pubtatordb

The goal of pubtatordb is to allow users to create and query a local version of the PubTator database. PubTator provides detailed annotations of abstracts found on PubMed. It is therefore very useful for directing research questions. While PubTator does provide an API, the use of a local database is more appropriate for high-throughput analyses. pubtatordb provides the tools necessary to download, setup, and query such a database.

Installation

You can install the released version of pubtatordb from CRAN with:

install.packages("pubtatordb")

The version on GitHub can be downloaded using the devtools package with:

install.packages("devtools")
devtools::install_github("MAMC-DCI/pubtatordb")

Example

Querying is only four steps away:

# Load the package.
library(pubtatordb)

# Download the data.
download_pt(getwd())

# Create the database.
pubtator_path <- file.path(getwd(), "PubTator")
pt_to_sql(
  pubtator_path,
  skip_behavior = FALSE,
  remove_behavior = TRUE,
  db_from_scratch = TRUE
)

# Create a connection to the database.
db_con <- pt_connector(pubtator_path)

# Query the data.
pt_select(
  db_con,
  "gene",
  columns = NULL,
  keys = NULL,
  keytype = NULL,
  limit = 5
)

Disclaimer

The views expressed are those of the author(s) and do not reflect the official policy of the Department of the Army, the Department of Defense or the U.S. Government.