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Is there a way to filter Pubmed search based on Citation index of the articles or Is there a way to retrieve an articles's citation index in pubmed

Is there a way to retrieve an article's citation index via Pubmed or Pubmed's eutils or any other way in Pubmed/Entrez? Or a way to filter the search results based on citation index in pubmed?

pubmed citation textmining
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updated by Crunk • Crunk • written by vigprasud vigprasud

Ohk. Thanks again.

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updated by Ram Ram • written by vigprasud vigprasud

2 answers

If by "citation index" you mean the number of times a paper is cited, then not really. The closest you'll come is the number of citations indexed in Pubmed Central. Using R:

library(rentrez)

get_pmc_cites <- function(pmid){
    res <- entrez_link(db="pmc", dbfrom="pubmed", id=pmid)
    return(length(res$pubmed_pmc_refs))
 }
get_pmc_cites(20203609)
# [1] 25

EDIT

Just noticed the summary xmls for pubmed have the PMC reference count, which might make multiple calls quicker:

recs <- entrez_summary(db="pubmed", id=c(20203609, 20203610))
sapply(rec, "[[", "PmcRefCount")
# [1] 25 200
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updated by Ram Ram • written by David W David W

Is there other literature databases that has citation index other than pubmed?

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written by vigprasud vigprasud

Not that I know of. Last time I looked at something like this I found the scopus api doesn't really work for this, Web Of Science is closed and Google Scholar has no api and has terms that expressly forbid scraping their html.

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written by David W David W

Ohk. Thanks again.

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updated by Ram Ram • written by vigprasud vigprasud

This script helps find the newest paper on Pubmed by query and count the cited of each article. The result is an HTML table. This is its web app version. The source code can be found in here.

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written by Crunk • Crunk

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