The USA National Center for Biotechnology Information (NCBI) is one of the world’s most important sources of biological information. NCBI databases like PubMed and GenBank contain mil lions of records describing bibliographic, genetic, genomic, and medical data. Here I present rentrez, a package which provides an R interface to 50 NCBI databases. The package is well-documented, contains an extensive suite of unit tests and has an active user base. The programmatic interface to the NCBI provided by rentrez allows researchers to query databases and download or import particular records into R sessions for subsequent analysis. The complete nature of the package, its extensive test-suite and the fact the package implements the NCBI’s usage policies all make rentrez a powerful aid to developers of new packages that perform more specific tasks.
Supplementary materials are available in addition to this article. It can be downloaded at RJ-2017-058.zip
ape, RISmed, pubmed.mineR, rentrez, reutils, rotl, fulltext, treemap
Phylogenetics, Environmetrics, Genetics, Graphics, OfficialStatistics, WebTechnologies
genomes, RMassBank, MeSHSim, genbankr
Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".
For attribution, please cite this work as
Winter, "The R Journal: rentrez: An R package for the NCBI eUtils API", The R Journal, 2017
BibTeX citation
@article{RJ-2017-058,
author = {Winter, David J.},
title = {The R Journal: rentrez: An R package for the NCBI eUtils API},
journal = {The R Journal},
year = {2017},
note = {https://doi.org/10.32614/RJ-2017-058},
doi = {10.32614/RJ-2017-058},
volume = {9},
issue = {2},
issn = {2073-4859},
pages = {520-526}
}