SMPDB 2.0: Big improvements to the small molecule pathway database

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Jewison, Timothy ^a   Su, Yilu ^a   Disfany, Fatemeh Miri ^a   Liang, Yongjie ^a   Knox, Craig ^a   MacIejewski, Adam ^a   Poelzer, Jenna ^a   Huynh, Jessica ^a   Zhou, You ^a   Arndt, David ^a   Djoumbou, Yannick ^a   Liu, Yifeng ^a   Deng, Lu ^a   Guo, An Chi ^a   Han, Beomsoo ^a   Pon, Allison ^a   Wilson, Michael ^a   Rafatnia, Shahrzad ^a   Liu, Philip ^a   Wishart, David S ^a,b  

^a UNIVERSITY OF ALBERTA   (Canada)

^b NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; DRUG; PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; DRUG ACTIVITY; DRUG METABOLISM; FACTUAL DATABASE; HUMAN; METABOLIC DISORDER; METABOLISM; MOLECULAR BIOLOGY; NONHUMAN; PHYSIOLOGY; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEIN QUATERNARY STRUCTURE; QUALITY CONTROL; SIGNAL TRANSDUCTION; SMALL MOLECULE PATHWAY DATABASE 2.0; STANDARDIZATION; TARGET ORGAN; APPLICATION SERVICE PROVIDER; DATA BASE; INFORMATION PROCESSING; INFORMATION SERVICE; INFORMATION SYSTEM; ONLINE SYSTEM; PATHWHIZ; CHEMICAL DATABASE; CHEMISTRY; COMPUTER GRAPHICS; INTERNET;

COMPUTER GRAPHICS; DATABASES, CHEMICAL; HUMANS; INTERNET; METABOLIC DISEASES; METABOLIC NETWORKS AND PATHWAYS; PHARMACEUTICAL PREPARATIONS; PROTEINS;

EID: 84891787534     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1067     Document Type: Article

References (15)

1. 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.
2. Keseler, I.M., Mackie, A., Peralta-Gil, M., Santos-Zavaleta, A., Gama-Castro, S., Bonavides-Martinez, C., Fulcher, C., Huerta, A.M., Kothari, A., Krummenacker, M. et al. (2013) EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res., 41, D605-D612.
3. Caspi, R., Altman, T., Dreher, K., Fulcher, C.A., Subhraveti, P., Keseler, I.M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L.A. et al. (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 40, D742-D753.
4. Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B. et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res., 39, D691-D697.
5. Pico, A.R., Kelder, T., van Iersel, M.P., Hanspers, K., Conklin, B.R. and Evelo, C. (2008) WikiPathways: pathway editing for the people. PLoS Biol., 6, e184.
6. Thorn, C.F., Klein, T.E. and Altman, R.B. (2013) PharmGKB: the Pharmacogenomics Knowledge Base. Methods Mol. Biol., 1015, 311-320.
7. Frolkis, A., Knox, C., Lim, E., Jewison, T., Law, V., Hau, D.D., Liu, P., Gautam, B., Ly, S., Guo, A.C. et al. (2010) SMPDB: The Small Molecule Pathway Database. Nucleic Acids Res., 38, D480-D487.
8. Stromback, L. and Lambrix, P. (2005) Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX. Bioinformatics, 21, 4401-4407.
9. Knox, C., Law, V., Jewison, T., Liu, P., Ly, S., Frolkis, A., Pon, A., Banco, K., Mak, C., Neveu, V. et al. (2011) DrugBank 3.0: a comprehensive resources for 'Omics' research on drugs. Nucleic Acids Res., 39, D1035-D1041.
10. Wishart, D.S., Jewison, T., Guo, A.C., Wilson, M., Knox, C., Liu, Y., Djoumbou, Y., Mandal, R., Aziat, F., Dong, E. et al. (2013) HMDB 3.0-The Human Metabolome Database in 2013. Nucleic Acids Res., 41, D801-D807.
11. UniProt Consortium. (2013) Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res., 41, D43-D47.
12. Webb, R.L. and Ma'ayan, A. (2011) Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. Source Code Biol. Med., 6, 5.
13. Hamosh, A., Scott, A.F., Amberger, J.S., Bocchini, C.A. and McKusick, V.A. (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res., 33, D514-D517.
14. Xia, J., Mandal, R., Sinelnikov, I.V., Broadhurst, D. and Wishart, D.S. (2012) MetaboAnalyst 2.0-A comprehensive server for metabolomic data analysis. Nucleic Acids Res., 40, W127-W133.
15. Xia, J. and Wishart, D.S. (2010) MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. Nucleic Acids Res., 38, W71-W77.