Metadata-Version: 2.3
Name: bionty
Version: 2.2.0
Summary: Basic biological entities, coupled to public ontologies [`source <https://github.com/laminlabs/bionty/blob/main/bionty/models.py>`__].
Author-email: Lamin Labs <open-source@lamin.ai>
Requires-Python: >=3.10,<3.14
Description-Content-Type: text/markdown
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Dist: lamindb>=2.0a1
Requires-Dist: lamindb_setup>=0.81.2
Requires-Dist: lamin_utils>=0.16.2
Requires-Dist: requests
Requires-Dist: pyyaml
Requires-Dist: laminci ; extra == "dev"
Requires-Dist: pre-commit ; extra == "dev"
Requires-Dist: pytest>=6.0 ; extra == "dev"
Requires-Dist: pytest-cov ; extra == "dev"
Requires-Dist: nbproject-test ; extra == "dev"
Requires-Dist: pronto ; extra == "dev"
Requires-Dist: pymysql ; extra == "dev"
Requires-Dist: bioregistry ; extra == "dev"
Project-URL: Home, https://github.com/laminlabs/bionty
Provides-Extra: dev

[![Stars](https://img.shields.io/github/stars/laminlabs/bionty?logo=GitHub&color=yellow)](https://github.com/laminlabs/bionty)
[![pypi](https://img.shields.io/pypi/v/bionty?color=blue&label=pypi%20package)](https://pypi.org/project/bionty)

# bionty: Registries for biological ontologies

- Access >20 public ontologies such as Gene, Protein, CellMarker, ExperimentalFactor, CellType, CellLine, Tissue, …
- Create records from entries in public ontologies using `.from_source()`.
- Access full underlying public ontologies via `.public()` to search & bulk-create records.
- Create in-house ontologies by extending public ontologies using hierarchical relationships among records (`.parents`).
- Use `.synonyms` and `.abbr` to manage synonyms.
- Safeguards against typos & duplications.
- Manage multiple ontology versions via `bionty.Source`.

Read the [docs](https://docs.lamin.ai/bionty).

