KEGG数据中全部代谢反应和代谢物注释信息的下载

KEGG数据中全部代谢反应和代谢物注释信息的下载

# 加载函数与R包 ----------------------------------------------------------------- library(KEGGREST) library(plyr) source("./RbioRXN-master/RbioRXN-master/R/get.kegg.all.R") source("./RbioRXN-master/RbioRXN-master/R/get.kegg.byId.R") ## KEGG数据...
# 加载函数与R包 -----------------------------------------------------------------
library(KEGGREST)
library(plyr)

source("./RbioRXN-master/RbioRXN-master/R/get.kegg.all.R")
source("./RbioRXN-master/RbioRXN-master/R/get.kegg.byId.R")

## KEGG数据库中的代谢反应和代谢物注释信息 -------------------------------------------------
keggAll = get.kegg.all()
## 这里需要消耗不少时间,加载提前下载好的数据
load("keggAll.Rdata")

## 查看代谢反应和代谢物的数量
dim(keggAll$reaction)
# [1] 11467    13
dim(keggAll$compound)
# [1] 18749    27

## 根据KEGG API接口查看代谢反应和代谢物信息
## http://rest.kegg.jp/info/reaction
# reaction         KEGG Reaction Database
# rn               Release 97.0+/12-31, Dec 20
# Kanehisa Laboratories
# 11,467 entries
## http://rest.kegg.jp/info/compound
# compound         KEGG Compound Database
# cpd              Release 97.0+/12-31, Dec 20
# Kanehisa Laboratories
# 18,749 entries

## 获取代谢信息的列名
colnames(keggAll$reaction)
# [1] "ENTRY"      "NAME"       "DEFINITION" "EQUATION"   "ENZYME"    
# [6] "RHEA"       "COMMENT"    "RCLASS"     "PATHWAY"    "ORTHOLOGY" 
# [11] "MODULE"     "REMARK"     "REFERENCE" 
colnames(keggAll$compound)
# [1] "ENTRY"      "NAME"       "FORMULA"    "EXACT_MASS" "MOL_WEIGHT" "REMARK"    
# [7] "REACTION"   "PATHWAY"    "MODULE"     "ENZYME"     "BRITE"      "ATOM"      
# [13] "BOND"       "CAS"        "PubChem"    "ChEBI"      "ChEMBL"     "PDB.CCD"   
# [19] "X3DMET"     "NIKKAJI"    "KNApSAcK"   "COMMENT"    "BRACKET"    "LIPIDMAPS" 
# [25] "LipidBank"  "SEQUENCE"   "REFERENCE" 


write.csv(reaction,file = "keggAllreaction.csv",row.names = F)
write.csv(compound,file = "keggAllcompound.csv",row.names = F)
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