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Tools for biomedical ontologies.

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Tools for biomedical ontologies.

💪 Getting Started

This package lets you get OBO Graphs from ontologies based on their OWL files, OBO files, or Bioregistry prefixes. Internally, it uses ROBOT to convert from these formats to OBO Graph JSON.

import bioontologies

# Get an ontology and convert to OBO Graph object via an OWL IRI
owl_iri = ""
parse_results = bioontologies.convert_to_obograph(owl_iri)

# Get an ontology and convert to OBO Graph object via an OBO IRI
obo_iri = ""
parse_results = bioontologies.convert_to_obograph(obo_iri)

# Get an ontology by its Bioregistry prefix
parse_results = bioontologies.get_obograph_by_prefix("go")
go_graph_document = parse_results.graph_document

🚀 Installation

The most recent release can be installed from PyPI with:

$ pip install bioontologies

The most recent code and data can be installed directly from GitHub with:

$ pip install git+

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.

🎁 Support

The Bioregistry was developed by the INDRA Lab, a part of the Laboratory of Systems Pharmacology and the Harvard Program in Therapeutic Science (HiTS) at Harvard Medical School.

💰 Funding

The development of this package is funded by the DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions

The final section of the README is for if you want to get involved by making a code contribution.

Development Installation

To install in development mode, use the following:

$ git clone git+
$ cd bioontologies
$ pip install -e .

🥼 Testing

After cloning the repository and installing tox with pip install tox, the unit tests in the tests/ folder can be run reproducibly with:

$ tox

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📖 Building the Documentation

The documentation can be built locally using the following:

$ git clone git+
$ cd bioontologies
$ tox -e docs
$ open docs/build/html/index.html

The documentation automatically installs the package as well as the docs extra specified in the setup.cfg. sphinx plugins like texext can be added there. Additionally, they need to be added to the extensions list in docs/source/

📦 Making a Release

After installing the package in development mode and installing tox with pip install tox, the commands for making a new release are contained within the finish environment in tox.ini. Run the following from the shell:

$ tox -e finish

This script does the following:

  1. Uses Bump2Version to switch the version number in the setup.cfg, src/bioontologies/, and docs/source/ to not have the -dev suffix
  2. Packages the code in both a tar archive and a wheel using build
  3. Uploads to PyPI using twine. Be sure to have a .pypirc file configured to avoid the need for manual input at this step
  4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
  5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use tox -e bumpversion minor after.

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