chembl_downloader

Don't worry about downloading/extracting ChEMBL or versioning - just use chembl_downloader to write code that knows how to download it and use it automatically.

Installation

$ pip install chembl-downloader

Download A Specific Version

import chembl_downloader

path = chembl_downloader.download(version='28')

After it's been downloaded and extracted once, it's smart and doesn't need to download again. It gets stored using pystow automatically in the ~/.data/chembl directory.

We'd like to implement something such that it could load directly into SQLite from the archive, but it appears this is a paid feature.

Download the Latest Version

First, you'll have to install bioversions with pip install bioversions, whose job it is to look up the latest version of many databases. Then, you can modify the previous code slightly by omitting the version keyword argument:

import chembl_downloader

path = chembl_downloader.download()

The version keyword argument is available for all functions in this package, but like the username and password will be omitted for brevity.

Automate Connection

Inside the archive is a single SQLite database file. Normally, people manually untar this folder then do something with the resulting file. Don't do this, it's not reproducible! Instead, the file can be downloaded and a connection can be opened automatically with:

import chembl_downloader

with chembl_downloader.cursor(version='28') as cursor:
    cursor.execute(...)  # run your query string
    rows = cursor.fetchall()  # get your results

You now know everything I can teach you. Please use these tools to do re-usable, reproducible science!

Store in a Different Place

If you want to store the data elsewhere using pystow (e.g., in pyobo I also keep a copy of this file), you can use the prefix argument.

import chembl_downloader

# It gets downloaded/extracted to 
# ~/.data/pyobo/raw/chembl/29/chembl_29/chembl_29_sqlite/chembl_29.db
path = chembl_downloader.download(prefix=['pyobo', 'raw', 'chembl'])

See the pystow documentation on configuring the storage location further.

Download via CLI

After installing, run the following CLI command to ensure it and send the path to stdout

$ chembl_downloader