SQLite database

The database is a SQLite database with the following schema:

The database stores the article information, the model output, and has consists of tables pertaining to specific metadata. The DOI of an article is used to link the tables together, as the DOI is unique to each article.

Creating the database

The database is created using the peptidedigest.create_database() function.

This function takes in the path to the database file and creates a new database at that location. It will not overwrite an existing database, so if you want to create a new database, you will need to use a new file path or name.

PYTHON

db_path = "path/to/article_database.db"
pd.create_database(db_path)

This will create a new database called article_database.db at the specified path.

Retrieving an article from the database

To retrieve an article from the database, you can use the peptidedigest.get_article() function.

PYTHON

doi = "10.1074/jbc.M117.805499"
article = pd.get_article(database, doi=doi, pmc_id=None)

And to retrieve all of them, you can use the peptidedigest.get_articles() function.

PYTHON

articles = pd.get_articles(database)

Deleting articles from the database

To delete an article from the database, you can use the peptidedigest.delete_article() function.

PYTHON

doi = "10.1074/jbc.M117.805499"
pd.delete_article(database, doi=doi, pmc_id=None):