The comparative toxicogenomics database: Update 2013

Nucleic Acids Research

Volumn 41, Issue D1, 2013, Pages

  Davis, Allan Peter ^a   Murphy, Cynthia Grondin ^a   Johnson, Robin ^b   Lay, Jean M ^b   Lennon Hopkins, Kelley ^b   Saraceni Richards, Cynthia ^b   Sciaky, Daniela ^b   King, Benjamin L ^b   Rosenstein, Michael C ^b   Wiegers, Thomas C ^a   Mattingly, Carolyn J ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b MOUNT DESERT ISLAND BIOLOGICAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENVIRONMENTAL CHEMICAL;

ARTICLE; BIOSTATISTICS; COMPARATIVE TOXICOGEOMICS DATABASE; COMPUTER INTERFACE; DATA ANALYSIS; DATA PROCESSING; ENVIRONMENTAL DISEASE; GENE INTERACTION; GENE PRODUCT; GENETIC DATABASE; GENOMICS; GENOTYPE ENVIRONMENT INTERACTION; INFORMATION PROCESSING DEVICE; MOLECULAR PATHOLOGY; PRIORITY JOURNAL; TOXICOGENOMICS;

COMPUTER GRAPHICS; DATABASES, CHEMICAL; DISEASE; INTERNET; SOFTWARE; TOXICOGENETICS;

EID: 84876467333     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks994     Document Type: Article

References (30)

1. Mortensen, H.M. and Euling, S.Y. (2011) Integrating mechanistic and polymorphism data to characterize human genetic susceptiblity for environmental chemical risk assessment in the 21st centruy. Toxicol. Appl. Pharmacol, February 1. (doi:10.1016/j.taap.2011.01.015; epub ahead of print).
2. Mahadevan, B., Snyder, R.D., Waters, M.D., Benz, R.D., Kemper, R.A., Tice, R.R. and Richard, A.M. (2011) Genetic toxicology in the 21st century: reflections and future directions. Environ. Mol. Mutagen., 52, 339-354.
3. Mattingly, C.J., Rosenstein, M.C., Davis, A.P., Colby, G.T., Forrest, J.N. and Boyer, J.L. (2006) The Comparative Toxicogenomics Database: a cross-species resource for building chemical-gene interaction networks. Toxicol. Sci., 92, 587-595.
4. Davis, A.P., King, B.L., Mockus, S., Murphy, C.G., Saraceni-Richards, C., Rosenstein, M., Wiegers, T. and Mattingly, C.J. (2011) The Comparative Toxicogenomics Database: update 2011. Nucleic Acids Res., 39, D1067-D1072.
5. 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.
6. Davis, A.P., Murphy, C.G., Rosenstein, M.C., Wiegers, T.C. and Mattingly, C.J. (2008) The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study. BMC Med. Genomics, 1, 48.
7. Davis, A.P., Wiegers, T.C., Rosenstein, M.C., Murphy, C.G. and Mattingly, C.J. (2011) The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database. Database, 2011, bar034.
8. Swanson, D.R. and Smalheiser, N.R. (1997) An interactive system for finding complementary literatures: a stimulus to scientific discovery. Artif. Intell., 91, 183-203.
9. Davis, A.P., Wiegers, T.C., Rosenstein, M.C. and Mattingly, C.J. (2012) MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database. Database, 2012, bar065.
10. Wiegers, T.C., Davis, A.P., Cohen, K.B., Hirschman, L. and Mattingly, C.J. (2009) Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD). BMC Bioinformatics, 10, 326.
11. Hirschman, L., Burns, G.A., Krallinger, M., Arighi, C., Cohen, K.B., Valencia, A., Wu, C.H., Chatr-Aryamontri, A., Dowel, K.G., Huala, E. et al. (2012) Text mining for the biocuration workflow. Database, 2012, bas020.
12. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene Ontology: tool for the unification of biology. Nat. Genet., 25, 25-29.
13. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. and Tanabe, M. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-D114.
14. Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Copinath, G., Jassal, B. et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res., 39, D691-D697.
15. de Matos, P., Alcantara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I., Turner, S. and Steinbeck, C. (2010) Chemical entities of biological interest: an update. Nucleic Acids Res., 38, D249-D254.
16. Wang, Y., Xiao, J., Suzek, T.O., Zhang, J., Wang, J., Zhou, Z., Han, L., Karapetyan, K., Dracheva, S., Shoemaker, B.A. et al. (2012) PubChem's bioassay database. Nucleic Acids Res., 40, D400-D412.
17. Schultheisz, R.J. (1981) TOXLINE: evolution of an online interactive bibliographic database. J. Am. Soc. Inf. Sci., 32, 421-429.
18. Hoffmann, R. (2008) A wiki for the life sciences where authorship matters. Nat. Genet., 40, 1047-1051.
19. Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., Dicuccio, M., Federhen, S. et al. (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 40, D13-D25.
20. Gaudet, P., Bairoch, A., Field, D., Sansone, S.A., Taylor, C., Attwood, T.K., Bateman, A., Blake, J.A., Bult, C.J., Cherry, J.M. et al. (2011) Towards BioDBcore: a community-defined information specification for biological database. Nucleic Acids Res., 39, D7-D10.
21. Davis, A.P., Rosenstein, M.C., Wiegers, T.C. and Mattingly, C.J. (2011) DiseaseComps: a metric that discovers similar diseases based upon common toxicogenomics profiles at CTD. Bioinformation, 7, 154-156.
22. Davis, A.P., Murphy, C.G., Saraceni-Richards, C.A., Rosenstein, M.C., Wiegers, T.C., Hampton, T.H. and Mattingly, C.J. (2009) GeneComps and ChemComps: a new CTD metric to identify genes and chemicals with shared toxicogenomic profiles. Bioinformation, 4, 173-174.
23. Kennedy, J. and Roerdink, J. (2012) Highlights of the 1st IEEE Symposium on biological data visualization. BMC Bioinformatics, 13(Suppl. 8), S1.
24. Suderman, M. and Hallett, M. (2007) Tools for visually exporing biological networks. Bioinformatics, 23, 2651-2659.
25. Gehlenborg, N., O'Donoghue, S.I., Baliga, N.S., Goesmann, A., Hibbs, M.A., Kitano, H., Kohlbacher, O., Neuweger, H., Schneider, R., Tenenbaum, D. et al. (2010) Visualization of omics data for system biology. Nat. Methods, 7, S56-S68.
26. Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B. and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
27. Coletti, M.H. and Bleich, H.L. (2001) Medical subject headings used to search the biomedical literature. J. Am. Med. Inform Assoc., 8, 317-323.
28. Amberger, J., Bocchini, C. and Hamosh, A. (2011) A new face and new challenges for Online Mendelian Inheritance in Man (OMIM). Hum. Mutat., 32, 564-567.
29. Mattingly, C.J., McKone, T.E., Callahan, M.A., Blake, J.A. and Hubal, E.A. (2012) Providing the missing link: the exposure science ontology ExO. Environ. Sci. Technol., 46, 3046-3053.
30. Pleil, J.D., Stiegel, M.A., Madden, M.C. and Sobus, J.R. (2011) Heat map visualization of complex environmental and biomarker measurements. Chemosphere, 84, 716-723.