Metabolic flux analysis requires both a reliable metabolic model and reliable metabolic profiles in characterizing metabolic reprogramming. Advances in analytic methodologies enable production of high-quality metabolomics datasets capturing isotopic flux. However, useful metabolic models can be difficult to derive due to the lack of relatively complete atom-resolved metabolic networks for a variety of organisms, including human. Here, we developed a neighborhood-specific graph coloring method that creates unique identifiers for each atom in a compound facilitating construction of an atom-resolved metabolic network. What is more, this method is guaranteed to generate the same identifier for symmetric atoms, enabling automatic identification of possible additional mappings caused by molecular symmetry. Furthermore, a compound coloring identifier derived from the corresponding atom coloring identifiers can be used for compound harmonization across various metabolic network databases, which is an essential first step in network integration. With the compound coloring identifiers, 8865 correspondences between KEGG (Kyoto Encyclopedia of Genes and Genomes) and MetaCyc compounds are detected, with 5451 of them confirmed by other identifiers provided by the two databases. In addition, we found that the Enzyme Commission numbers (EC) of reactions can be used to validate possible correspondence pairs, with 1848 unconfirmed pairs validated by commonality in reaction ECs. Moreover, we were able to detect various issues and errors with compound representation in KEGG and MetaCyc databases by compound coloring identifiers, demonstrating the usefulness of this methodology for database curation.

中文翻译：

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通过特定于邻域的图着色方法生成的原子标识符可实现跨代谢数据库的化合物协调。

代谢通量分析在表征代谢重编程时既需要可靠的代谢模型又需要可靠的代谢谱。分析方法学的进步使得能够生成捕获同位素通量的高质量代谢组学数据集。然而，由于缺乏包括人在内的多种生物的相对完整的原子解析代谢网络，可能难以得出有用的代谢模型。在这里，我们开发了一种邻域特定的图形着色方法，该方法为化合物中的每个原子创建了唯一的标识符，从而促进了原子分解代谢网络的构建。而且，该方法可确保为对称原子生成相同的标识符，从而能够自动识别由分子对称性引起的可能的其他映射。此外，可以将衍生自相应原子着色标识符的化合物着色标识符用于跨各种代谢网络数据库的化合物协调，这是网络集成中必不可少的第一步。使用化合物着色识别符，可以检测到KEGG（基因与基因组京都百科全书）与MetaCyc化合物之间的8865对应关系，其中有5451个被两个数据库提供的其他识别符所证实。此外，我们发现反应的酶委员会编号（EC）可用于验证可能的对应对，其中1848个未确认对通过反应EC的通用性进行验证。此外，我们还可以通过化合物着色标识符检测KEGG和MetaCyc数据库中化合物表示的各种问题和错误，