| Type: | Package |
| Title: | Create and Query a Local 'PubTator' Database |
| Version: | 0.1.4 |
| Maintainer: | Zachary Colburn <zcolburn@gmail.com> |
| Description: | '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. |
| 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: | 7.0.0 |
| NeedsCompilation: | no |
| Packaged: | 2019-11-22 19:06:37 UTC; zcolburn |
| Author: | Zachary Colburn [aut, cre], Madigan Army Medical Center - Department of Clinical Investigation [cph, fnd] |
| Repository: | CRAN |
| Date/Publication: | 2019-11-22 19:30:02 UTC |
Download PubTator data via ftp.
Description
Download PubTator data via ftp.
Usage
download_pt(pubtator_parent_path, ...)
Arguments
pubtator_parent_path |
The path to the directory where the PubTator data folder will be created. |
... |
Additional arguments to dir.create and download.file. |
Value
The path to the newly created directory. This can be passed to other functions as the pt_path argument.
Examples
# Use the full path. The files are large. Writing somewhere other than the
# temp directory is recommended.
download_path <- tempdir()
download_pt(dowload_path)
Make a path to the PubTator sqlite file.
Description
Make a path to the PubTator sqlite file.
Usage
make_pubtator_sqlite_path(pt_path)
Arguments
pt_path |
A character string indicating the full path of the directory containing the pubtator gz files to be extracted. |
Value
A character string indicating the full path to the sqlite file.
List the column names for a table in the PubTator sqlite database
Description
List the column names for a table in the PubTator sqlite database
Usage
pt_columns(db_con, table_name)
Arguments
db_con |
A connection to the PubTator sqlite database, as created via pubator_connector. |
table_name |
The name of the table of interest. Valid tables can be found using pt_tables. Capitalization does not matter. |
Value
A character vector of the column names for a given table.
Examples
db_con <- pt_connector(pt_path)
pubtator_columns(db_con, "gene")
Connect to pubtator.sqlite
Description
Connect to pubtator.sqlite
Usage
pt_connector(pt_path)
Arguments
pt_path |
A character string indicating the full path of the directory containing the pubtator gz files to be extracted. |
Value
A SQLiteConnection
Examples
pt_connector("D:/Reference_data/PubTator")
Retrieve data from the PubTator database.
Description
Retrieve data from the PubTator database.
Usage
pt_select(
db_con,
table_name,
columns = NULL,
keys = NULL,
keytype = NULL,
limit = Inf
)
Arguments
db_con |
A connection to the PubTator sqlite database, as created via pubator_connector. |
table_name |
The name of the table of interest. Valid tables can be found using pt_tables. Capitalization does not matter. |
columns |
A character vector of the names of the columns of interest. Capitalization does not matter. |
keys |
A vector specifying which values must be in the keytype column to enable retrieval. No filtering is performed if keys = NULL. |
keytype |
The column in which the keys should be searched for. |
limit |
The maximum number of rows the query should return. All rows passing filtering (if any) are returned if limit = Inf. |
Value
A data.frame.
Examples
db_con <- pt_connector(pt_path)
pt_select(
db_con,
"gene",
columns = c("ENTREZID","Resource","MENTIONS","PMID"),
keys = c("7356", "4199", "7018"),
keytype = "ENTREZID",
limit = 10
)
List the tables in the PubTator sqlite database
Description
List the tables in the PubTator sqlite database
Usage
pt_tables(db_con)
Arguments
db_con |
A connection to the PubTator sqlite database, as created via pubator_connector. |
Value
A character vector of the names of the tables found in the database.
Examples
db_con <- pt_connector(pt_path)
pt_tables(db_con)
Create sqlite database from the pubtator data.
Description
Create sqlite database from the pubtator data.
Usage
pt_to_sql(pt_path, skip_behavior = TRUE, remove_behavior = FALSE)
Arguments
pt_path |
A character string indicating the full path of the directory containing the pubtator gz files to be extracted. |
skip_behavior |
TRUE/FALSE indicating whether the file should be re-extracted if it has already been extracted. |
remove_behavior |
TRUE/FALSE indicating whether the gz files should be removed following successful extraction. |
Examples
download_path <- tempdir()
current_dir <- getwd()
setwd(download_path)
pt_to_sql("PubTator")
setwd(current_dir)
See the citations for PubTator
Description
See the citations for PubTator
Usage
pubtator_citations()
Examples
pubtator_citations()
NCBI's ftp url definition for PubTator.
Description
NCBI's ftp url definition for PubTator.
Usage
pubtator_ftp_url()
Value
A character string giving the ftp url for PubTator.
Table and dataset definitions
Description
Table and dataset definitions
Usage
pubtator_tables()
Value
A character vector where names are table names and values are dataset names.