pubtatordb

Create and Query a Local 'PubTator' Database

'PubTator' <https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/> is a National Center for Biotechnology Information (NCBI) tool that enhances the annotation of articles on PubMed <https://www.ncbi.nlm.nih.gov/pubmed/>. It makes it possible to rapidly identify potential relationships between genes or proteins using text mining techniques. In contrast, manually searching for and reading the annotated articles would be very time consuming. 'PubTator' offers both an online interface and a RESTful API, however, neither of these approaches are well suited for frequent, high-throughput analyses. The package 'pubtatordb' provides a set of functions that make it easy for the average R user to download 'PubTator' annotations, create, and then query a local version of the database.

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Description file content

Package
pubtatordb
Type
Package
Title
Create and Query a Local 'PubTator' Database
Version
0.1.3
Maintainer
Zachary Colburn
Description
'PubTator' is a National Center for Biotechnology Information (NCBI) tool that enhances the annotation of articles on PubMed . It makes it possible to rapidly identify potential relationships between genes or proteins using text mining techniques. In contrast, manually searching for and reading the annotated articles would be very time consuming. 'PubTator' offers both an online interface and a RESTful API, however, neither of these approaches are well suited for frequent, high-throughput analyses. The package 'pubtatordb' provides a set of functions that make it easy for the average R user to download 'PubTator' annotations, create, and then query a local version of the database.
License
MIT + file LICENSE
Encoding
UTF-8
LazyData
true
Suggests
covr, testthat, knitr, rmarkdown
Imports
DBI, R.utils, RSQLite, assertthat, dplyr, readr
VignetteBuilder
knitr
RoxygenNote
6.1.1
NeedsCompilation
no
Packaged
2019-03-13 15:35:56 UTC; mamcdci
Author
Zachary Colburn [aut, cre], Madigan Army Medical Center - Department of Clinical Investigation [cph, fnd]
Repository
CRAN
Date/Publication
2019-03-13 16:00:03 UTC

install.packages('pubtatordb')

0.1.3

10 days ago

Zachary Colburn

MIT + file LICENSE

Imports

DBI, R.utils, RSQLite, assertthat, dplyr, readr

Suggests

covr, testthat, knitr, rmarkdown

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