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.
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 below in this vignette.
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 below.
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.
Improved Support for Book Document Records. The revised epm_fetch()
function now supports the download and the identification of raw
Book Document Records in either xml
or medline format. Note that epm_parse() is still incompatible with
this kind of records.
The latest version (3.1.3) of the library is hosted on GitHub, and you can install it using the devtools R library as follows.
devtools::install_github("dami82/easyPubMed")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.