easyPubMed (version 2.13)

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, getKeywords = FALSE, 
                     getAuthors = TRUE)

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 (integer). Maximum number of characters to be extracted from the Article Abstract field. Set max_chars to -1 for extracting the full-length abstract. Set max_chars to 0 to extract no abstract.

getKeywords

Logical. If TRUE, an attempt to extract article Keywords will be made.

getAuthors

Logical. If FALSE, author information won't be extracted. This will considerably speed up the operation.

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), keywords, 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. If information about authors are not required, set 'getAuthors' = TRUE.

References

https://www.data-pulse.com/dev_site/easypubmed/

Examples

# NOT RUN {
try({
  ## Display some contents
  data("EPMsamples")
  #display Query String used for collecting the data
  print(EPMsamples$NUBL_1618$qry_st)
  #Get records
  BL_list <- EPMsamples$NUBL_1618$rec_lst
  cat(BL_list[[1]])
  # cast PM recort to data.frame
  BL_df <- article_to_df(BL_list[[1]], max_chars = 0)
  print(BL_df)
}, silent = TRUE)

# }
# NOT RUN {
## Query PubMed, retrieve a selected citation and format it as a data frame
dami_query <- "Damiano Fantini[AU] AND 2017[PDAT]"
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[[1]], autofill = FALSE)
article_to_df(pubmedArticle = dami_abstracts_list[[2]], autofill = TRUE, max_chars = 300)[1:2,]
# }
# NOT RUN {
# }