pmparser
enables one to easily create and maintain a relational database of data from PubMed/MEDLINE. pmparser
can download the publicly available XML files, parse them, incorporate PubMed’s regular updates, and combine the data with the NIH Open Citation Collection. PMDB, our implementation of the database, is available on Zenodo (as a PostgreSQL dump) and on Google BigQuery. For a detailed description of pmparser
and PMDB, check out the article.
Installation
Option 1: CRAN
install.packages('pmparser')
Option 2: Hughey Lab Drat Repository
-
Install
BiocManager
.if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager')
-
If you use RStudio, go to Tools → Global Options… → Packages → Add… (under Secondary repositories), then enter:
- Name: hugheylab
- Url: https://hugheylab.github.io/drat/
You only have to do this once. Then you can install or update the package by entering:
BiocManager::install('pmparser')
Alternatively, you can install or update the package by entering:
BiocManager::install('pmparser', site_repository = 'https://hugheylab.github.io/drat/')
Usage
See the examples and detailed guidance in the reference documentation.