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I have a protein refseq (eg, NP_000029). How can I get the corresponding gene ID (ag, APC) from NCBI using an R package?

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  • $\begingroup$ Hi @ElizaGanguly Is efetch not appropriate here? $\endgroup$
    – M__
    Commented Dec 4, 2020 at 15:32

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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")
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