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Original Articles

Public Databases Supporting Computational Toxicology

Pages 218-231 | Published online: 21 Jun 2010

REFERENCES

  • Balls , M. 2009 . The three Rs and the humanity criterion, an abridged version of The principles of humane experimental technique by , Edited by: Russel , W. M. S. and Burch , R. L. Nottinghame, , UK : Fund for the Replacement of Animals in Medical Experiments (FRAME) .
  • Collins , F. S. , Gray , G. M. and Bucher , J. R. 2008 . Toxicology. Transforming environmental health protection . Science , 319 : 906 – 907 .
  • Davis , A. P. , Murphy , C. G. , Saraceni-Richards , C. A. , Rosenstein , M. C. , Wiegers , T. C. and Mattingly , C. J . 2009 . Comparative toxicogenomics database: A knowledgebase and discovery tool for chemical-gene-disease networks . Nucleic Acids Res. , 37 : D786 – D792 .
  • Dix , D. J. , Houck , K. A. , Martin , Richard M. T. A. M. , A , M , Setzer , R. W. and Kavlock , R. J. 2007 . The ToxCast program for prioritizing toxicity testing of environmental chemicals . Toxicol. Sci. , 95 : 5 – 12 .
  • Fostel , J. , Choi , D. , Zwickl , C. , Morrison , N. , Rashid , A. , Hasan , A. , Bao , W. , Richard , A. , Tong , W. , Bushel , P. R. , Brown , R. , Bruno , M. , Cunningham , M. L. , Dix , D. , Eastin , W. , Frade , C. , Garcia , A. , Heinloth , A. , Irwin , R. , Madenspacher , J. , Merrick , B. A. , Papoian , T. , Paules , R. , Rocca-Serra , P. , Sansone , A. S. , Stevens , J. , Tomer , K. , Yang , C. and Waters , M. 2005 . Chemical effects in biological systems—Data dictionary (CEBS-DD): A compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and omics data . Toxicol. Sci. , 88 : 585 – 601 .
  • Fostel , J. M. , Burgoon , L. , Zwickl , C. , Lord , P. , Corton , J. C. , Bushel , P. R , Cunningham , M. , Fan , L. , Edwards , S. W. , Hester , S. , Stevens , J. , Tong , W. , Waters , M. , Yang , C. and Tennant , R. 2007 . Toward a checklist for exchange and interpretation of data from a toxicology study . Toxicol. Sci. , 99 : 26 – 34 .
  • Gohlke , J. M. , Thomas , R. , Zhang , Y. , Rosenstein , M. C. , Davis , A. P. , Murphy , C. , Becker , K. G. , Mattingly , C. J. and Portier , C. J. 2009 . Genetic and environmental pathways to complex diseases . BMC Syst. Biol. , 3 : 46
  • Gold , L. S. , Manley , N. B. , Slone , T. H. and Ward , J. M. 2001 . Compendium of chemical carcinogens by target organ: Results of chronic bioassays in rats, mice, hamsters, dogs, and monkeys . Toxicol. Pathol. , 29 : 639 – 652 .
  • Gold, L. S. 2008. Carcinogenic potency database. http://potency.berkeley.edu/index.html
  • Jenssen , T. K. , Laegreid , A. , Komorowski , J. and Hovig , E. 2001 . A literature network of human genes for high-throughput analysis of gene expression . Nat. Genet. , 28 : 21 – 28 .
  • Jenssen, T. K., Laegreid, A., Komorowski, J., and Hovig, E. 2009. PubGene. http://www.pubgene.org
  • Judson , R. , Richard , A. M. , Dix , D. J. , Houck , K. , Martin , M. T. , Kavlock , R. J. , Dellarco , V. , Henry , T. , Holderman , T. , Sayre , P. , Tan , S. , Carpenter , T. and Smith , E. 2009 . The toxicity data landscape for environmental chemicals . Environ. Health. Perspect. , 117 : 685 – 695 .
  • Judson , R. S. , Houck , K. A. , Kavlock , R. J. , Knudsen , K. B. , Martin , M. T. , Mortensen , H. M. , Reif , D. M. , Richard , A. M. , Rotroff , D. M. , Shah , I. and Dix , D. J. Predictive in vitro screening of environmental chemicals—The ToxCast Project . Environ Health Perspect. , 118 485 – 492 .
  • Judson , R. , Richard , A. , Dix , D. , Houck , K. , Elloumi , F. , Martin , M. , Cathey , T. , Transue , T. R. , Spencer , R. and Wolf , M. 2008 . ACToR—Aggregated Computational Toxicology Resource . Toxicol. Appl. Pharmacol. , 233 : 7 – 13 .
  • Kavlock , R. J. , Austin , C. P. and Tice , R. R. 2009 . Toxicity testing in the 21st century: implications for human health risk assessment . Risk Anal. , 29 : 485 – 487 . discussion 92–97
  • Knudsen , T. B. , Martin , M. T. , Kavlock , R. J. , Judson , R. J. , Dix , D. J. and Singh , A.V. 2009 . Profiling the activity of environmental chemicals in prenatal developmental toxicity studies using the U.S. EPA's ToxRefDB . Reprod. Toxicol. , 28 : 209 – 219 .
  • Martin , M. T. , Judson , R. S. , Reif , D. M. , Kavlock , R. J. and Dix , D. J. 2009a . Profiling chemicals based on chronic toxicity results from the U.S. EPA ToxRef database . Environ. Health. Perspect. , 117 : 392 – 399 .
  • Martin , M. T . , Mendez , E. , Corum , D. G. , Judson , R. S. , Kavlock , R. J. , Rotroff , D. M. and Dix , D. J. 2009b . Profiling the reproductive toxicity of chemicals from multigeneration studies in the toxicity reference database (ToxRefDB) . Toxicol. Sci. , 110 : 181 – 190 .
  • Mattingly , C. J. , Rosenstein , M. C. , Davis , A. P. , Colby , G. T. , Forrest , J. N. Jr. and Boyer , J. L. 2006 . The comparative toxicogenomics database: A cross-species resource for building chemical-gene interaction networks . Toxicol. Sci. , 92 : 587 – 595 .
  • National Research Council . 2007 . Toxicity testing in the 21st century: A vision and a strategy , Vol. Washington, DC , National Academies Press .
  • Richard , A. M. , Yang , C. and Judson , R. 2008a . Toxicity data informatics: Supporting a new paradigm for toxicity prediction . Toxicol. Mechanisms Methods , 18 : 103 – 118 .
  • Richard , A. M. , Gold , L. S. and Nicklaus , M. C. 2006 . Chemical structure indexing of toxicity data on the Internet: Moving toward a flat world . Curr. Opin. Drug Discov. Dev. , 9 : 314 – 325 .
  • Richard, A. M., Wolf, M. A., and Burch, J. 2008b. DSSTox EPA Integrated Risk Information System (IRIS) toxicity review data: SDF file and documentation. www.epa.gov/ncct/dsstox
  • Richard , A. M. and Williams , C. R. 2003 . “ Public sources of mutagenicity and carcinogenicity data: Use in structure–activity relationship models ” . In QSARS of mutagens and carcinogens , Edited by: Benigni , R. 145 – 173 . New York : CRC Press .
  • Russom , C. L. 2002 . Mining environmental toxicology information: Web resources . Toxicology , 173 : 75 – 88 .
  • Russom, C. L., Williams, C. R., Stewart, T. W., Swank, A. E., and Richard, A. M. 2008. DSSTox EPA Fathead Minnow Acute Toxicity Database (EPAFHM): SDF files and documentation. www.epa.gov/ncct/dsstox
  • Smith , B. , Ashburner , M. , Rosse , C. , Bard , J. , Bug , W. , Ceusters , W. , Goldberg , L. J. , Eilbeck , K. , Ireland , A. , Mungall , C. J. , Leontis , M. , Rocca-Serra , P. , Ruttenberg , A., S. , Sansone , A. , Scheuermann , R. H. , Shah , N. , Whetzel , P. L. and S. Lewis , S. 2007 . The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration . Nat. Biotechnol. , 25 : 1251 – 1255 .
  • U.S. Environmental Protection Agency. 2008. EPA ToxCast. http://www.epa.gov/ncct/toxcast
  • Viceconti , M. , Clapworthy , G. and Van Sint Jan , S. 2008 . The virtual physiological human—A European initiative for in silico human modelling . J. Physiol. Sci. , 58 : 441 – 446 .
  • Waters , M. , Stasiewicz , S. , Merrick , B. A. , Tomer , K. , Bushel , P. , Paules , R. , Stegman , N. , Nehls , G. , Yost , K. J. , Johnson , C. H. , Gustafson , S. F. , Xirasagar , S. , Xiao , N. , Huang , C. C. , Boyer , P. , Chan , C. C. , Pan , Q. , Gong , H. , Taylor , J. , Choi , D. , Rashid , A. , Ahmed , A. , Howle , R. , Selkirk , J. , Tennant , R. and Fostel , J. 2008 . CEBS—Chemical Effects in Biological Systems: A public data repository integrating study design and toxicity data with microarray and proteomics data . Nucleic Acids Res. , 36 : D892 – D900 .
  • Wishart , D. S. , Knox , C. , Guo , A. C. , Cheng , D. , Shrivastava , S. , Tzur , D. , Gautam , B. and Hassanali , M. 2008 . DrugBank: A knowledgebase for drugs, drug actions and drug targets . Nucleic Acids Res. , 36 : D901 – D906 .
  • Wishart , D. S. , Knox , C. , Guo , A. C. , Shrivastava , S. , Hassanali , M. , Stothard , P. , Chang , Z. and Woolsey , J. 2006 . DrugBank: A comprehensive resource for in silico drug discovery and exploration . Nucleic Acids Res. , 34 : D668 – D672 .
  • Yang , C. , Benz , R. D. and Cheeseman , M. A. 2006 . Landscape of current toxicity databases and database standards . Curr. Opin. Drug Discov. Dev. , 9 : 124 – 133 .

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