Package: pubtatordb 0.1.4
Zachary Colburn
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.
Authors:
pubtatordb_0.1.4.tar.gz
pubtatordb_0.1.4.zip(r-4.5)pubtatordb_0.1.4.zip(r-4.4)pubtatordb_0.1.4.zip(r-4.3)
pubtatordb_0.1.4.tgz(r-4.5-any)pubtatordb_0.1.4.tgz(r-4.4-any)pubtatordb_0.1.4.tgz(r-4.3-any)
pubtatordb_0.1.4.tar.gz(r-4.5-noble)pubtatordb_0.1.4.tar.gz(r-4.4-noble)
pubtatordb_0.1.4.tgz(r-4.4-emscripten)pubtatordb_0.1.4.tgz(r-4.3-emscripten)
pubtatordb.pdf |pubtatordb.html✨
pubtatordb/json (API)
NEWS
| # Install 'pubtatordb' in R: |
| install.packages('pubtatordb', repos = c('https://mamc-dci.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mamc-dci/pubtatordb/issues
Last updated 5 years agofrom:518c24fd7d. Checks:9 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 09 2025 |
| R-4.5-win | OK | Mar 09 2025 |
| R-4.5-mac | OK | Mar 09 2025 |
| R-4.5-linux | OK | Mar 09 2025 |
| R-4.4-win | OK | Mar 09 2025 |
| R-4.4-mac | OK | Mar 09 2025 |
| R-4.4-linux | OK | Mar 09 2025 |
| R-4.3-win | OK | Mar 09 2025 |
| R-4.3-mac | OK | Mar 09 2025 |
Exports:download_ptpt_columnspt_connectorpt_selectpt_tablespt_to_sqlpubtator_citations
Dependencies:assertthatbitbit64blobcachemclicliprcpp11crayonDBIdplyrfansifastmapgenericsgluehmslifecyclemagrittrmemoisepillarpkgconfigplogrprettyunitsprogressR.methodsS3R.ooR.utilsR6readrrlangRSQLitetibbletidyselecttzdbutf8vctrsvroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Download PubTator data via ftp. | download_pt |
| Make a path to the PubTator sqlite file. | make_pubtator_sqlite_path |
| List the column names for a table in the PubTator sqlite database | pt_columns |
| Connect to pubtator.sqlite | pt_connector |
| Retrieve data from the PubTator database. | pt_select |
| List the tables in the PubTator sqlite database | pt_tables |
| Create sqlite database from the pubtator data. | pt_to_sql |
| See the citations for PubTator | pubtator_citation pubtator_citations |
| NCBI's ftp url definition for PubTator. | pubtator_ftp_url |
| Table and dataset definitions | pubtator_tables |
