KEGG 数据库扩展用于刻画生物圈基因组与通路
KEGG for characterizing genomes and pathways in the biosphere
KEGG 数据库以分子连线图形式组织细胞与生物体层面功能知识，其 KO（KEGG Orthology）数据集把特定生物中的实验证据推广到其他生物，通路图与 module 等分子网络以 KO 为节点，因此从基因组到通路的 KEGG mapping 可适用于任何生物。随着 KO 数量增加和 KO 注释率提升，KEGG mapping 的适用范围进一步扩大。现在基因组中的 KO 集合与代谢通路中的 module 集合被用于刻画生物圈中的多种数据对象，包括生物、生物类群、微生物组、病毒及其组合，如内共生体—宿主、微生物组—宿主和病毒—宿主关系。
来源：Nucleic Acids Research · doi.org
The KEGG database (https://www.kegg.jp) has been developed as a model of the biological systems. By organizing knowledge of cellular and organism-level functions in the form of molecular wiring diagrams, the model enables generating new knowledge and finding practical applications. The KO (KEGG Orthology) dataset plays the basic role of organizing knowledge. KO is an ortholog with functional relevance, generalizing experimental evidence in specific organisms to other organisms. KEGG molecular networks, including pathway maps and modules, are generic networks with KOs as network nodes, and thus KEGG mapping from genomes to pathways can be applied to any organism. As the number of KOs increases and the KO annotation rate improves, KEGG mapping is further expanded. A set of KOs in the genome and a set of modules in the metabolic pathways are now used to characterize various data objects in the biosphere, including organisms, organism groups, microbiomes, viruses, and their combinations, such as endosymbiont–host, microbiome–host, and virus–host relationships. Furthermore, a simple measure of similarity either by KO compositions or module compositions is introduced to compare organism groups. The resulting similarity dendrograms possibly reflect similarity of cellular functions or, more specifically, metabolic functions, which can be compared with phylogenetic trees.