I have a protein refseq (eg, NP_000029). How can I get the corresponding gene ID (ag, APC) from NCBI using an R package?
1
-
$\begingroup$ Hi @ElizaGanguly Is efetch not appropriate here? $\endgroup$– M__ ♦Dec 4, 2020 at 15:32
Add a comment
|
1 Answer
$\begingroup$
$\endgroup$
You can do this with the reutils package, which provides an API to NCBI's E-utilities. Here's an example for your specific question:
install.packages("reutils")
library(reutils)
# Get universal identifier
uid <- esearch("NP_000029", db = "gene")
# Fetch summary
sm <- esummary(uid, db = "gene")
# Extract specific tag
sm$xmlValue("//Name")
answered Dec 4, 2020 at 11:07