read_pubmed_jats: Convert JATS-file from PubMed into a data frame

In JulFriedrich/miRetrieve: miRNA Text Mining in Abstracts

Description

Convert JATS-file from PubMed into a data frame.

Usage

read_pubmed_jats(jats_file, topic = NULL)

Arguments

jats_file	JATS-file, downloaded from PubMed.
topic	String. Optional. If provided, adds a "Topic" column containing topic.

Details

Converts an JATS-file from PubMed into a data frame. The JATS-file should contain PubMed-IDs, abstracts from research articles, abstract title, publication year, abstract language, and article type. The data frame created holds at least six columns, namely

• PMID, containing the PubMed-ID,

• Year, containing the publication year,

• Title, containing the title of the abstracts,

• Abstract, containing the actual abstract,

• Language, containing the language(s) of the paper,

• Type, containing the article type.

If topic is provided, a "Topic" column is added, assigning all abstracts in df to topic.

read_pubmed() is faster than read_pubmed_jats() and thus recommended.

Value

Data frame containing PubMed-IDs, abstracts, abstract titles, publication years, languages, and article types.

See Also

read_pubmed()

Other external data functions: read_pubmed(), save_excel(), save_plot()

JulFriedrich/miRetrieve documentation built on Sept. 20, 2021, 11:37 p.m.