easyPubMed (version 3.1.6)

easyPubMed-package: Retrieve and Process Scientific Publication Records from Pubmed

Description

Query NCBI Entrez and retrieve PubMed records in XML or TXT format. PubMed records can be downloaded and saved as XML or text files. Data integrity is enforced during data download, allowing to retrieve and save very large number of records effortlessly. PubMed records can be processed to extract publication- and author-specific information.

Author

Damiano Fantini

Details

This software is based on the information included in the Entrez Programming Utilities Help manual authored by Eric Sayers, PhD and available on the NCBI Bookshelf (NBK25500). This R library is NOT endorsed, supported, maintained NOR affiliated with NCBI.

References

• Tutorials and Help Webpage: https://www.data-pulse.com/dev_site/easypubmed/

• NCBI PubMed Help Manual: https://pubmed.ncbi.nlm.nih.gov/help/

• Entrez Programming Utilities Help (NBK25500): https://www.ncbi.nlm.nih.gov/books/NBK25500/

See Also

Useful links:

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

Examples

## Example 01: retrieve data in XML format, extract info, show
# Note: a time limit can be set in order to kill the operation when/if 
# the NCBI/Entrez server becomes unresponsive.
setTimeLimit(elapsed = 4.9)
try({
  my_query_string <- 'Damiano Fantini[AU] AND "2018"[PDAT]'
  epm <- epm_query(my_query_string)
  epm <- epm_fetch(epm)
  epm <- epm_parse(epm, max_authors = 5, max_references = 10)
  processed_data <- get_epm_data(epm)
  utils::head(processed_data)
}, silent = TRUE)
setTimeLimit(elapsed = Inf)

if (FALSE) {
## Example 02: retrieve data in medline format
my_query_string <- 'Damiano Fantini[AU] AND "2018"[PDAT]'
epm <- epm_query(my_query_string)
epm <- epm_fetch(epm, format = 'medline')
medline_data <- get_epm_raw(epm)
first_record <- medline_data[[1]] 
cat(first_record, sep = '\n')


## Additional Examples: show easyPubMed Vignette
library(easyPubMed)
vignette("easyPubMed_demo")

}