Traceability, reproducibility and wiki-exploration for "a-la-carte" reconstructions of genome-scale metabolic models
Traceability, reproducibility and wiki-exploration for "a-la-carte" reconstructions of genome-scale metabolic models
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DOI：
10.1371/journal.pcbi.1006146
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发表时间：
2018-05-01
影响因子：
4.3
通讯作者：
Siegel, Anne
中科院分区：
文献类型：
--
作者：
Aite, Meaziane;Chevallier, Marie;Siegel, Anne
基因组规模的代谢模型已成为全球微生物代谢分析的首选工具，其重建已达到高标准的质量和可靠性。这一领域的改进伴随着一些主要平台和数据库的发展，以及个体生物信息学方法的爆炸式增长。因此，许多最新的模型都来自于“点菜”管道，结合使用平台，个人工具和生物专业知识，以提高重建质量。虽然非常有用，但引入几乎不相互作用的异构工具会导致重建过程中的可追溯性和再现性损失。这代表了一个真实的障碍，特别是当考虑较少研究的物种时，其代谢重建可以从与相关生物体的高质量模型的比较中大大受益。这项工作提出了一个适应性强的工作空间AuReMe，用于可持续重建或改进涉及个性化管道的基因组规模代谢模型。在每个步骤中，存储与通过方法对模型进行的修改相关的相关信息。这确保了无论使用何种工具组合，该过程都是可重现的并有记录的。此外，工作空间建立了一种浏览代谢模型及其元数据的方法，通过自动生成专门用于监测和促进重建过程的自组织本地wiki。AuReMe支持基于RDF数据库的探索和语义查询。我们说明了这个工作区如何允许处理，在一个综合的方式，非模式生物，如极端细菌或真核藻类的代谢重建。在相关的应用中，后者的重建导致了代谢途径的推定进化见解。
Genome-scale metabolic models have become the tool of choice for the global analysis of microorganism metabolism, and their reconstruction has attained high standards of quality and reliability. Improvements in this area have been accompanied by the development of some major platforms and databases, and an explosion of individual bioinformatics methods. Consequently, many recent model s result from "a la carte" pipelines, combining the use of platforms, individual tools and biological expertise to enhance the quality of the reconstruction. Although very useful, introducing heterogeneous tools, that hardly interact with each other, causes loss of traceability and reproducibility in the reconstruction process. This represents a real obstacle, especially when considering less studied species whose metabolic reconstruction can greatly benefit from the comparison to good quality models of related organisms. This work proposes an adaptable workspace, AuReMe, for sustainable reconstructions or improvements of genome-scale metabolic models involving personalized pipelines. At each step, relevant information related to the modifications brought to the model by a method is stored. This ensures that the process is reproducible and documented regardless of the combination of tools used. Additionally, the workspace establishes a way to browse metabolic models and their metadata through the automatic generation of ad-hoc local wikis dedicated to monitoring and facilitating the process of reconstruction. AuReMe supports exploration and semantic query based on RDF databases. We illustrate how this workspace allowed handling, in an integrated way, the metabolic reconstructions of non-model organisms such as an extremophile bacterium or eukaryote algae. Among relevant applications, the latter reconstruction led to putative evolutionary insights of a metabolic pathway.