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PubTator is an NCBI product that contains detailed annotations of abstracts found on PubMed. This makes it a very useful research tool. While PubTator does provide an API, the use of an API is inconvenient for high-throughput analyses and also requires a guaranteed internet connection. Querying a local PubTator database is better suited for high-throughput analyses. The package pubtatordb makes it easy to quickly start using a local copy of PubTator's data.
You can install the released version of pubtatordb from CRAN with:
The version on GitHub can be downloaded using the devtools package with:
Load the package.
# Load the package. library(pubtatordb)
After loading the package, database setup and querying can be accomplished in four steps.
After the user manually creates a folder to store the data, the user can define the path to that folder and then download the data to that location:
# Download the data. # Use the full path. Writing to the temp directory is not recommended. download_dir <- tempdir() download_pt(download_dir)
After defining the path to the download directory created above, the database can be created with:
# Define the data directory, a subdirectory of the above directory. pubtator_path <- file.path(download_dir, "PubTator") # Create the database. pt_to_sql( pubtator_path, skip_behavior = FALSE, remove_behavior = TRUE )
If the .gz files from PubTator have already been extracted, their extraction can be skipped with the skip_behavior argument. After their insertion into the database, both the .gz and uncompressed files can be removed using the remove_behavior argument.
A connection can be created to the database using pt_connector. Note that this is a wrapper for the dbConnect function of the DBI package.
# Create a connection to the database. db_con <- pt_connector(pubtator_path)
Querying the data is accomplished using the pt_select function. The first five rows of the gene table can be selected with:
# Query the data. pt_select( db_con, "gene", columns = NULL, keys = NULL, keytype = NULL, limit = 5 )
The first five results for PMIDs in which the genes with ENTREZ IDs 7356 or 4199 were mentioned can be selected with:
# Query the data. pt_select( db_con, "gene", columns = c("PMID", "ENTREZID"), keys = c("7356", "4199"), keytype = "ENTREZID", limit = 5 )
PubTator has several datasets. The names of tables in the database can be obtained with:
The column names for a particular table can be accessed with:
The citation information for PubTator can be found on the PubTator website or with:
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.
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