SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database

被引：338

作者：

Jewison, Timothy ^{[1
]}

Su, Yilu ^{[1
]}

Disfany, Fatemeh Miri ^{[1
]}

Liang, Yongjie ^{[1
]}

Knox, Craig ^{[1
]}

Maciejewski, Adam ^{[1
]}

Poelzer, Jenna ^{[1
]}

Huynh, Jessica ^{[1
]}

Zhou, You ^{[1
]}

Arndt, David ^{[1
]}

Djoumbou, Yannick ^{[1
]}

Liu, Yifeng ^{[1
]}

Deng, Lu ^{[1
]}

Guo, An Chi ^{[1
]}

Han, Beomsoo ^{[1
]}

Pon, Allison ^{[1
]}

Wilson, Michael ^{[1
]}

Rafatnia, Shahrzad ^{[1
]}

Liu, Philip ^{[1
]}

Wishart, David S. ^{[1
,2
,3
]}

机构：

[1] Univ Alberta, Dept Comp Sci, Edmonton, AB T6G 2E8, Canada

[2] Univ Alberta, Dept Biol Sci, Edmonton, AB T6G 2E8, Canada

[3] Natl Inst Nanotechnol, Edmonton, AB T6G 2M9, Canada

来源：

NUCLEIC ACIDS RESEARCH | 2014年 / 42卷 / D1期

关键词：

D O I：

10.1093/nar/gkt1067

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

The Small Molecule Pathway Database (SMPDB, http://www.smpdb.ca) is a comprehensive, colorful, fully searchable and highly interactive database for visualizing human metabolic, drug action, drug metabolism, physiological activity and metabolic disease pathways. SMPDB contains >600 pathways with nearly 75% of its pathways not found in any other database. All SMPDB pathway diagrams are extensively hyperlinked and include detailed information on the relevant tissues, organs, organelles, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Since its last release in 2010, SMPDB has undergone substantial upgrades and significant expansion. In particular, the total number of pathways in SMPDB has grown by >70%. Additionally, every previously entered pathway has been completely redrawn, standardized, corrected, updated and enhanced with additional molecular or cellular information. Many SMPDB pathways now include transporter proteins as well as much more physiological, tissue, target organ and reaction compartment data. Thanks to the development of a standardized pathway drawing tool (called PathWhiz) all SMPDB pathways are now much more easily drawn and far more rapidly updated. PathWhiz has also allowed all SMPDB pathways to be saved in a BioPAX format. Significant improvements to SMPDB's visualization interface now make the browsing, selection, re-coloring and zooming of pathways far easier and far more intuitive. Because of its utility and breadth of coverage, SMPDB is now integrated into several other databases including HMDB and DrugBank.

引用

页码：D478 / D484

页数：7

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