linux下kegg注释软件,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)