pmApiRequest: Gather bibliographic content from PubMed database using NCBI entrez APIs

Description

It gathers metadata about publications from the NCBI PubMed database. The use of NCBI PubMed APIs is entirely free, and doesn't necessarily require an API key. The function pmApiRequest queries NCBI PubMed using an entrez query formulated through the Entrez query language or the helper function pmQueryBuild.

Usage

pmApiRequest(query, limit, api_key = NULL, batch_size = 200)

Value

a list D composed by 5 objects:

data		It is the xml-structured list containing the bibliographic metadata collection downloaded from the PubMed database.
query		It a character object containing the original query formulated by the user.
query_translation		It a character object containing the query, translated by the NCBI Automatic Terms Translation system and submitted to the PubMed database.
records_downloaded		It is an integer object indicating the total number of records downloaded and stored in "data".
total_count		It is an integer object indicating the total number of records matching the query (stored in the "query_translation" object").

To obtain a free access to NCBI API, please visit: https://pmc.ncbi.nlm.nih.gov/tools/developers/

To obtain more information about how to write a NCBI search query, please visit: https://pubmed.ncbi.nlm.nih.gov/help/#search-tags

Arguments

query: is a character. It contains a search query formulated using the Entrez query language.
limit: is numeric. It indicates the max number of records to download.
api_key: is a character. It contains a valid API key for the NCBI E-utilities. Default is api_key=NULL. The API key can also be set via the environment variable PUBMED_API_KEY or ENTREZ_KEY.
batch_size: is numeric. The number of records to download per API request. Default is 200.

Details

Official API documentation is https://www.ncbi.nlm.nih.gov/books/NBK25500/.

Examples

Run this code


# \donttest{
query <- "bibliometric*[Title/Abstract] AND english[LA]
          AND Journal Article[PT] AND 2000:2020[DP]"
 D <- pmApiRequest(query = query, limit = 100, api_key = NULL)
# }