Entrez and RISmed library for pubmed data mining

Question

I'm using this "RISmed" library to do some query of my gene or protein of interest and the output comes with pubmed ID basically, but most of the times it consist of non-specific hits as well which are not my interest. As I can only see the pubmed ID I have to manually put those returned ID and search them in NCBI to see if the paper is of my interest or not.

Question: Is there a way to to return the abstract of the paper or summary sort of along with its pumed ID , which can be implemented in R?

If anyone can help it would be really great..

zx8754 zx8754 · Accepted Answer · 2016-12-19T13:25:14

Using the example from the manuals we need EUtilsGet function.

library(RISmed)

search_topic <- 'copd'
search_query <- EUtilsSummary(search_topic, retmax = 10,
                              mindate = 2012, maxdate = 2012)
summary(search_query)

# see the ids of our returned query
QueryId(search_query)

# get actual data from PubMed
records <- EUtilsGet(search_query)
class(records)

# store it
pubmed_data <- data.frame('Title' = ArticleTitle(records),
                          'Abstract' = AbstractText(records))

Entrez and RISmed library for pubmed data mining

1 Answers