Witting Michael, Hastings Janna, Rodriguez Nicolas, Joshi Chintan J, Hattwell Jake P N, Ebert Paul R, van Weeghel Michel, Gao Arwen W, Wakelam Michael J O, Houtkooper Riekelt H, Mains Abraham, Le Novère Nicolas, Sadykoff Sean, Schroeder Frank, Lewis Nathan E, Schirra Horst-Joachim, Kaleta Christoph, Casanueva Olivia
Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany.
Chair of Analytical Food Chemistry, Technische Universtität München, Freising, Germany.
Front Mol Biosci. 2018 Nov 14;5:96. doi: 10.3389/fmolb.2018.00096. eCollection 2018.
Metabolism is one of the attributes of life and supplies energy and building blocks to organisms. Therefore, understanding metabolism is crucial for the understanding of complex biological phenomena. Despite having been in the focus of research for centuries, our picture of metabolism is still incomplete. Metabolomics, the systematic analysis of all small molecules in a biological system, aims to close this gap. In order to facilitate such investigations a blueprint of the metabolic network is required. Recently, several metabolic network reconstructions for the model organism have been published, each having unique features. We have established the WormJam Community to merge and reconcile these (and other unpublished models) into a single consensus metabolic reconstruction. In a series of workshops and annotation seminars this model was refined with manual correction of incorrect assignments, metabolite structure and identifier curation as well as addition of new pathways. The WormJam consensus metabolic reconstruction represents a rich data source not only for network-based approaches like flux balance analysis, but also for metabolomics, as it includes a database of metabolites present in , which can be used for annotation. Here we present the process of model merging, correction and curation and give a detailed overview of the model. In the future it is intended to expand the model toward different tissues and put special emphasizes on lipid metabolism and secondary metabolism including ascaroside metabolism in accordance to their central role in physiology.
新陈代谢是生命的属性之一，为生物体提供能量和组成成分。因此，理解新陈代谢对于理解复杂的生物现象至关重要。尽管几个世纪以来新陈代谢一直是研究的焦点，但我们对新陈代谢的认识仍然不完整。代谢组学旨在系统分析生物系统中的所有小分子，以填补这一空白。为了便于此类研究，需要一个代谢网络蓝图。最近，已经发表了几种模式生物的代谢网络重建，每种都有其独特的特点。我们建立了WormJam社区，将这些（以及其他未发表的模型）合并并协调成一个单一的共识代谢重建。在一系列研讨会和注释研讨会上，通过人工纠正错误分配、代谢物结构和标识符管理以及添加新途径对该模型进行了完善。WormJam共识代谢重建不仅是基于网络的方法（如通量平衡分析）的丰富数据源，也是代谢组学的丰富数据源，因为它包含了存在于[具体生物名称]中的代谢物数据库，可用于注释。在这里，我们展示了模型合并、校正和管理的过程，并对该模型进行了详细概述。未来，我们打算将该模型扩展到不同组织，并特别强调脂质代谢和次生代谢，包括ascaroside代谢，因为它们在[具体生物名称]生理学中具有核心作用。
