e   Jeliazkova, Nina ^f   Jeliazkov, Vedrin ^f   Maggioni, Silvia ^b   Miller, Scott ^c   Myatt, Glenn ^c   Rautenberg, Michael ^e   Stacey, Glyn ^d   Willighagen, Egon ^a   Wiseman, Jeff ^g   Hardy, Barry ^h  

^a KAROLINSKA INSTITUTE   (Sweden)

^b MARIO NEGRI INSTITUTE FOR PHARMACOLOGICAL RESEARCH   (Italy)

^c Leadscope Inc   (United States)

^d NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL   (United Kingdom)

^e In Silico Toxicology   (Switzerland)

^f IDEACONSULT LTD   (Bulgaria)

^g Pharmatrope Ltd   (United States)

^h Douglas Connect GmbH   (Switzerland)

Author keywords

Alternative Testing Strategies; Bioinformatics; Cellular models; Cheminformatics; Data warehouse; Databases; Electron transport; Gene expression; OpenTox; Oxidation; Predictive toxicology; Redox chemistry; Reference compounds; Repeated dose toxicity testing; Semantic web; SEURAT 1; ToxBank; Toxicogenomics; Toxicology; Wikis

Indexed keywords

DATA WAREHOUSES; ELECTRONIC DATA INTERCHANGE; GENE EXPRESSION; SAFETY TESTING; SEMANTIC WEB;

ALTERNATIVE TESTING STRATEGY; ANIMAL TESTING; CELLULAR MODELING; CHEMINFORMATICS; ELECTRON TRANSPORT; GENES EXPRESSION; OPENTOX; PREDICTIVE TOXICOLOGY; REDOX CHEMISTRY; REFERENCE COMPOUNDS; REPEATED-DOSE TOXICITY TESTING; SAFETY EVALUATION ULTIMATELY REPLACING ANIMAL TESTING-1; SAFETY EVALUATIONS; SEMANTIC-WEB; TESTING STRATEGIES; TOXBANK; TOXICITY TESTING; TOXICOGENOMICS; TOXICOLOGY; WIKI;

TOXICITY;

BIOMATERIAL; GOLD COMPLEX;

ARTICLE; COMPUTER MODEL; DATA BASE; GENOMICS; IN VIVO STUDY; INFORMATION PROCESSING; INFORMATION SERVICE; PREDICTION; PRIORITY JOURNAL; REFERENCE DATABASE; TECHNOLOGY; TOXICITY TESTING;

EID: 84873038959     PISSN: 18681743     EISSN: 18681751     Source Type: Journal    
DOI: 10.1002/minf.201200114     Document Type: Article

References (94)

1. SEURAT-1, available from, http://www.seurat-1.eu/, 2012.
2. Seventh Framework Programme (FP7), available from, http://cordis.europa. eu/fp7/home-en.html, 2012.
3. Cosmetics Europe, available from, http://www.cosmeticseurope.eu, 2012.
4. A. R. Boobis, J. E. Doe, B. Heinrich-Hirsch, M. E. Meek, S. Munn, M. Ruchirawat, etal., Crit. Rev. Toxicol. 2008, 38, 87-96.
5. G. T. Ankley, R. S. Bennett, R. J. Erickson, D. J. Hoff, M. W. Hornung, R. D. Johnson, etal., Environ Toxicol Chem. 2010, 29, 730-41.
6. K. Boekelheide, M. E. Andersen, ALTEX 2010, 27, 243-52.
7. D. Krewski, D. Acosta Jr., M. H. Andersen, Anderson, J. C. Bailar, 3rd, K. Boekelheide, etal., J. Toxicol. Environ. Health B Crit. Rev. 2010, 13, 51-138.
8. T. Gocht, M. Schwarz, SEURAT-1-Towards the replacement of in vivo repeated dose systemic toxicity testing, Vol.2, ISBN, 978-2-9539634-1-0, Coach consortium, 2012.
9. COSMOS, available from, http://www.cosmos-tox.eu/, 2012.
10. A. Tonnelier, S. Coecke, J. M. Zaldivar, Arch Toxicol. 2012, 86, 393-403.
11. DETECTIVE, available from, http://www.detect-iv-e.eu/, 2012.
12. M. Wiesinger, B. Mayer, P. Jennings, A. Lukas, Toxicol In Vitro. 2012, 26, 956-62.
13. HeMiBio, available from, http://www.hemibio.eu/
14. M. Vinken, M. Pauwels, G. Ates, M. Vivier, T.Vanhaecke, V. Rogiers, Arch Toxicol. 2012, 86, 405-12.
15. NOTOX, available from, http://www.notox-sb.eu/, 2012.
16. B. Hardy, G. Apic, P. Carthew, D. Clark, D. Cook, I. Dix, etal., ALTEX 2012, 29, 129-37.
17. B. Hardy, G. Apic, P. Carthew, D. Clark, D. Cook, I. Dix, etal., ALTEX 2012, 29, 139-56.
18. Screentox, available from, http://www.scrtox.eu/, 2012.
19. S. Colleoni, C. Galli, J. A. Gaspar, K. Meganathan, S. Jagtap, J. Hescheler, etal., Toxicol. Sci. 2011, 124, 370-377.
20. P. Sartipy, P. Bjorquist, Stem Cells 2011, 29, 744-748.
21. F. Pistollato, S. Bremer-Hoffmann, L. Healy, L. Young, G. Stacey, Expert. Opin. Drug Metab. Toxicol. 2012, 8, 239-57.
22. J. Synnergren, C. Ameen, A. Jansson, P. Sartipy, Physiol. Genomics. 2012, 44, 245-58.
23. ToxBank, available from, http://toxbank.net/, 2012.
24. Gold Compounds Wiki (GCW), available from, http://wiki.toxbank.net, 2012.
25. S. Coecke, M. Balls, G. Bowe, J. Davis, G. Gstraunthaler, T. Hartung, etal., Altern. Lab. Anim. 2005, 33, 261-287.
26. International Stem Cell Banking Initiative, Stem Cell Rev. 2009, 5, 301-314.
27. OpenTox, available from, http://www.opentox.org/, 2012.
28. B. Hardy, N. Douglas, C. Helma, M. Rautenberg, N. Jeliazkova, V. Jeliazkov, etal., J. Cheminform. 2010, 2, 7.
29. N. Jeliazkova, V. Jeliazkov, J. Cheminform. 2011, 3, 18.
30. E. L. Willighagen, N. Jeliazkova, B. Hardy, R. C. Grafstrom, O. Spjuth, BMC Res. Notes. 2011, 4, 487.
31. O. Tcheremenskaia, R. Benigni, I. Nikolova, N. Jeliazkova, S. E. Escher, M. Batke, etal., J. Biomed. Semantics 2012, 3 Suppl 1, S 7.
32. RESTful webservices, R.T. Fielding, R.N. Taylor, ACM Transactions on Internet Technology (TOIT), New York, Association for Computing Machinery, 2002-05, 2 (2), 115-150.
33. S. A. Sansone, P. Rocca-Serra, D. Field, E. Maguire, C. Taylor, O. Hofmann, etal., Nat Genet. 2012, 44, 121-126.
34. D. J. Wild, Y. Ding, A. P. Sheth, L. Harland, E. M. Gifford, M. S. Lajiness, Drug Discov. Today 2012, 17, 469-474.
35. K. Holtzblatt, J. Burns Wendell, S. Wood, Rapid Contextual Design, A How-to Guide to Key Techniques for User-Centered Design, Elsevier, 2005.
36. M. Chen, M. Zhang, J. Borlak, W. Tong, Toxicol. Sci. 2012.
37. T. Uehara, A. Ono, T. Maruyama, I. Kato, H. Yamada, Y. Ohno, etal., Mol. Nutr. Food Res. 2010, 54, 218-227.
38. B. Ganter, S. Tugendreich, C. I. Pearson, E. Ayanoglu, S. Baumhueter, K. A. Bostian, etal., J. Biotechnol. 2005, 119, 219-244.
39. A. P. Davis, B. L. King, S. Mockus, C. G. Murphy, C. Saraceni-Richards, M. Rosenstein, etal., Nucleic Acids Res. 2011, 39, D 1067-72.
40. B. Zhang, S. Kirov, J. Snoddy, Nucleic Acids Res. 2005, 33, W 741-748.
41. D. Szklarczyk, A. Franceschini, M. Kuhn, M. Simonovic, A. Roth, P. Minguez, etal., Nucleic Acids Res. 2011, 39, D 561-568.
42. C. F. Taylor, D. Field, S. A. Sansone, J. Aerts, R. Apweiler, M. Ashburner, etal., Nat. Biotechnol. 2008, 26, 889-896.
43. W. A. Warr, J. Comput. Aided Mol. Des. 2012, 26, 801-804.
44. MAQC Consortium, Nat. Biotechnol. 2010, 28(8), 827-838.
45. RDF, J.J. Carroll, G. Klyne, "Resource Description Framework (RDF), Concepts and Syntax", Technical Report, W3C, 2004.
46. OpenAM, available from, http://openam.forgerock.org, 2012.
47. Semantic Web, available from, http://semanticweb.org, 2012.
48. M. Samwald, A. Jentzsch, C. Bouton, C. S. Kallesøe, E. Willighagen, J. Hajagos, M. S. Marshall, E. Prud'hommeaux, O. Hassenzadeh, E. Pichler, S. Stephens, J. Cheminform. 2011, 3(1), 19.
49. A.J. Williams, L. Harland, P. Groth, S. Pettifer, C. Chichester, E.L. Willighagen, etal., Drug Discov Today. 2012, 17(21-22), 1188-1189
50. M. J. Gomez-Lechon, L. Tolosa, J. V. Castell, M. T. Donato, Toxicol. In Vitro 2010, 24, 1879-1889.
51. M. M. Schmidt, R. Dringen, Front. Neuroenergetics 2009, 1, 1.
52. B. Coles, I. Wilson, P. Wardman, J. A. Hinson, S. D. Nelson, B. Ketterer, Arch Biochem Biophys. 1988, 264, 253-260.
53. A. T. Jacobs, L. J. Marnett, Acc. Chem. Res. 2010, 43, 673-683.
54. S. Hoogendoorn, L. Willems, B. Florea, H. Overkleeft, Angew. Chem. Int. Ed. Engl. 2011, 50, 5434-5436.
55. W. Tang, Expert. Opin. Drug Metab. Toxicol. 2007, 3, 407-420.
56. T. O'Brien, G. Babcock, J. Cornelius, M. Dingeldein, G. Talaska, D. Warshawsky, etal., Toxicol. Appl. Pharmacol. 2000, 164, 280-290.
57. F. P. Guengerich, K. O. Arneson, K. M. Williams, Z. Deng, T. M. Harris, Chem. Res. Toxicol. 2002, 15, 780-792.
58. W. H. Koppenol, J. Am. Chem. Soc. 2007, 129, 9686-9690.
59. M. Floreani, F. Carpenedo, Gen. Pharmacol. 1995, 26, 1757-1764.
60. J. M. Karczewski, J. G. Peters, J. Noordhoek, Biochem. Pharmacol. 1999, 57, 27-37.
61. R. H. Haefeli, M. Erb, A. C. Gemperli, D. Robay, I. Courdier Fruh, C. Anklin, etal. PLoS One 2011, 6, e 17963.
62. Y. Wen, W. Li, E. C. Poteet, L. Xie, C. Tan, L. J. Yan, etal., J. Biol. Chem. 2011, 286, 16504-16515.
63. J. A. Hinson, D. W. Roberts, L. P. James, Handb. Exp. Pharmacol. 2010, 369-405.
64. Y. Song, G. R. Buettner, Free Radic. Biol. Med. 2010, 49, 919-962.
65. T. Castillo, D. R. Koop, S. Kamimura, G. Triadafilopoulos, H. Tsukamoto, Hepatology 1992, 16, 992-996.
66. L. E. Fleming, in Case Studies in Environmental Medicine (Eds:, A.M. Pope, D.P. Rall,), National Academies Press, Washington, DC, 1995. p. 249-266.
67. L. W. Weber, M. Boll, A. Stampfl, Crit. Rev. Toxicol. 2003, 33, 105-136.
68. M. Boll, L. W. Weber, E. Becker, A. Stampfl, Z. Naturforsch. C 2001, 56, 649-659.
69. P. Seeman, Biochem. Pharmacol. 1977, 26, 1741-1748.
70. N. Anderson, J. Borlak, FEBS Lett. 2006, 580, 5533-5540.
71. S. Nadanaciva, A. Bernal, R. Aggeler, R. Capaldi, Y. Will, Toxicol. In Vitro 2007, 21, 902-911.
72. J. W. Kesterson, G. R. Granneman, J. M. Machinist, Hepatology 1984, 4, 1143-1152.
73. C. J. Phiel, F. Zhang, E. Y. Huang, M. G. Guenther, M. A. Lazar, P. S. Klein, J. Biol. Chem. 2001, 276, 36734-36741.
74. F. De Ponti, E. Poluzzi, A. Cavalli, M. Recanatini, N. Montanaro, Drug Saf. 2002, 25, 263-286.
75. M. T. Martin, D. J. Dix, R. S. Judson, R. J. Kavlock, D. M. Reif, A. M. Richard, etal., Chem. Res. Toxicol. 2010, 23, 578-590.
76. R. Tirumalai, T. Rajesh Kumar, K. H. Mai, S. Biswal, Toxicol Lett. 2002, 132, 27-36.
77. G. Olmos, I. Conde, I. Arenas, L. Del Peso, C. Castellanos, M. O. Landazuri, etal., Cell Signal. 2007, 19, 2098-2105.
78. I. M. Copple, C. E. Goldring, R. E. Jenkins, A. J. Chia, L. E. Randle, J. D. Hayes, etal. Hepatology 2008, 48, 1292-1301.
79. Y. L. Chua, E. Dufour, E. P. Dassa, P. Rustin, H. T. Jacobs, C. T. Taylor, etal., J. Biol. Chem. 2010, 285, 31277-31284.
80. A. V. Pointon, T. M. Walker, K. M. Phillips, J. Luo, J. Riley, S. D. Zhang, etal., PLoS One 2010, 5, e 12733.
81. E. M. Sparkenbaugh, Y. Saini, K. K. Greenwood, J. J. LaPres, J. P. Luyendyk, B. L. Copple, etal., J. Pharmacol. Exp. Ther. 2011, 338, 492-502.
82. N. J. Allen, R. Karadottir, D. Attwell, J. Neurosci. 2005, 25, 848-859.
83. J. R. Williamson, J. Biol. Chem. 1967, 242, 4476-4485.
84. A. L. Nieminen, A. K. Saylor, B. Herman, J. J. Lemasters, Am. J. Physiol. 1994, 267, C 67-74.
85. H. Sawada, K. Takami, S. Asahi, Toxicol. Sci. 2005, 83, 282-292.
86. K. Fattinger, C. Funk, M. Pantze, C. Weber, J. Reichen, B. Stieger, etal., Clin. Pharmacol. Ther. 2001, 69, 223-231.
87. R. P. Robinson, J. A. Bartlett, P. Bertinato, A. J. Bessire, J. Cosgrove, P. M. Foley, etal., Bioorg. Med. Chem. Lett. 2011, 21, 4150-4154.
88. H. M. Mehendale, Toxicol. Pathol. 2005, 33, 41-51.
89. S. A. Jung, Y. H. Chung, N. H. Park, S. S. Lee, J. A. Kim, S. H. Yang, etal., Scand. J. Gastroenterol. 2000, 35, 969-975.
90. S. Hoehme, M. Brulport, A. Bauer, E. Bedawy, W. Schormann, M. Hermes, etal., Proc. Natl. Acad. Sci. USA 2010, 107, 10371-10376.
91. P. Hytiroglou, H. Tobias, R. Saxena, M. Abramidou, C. S. Papadimitriou, N. D. Theise, Am. J. Clin. Pathol. 2004, 121, 324-329.
92. K. Lindsay, A. D. Fraser, A. Layton, M. Goodfield, H. Gruss, A. Gough, Rheumatology (Oxford), 2009, 48, 569-572.
93. J. M. Kremer, Arthritis Rheum. 2004, 50, 1370-1382.
94. J. S. Moffit, P. H. Koza-Taylor, R. D. Holland, M. S. Thibodeau, R. D. Beger, M. P. Lawton, etal., Toxicol. Appl. Pharmacol. 2007, 222, 169-79.