3 Search PubMed records

getPubmed function utilizes europepmc to easily get PubMed records by searching paper abstract.

Users need to input the term argument; if there is any supplement information, the keys parameter is available.

For example, if user wants to check papers for genes “Tp53”, “Brca1,” and “Tet2” research of mouse stem cells:

term <- c("Tp53", "Brca1", "Tet2")
keys <- c("stem cell", "mouse")
l <- getPubmed(term, keys)
names(l)

## [1] "Tp53"  "Brca1" "Tet2"

head(l$Tp53, 5)

## # A tibble: 5 × 28
##   id      source pmid  doi   title authorString journalTitle issue journalVolume
##   <chr>   <chr>  <chr> <chr> <chr> <chr>        <chr>        <chr> <chr>        
## 1 358640… MED    3586… 10.1… "Bia… Ohno T, Aka… Nat Commun   1     13           
## 2 354091… MED    3540… 10.3… "Enh… Gringmuth M… Int J Mol S… 7     23           
## 3 357633… MED    3576… 10.1… "Deg… Sellar RS, … J Clin Inve… <NA>  <NA>         
## 4 PPR467… PPR    <NA>  10.1… "Bia… Ohno T, Aka… <NA>         <NA>  <NA>         
## 5 354353… MED    3543… 10.1… "Ide… Thirouard L… Adv Sci (We… 17    9            
## # … with 19 more variables: pubYear <chr>, journalIssn <chr>, pageInfo <chr>,
## #   pubType <chr>, isOpenAccess <chr>, inEPMC <chr>, inPMC <chr>, hasPDF <chr>,
## #   hasBook <chr>, hasSuppl <chr>, citedByCount <int>, hasReferences <chr>,
## #   hasTextMinedTerms <chr>, hasDbCrossReferences <chr>, hasLabsLinks <chr>,
## #   hasTMAccessionNumbers <chr>, firstIndexDate <chr>,
## #   firstPublicationDate <chr>, pmcid <chr>

NOTICE: A minor update has been made in version 0.8.6 or above. Argument keys is replaced with add_term for easy understanding, and the num parameter is added to specify the number of returned records.

term <- c("Tp53", "Brca1", "Tet2")
add_term <- c("stem cell", "mouse")
l <- getPubmed(term, add_term, num = 30)
# set "num" larger to get all records
all <- getPubmed(term, add_term, num = 666666)