Improving reproducibility of cheminformatics workflows with chembl-downloader

TL;DR

This paper introduces chembl-downloader, a Python package that enables reproducible, up-to-date access to ChEMBL data, improving transparency and consistency in cheminformatics workflows.

Contribution

The paper presents a new Python tool that simplifies reproducible access to current and specific versions of ChEMBL data for cheminformatics research.

Findings

Provides reproducible data acquisition from ChEMBL

Enables access to latest or specific ChEMBL versions

Facilitates transparent and up-to-date datasets

Abstract

Many modern cheminformatics workflows derive datasets from ChEMBL, but few of these datasets are published with accompanying code for their generation. Consequently, their methodologies (e.g., selection, filtering, aggregation) are opaque, reproduction is difficult, and interpretation of results therefore lacks important context. Further, such static datasets quickly become out-of-date. For example, the current version of ChEMBL is v35 (as of December 2024), but ExCAPE-DB uses v20, Deep Confidence uses v23, the consensus dataset from Isigkeit _et al._ (2022) uses v28, and Papyrus uses v30. Therefore, there is a need for tools that provide reproducible bulk access to the latest (or a given) version of ChEMBL in order to enable researchers to make their derived datasets more transparent, updatable, and trustworthy. This article introduces `chembl-downloader`, a Python package for the reproducible acquisition, access, and manipulation of ChEMBL data through its FTP server. It can be downloaded under the MIT license from https://github.com/cthoyt/chembl-downloader and installed from PyPI with `pip install chembl-downloader.`