Genome scale metabolic models (GSMs) are a representation of the current knowledge on the metabolism of a given organism or superorganism. They group metabolites, genes, enzymes and reactions together to form a mathematical model and representation that can be used to analyze metabolic networks in silico or used for analysis of omics data. Beside correct mass and charge balance, correct structural annotation of metabolites represents an important factor for analysis of these metabolic networks. However, several metabolites in different GSMs have no or only partial structural information associated with them. Here, a new systematic nomenclature for acyl-based metabolites such as fatty acids, acyl-carnitines, acyl-coenzymes A or acyl-carrier proteins is presented. This nomenclature enables one to encode structural details in the metabolite identifiers and improves human readability of reactions. As proof of principle, it was applied to the fatty acid biosynthesis and degradation in the Caenorhabditis elegans consensus model WormJam.

中文翻译：

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关于基因组规模代谢模型中脂肪酰基化合物标准化标识符的建议及其在 WormJam 秀丽隐杆线虫模型中的应用。


基因组规模代谢模型（GSM）代表了给定生物体或超有机体代谢的当前知识。他们将代谢物、基因、酶和反应组合在一起，形成数学模型和表示形式，可用于在计算机中分析代谢网络或用于组学数据分析。除了正确的质量和电荷平衡之外，代谢物的正确结构注释也是分析这些代谢网络的重要因素。然而，不同 GSM 中的几种代谢物没有或只有部分与之相关的结构信息。在此，提出了基于酰基的代谢物（例如脂肪酸、酰基肉碱、酰基辅酶 A 或酰基载体蛋白）的新系统命名法。这种命名法使人们能够对代谢物标识符中的结构细节进行编码，并提高人类对反应的可读性。作为原理证明，它被应用于秀丽隐杆线虫共识模型 WormJam 中的脂肪酸生物合成和降解。