Month: February 2016

1. bta里的pathway个数在不断增加，过去抓取的和现在的混着用就会出错；
2. 批量下载KEGG Mapper生成的图像时，由于网络状况可能导致下载不完全，请一定仔细核实数目是否对应，图像是否完整；

在KEGG中，分子水平上的功能保存在KO（KEGG Orthology）数据库中。这些功能与直系同源组联系在一起，以此来使得一个特殊物种的实验数据可以被扩展到其他物种。KEGG中的基因组注释是直系同源注释，其方式为，为GENES数据库中的每个基因制定KO identifiers (K numbers) 。对于原始数据，像由RefSeq或者GenBank给出的基因名和描述，即使他们和KO的分配不一致，KEGG也不会做任何修改。

将KO的条目与功能表征的序列数据的实验证据联系在一起的工作，已经开始了，并且现在已经展示在REFERENCE下的SEQUENCE子域中。而且，基因组层面的“KEGG GENES”（http://www.genome.jp/kegg/genes.html）集合已经被扩展，使其可以将蛋白数据也包含在附录中。最终KO数据库将覆盖所有的功能表征蛋白序列信息（另见”KEGG Enzyme”（http://www.genome.jp/kegg/annotation/enzyme.html））。

In KEGG, molecular-level functions are stored in the KO (KEGG Orthology) database and associated with ortholog groups in order to enable extension of experimental evidence in a specific organism to other organisms. Genome annotation in KEGG is ortholog annotaion, assigning KO identifiers (K numbers) to individual genes in the GENES database. No updates are made to original data, such as gene names and descriptions given by RefSeq or GenBank, even if they are inconsistent with the KO assignment.

Major efforts have been initated to associate each KO entry with experimental evidence of functionally characterized sequence data, now shown in the SEQUENCE subfield of the REFERENCE field. Furthermore, the genome-based collection of KEGG GENES has been expanded to allow individual protein data to be included in the addendum category. Eventually the KO database will cover all knowledge on functionally characterized protein sequences (see also KEGG Enzyme).

一般来说，KO对功能直系同源的划分是定义在KEGG分子网络的语境中（KEGG pathway maps, BRITE hierarchies and KEGG modules）。KEGG分子网络实际上是由K numbers标识的网络节点表示的。KOs和相应的分子网络的关系呗存储在下面这个系统中。

KEGG Orthology （KO）

将功能信息和直系同源组关联在一起这个功能是KEGG资源的一个独特的功能。基于有限总量的实验数据生成的对序列相似性的预测被预先定义好在KEGG中。如同在BlastKOALA和其他工具中实现的那样，对KEGG GENES的序列相似性搜索是针对K numbers的。一旦一个K numbers被指定给基因组中的基因，KEGG pathways maps, Brite hierarchies,和KEGG modules都会自动重建。如此一来，就能对较高水平的功能有一个生物学上的科学的诠释。

In general KO grouping of functional orthologs is defined in the context of KEGG molecular networks (KEGG pathway maps, BRITE hierarchies and KEGG modules), which are in fact represented as networks of nodes identified by K numbers. The relationships between KOs and corresponding molecular networks are represented in the following KO system.

KEGG Orthology (KO)The fact that functional information is associated with ortholog groups is a unique aspect of the KEGG resource. The sequence similarity based inference as a generalization of limited amount of experimental evidence is predefined in KEGG. As implemented in BlastKOALA and other tools, the sequence similarity search against KEGG GENES is a search for most appropriate K numbers. Once K numbers are assigned to genes in the genome, the KEGG pathways maps, Brite hierarchies, and KEGG modules are automatically reconstructed, enabling biological interpretation of high-level functions.