easyPubMed (version 2.3)

article_to_df: Extract Data from a PubMed Record

Description

Extract publication-specific information from a PubMed record driven by XML tags. The input record is a string (character-class vector of length 1) and includes PubMed-specific XML tags. Data are returned as a data frame where each row corresponds to one of the authors of the PubMed article.

Usage

article_to_df(pubmedArticle, autofill = FALSE, max_chars = 500)

Arguments

pubmedArticle

String including one PubMed record.

autofill

Logical. If TRUE, missing affiliations are automatically imputed based on other non-NA addresses from the same record.

max_chars

Numeric (>=0). Maximum number of characters to be extracted from the Article Abstract field.

Value

Data frame including the extracted features. Each row correspond a different author.

Details

Given one Pubmed Article record, this function will automatically extract a set of features. Extracted information include: PMID, DOI, article title, article abstract, publication date (year, month, day), journal name (title, abbreviation) and a set of author-specific info (names, affiliation, email address). Each row of the output data frame corresponds to one of the authors of the PubMed record. Author-independent info (publication ID, title, journal, date) are identical across all rows.

References

http://www.biotechworld.it/bioinf/2016/01/05/querying-pubmed-via-the-easypubmed-package-in-r/

Examples

# NOT RUN {
#
# Query PubMed, retrieve a selected citation and format it as a data frame
dami_query <- "Damiano Fantini[AU]"
dami_on_pubmed <- get_pubmed_ids(dami_query)
dami_abstracts_xml <- fetch_pubmed_data(dami_on_pubmed)
dami_abstracts_list <- articles_to_list(dami_abstracts_xml)
article_to_df(pubmedArticle = dami_abstracts_list[[4]], autofill = FALSE, max_chars = 100)
article_to_df(pubmedArticle = dami_abstracts_list[[4]], autofill = TRUE, max_chars = 300)[1:2,]
# }