Metadata-Version: 2.4
Name: aoptk
Version: 0.3.2
Summary: Tools to support data mining for the development of (q)AOPs
Author-email: Robin Durník <rdurnik@gmail.com>, Helge Hecht <helge.hecht@recetox.muni.cz>
License: MIT License
        
        Copyright (c) 2025, Robin Durník
        
        Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
        documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
        rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit
        persons to whom the Software is furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
        Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
        WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
        COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
        OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Project-URL: Repository, https://github.com/rdurnik/aoptk
Project-URL: Issues, https://github.com/rdurnik/aoptk/issues
Project-URL: ReadTheDocs, https://aoptk.readthedocs.io
Keywords: AOP, toxicology, data mining, ai, machine learning, data analysis
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pandas
Requires-Dist: pymupdf<=1.27
Requires-Dist: requests
Requires-Dist: scipy>=1.16.3
Requires-Dist: scispacy
Requires-Dist: numpy<2.0,>=1.26
Requires-Dist: spacy<3.8.0,>=3.0.0
Requires-Dist: beautifulsoup4
Requires-Dist: biopython
Requires-Dist: transformers
Requires-Dist: torch
Requires-Dist: openpyxl
Requires-Dist: click>=8.1
Requires-Dist: openai
Requires-Dist: python-dotenv
Requires-Dist: setuptools
Requires-Dist: spacy-layout
Requires-Dist: tenacity
Provides-Extra: dev
Requires-Dist: build; extra == "dev"
Requires-Dist: bumpversion; extra == "dev"
Requires-Dist: coverage[toml]; extra == "dev"
Requires-Dist: pytest; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: ruff; extra == "dev"
Requires-Dist: sphinx; extra == "dev"
Requires-Dist: sphinx_rtd_theme; extra == "dev"
Requires-Dist: sphinx-autoapi; extra == "dev"
Requires-Dist: myst_parser; extra == "dev"
Requires-Dist: jupyter; extra == "dev"
Requires-Dist: ipykernel; extra == "dev"
Requires-Dist: fuzzywuzzy; extra == "dev"
Requires-Dist: pytest-mock; extra == "dev"
Requires-Dist: boto3; extra == "dev"
Provides-Extra: docs
Requires-Dist: sphinx; extra == "docs"
Requires-Dist: sphinx_rtd_theme; extra == "docs"
Requires-Dist: sphinx-autoapi; extra == "docs"
Requires-Dist: myst_parser; extra == "docs"
Provides-Extra: publishing
Requires-Dist: build; extra == "publishing"
Requires-Dist: twine; extra == "publishing"
Requires-Dist: wheel; extra == "publishing"
Dynamic: license-file

## 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.

## Badges


| fair-software.eu recommendations | |
| :-- | :--  |
| (1/5) code repository              | [![github repo badge](https://img.shields.io/badge/github-repo-000.svg?logo=github&labelColor=gray&color=blue)](https://github.com/rdurnik/aoptk) |
| (2/5) license                      | [![github license badge](https://img.shields.io/github/license/rdurnik/aoptk)](https://github.com/rdurnik/aoptk) |
| (3/5) community registry           | [![RSD](https://img.shields.io/badge/rsd-aoptk-00a3e3.svg)](https://www.research-software.nl/software/aoptk) [![workflow pypi badge](https://img.shields.io/pypi/v/aoptk.svg?colorB=blue)](https://pypi.python.org/project/aoptk/) |
| (4/5) citation                     | [![DOI](https://zenodo.org/badge/DOI/<replace-with-created-DOI>.svg)](https://doi.org/<replace-with-created-DOI>)|
| (5/5) checklist                    | [![workflow cii badge](https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>/badge)](https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>) |
| howfairis                          | [![fair-software badge](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B-yellow)](https://fair-software.eu) |
| **Other best practices**           | &nbsp; |
| Static analysis                    | [![workflow scq badge](https://sonarcloud.io/api/project_badges/measure?project=rdurnik_aoptk&metric=alert_status)](https://sonarcloud.io/dashboard?id=rdurnik_aoptk) |
| Coverage                           | [![workflow scc badge](https://sonarcloud.io/api/project_badges/measure?project=rdurnik_aoptk&metric=coverage)](https://sonarcloud.io/dashboard?id=rdurnik_aoptk) || Documentation                      | [![Documentation Status](https://readthedocs.org/projects/aoptk/badge/?version=latest)](https://aoptk.readthedocs.io/en/latest/?badge=latest) || **GitHub Actions**                 | &nbsp; |
| Build                              | [![build](https://github.com/rdurnik/aoptk/actions/workflows/build.yml/badge.svg)](https://github.com/rdurnik/aoptk/actions/workflows/build.yml) |
| Citation data consistency          | [![cffconvert](https://github.com/rdurnik/aoptk/actions/workflows/cffconvert.yml/badge.svg)](https://github.com/rdurnik/aoptk/actions/workflows/cffconvert.yml) || SonarCloud                         | [![sonarcloud](https://github.com/rdurnik/aoptk/actions/workflows/sonarcloud.yml/badge.svg)](https://github.com/rdurnik/aoptk/actions/workflows/sonarcloud.yml) |## How to use aoptk


## Installation

To install aoptk from GitHub repository, do:

```console
git clone git@github.com:rdurnik/aoptk.git
cd aoptk
python -m pip install .
```

## Documentation

TBA

## Contributing

If you want to contribute to the development of aoptk,
have a look at the [contribution guidelines](CONTRIBUTING.md).

## Credits

This package was created with [Copier](https://github.com/copier-org/copier) and the [NLeSC/python-template](https://github.com/NLeSC/python-template).
