The Comparative Toxicogenomics Database: Update 2019

Nucleic Acids Research

Volumn 47, Issue D1, 2019, Pages D948-D954

  Davis, Allan Peter ^a   Grondin, Cynthia J ^a   Johnson, Robin J ^a   Sciaky, Daniela ^a   McMorran, Roy ^b   Wiegers, Jolene ^a   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

ANATOMICAL CONCEPTS; ARTICLE; CHEMICAL DATABASE; CHEMICAL GENETICS; COMPARATIVE TOXICOGENOMICS DATABASE; DATA BASE; ENVIRONMENTAL EXPOSURE; HUMAN; INFORMATION PROCESSING; MEDICAL TERMINOLOGY; PATHOGENESIS; PHENOTYPE; PREDICTIVE VALUE; PRIORITY JOURNAL; TAXONOMY; TOXICOGENETICS; VOCABULARY; CONTROLLED VOCABULARY; DISEASES; DRUG DATABASE; GENETICS;

DATABASES, PHARMACEUTICAL; DISEASE; ENVIRONMENTAL EXPOSURE; HUMANS; PHENOTYPE; TOXICOGENETICS; VOCABULARY, CONTROLLED;

EID: 85059795504     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gky868     Document Type: Article

References (41)

1. 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.
2. 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.
3. Davis, A.P., Murphy, C.G., Johnson, R., Lay, J.M., Lennon-Hopkins, K., Saraceni-Richards, C., Sciaky, D., King, B.L., Rosenstein, M.C., Wiegers, T.C. et al. (2013) The Comparative Toxicogenomics Database: update 2013. Nucleic Acids Res., 41, D1104-D1114.
4. Davis, A.P., Grondin, C.J., Lennon-Hopkins, K., Saraceni-Richards, C., Sciaky, D., King, B.L., Wiegers, T.C. and Mattingly, C.J. (2015) The Comparative Toxicogenomics Database's 10th year anniversary: update 2015. Nucleic Acids Res., 43, D914-D920.
5. Davis, A.P., Grondin, C.J., Johnson, R.J., Sciaky, D., King, B.L., McMorran, R., Wiegers, J., Wiegers, T.C. and Mattingly, C.J. (2017) The Comparative Toxicogenomics Database: update 2017. Nucleic Acids Res., 45, D972-D978.
6. 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.
7. 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.
8. Mattingly, C.J., Rosenstein, M.C., Colby, G.T., Forrest, J.N. and Boyer, J.L. (2006) The Comparative Toxicogenomics Database (CTD): a resource for comparative toxicological studies. J. Exp. Zool. A Comp. Exp. Biol., 305, 689-692.
9. 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.
10. 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.
11. Davis, A.P., Wiegers, T.C., Roberts, P.M., King, B.L., Lay, J.M., Lennon-Hopkins, K., Sciaky, D., Johnson, R., Keating, H., Greene, N. et al. (2013) A CTD-Pfizer collaboration: manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions. Database, 2013, bat080.
12. Davis, A.P., Wiegers, T.C., Wiegers, J., Johnson, R.J., Sciaky, D., Grondin, C.J. and Mattingly, C.J. (2018) Chemical-induced phenotypes at CTD help to inform the pre-disease state and construct adverse outcome pathways. Toxicol. Sci., 165, 145-156.
13. 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.
14. Davis, A.P., Rosenstein, M.C., Wiegers, T.C. and Mattingly, C.J. (2011) Disease Comps: a metric that discovers similar diseases based upon common toxicogenomic profiles at CTD. Bioinformation, 7, 154-156.
15. 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.
16. Davis, A.P., Wiegers, T.C., King, B.L., Wiegers, J., Grondin, C.J., Sciaky, D., Johnson, R.J. and Mattingly, C.J. (2016) Generating Gene Ontology-disease inferences to explore mechanisms of human disease at the Comparative Toxicogenomics Database. PLoS One, 11, e0155530.
17. 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.
18. Grondin, C.J., Davis, A.P., Wiegers, T.C., King, B.L., Wiegers, J.A., Reif, D.M., Hoppin, J.A. and Mattingly, C.J. (2016) Advancing exposure science through chemical data curation and integration in the Comparative Toxicogenomics Database. Environ. Health Perspect., 124, 1592-1599.
19. Grondin, C.J., Davis, A.P., Wiegers, T.C., Wiegers, J.A. and Mattingly, C.J. (2018) Accessing an expanded exposure science module at the Comparative Toxicogenomics Database. Environ. Health Perspect., 126, 014501.
20. Planchart, A., Green, A., Hoyo, C. and Mattingly, C.J. (2018) Heavy metal exposure and metabolic syndrome: evidence from human and model system studies. Curr. Environ. Health Rep., 5, 110-124.
21. Pelletier, D., Wiegers, T.C., Enayetallah, A., Kibbey, C., Gosink, M., Koza-Taylor, P., Mattingly, C.J. and Lawton, M. (2016) ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings. Database, 2016, baw062.
22. Wilkinson, M.D., Dumontier, M., Aalbersberg, I.J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.W., da Silva Santos, L.B., Bourne, P.E. et al. (2016) The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data, 3, 160018.
23. Mattingly, C.J., Boyles, R., Lawler, C.P., Haugen, A.C., Dearry, A. and Haendel, M. (2016) Laying a community-based foundation for data-driven semantic standards in environmental health sciences. Environ. Health Perspect., 124, 1136-1140.
24. McQuilton, P., Gonzalez-Beltran, A., Rocca-Serra, P., Thurston, M., Lister, A., Maguire, E. and Sansone, S.A. (2016) BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences. Database, 2016, baw075.
25. 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 databases. Database, 2011, baq027.
26. Davis, A.P., Johnson, R.J., Lennon-Hopkins, K., Sciaky, D., Rosenstein, M.C., Wiegers, T.C. and Mattingly, C.J. (2012) Targeted journal curation as a method to improve data currency at the Comparative Toxicogenomics Database. Database, 2012, bas051.
27. Davis, A.P., Wiegers, T.C., Johnson, R.J., Lay, J.M., Lennon-Hopkins, K., Saraceni-Richards, C., Sciaky, D., Murphy, C.G. and Mattingly, C.J. (2013) Text mining effectively scores and ranks the literature for improving chemical-gene-disease curation at the Comparative Toxicogenomics Database. PLoS One, 8, e58201.
28. King, B.L., Davis, A.P., Rosenstein, M.C., Wiegers, T.C. and Mattingly, C.J. (2012) Ranking transitive chemical-disease inferences using local network topology in the Comparative Toxicogenomics Database. PLoS One, 7, e46524.
29. 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.
30. Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y. and Morishima, K. (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res., 45, D353-D361.
31. Fabregat, A., Jupe, S., Matthews, L., Sidiropoulos, K., Gillespie, M., Garapati, P., Haw, R., Jassal, B., Kominger, F., May, B. et al. (2018) The Reactome pathway knowledgebase. Nucleic Acids Res., 46, D649-D655.
32. Chatr-Aryamontri, A., Oughtred, R., Boucher, L., Rust, J., Chang, C., Kolas, N.K., O'Donnell, L., Oster, S., Theesfeld, C., Sellam, A. et al. (2017) The BioGRID interaction database: 2017 update. Nucleic Acids Res., 45, D369-D379.
33. Galperin, M.Y., Fernandez-Suarez, X.M. and Rigden, D.J. (2017) The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. Nucleic Acids Res., 45, D1-D11.
34. Federhen, S. (2012) The NCBI Taxonomy database. Nucleic Acids Res., 40, D136-D143.
35. 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.
36. Agarwala, R., Barrett, T., Beck, J., Benson, D.A., Bollin, C., Bolton, E., Bourexis, D., Brister, J.R., Bryant, S.H., Canese, K. et al. (2018) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 46, D8-D13.
37. Deans, A.R., Lewis, S.E., Huala, E., Anzaldo, S.S., Ashburner, M., Balhoff, J.P., Blackburn, D.C., Blake, J.A., Burleigh, J.G., Chanet, B. et al. (2015) Finding our way through phenotypes. PLoS Biol., 13, e1002033.
38. Oki, N.O., Nelms, M.D., Bell, S.M., Mortensen, H.M. and Edwards, S.W. (2016) Accelerating adverse outcome pathway development using publicly available data sources. Curr. Environ. Health Rep., 3, 53-63.
39. Amberger, J.S., Bocchini, C.A., Schiettecatte, F., Scott, A.F. and Hamosh, A. (2015) OMIM.org: Online Mendelian Inheritance in Man (OMIM), an online catalog of human genes and genetic disorders. Nucleic Acids Res., 43, D789-D798.
40. Kibbe, W.A., Arze, C., Felix, V., Mitraka, E., Bolton, E., Fu, G., Mungall, C.J., Binder, J.X., Malone, J., Vasant, D. et al. (2015) Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Res., 43, D1071-D1078.
41. 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.