easyPubMed: Query NCBI Entrez and retrieve PubMed records in XML or TXT format

Latest version: easyPubMed, version 3.01 (available on GitHub)

easyPubMed is an open-source R interface to the Entrez Programming Utilities aimed at allowing programmatic access to PubMed in the R environment. The package is suitable for downloading large number of records, and includes a collection of functions to perform basic processing of the Entrez/PubMed query responses. The library supports either XML or TXT (“medline”) format.

New features of easyPubMed, version 3.01

  • Simplified Pipeline. The process of retrieving and analyzing Pubmed records has been updated and simplified. The revised pipeline includes three steps: 1) submit a query; 2) fetch records; 3) extract information. The corresponding functions are discussed in the vignette you’ll find below.
  • Automatic Job splitting into Sub-Queries. The Entrez server imposes a strict n=10,000 limit to the number of records that can be programmatically retrieved from a single query. Whenever possible, the easyPubMed library automatically attempts to split queries returning large number of records into lists of smaller, manageable queries.
  • The easyPubMed S4 Class. Here we introduce a new S4 class (easyPubMed) that was designed to better store and manage query information, retrieved records and associated meta-data. This S4 class comes with a series of methods and is aimed at improving data handling and analysis reproducibility. Raw or processed data can be obtained from an easyPubMed object via the appropriate getter functions (as discussed below).
  • Additional Parsed Fields. The new epm_parse() function supports extraction of additional information from Pubmed records (compared to previous versions of this R library). Extracted fields now include mesh_codes, grant_ids, references and conflict of interest statements (cois) among others. For more information, see the examples included in the vignette.
  • Compact Output. Unlike previous versions of easyPubMed, it is now possible to collapse author information (i.e., author names) into a single string. This way, the output (parsed data.frame) only includes one row per record.

Installation

The latest version (3.01) of the library is hosted on GitHub, and you can install it using the devtools R library as follows.

devtools::install_github('dami82/easyPubMed', force = 'TRUE', build_vignettes = TRUE)

Notes & Info

  • easyPubMed is an open-source software, under the GPL-3 license and comes with ABSOLUTELY NO WARRANTY. For more questions about the GPL-3 license terms, see www.gnu.org/licenses.
  • This R library was written 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.
  • There is only one person maintaining this R package: I work on code updates in my spare time and for free. Take-home message: please, be patient.

Vignette / Getting Started

https://www.data-pulse.com/projects/Rlibs/vignettes/easyPubMed_demo.html