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talk with NCBI entrez using R
https://docs.ropensci.org/rentrez
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entrez_link sometimes doesn't return "$nuccore_pubmed" #184

Closed niki0211 closed 1 year ago

niki0211 commented 1 year ago

I am trying to download sequences from NCBI and I also want to retrieve some summary info with entrez_summary.

Therefore I am using "entrez_link" but sometimes exactly the same request result in different results. Specifically the "nuccore_pubmed" value is sometimes not returned but only "nuccore_pubmed_weighted".

Here is an example request with a specific ID.

linked <- entrez_link(dbfrom = "nucleotide", db = "pubmed", id = "ON597769.1")

Sometime I get the PubmedId back, sometimes not. See screenshot:

grafik

niki0211 commented 1 year ago

I also observed that it happens for some IDs more frequently than for others....

allenbaron commented 1 year ago

This probably has nothing to do with rentrez and is likely an issue at NCBI. Have you tried the commandline Entrez Utils to see if you get the same results?

I noticed a number of irregularities in PubMed related searches through rentrez, Entrez Utils, and PubMed itself throughout Oct & Nov.

niki0211 commented 1 year ago

Alright, thanks for the hint. I try to compare the result with commandline Entrez Utils but I don't know how to run the same command. Since "elink" does not allow to specify "dbfrom".

allenbaron commented 1 year ago

See https://www.ncbi.nlm.nih.gov/books/NBK25499/#_chapter4ELink.

niki0211 commented 1 year ago

Thanks for the link. I will use edirect to double-check my results. However, it seems to be not a problem anymore...It just works fine although I didn't change anything. So maybe you were right and it was some kind of NCBI issue.