An editor for pathway drawing and data visualization in the Biopathways Workbench.
An editor for pathway drawing and data visualization in the Biopathways Workbench.
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DOI：
10.1186/1752-0509-3-99
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发表时间：
2009-10-02
影响因子：
--
通讯作者：
Subramaniam S
中科院分区：
文献类型：
--
作者：
Byrnes RW;Cotter D;Maer A;Li J;Nadeau D;Subramaniam S
途径模型是许多系统生物学的基础。它们通常使用为此目的设计的程序来构建。构建新的模型通常需要同时访问不同类型的实验数据，充分表征的生物化合物和分子中间体的数据库，以及参考模型途径。然而，很少有软件应用程序在单个用户界面内提供所有这些能力。Pathway Editor是一个用Java编程语言编写的程序，允许从头创建和下载LIPID MAPS（脂质代谢和途径策略）和KEGG脂质代谢途径，以及代谢脂质组分的时间依赖性变化。通过Java Web Start访问，该程序从LIPID MAPS Pathway数据库（Pathway）以及LIPID MAPS Web服务器下载路径。数据来自于由实验室的LIPID MAPS联盟进行的代谢组学（脂质组学）、微阵列和蛋白质阵列实验，并按实验进行排列。提供了一种在绘图面板上参照数据库对象和时间过程数据创建、连接和注释节点和进程的工具。节点和交互布局以及数据显示可以根据需要在路径图中配置。用户可以扩展图表，也可以从文件中读取和写入数据和非脂质组学KEGG路径。XML格式的途径图，包含引用特定化合物和实验的数据库标识符，可以保存到本地文件中供后续使用。该程序是建立在一个类库，称为Biopathways库，可以在不同的文件格式和数据库对象之间转换。该特征的一个示例以对包含在本地文件系统中的SBML（系统生物学标记语言）中的模型的读/构造/写访问的形式提供。包括访问多种实验数据类型和途径图在一个单一的界面，通过连接到一个在线数据库，自动更新，并专注于注释，包括参考标准化的脂质命名以及常见的脂质名称，支持的观点，途径编辑器代表了一个显着的，切实可行的贡献，目前的途径建模工具。
Pathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose. Constructing new models generally requires simultaneous access to experimental data of diverse types, to databases of well-characterized biological compounds and molecular intermediates, and to reference model pathways. However, few if any software applications provide all such capabilities within a single user interface. The Pathway Editor is a program written in the Java programming language that allows de-novo pathway creation and downloading of LIPID MAPS (Lipid Metabolites and Pathways Strategy) and KEGG lipid metabolic pathways, and of measured time-dependent changes to lipid components of metabolism. Accessed through Java Web Start, the program downloads pathways from the LIPID MAPS Pathway database (Pathway) as well as from the LIPID MAPS web server . Data arises from metabolomic (lipidomic), microarray, and protein array experiments performed by the LIPID MAPS consortium of laboratories and is arranged by experiment. Facility is provided to create, connect, and annotate nodes and processes on a drawing panel with reference to database objects and time course data. Node and interaction layout as well as data display may be configured in pathway diagrams as desired. Users may extend diagrams, and may also read and write data and non-lipidomic KEGG pathways to and from files. Pathway diagrams in XML format, containing database identifiers referencing specific compounds and experiments, can be saved to a local file for subsequent use. The program is built upon a library of classes, referred to as the Biopathways Workbench, that convert between different file formats and database objects. An example of this feature is provided in the form of read/construct/write access to models in SBML (Systems Biology Markup Language) contained in the local file system. Inclusion of access to multiple experimental data types and of pathway diagrams within a single interface, automatic updating through connectivity to an online database, and a focus on annotation, including reference to standardized lipid nomenclature as well as common lipid names, supports the view that the Pathway Editor represents a significant, practicable contribution to current pathway modeling tools.
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