一、介绍

KEGG 是一个数据库资源，用于从分子水平信息，特别是基因组测序和其他高通量产生的大规模分子数据集，了解生物系统（如细胞、有机体和生态系统）的高级功能和效用实验技术。

KEGGREST允许访问 KEGG REST API。由于 KEGG 在 2012 年 12 月 31 日禁用了 KEGG SOAP 服务器（这意味着该KEGGSOAP包将不再工作），KEGGREST因此可以作为替代品。

二、使用方法

> library(KEGGREST)
#KEGG 公开了许多数据库,通过listDatabases进行查看
> listDatabases()
 [1] "pathway"  "brite"    "module"   "ko"       "genome"   "vg"
 [7] "ag"       "compound" "glycan"   "reaction" "rclass"   "enzyme"
[13] "disease"  "drug"     "dgroup"   "environ"  "genes"    "ligand"
[19] "kegg"
> pathway<-keggLink("pathway", "dre")#dre是斑马鱼，这里选择自己要看的物种
> pathway[1]
  dre:100000026
"path:dre00010"
> ko<-keggList("ko")
> ko[1]
                                          ko:K00001
"E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]"
#获取特定条目
>query <- keggGet(c("hsa:10458", "ece:Z5100"))
> names(query[[1]])
 [1] "ENTRY"     "SYMBOL"    "NAME"      "ORTHOLOGY" "ORGANISM"  "PATHWAY"
 [7] "NETWORK"   "BRITE"     "POSITION"  "MOTIF"     "DBLINKS"   "STRUCTURE"
[13] "AASEQ"     "NTSEQ"
> query[[1]]$"PATHWAY"
                               hsa04520                                hsa04810
                    "Adherens junction"      "Regulation of actin cytoskeleton"
                               hsa05130                                hsa05135
"Pathogenic Escherichia coli infection"                    "Yersinia infection"
> query[[1]]$"NAME"
[1] "(RefSeq) BAR/IMD domain containing adaptor protein 2"
> query[[1]]$"ENTRY"
    CDS
"10458"
#按关键字搜索
> head(keggFind("genes", c("shiga", "toxin")))
                                                              ece:Z1464
"stx2A; shiga-like toxin II A subunit encoded by bacteriophage BP-933W"
                                                              ece:Z1465
"stx2B; shiga-like toxin II B subunit encoded by bacteriophage BP-933W"
                                                              ece:Z3343
  "stx1B; shiga-like toxin 1 subunit B encoded within prophage CP-933V"
                                                              ece:Z3344
  "stx1A; shiga-like toxin 1 subunit A encoded within prophage CP-933V"
                                                           ecs:ECs_1205
                                       "stx2A; Shiga toxin 2 subunit A"
                                                           ecs:ECs_1206
                                       "stx2B; Shiga toxin 2 subunit B"
#转换标识符
> keggConv("ncbi-proteinid", c("hsa:10458", "ece:Z5100"))
                 hsa:10458                  ece:Z5100
"ncbi-proteinid:NP_059345"  "ncbi-proteinid:AAG58814"

参考：
http://www.bioconductor.org/packages/release/bioc/vignettes/KEGGREST/inst/doc/KEGGREST-vignette.html