KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database.
KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database.
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DOI：
10.1186/1471-2105-10-324
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发表时间：
2009-10-08
影响因子：
3
通讯作者：
Kolisis FN
中科院分区：
文献类型：
--
作者：
Moutselos K;Kanaris I;Chatziioannou A;Maglogiannis I;Kolisis FN
KEGG通路数据库是一个有价值的代谢通路图集合。然而，从KEGG Pathway数据中产生具有模拟能力的代谢网络是一项具有挑战性的复杂工作，无论已经开发出用于该范围的工具。最初用于说明目的，通过KGML （KEGG标记语言）文件的KEGG Pathways可以提供完整的反应集并引入物种版本，这为细胞代谢模拟建模的范围提供了优势。在这个项目中，KEGGconverter也是作为一个基于web的应用程序来描述和实现的，它使用KGML文件作为源文件，以便为仿真目的构建完整功能的集成路径SBML模型。一个从KEGG整合六种人类代谢途径的案例研究描述了KEGGconverter自动生成合并并转换为SBML全功能途径模型的能力，并通过默认动力学得到增强。通过与其他最新的相关软件工具进行比较，证明所开发工具的适用性，以完成相同的数据融合和转换任务，从而说明问题和相关工作流程。此外，KEGGconverter允许在生成的模型中包含额外的反应，这些反应表示与邻近路径的通量串扰，从而提高了模拟精度。这些额外的反应是通过利用KEGG Pathways数据库元素的相关语义信息引入的。介绍了基于web的应用程序的体系结构和功能。通过只输入KGML文件，KEGGconverter能够生成适合模拟任务的代谢途径的集成类似物。web应用程序作为一个用户友好的外壳，透明地实现自动生化正确路径合并，转换为SBML格式，适当的重命名物种，并为相关反应插入默认的动力学性质。该工具可在以下网址下载：
The KEGG Pathway database is a valuable collection of metabolic pathway maps. Nevertheless, the production of simulation capable metabolic networks from KEGG Pathway data is a challenging complicated work, regardless the already developed tools for this scope. Originally used for illustration purposes, KEGG Pathways through KGML (KEGG Markup Language) files, can provide complete reaction sets and introduce species versioning, which offers advantages for the scope of cellular metabolism simulation modelling. In this project, KEGGconverter is described, implemented also as a web-based application, which uses as source KGML files, in order to construct integrated pathway SBML models fully functional for simulation purposes. A case study of the integration of six human metabolic pathways from KEGG depicts the ability of KEGGconverter to automatically produce merged and converted to SBML fully functional pathway models, enhanced with default kinetics. The suitability of the developed tool is demonstrated through a comparison with other state-of-the art relevant software tools for the same data fusion and conversion tasks, thus illustrating the problems and the relevant workflows. Moreover, KEGGconverter permits the inclusion of additional reactions in the resulting model which represent flux cross-talk with neighbouring pathways, providing in this way improved simulative accuracy. These additional reactions are introduced by exploiting relevant semantic information for the elements of the KEGG Pathways database. The architecture and functionalities of the web-based application are presented. KEGGconverter is capable of producing integrated analogues of metabolic pathways appropriate for simulation tasks, by inputting only KGML files. The web application acts as a user friendly shell which transparently enables the automated biochemically correct pathway merging, conversion to SBML format, proper renaming of the species, and insertion of default kinetic properties for the pertaining reactions. The tool is available at:
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影响因子：
46.9
作者：
Le Novère, N;Finney, A;Wanner, BL
通讯作者：
Wanner, BL
影响因子：
5.8
作者：
Bornstein, Benjamin J.;Keating, Sarah M.;Hucka, Michael
通讯作者：
Hucka, Michael
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J
DOI：
10.1093/bioinformatics/btp167
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Zhang JD;Wiemann S
通讯作者：
Wiemann S
影响因子：
3
作者：
Junker BH;Klukas C;Schreiber F
通讯作者：
Schreiber F