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March 21, 2019 21:57
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quickly whipped up something to fetch citing articles from pubmed
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| # essentially same as before but now restructured into a function: getCitingPMIDs() | |
| getCitingPMIDs <- function(PMID) { | |
| lines <- readLines(paste0("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&linkname=pubmed_pubmed_citedin&id=", PMID)) # construct quering URL using the PMID parameter in resTargetRecord, and fetch its contents into object lines | |
| citingPMIDs <- sub("^.*(<Id>)(.*)(</Id>)", "\\2", lines[grep("<Id>", lines)]) # filter out lines in lines that contain <Id> and then filter out the content between <Id> and </Id>.Store in object citingPMIDs | |
| citingPMIDs <- citingPMIDs[-1] # remove first entry in citingPMIDs, which is the target record | |
| return(citingPMIDs) | |
| } | |
| library(RISmed) | |
| resTarget <- EUtilsSummary("10.1371/journal.pone.0166600") # search for your target record (here I used one of my own articled search for by DOI) | |
| resTarget@PMID # the target records PMID is in resTarget@PMID | |
| citingPMIDs <- getCitingPMIDs(resTarget@PMID) | |
| resCitingRecords <- EUtilsGet(citingPMIDs) # feed citingPMIDs into EUtilsGet to receive their records | |
| resCitingRecords@ArticleTitle # titles of citing articles |
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annotated it somewhat.