Cheminformatics and Metabolism, European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Bioinformatics. 2013 Sep 1;29(17):2213-5. doi: 10.1093/bioinformatics/btt342. Epub 2013 Jun 13.
Genome-scale metabolic models often lack annotations that would allow them to be used for further analysis. Previous efforts have focused on associating metabolites in the model with a cross reference, but this can be problematic if the reference is not freely available, multiple resources are used or the metabolite is added from a literature review. Associating each metabolite with chemical structure provides unambiguous identification of the components and a more detailed view of the metabolism. We have developed an open-source desktop application that simplifies the process of adding database cross references and chemical structures to genome-scale metabolic models. Annotated models can be exported to the Systems Biology Markup Language open interchange format.
Source code, binaries, documentation and tutorials are freely available at http://johnmay.github.com/metingear. The application is implemented in Java with bundles available for MS Windows and Macintosh OS X.
基因组规模代谢模型通常缺乏可用于进一步分析的注释。以前的工作主要集中在将模型中的代谢物与交叉引用相关联，但如果参考资源不可用、使用了多个资源或代谢物是从文献综述中添加的，则这可能会有问题。将每个代谢物与化学结构相关联可提供组件的明确标识，并更详细地了解代谢情况。我们开发了一个开源桌面应用程序，可简化将数据库交叉引用和化学结构添加到基因组规模代谢模型中的过程。已注释的模型可以导出到系统生物学标记语言开放交换格式。
源代码、二进制文件、文档和教程可在 http://johnmay.github.com/metingear 上免费获得。该应用程序是用 Java 编写的，有适用于 MS Windows 和 Macintosh OS X 的捆绑包。
