pmApiRequest {pubmedR}

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 necessary require an API key. The function pmApiRequest queries NCBI PubMed using an entrez query formulated through the function pmQueryBuild.

Usage

pmApiRequest(query, limit, api_key = NULL)

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 API keys for the NCBI E-utilities.

Details

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

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_counts		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://www.ncbi.nlm.nih.gov/pmc/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

See Also

pmQueryTotalCount

pmApi2df

Examples

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