Tools for biomedical ontologies.
Project description
Bioontologies
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 = "http://purl.obolibrary.org/obo/go.owl"
parse_results = bioontologies.convert_to_obograph(owl_iri)
# Get an ontology and convert to OBO Graph object via an OBO IRI
obo_iri = "http://purl.obolibrary.org/obo/go.obo"
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+https://github.com/biopragmatics/bioontologies.git
👐 Contributing
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md 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+https://github.com/biopragmatics/bioontologies.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+https://github.com/biopragmatics/bioontologies.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/conf.py.
📦 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:
- Uses Bump2Version to switch the version number in the
setup.cfg,src/bioontologies/version.py, anddocs/source/conf.pyto not have the-devsuffix - Packages the code in both a tar archive and a wheel using
build - Uploads to PyPI using
twine. Be sure to have a.pypircfile configured to avoid the need for manual input at this step - Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
- 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 minorafter.
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