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Questions - rentrez

How do I provide my Identity / Email when connecting to NCBI through Rentrez?

My project head is telling me that its unacceptable to connect with NCBI to retrieve sequence entries without sending along identifying information such as our institution email. They claim this means...
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BioInfoMan28

r

bioinformatics

ncbi

rentrez

Votes: 0

Answers: 1

Latest Answer

It seems like you need an API key. You can get one from your NCBI account interactively, and it needs to be specified in your .bash_profile (at least on a mac, using bash, not sure your OS / terminal ...
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Nick

Using R to fetch a Pubmed abstract by using its title

I have been trying for a while to fetch Pubmed abstracts by using its title. For istance, if I put the following title on the pubmPd mask @ https://pubmed.ncbi.nlm.nih.gov/ : A Pituitary-Derived MEG3 ...
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Arturo

r

pubmed

rentrez

Votes: 0

Answers: 2

Latest Answer

We can use rvest to get the abstract by submitting form. library(rvest) library(dplyr) # URL url = 'https://pubmed.ncbi.nlm.nih.gov/' ncbi <- html_session(url) # Grab the Form search <- ncbi %...
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Nad Pat

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