登錄KO (KEGG ORTHOLOGY) Database，進(jìn)入下圖頁(yè)面：
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點(diǎn)擊進(jìn)入KEGG Orthology (KO)，進(jìn)入下圖界面：
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右鍵復(fù)制鏈接，讀入R來解析json文件。
library(rjson)
library(jsonlite)
library(tidyverse)
KO <- fromJSON("https://www.kegg.jp/kegg-bin/download_htext?htext=ko00001&format=json&filedir=")#下載并解析JSON文件
KO$name <- NULL
KO <- as.data.frame(KO) %>%
unnest(cols = c("children.name","children.children"),names_repair = tidyr_legacy) %>%#重要函數(shù)
unnest(cols = c("children.name","name","children"),names_repair = tidyr_legacy) %>%
unnest(cols = c("children.name","name","name1","children"),names_repair = tidyr_legacy)
colnames(KO) <- c("L1","L2","L3","KO")
KO %<>% #整理KEGG ORTHOLOGY
select(last_col(),everything()) %>%
separate(col = "KO",sep = " ",into = c("KO","Description")) %>%
separate(col = "L1",sep = " ",into = c("L1_ID","L1"),extra = "merge") %>%
filter(!L1_ID %in% c("09180","09190")) %>% #去除BRITE hierarchies和Not Included in Pathway or Brite兩大類
separate(col = "L2",sep = " ",into = c("L2_ID","L2"),extra = "merge") %>%
separate(col = "L3",sep = " ",into = c("L3_ID","L3"),extra = "merge") %>%
separate(col = "L3",sep = " \\[PATH:",into = c("L3","PathwayID")) %>%
mutate(PathwayID=str_remove(PathwayID,pattern = "\\]")) %>%
drop_na()#KEGG ORTHOLOGY等級(jí)有缺失的刪掉
head(KO)
# A tibble: 6 x 9
# KO Description L1_ID L1 L2_ID L2 L3_ID L3 PathwayID
# <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
# 1 K00844 HK; hexokinase [EC:2.7.1.1] 09100 Metabolism 09101 Carbohydrate metabolism 00010 Glycolysis / Gluconeo~ ko00010
# 2 K12407 GCK; glucokinase [EC:2.7.1.2] 09100 Metabolism 09101 Carbohydrate metabolism 00010 Glycolysis / Gluconeo~ ko00010
# 3 K00845 glk; glucokinase [EC:2.7.1.2] 09100 Metabolism 09101 Carbohydrate metabolism 00010 Glycolysis / Gluconeo~ ko00010
# 4 K25026 glk; glucokinase [EC:2.7.1.2] 09100 Metabolism 09101 Carbohydrate metabolism 00010 Glycolysis / Gluconeo~ ko00010
# 5 K01810 GPI, pgi; glucose-6-phosphate isomerase [EC:5.3.1.9] 09100 Metabolism 09101 Carbohydrate metabolism 00010 Glycolysis / Gluconeo~ ko00010
# 6 K06859 pgi1; glucose-6-phosphate isomerase, archaeal [EC:5.3.1.9] 09100 Metabolism 09101 Carbohydrate metabolism 00010 Glycolysis / Gluconeo~ ko00010
