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1. DrugBank 6.0: the DrugBank Knowledgebase for 2024

Author

Knox, Craig, primary, Wilson, Mike, additional, Klinger, Christen M, additional, Franklin, Mark, additional, Oler, Eponine, additional, Wilson, Alex, additional, Pon, Allison, additional, Cox, Jordan, additional, Chin, Na Eun (Lucy), additional, Strawbridge, Seth A, additional, Garcia-Patino, Marysol, additional, Kruger, Ray, additional, Sivakumaran, Aadhavya, additional, Sanford, Selena, additional, Doshi, Rahil, additional, Khetarpal, Nitya, additional, Fatokun, Omolola, additional, Doucet, Daphnee, additional, Zubkowski, Ashley, additional, Rayat, Dorsa Yahya, additional, Jackson, Hayley, additional, Harford, Karxena, additional, Anjum, Afia, additional, Zakir, Mahi, additional, Wang, Fei, additional, Tian, Siyang, additional, Lee, Brian, additional, Liigand, Jaanus, additional, Peters, Harrison, additional, Wang, Ruo Qi (Rachel), additional, Nguyen, Tue, additional, So, Denise, additional, Sharp, Matthew, additional, da Silva, Rodolfo, additional, Gabriel, Cyrella, additional, Scantlebury, Joshua, additional, Jasinski, Marissa, additional, Ackerman, David, additional, Jewison, Timothy, additional, Sajed, Tanvir, additional, Gautam, Vasuk, additional, and Wishart, David S, additional

Published
2023
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2. DrugBank 6.0: the DrugBank Knowledgebase for 2024.

Author

Knox, Craig, Wilson, Mike, Klinger, Christen M, Franklin, Mark, Oler, Eponine, Wilson, Alex, Pon, Allison, Cox, Jordan, Chin, Na Eun (Lucy), Strawbridge, Seth A, Garcia-Patino, Marysol, Kruger, Ray, Sivakumaran, Aadhavya, Sanford, Selena, Doshi, Rahil, Khetarpal, Nitya, Fatokun, Omolola, Doucet, Daphnee, Zubkowski, Ashley, and Rayat, Dorsa Yahya

Published
2024
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3. T3DB: the toxic exposome database

Author

Wishart, David, Arndt, David, Pon, Allison, Sajed, Tanvir, Guo, An Chi, Djoumbou, Yannick, Knox, Craig, Wilson, Michael, Liang, Yongjie, Grant, Jason, Liu, Yifeng, Goldansaz, Seyed Ali, and Rappaport, Stephen M.

Published
2015
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5. SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database

Author

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

Published
2014
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8. PathBank: a comprehensive pathway database for model organisms

Author

Wishart, David S., Li, Carin, Marcu, Ana, Badran, Hasan, Pon, Allison, Budinski, Zachary, Patron, Jonas, Lipton, Debra, Cao, Xuan, Oler, Eponine, Li, Krissa, Paccoud, Maïlys, Hong, Chelsea, Guo, An C., Chan, Christopher, Wei, William, Ramirez-Gaona, Miguel, Wishart, David S., Li, Carin, Marcu, Ana, Badran, Hasan, Pon, Allison, Budinski, Zachary, Patron, Jonas, Lipton, Debra, Cao, Xuan, Oler, Eponine, Li, Krissa, Paccoud, Maïlys, Hong, Chelsea, Guo, An C., Chan, Christopher, Wei, William, and Ramirez-Gaona, Miguel

Abstract

PathBank (www.pathbank.org) is a new, comprehensive, visually rich pathway database containing more than 110 000 machine-readable pathways found in 10 model organisms (Homo sapiens, Bos taurus, Rattus norvegicus, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, Escherichia coli and Pseudomonas aeruginosa). PathBank aims to provide a pathway for every protein and a map for every metabolite. This resource is designed specifically to support pathway elucidation and pathway discovery in transcriptomics, proteomics, metabolomics and systems biology. It provides detailed, fully searchable, hyperlinked diagrams of metabolic, metabolite signaling, protein signaling, disease, drug and physiological pathways. All PathBank pathways include information on the relevant organs, organelles, subcellular compartments, cofactors, molecular locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to the rich data contained in public chemical databases such as HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All PathBank pathways are accompanied with references and detailed descriptions which provide an overview of the pathway, condition or processes depicted in each diagram. Every PathBank pathway is downloadable in several machine-readable and image formats including BioPAX, SBML, PWML, SBGN, RXN, PNG and SVG. PathBank also supports community annotations and submissions through the web-based PathWhiz pathway illustrator. The vast majority of PathBank's pathways (>95%) are not found in any other public pathway database.

Published
2020

9. PathBank: a comprehensive pathway database for model organisms

Author

Wishart, David S, primary, Li, Carin, additional, Marcu, Ana, additional, Badran, Hasan, additional, Pon, Allison, additional, Budinski, Zachary, additional, Patron, Jonas, additional, Lipton, Debra, additional, Cao, Xuan, additional, Oler, Eponine, additional, Li, Krissa, additional, Paccoud, Maïlys, additional, Hong, Chelsea, additional, Guo, An C, additional, Chan, Christopher, additional, Wei, William, additional, and Ramirez-Gaona, Miguel, additional

Published
2019
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11. HMDB 4.0: the human metabolome database for 2018

Author

Wishart, David S, primary, Feunang, Yannick Djoumbou, additional, Marcu, Ana, additional, Guo, An Chi, additional, Liang, Kevin, additional, Vázquez-Fresno, Rosa, additional, Sajed, Tanvir, additional, Johnson, Daniel, additional, Li, Carin, additional, Karu, Naama, additional, Sayeeda, Zinat, additional, Lo, Elvis, additional, Assempour, Nazanin, additional, Berjanskii, Mark, additional, Singhal, Sandeep, additional, Arndt, David, additional, Liang, Yonjie, additional, Badran, Hasan, additional, Grant, Jason, additional, Serra-Cayuela, Arnau, additional, Liu, Yifeng, additional, Mandal, Rupa, additional, Neveu, Vanessa, additional, Pon, Allison, additional, Knox, Craig, additional, Wilson, Michael, additional, Manach, Claudine, additional, and Scalbert, Augustin, additional

Published
2017
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12. DrugBank 5.0: a major update to the DrugBank database for 2018

Author

Wishart, David S, primary, Feunang, Yannick D, additional, Guo, An C, additional, Lo, Elvis J, additional, Marcu, Ana, additional, Grant, Jason R, additional, Sajed, Tanvir, additional, Johnson, Daniel, additional, Li, Carin, additional, Sayeeda, Zinat, additional, Assempour, Nazanin, additional, Iynkkaran, Ithayavani, additional, Liu, Yifeng, additional, Maciejewski, Adam, additional, Gale, Nicola, additional, Wilson, Alex, additional, Chin, Lucy, additional, Cummings, Ryan, additional, Le, Diana, additional, Pon, Allison, additional, Knox, Craig, additional, and Wilson, Michael, additional

Published
2017
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20. Pathways with PathWhiz

Author

Pon, Allison, primary, Jewison, Timothy, additional, Su, Yilu, additional, Liang, Yongjie, additional, Knox, Craig, additional, Maciejewski, Adam, additional, Wilson, Michael, additional, and Wishart, David S., additional

Published
2015
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21. T3DB: the toxic exposome database

Author

Wishart, David, primary, Arndt, David, additional, Pon, Allison, additional, Sajed, Tanvir, additional, Guo, An Chi, additional, Djoumbou, Yannick, additional, Knox, Craig, additional, Wilson, Michael, additional, Liang, Yongjie, additional, Grant, Jason, additional, Liu, Yifeng, additional, Goldansaz, Seyed Ali, additional, and Rappaport, Stephen M., additional

Published
2014
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22. SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database

Author

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

Published
2013
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27. DrugBank 5.0: a major update to the DrugBank database for 2018.

Author

Wishart DS, Feunang YD, Guo AC, Lo EJ, Marcu A, Grant JR, Sajed T, Johnson D, Li C, Sayeeda Z, Assempour N, Iynkkaran I, Liu Y, Maciejewski A, Gale N, Wilson A, Chin L, Cummings R, Le D, Pon A, Knox C, and Wilson M

Subjects
Drug Interactions, Food-Drug Interactions, Metabolome drug effects, Polymorphism, Single Nucleotide, Transcriptome drug effects, User-Computer Interface, Databases, Pharmaceutical
Abstract

DrugBank (www.drugbank.ca) is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. First described in 2006, DrugBank has continued to evolve over the past 12 years in response to marked improvements to web standards and changing needs for drug research and development. This year's update, DrugBank 5.0, represents the most significant upgrade to the database in more than 10 years. In many cases, existing data content has grown by 100% or more over the last update. For instance, the total number of investigational drugs in the database has grown by almost 300%, the number of drug-drug interactions has grown by nearly 600% and the number of SNP-associated drug effects has grown more than 3000%. Significant improvements have been made to the quantity, quality and consistency of drug indications, drug binding data as well as drug-drug and drug-food interactions. A great deal of brand new data have also been added to DrugBank 5.0. This includes information on the influence of hundreds of drugs on metabolite levels (pharmacometabolomics), gene expression levels (pharmacotranscriptomics) and protein expression levels (pharmacoprotoemics). New data have also been added on the status of hundreds of new drug clinical trials and existing drug repurposing trials. Many other important improvements in the content, interface and performance of the DrugBank website have been made and these should greatly enhance its ease of use, utility and potential applications in many areas of pharmacological research, pharmaceutical science and drug education., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2018
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28. HMDB 4.0: the human metabolome database for 2018.

Author

Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, Vázquez-Fresno R, Sajed T, Johnson D, Li C, Karu N, Sayeeda Z, Lo E, Assempour N, Berjanskii M, Singhal S, Arndt D, Liang Y, Badran H, Grant J, Serra-Cayuela A, Liu Y, Mandal R, Neveu V, Pon A, Knox C, Wilson M, Manach C, and Scalbert A

Subjects
Databases, Chemical, Gas Chromatography-Mass Spectrometry, Humans, Metabolic Networks and Pathways, Metabolomics, Nuclear Magnetic Resonance, Biomolecular, Tandem Mass Spectrometry, User-Computer Interface, Databases, Factual, Metabolome
Abstract

The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards. This year's update, HMDB 4.0, represents the most significant upgrade to the database in its history. For instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60. Significant improvements have also been made to the HMDB's chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. A great deal of brand new data has also been added to HMDB 4.0. This includes large quantities of predicted MS/MS and GC-MS reference spectral data as well as predicted (physiologically feasible) metabolite structures to facilitate novel metabolite identification. Additional information on metabolite-SNP interactions and the influence of drugs on metabolite levels (pharmacometabolomics) has also been added. Many other important improvements in the content, the interface, and the performance of the HMDB website have been made and these should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2018
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