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        "author": "Daniel Himmelstein",
        "author_email": "daniel.himmelstein@gmail.com",
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        "classifiers": [
            "Intended Audience :: Science/Research",
            "License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Information Analysis"
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        "description": "# obonet: load OBO-formatted ontologies into networkx\n\n[![Build Status](https://travis-ci.org/dhimmel/obonet.svg?branch=master)](https://travis-ci.org/dhimmel/obonet)\n\nRead OBO-formatted ontologies in Python.\n`obonet` is\n\n+ user friendly\n+ no nonsense\n+ pythonic\n+ modern\n+ simple and tested\n+ lightweight\n+ [`networkx`](https://networkx.readthedocs.io/en/stable/overview.html) leveraging\n\nThis Python 3.4+ package loads OBO serialized ontologies into networks.\nThe function `obonet.read_obo()` takes an `.obo` file and returns a [`networkx.MultiDiGraph`](https://networkx.github.io/documentation/stable/reference/classes/multigraph.html) representation of the ontology.\nThe parser was designed for the OBO specification version [1.2](https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html) & [1.4](https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html).\n\n## Usage\n\nThis package is designed and tested on python \u2265 3.4.\nOBO files can be read from a path, URL, or open file handle.\nCompression is inferred from the path's extension.\nSee example usage below:\n\n```python\nimport networkx\nimport obonet\n\n# Read the taxrank ontology\nurl = 'https://github.com/dhimmel/obonet/raw/master/tests/data/taxrank.obo'\ngraph = obonet.read_obo(url)\n\n# Or read the xz-compressed taxrank ontology\nurl = 'https://github.com/dhimmel/obonet/raw/master/tests/data/taxrank.obo.xz'\ngraph = obonet.read_obo(url)\n\n# Number of nodes\nlen(graph)\n\n# Number of edges\ngraph.number_of_edges()\n\n# Check if the ontology is a DAG\nnetworkx.is_directed_acyclic_graph(graph)\n\n# Mapping from term ID to name\nid_to_name = {id_: data.get('name') for id_, data in graph.nodes(data=True)}\nid_to_name['TAXRANK:0000006']  # TAXRANK:0000006 is species\n\n# Find all superterms of species. Note that networkx.descendants gets\n# superterms, while networkx.ancestors returns subterms.\nnetworkx.descendants(graph, 'TAXRANK:0000006')\n```\n\nFor a more detailed tutorial, see the [**Gene Ontology example notebook**](https://github.com/dhimmel/obonet/blob/master/examples/go-obonet.ipynb).\n\n## Installation\n\n[![PyPI](https://img.shields.io/pypi/v/obonet.svg)](https://pypi.org/project/hetio/)\n\nThe recommended approach is to install the latest release from [PyPI](https://pypi.org/project/hetio/) using:\n\n```sh\npip install obonet\n```\n\nHowever, if you'd like to install the most recent version from GitHub, use:\n\n```sh\npip install git+https://github.com/dhimmel/obonet.git#egg=obonet\n```\n\n## Contributing\n\n[![GitHub issues](https://img.shields.io/github/issues/dhimmel/obonet.svg)](https://github.com/dhimmel/obonet/issues)\n\nWe welcome feature suggestions and community contributions.\nCurrently, only reading OBO files is supported.\nPlease open an issue if you're interested in writing OBO files in Python.\n\n## Release instructions\n\nThis section is only relevant for project maintainers.\nTravis CI deployments are used to upload releases to [PyPI](https://pypi.org/project/hetio).\nTo create a new release, do the following:\n\n1. Bump the `__version__` in [`obonet/__init__.py`](https://github.com/dhimmel/obonet/blob/master/obonet/__init__.py).\n\n3. Run the following commands:\n    \n  ```sh\n  TAG=v`python setup.py --version`\n  git add obonet/__init__.py\n  git commit --message=\"Upgrade to $TAG\"\n  git push\n  git tag --annotate $TAG --message=\"Upgrade to $TAG\"\n  git push --tags\n  ```",
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