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توضیحات

Tools for biomedical ontologies.

ویژگی	مقدار
سیستم عامل	OS Independent
نام فایل	bioontologies-0.2.1
نام	bioontologies
نسخه کتابخانه	0.2.1
نگهدارنده	['Charles Tapley Hoyt']
ایمیل نگهدارنده	['cthoyt@gmail.com']
نویسنده	Charles Tapley Hoyt
ایمیل نویسنده	cthoyt@gmail.com
آدرس صفحه اصلی	https://github.com/biopragmatics/bioontologies
آدرس اینترنتی	https://pypi.org/project/bioontologies/
مجوز	MIT

<h1 align="center"> Bioontologies </h1> <p align="center"> <a href="https://github.com/biopragmatics/bioontologies/actions?query=workflow%3ATests"> <img alt="Tests" src="https://github.com/biopragmatics/bioontologies/workflows/Tests/badge.svg" /> </a> <a href="https://pypi.org/project/bioontologies"> <img alt="PyPI" src="https://img.shields.io/pypi/v/bioontologies" /> </a> <a href="https://pypi.org/project/bioontologies"> <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/bioontologies" /> </a> <a href="https://github.com/biopragmatics/bioontologies/blob/main/LICENSE"> <img alt="PyPI - License" src="https://img.shields.io/pypi/l/bioontologies" /> </a> <a href='https://bioontologies.readthedocs.io/en/latest/?badge=latest'> <img src='https://readthedocs.org/projects/bioontologies/badge/?version=latest' alt='Documentation Status' /> </a> <a href="https://codecov.io/gh/biopragmatics/bioontologies/branch/main"> <img src="https://codecov.io/gh/biopragmatics/bioontologies/branch/main/graph/badge.svg" alt="Codecov status" /> </a> <a href="https://github.com/cthoyt/cookiecutter-python-package"> <img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-snekpack-blue" /> </a> <a href='https://github.com/psf/black'> <img src='https://img.shields.io/badge/code%20style-black-000000.svg' alt='Code style: black' /> </a> <a href="https://github.com/biopragmatics/bioontologies/blob/main/.github/CODE_OF_CONDUCT.md"> <img src="https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg" alt="Contributor Covenant"/> </a> </p> Tools for biomedical ontologies. ## 💪 Getting Started This package lets you get OBO Graphs from ontologies based on their OWL files, OBO files, or [Bioregistry](https://bioregistry.io) prefixes. Internally, it uses [ROBOT](https://robot.obolibrary.org) to convert from these formats to [OBO Graph JSON](https://github.com/geneontology/obographs). ```python 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](https://pypi.org/project/bioontologies/) with: ```bash $ pip install bioontologies ``` The most recent code and data can be installed directly from GitHub with: ```bash $ 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](https://github.com/biopragmatics/bioontologies/blob/master/.github/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](https://indralab.github.io), a part of the [Laboratory of Systems Pharmacology](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/about/) and the [Harvard Program in Therapeutic Science (HiTS)](https://hits.harvard.edu) at [Harvard Medical School](https://hms.harvard.edu/). ### 💰 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](https://github.com/audreyfeldroy)'s [cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s [cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack) template. ## 🛠️ For Developers <details> <summary>See developer instructions</summary> 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: ```bash $ 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: ```shell $ tox ``` Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/biopragmatics/bioontologies/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```shell $ 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`](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`](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: ```shell $ tox -e finish ``` This script does the following: 1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`, `src/bioontologies/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix 2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build) 3. Uploads to PyPI using [`twine`](https://github.com/pypa/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. </details>

نیازمندی

مقدار	نام
>=0.5.86	bioregistry
>=0.3.0	curies
-	requests
-	pydantic
-	typing-extensions
-	pystow
-	sphinx
-	sphinx-rtd-theme
-	sphinx-click
-	sphinx-autodoc-typehints
-	sphinx-automodapi
-	m2r2
-	pytest
-	coverage

زبان مورد نیاز

مقدار	نام
>=3.7	Python

نحوه نصب

نصب پکیج whl bioontologies-0.2.1:

pip install bioontologies-0.2.1.whl

نصب پکیج tar.gz bioontologies-0.2.1:

pip install bioontologies-0.2.1.tar.gz