3 Search PubMed records

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

You need to input the term argument; if you want to add supplementary information, you can use the keys parameter.

For example, if you want to find papers about genes “Tp53”, “Brca1”, and “Tet2” in the context of mouse stem cell research:

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 × 29
##   id       source pmid     pmcid     doi   title authorString journalTitle issue
##   <chr>    <chr>  <chr>    <chr>     <chr> <chr> <chr>        <chr>        <chr>
## 1 42278500 MED    42278500 PMC13257… 10.3… Wild… Cart JB, Zh… Int J Mol S… 11   
## 2 41814002 MED    41814002 PMC12987… 10.1… CDK4… Chan ICC, Z… Nat Genet    3    
## 3 42069772 MED    42069772 <NA>      10.1… NELF… Su X, Yang … Nat Commun   1    
## 4 41160778 MED    41160778 <NA>      10.1… The … Semba Y, Ya… Blood        6    
## 5 41758987 MED    41758987 <NA>      10.1… MDM4… Sharma R, B… Blood        2    
## # … with 20 more variables: journalVolume <chr>, 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>, versionNumber <int>

NOTICE: A minor update has been made in version 0.8.6 or above. Argument keys is replaced with add_term for easier 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)