Rentrez Search Exercises

Exercise Answers

1: DOI Search

ex1_paper <- entrez_search(db="pubmed", term="10.1111/nyas.13259[doi]")
ex1_summary <- entrez_summary(db="pubmed", ex1_paper$ids)
ex1_summary$title

## [1] "Genome privacy: challenges, technical approaches to mitigate risk, and ethical considerations in the United States."

ex1_summary$authors

##             name authtype clusterid
## 1         Wang S   Author          
## 2        Jiang X   Author          
## 3        Singh S   Author          
## 4       Marmor R   Author          
## 5       Bonomi L   Author          
## 6          Fox D   Author          
## 7          Dow M   Author          
## 8 Ohno-Machado L   Author

ex1_summary$source

## [1] "Ann N Y Acad Sci"

ex1_summary$pubdate

## [1] "2017 Jan"

2. Keyword search

another_r_search <- entrez_search(db="pubmed", term="Natural Language Processing", retmax=40)
another_r_search

3: Using Qualifiers:

entrez_search(db="sra",
              term="(Tetrahymena thermophila[ORGN] OR Tetrahymena borealis[ORGN]) AND 2013:2015[PDAT]",
              retmax=0)

## Entrez search result with 75 hits (object contains 0 IDs and no web_history object)
##  Search term (as translated):  ("Tetrahymena thermophila"[Organism] OR "Tetrahyme ...

4: Mesh search

entrez_search(db   = "pubmed",
              term = "(vivax malaria[MeSH]) AND (folic acid antagonists[MeSH])")

## Entrez search result with 12 hits (object contains 12 IDs and no web_history object)
##  Search term (as translated):  "malaria, vivax"[MeSH Terms] AND "folic acid antag ...