This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Is there way to do batchquery and obtain ATC codes for pubchem CIDs?

Hello,

I have large list of chemicals with common drug names and pubchem CIDs. I want to add the Anatomical Therapeutic Chemical (ATC) Classification System -codes (ATC codes), for each one of them. I notice that pubchem provides this info in the compound summary page. Is there a way to do batch query and obtain ATC codes? (or) is there any website or tool to get this info,i.e., given a pubchem CID obtain ATC codes?

Thanks, Diwan

pubchem cid atc codes
• 5,510 views • link
updated by Biostar Biostar • written by Diwan Diwan

Diwan, were you able to solve this question? The pubchem API doesn't let you retrieve ATC codes as far as I can see

• 0 views • link
written by fr fr

2 answers

Hi RF, My solution is given below. HTH 

 
 #install.packages('httr')
  library(httr)
 #install.packages("RCurl")
  library(RCurl)
 #install.packages("RJSONIO")
  library(RJSONIO)
 #install.packages("plyr")
  library(plyr)



getATC <- function(cidnum){
pubchem_url_in<-paste('https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/',cidnum,'/JSON',sep='')
pubchempage <- GET(pubchem_url_in) 
page_text <- content(pubchempage,as='text')
page_test2 <- fromJSON(page_text)
ATC_parse1  <- grep('www.whocc.no',unlist(page_test2),value=T)
ATC_parse2 <- ATC_parse1[2]
ATCout1 <-strsplit(strsplit(ATC_parse2,'code=')[[1]][2],'&showdescription')[[1]][1]
return(c(cidnum,ATCout1))
}



getATC('3385')



 #For many CID query
cidnum_few<-c('5453','3385','3199')
testout <- lapply(cidnum_few,getATC)
cid_getatc <- do.call(rbind,testout)
• 0 views • link
written by Diwan Diwan

Thanks so much for your help, this is very useful!

• 0 views • link
written by fr fr

The pubchem API can do this task.

• 1 views • link
written by Zhilong Jia Zhilong Jia

Log in to answer this question.

More posts like this