Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

The use of multiple omics techniques (i.e., genomics, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets of life science. Omics techniques provide a more holistic molecular perspective of studied biological systems compared to traditional approaches. However, due to their inherent data differences, integrating multiple omics platforms remains an ongoing challenge for many researchers. As metabolites represent the downstream products of multiple interactions between genes, transcripts, and proteins, metabolomics, the tools and approaches routinely used in this field could assist with the integration of these complex multi-omics data sets. The question is, how? Here we provide some answers (in terms of methods, software tools and databases) along with a variety of recommendations and a list of continuing challenges as identified during a peer session on multi-omics integration that was held at the recent Australian and New Zealand Metabolomics Conference' (ANZMET 2018) in Auckland, New Zealand (Sept. 2018). We envisage that this document will serve as a guide to metabolomics researchers and other members of the community wishing to perform multi-omics studies. We also believe that these ideas may allow the full promise of integrated multi-omics research and, ultimately, of systems biology to be realized.

多种组学技术（即基因组学、转录组学、蛋白质组学和代谢组学）的使用在生命科学的各个方面正变得越来越流行。与传统方法相比，组学技术为所研究的生物系统提供了更全面的分子视角。然而，由于其固有的数据差异，整合多个组学平台对许多研究人员来说仍然是一个持续的挑战。由于代谢物是基因、转录本和蛋白质之间多种相互作用的下游产物，代谢组学以及该领域常规使用的工具和方法可以协助整合这些复杂的多组学数据集。问题是，如何做到呢？在此，我们提供一些答案（在方法、软件工具和数据库方面），以及一系列建议和在新西兰奥克兰举行的近期澳大利亚和新西兰代谢组学会议（ANZMET 2018，2018年9月）上关于多组学整合的同行会议期间所确定的一系列持续挑战。我们设想这份文件将作为代谢组学研究人员以及希望进行多组学研究的其他社区成员的指南。我们还相信这些想法可能使综合多组学研究以及最终使系统生物学的全部潜力得以实现。