AraCyc: A biochemical pathway database for Arabidopsis
AraCyc: A biochemical pathway database for Arabidopsis
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DOI：
10.1104/pp.102.017236
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发表时间：
2003-06-01
期刊：
影响因子：
7.4
通讯作者：
Rhee, SY
中科院分区：
文献类型：
--
作者：
Mueller, LA;Zhang, PF;Rhee, SY
Aracyc是一个数据库，该数据库包含拟南芥信息资源（http://www.arabidopsis.org）开发的拟南芥的生化途径。 Aracyc的目的是通过基于用户友好的Web界面尽可能完全代表拟南芥代谢。目前，它具有170多个途径，其中包括有关化合物，中间体，辅因子，反应，基因，蛋白质和蛋白质亚细胞位置的信息。该数据库使用途径工具软件，该软件使用户可以将数据库中所有途径的视图可视化到化合物的单个化学结构。该数据库是使用途径工具的病理模块构建的，该模块是Metacyc，该模块是来自150多种物种的一系列途径，作为参考数据库。该最初的构建是手动完善和注释的。从文献中添加了20多种植物特异性途径，包括胡萝卜素，黄铜固醇和吉布雷林生物合成。未来几个月将添加40多种植物途径的列表。将数据库的初始自动构建的质量与手动改进的版本进行了比较，而Ecocyc是使用相同的软件系统的Escherichia Coli数据库，该软件系统已经手动注释了很多年。此外，开发了Perl接口PerlCYC，允许程序员从流行的Perl语言访问Pathway Tools数据库。 Aracyc可在拟南芥信息资源网站（http://www.arabidopsis.org/tools/aracyc）的“工具”部分上找到。
AraCyc is a database containing biochemical pathways of Arabidopsis, developed at The Arabidopsis Information Resource (http://www.arabidopsis.org). The aim of AraCyc is to represent Arabidopsis metabolism as completely as possible with a user-friendly Web-based interface. It presently features more than 170 pathways that include information on compounds, intermediates, cofactors, reactions, genes, proteins, and protein subcellular locations. The database uses Pathway Tools software, which allows the users to visualize a bird's eye view of all pathways in the database down to the individual chemical structures of the compounds. The database was built using Pathway Tools' Pathologic module with MetaCyc, a collection of pathways from more than 150 species, as a reference database. This initial build was manually refined and annotated. More than 20 plant-specific pathways, including carotenoid, brassinosteroid, and gibberellin biosyntheses have been added from the literature. A list of more than 40 plant pathways will be added in the coming months. The quality of the initial, automatic build of the database was compared with the manually improved version, and with EcoCyc, an Escherichia coli database using the same software system that has been manually annotated for many years. In addition, a Perl interface, PerlCyc, was developed that allows programmers to access Pathway Tools databases from the popular Perl language. AraCyc is available at the tools section of The Arabidopsis Information Resource Web site (http://www.arabidopsis.org/tools/aracyc).