dujm/Literature_mining_PubMed

An app for myself to search PubMed literature

How to download PubMed literature into a csv table in 5 steps?

I. Try my online app

• URL: https://duju.shinyapps.io/PubMed-Literature-Search

II. Download PubMed content using RISmed package

1. Install RIS medpackage in R

Documentation

install.packages(RISmed)

2. Define a query

Use keywords(e.g. PTEN), database (pubmed), limit of the number of results (e.g. 500)

library(RISmed)
res <- EUtilsSummary("PTEN", type="esearch", db="pubmed", retmax=500)

3. Download the results of your query

EUtilsGet(res,type="efetch",db="pubmed")
QueryCount(res) # No. of results returned
summary(res) # Summary of your query

4. Gather information for your output file

y <- YearPubmed(EUtilsGet(res)) # Year of publication
t<-ArticleTitle(EUtilsGet(res)) # Title
a <-AbstractText(EUtilsGet(res)) # Abstract

Authors

at <- Author(EUtilsGet(res))
at1 <-lapply(at, `[[`, 1) # Extract the first row of each list because I only need the 1st author
at_first<-lapply(at1, `[[`, 1) # Extract the first element of each row
at_first_row <- as.data.frame(at_first) # Format as dataframe
at_first_column <- t(at_first_row)  # Convert row to column using transpose t()  

5. Output to a .csv file

myresults <- data.frame('1stAuthor'= at_first_column,'year' = y, 'Title'=t,'Abstract'=a)  
write.csv(myresults, file = "pubmed_literature.csv",row.names = FALSE)