How to do it…

Let's perform the following steps to perform a PubMed literature search using R:

  1. Load the pubmed.mineR and RISmed libraries into your R session.
  2. Create an object containing keywords.
  3. Parse the keyword term to create a query term into the form of PubMed search_query.
  4. Parse the search_query term to get the search results.
  5. Retrieve the relevant information from the output objects.

Here is the code to perform the preceding tasks mentioned:

        library(pubmed.mineR)
library(RISmed)
keyword <- "Deep Learning"
search_query <- EUtilsSummary(keyword, retmax=10)
summary(search_query)
fetch <- EUtilsGet(search_query)
  1. The fetch object contains all the information you might be interested in. Here is the list of objects that you can extract from it:
  1. The fetch object that you have created contains a lot of internal information but you might be only interested in some of it. So, the next step is to retrieve some of the fields that you might be interested in, especially Title, ArticleTitle, AbstractText, and YearPubmed along with PMID:
        pmid <- PMID(fetch)
years <- YearPubmed(fetch)
Jtitle <- Title(fetch)
articleTitle <- ArticleTitle(fetch)
abstracts <- AbstractText(fetch)
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