aoptk 0.4.2

Tools to support data mining for the development of (q)AOPs

AOP-toolkit (aoptk)

AOP-toolkit (aoptk) is a Python package for mining and analyzing toxicological and biomedical literature. Originally developed to support the construction of Adverse Outcome Pathways (AOPs), it provides general-purpose tools for retrieving, processing, and analyzing scientific publications.

The toolkit enables users to collect literature from databases such as PubMed Central and Europe PMC, extract information from full-text articles, analyze unstructured text and images using large language models, and normalize chemical names across publications to improve data consistency and interoperability.

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Installation

You can install aoptk in multiple ways depending on your workflow.

Install from PyPI (with uv)

python -m pip install aoptk

Install from BioConda

conda install -c bioconda aoptk

Install from source (with uv)

git clone [e-mail]:rdurnik/aoptk.git
cd aoptk
uv sync --frozen
uv pip install .

Documentation

TBA

Contributing

If you want to contribute to the development of aoptk, have a look at the contribution guidelines.

Credits

This package was created with Copier and the NLeSC/python-template.