Byrnes Robert W, Cotter Dawn, Maer Andreia, Li Joshua, Nadeau David, Subramaniam Shankar
San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093-0505, USA.
BMC Syst Biol. 2009 Oct 2;3:99. doi: 10.1186/1752-0509-3-99.
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 http://www.lipidmaps.org. 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.
通路模型是许多系统生物学研究的基础。它们通常使用专门为此目的设计的程序构建。构建新模型通常需要同时访问多种类型的实验数据、特征明确的生物化合物和分子中间体数据库以及参考模型通路。然而，几乎没有软件应用程序能在单个用户界面中提供所有这些功能。
通路编辑器是一个用Java编程语言编写的程序，它允许从头创建通路，并下载LIPID MAPS（脂质代谢物和通路策略）和KEGG脂质代谢通路，以及代谢脂质成分随时间变化的测量数据。通过Java Web Start访问该程序，它可从LIPID MAPS通路数据库（Pathway）以及LIPID MAPS网络服务器http://www.lipidmaps.org下载通路。数据来源于LIPID MAPS实验室联盟进行的代谢组学（脂质组学）、微阵列和蛋白质阵列实验，并按实验进行整理。该程序提供了相关功能，可参照数据库对象和时程数据在绘图面板上创建、连接和注释节点及过程。节点和相互作用的布局以及数据显示可根据需要在通路图中进行配置。用户可以扩展图表，还能与文件之间读写数据以及非脂质组学的KEGG通路。包含引用特定化合物和实验的数据库标识符的XML格式通路图可以保存到本地文件以供后续使用。该程序基于一个类库构建，即生物通路工作台，它可在不同文件格式和数据库对象之间进行转换。此功能的一个示例是以对本地文件系统中包含的SBML（系统生物学标记语言）模型的读/构建/写访问的形式提供的。
在单个界面中包含对多种实验数据类型和通路图的访问、通过与在线数据库的连接实现自动更新，以及专注于注释，包括参考标准化脂质命名法和常见脂质名称，这些都支持了这样一种观点，即通路编辑器对当前的通路建模工具做出了重大且实用的贡献。
