PathwayBooster: a tool to support the curation of metabolic pathways.
PathwayBooster: a tool to support the curation of metabolic pathways.
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DOI：
10.1186/s12859-014-0447-2
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发表时间：
2015-03-15
影响因子：
3
通讯作者：
Pinney JW
中科院分区：
文献类型：
--
作者：
Liberal R;Lisowska BK;Leak DJ;Pinney JW
尽管最近在自动生成代谢重建草案方面取得了一些进展，但手动管理这些网络以生成高质量的基因组规模代谢模型仍然是一项劳动密集型且具有挑战性的任务。我们推出 PathwayBooster，这是一种开源软件工具，支持代谢模型的手动比较和管理。它将 GenBank 文件和其他来源的基因注释与从代谢数据库 BRENDA 和 KEGG 检索的信息相结合，生成一组通路图和报告，总结给定生物体代谢网络中存在反应的证据。通过比较共同框架内的多个证据来源，PathwayBooster 帮助管理者识别可能的假阳性（错误注释的酶）和假阴性（通路孔）反应。反应证据可以从同一基因组和/或一组密切相关的生物体的替代注释中获取。通过整合和可视化来自多个来源的证据，PathwayBooster 减少了管理代谢模型所需的手动工作。该软件可在线获取：http://www.theosysbio.bio.ic.ac.uk/resources/pathwaybooster/。本文的在线版本 (doi:10.1186/s12859-014-0447-2) 包含补充材料，可供授权用户使用。
Despite several recent advances in the automated generation of draft metabolic reconstructions, the manual curation of these networks to produce high quality genome-scale metabolic models remains a labour-intensive and challenging task. We present PathwayBooster, an open-source software tool to support the manual comparison and curation of metabolic models. It combines gene annotations from GenBank files and other sources with information retrieved from the metabolic databases BRENDA and KEGG to produce a set of pathway diagrams and reports summarising the evidence for the presence of a reaction in a given organism’s metabolic network. By comparing multiple sources of evidence within a common framework, PathwayBooster assists the curator in the identification of likely false positive (misannotated enzyme) and false negative (pathway hole) reactions. Reaction evidence may be taken from alternative annotations of the same genome and/or a set of closely related organisms. By integrating and visualising evidence from multiple sources, PathwayBooster reduces the manual effort required in the curation of a metabolic model. The software is available online at http://www.theosysbio.bio.ic.ac.uk/resources/pathwaybooster/. The online version of this article (doi:10.1186/s12859-014-0447-2) contains supplementary material, which is available to authorized users.
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影响因子：
3
作者：
Choi, Kwangmin;Kim, Sun
通讯作者：
Kim, Sun
影响因子：
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作者：
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通讯作者：
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影响因子：
5.8
作者：
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通讯作者：
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