SMPDB 2.0: big improvements to the Small Molecule Pathway Database.
SMPDB 2.0: big improvements to the Small Molecule Pathway Database.
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DOI：
10.1093/nar/gkt1067
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发表时间：
2014-01
影响因子：
14.9
通讯作者：
Wishart DS
中科院分区：
文献类型：
--
作者：
Jewison T;Su Y;Disfany FM;Liang Y;Knox C;Maciejewski A;Poelzer J;Huynh J;Zhou Y;Arndt D;Djoumbou Y;Liu Y;Deng L;Guo AC;Han B;Pon A;Wilson M;Rafatnia S;Liu P;Wishart DS
小分子通路数据库（SMPDB，http://www.smpdb.ca）是一个全面、丰富多彩、完全可搜索且高度交互的数据库，用于可视化人体代谢、药物作用、药物代谢、生理活动和代谢疾病通路。 SMPDB 包含超过 600 条路径，其中近 75% 的路径在任何其他数据库中都找不到。所有 SMPDB 通路图均具有广泛的超链接，包括相关组织、器官、细胞器、亚细胞区室、蛋白质辅因子、蛋白质位置、代谢物位置、化学结构和蛋白质四级结构的详细信息。自 2010 年上次发布以来，SMPDB 经历了大幅升级和显着扩展。特别是，SMPDB 中的路径总数增长了 >70%。此外，之前输入的每条途径都已通过额外的分子或细胞信息完全重新绘制、标准化、纠正、更新和增强。许多 SMPDB 通路现在包括转运蛋白以及更多的生理、组织、靶器官和反应区室数据。由于标准化路径绘制工具（称为 PathWhiz）的开发，所有 SMPDB 路径现在都更容易绘制并且更新更快。 PathWhiz 还允许将所有 SMPDB 路径保存为 BioPAX 格式。 SMPDB 可视化界面的重大改进现在使路径的浏览、选择、重新着色和缩放变得更加容易和直观。由于其实用性和覆盖面广度，SMPDB 现在已集成到其他几个数据库中，包括 HMDB 和 DrugBank。
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, recoloring 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.
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DOI：
10.1007/978-1-62703-435-7_20
发表时间：
2013
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
--
作者：
Thorn, Caroline F;Klein, Teri E;Altman, Russ B
通讯作者：
Altman, Russ B
影响因子：
14.9
作者：
Kanehisa M;Goto S;Sato Y;Furumichi M;Tanabe M
通讯作者：
Tanabe M
影响因子：
14.9
作者：
Frolkis A;Knox C;Lim E;Jewison T;Law V;Hau DD;Liu P;Gautam B;Ly S;Guo AC;Xia J;Liang Y;Shrivastava S;Wishart DS
通讯作者：
Wishart DS
影响因子：
14.9
作者：
Wishart DS;Jewison T;Guo AC;Wilson M;Knox C;Liu Y;Djoumbou Y;Mandal R;Aziat F;Dong E;Bouatra S;Sinelnikov I;Arndt D;Xia J;Liu P;Yallou F;Bjorndahl T;Perez-Pineiro R;Eisner R;Allen F;Neveu V;Greiner R;Scalbert A
通讯作者：
Scalbert A
影响因子：
14.9
作者：
Keseler IM;Mackie A;Peralta-Gil M;Santos-Zavaleta A;Gama-Castro S;Bonavides-Martínez C;Fulcher C;Huerta AM;Kothari A;Krummenacker M;Latendresse M;Muñiz-Rascado L;Ong Q;Paley S;Schröder I;Shearer AG;Subhraveti P;Travers M;Weerasinghe D;Weiss V;Collado-Vides J;Gunsalus RP;Paulsen I;Karp PD
通讯作者：
Karp PD