Institute of Biochemistry and Molecular Biology, College of Life Science, National Yang-Ming University, No. 155, Sec. 2, Li-Nong St, Taipei City, Taiwan 11221, R.O.C.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W124-31. doi: 10.1093/nar/gkq499. Epub 2010 Jun 10.
New pathway databases generally display pathways by retrieving information from a database dynamically. Some of them even provide their pathways in SBML or other exchangeable formats. Integrating these models is a challenging work, because these models were not built in the same way. Pathways integration Tool (PINT) may integrate the standard SBML files. Since these files may be obtained from different sources, any inconsistency in component names can be revised by using an annotation editor upon uploading a pathway model. This integration function greatly simplifies the building of a complex model from small models. To get new users started, about 190 curated public models of human pathways were collected by PINT. Relevant models can be selected and sent to the workbench by using a user-friendly query interface, which also accepts a gene list derived from high-throughput experiments. The models on the workbench, from either a public or a private source, can be integrated and painted. The painting function is useful for highlighting important genes or even their expression level on a merged pathway diagram, so that the biological significance can be revealed. This tool is freely available at http://csb2.ym.edu.tw/pint/.
新的通路数据库通常通过从数据库中动态检索信息来显示通路。其中一些甚至提供 SBML 或其他可交换格式的通路。整合这些模型是一项具有挑战性的工作，因为这些模型不是以相同的方式构建的。通路整合工具（PINT）可以整合标准的 SBML 文件。由于这些文件可能来自不同的来源，因此在上载通路模型时，可以使用注释编辑器来修改组件名称中的任何不一致之处。此集成功能极大地简化了从小型模型构建复杂模型的过程。为了让新用户入门，PINT 收集了大约 190 个人类通路的经过策展的公共模型。可以使用用户友好的查询界面选择相关模型并将其发送到工作台，该界面还接受来自高通量实验的基因列表。来自公共或私人来源的工作台模型可以进行整合和绘制。绘制功能可用于突出显示合并通路图上的重要基因甚至它们的表达水平，从而揭示生物学意义。该工具可在 http://csb2.ym.edu.tw/pint/ 免费获得。
