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It also facilitates data interchange between common formats and databases such as\n`NetworkX <http://networkx.github.io/>`_, JSON, CSV, SIF, `Cytoscape <http://www.cytoscape.org/>`_,\n`CX <http://www.home.ndexbio.org/data-model/>`_, `NDEx <https://github.com/pybel/pybel2cx>`_, SQL, and\n`Neo4J <https://neo4j.com>`_.\n\nIts companion package, `PyBEL Tools <http://pybel-tools.readthedocs.io/>`_, contains a\nsuite of functions and pipelines for analyzing the resulting biological networks.\n\nWe realize there we have a name conflict with the python wrapper for the cheminformatics package, OpenBabel. If you're\nlooking for their python wrapper, see `here <https://github.com/openbabel/openbabel/tree/master/scripts/python>`_.\n\nCitation\n--------\nIf you find PyBEL useful for your work, please consider citing:\n\n.. [1] Hoyt, C. T., *et al.* (2017). `PyBEL: a Computational Framework for Biological Expression Language\n       <https://doi.org/10.1093/bioinformatics/btx660>`_. Bioinformatics, 34(December), 1\u20132.\n\nGetting Started\n---------------\nThis example illustrates how the `Selventa Small Corpus <https://wiki.openbel.org/display/home/Summary+of+Large+and+Small+BEL+Corpuses>`_\ncan be loaded.\n\n.. code-block:: python\n\n   >>> import pybel\n   >>> graph = pybel.from_url('http://resources.openbel.org/belframework/20150611/knowledge/small_corpus.bel')\n   >>> graph.number_of_nodes()  # Will be smaller than expected because we have the most strict settings enabled\n   1207\n\nMore examples can be found in the `documentation <http://pybel.readthedocs.io>`_ and in the\n`PyBEL Notebooks <https://github.com/pybel/pybel-notebooks>`_ repository.\n\nPyBEL also installs a command line interface with the command :code:`pybel` for simple utilities such as data\nconversion. In this example, a BEL document is compiled then exported to `GraphML <http://graphml.graphdrawing.org/>`_\nfor viewing in Cytoscape.\n\n.. code-block:: sh\n\n    $ pybel compile ~/Desktop/example.bel\n    $ pybel serialize ~/Desktop/example.bel --graphml ~/Desktop/example.graphml\n\nIn Cytoscape, open with :code:`Import > Network > From File`.\n\nInstallation |pypi_version| |python_versions| |pypi_license|\n------------------------------------------------------------\nPyBEL can be installed easily from `PyPI <https://pypi.python.org/pypi/pybel>`_ with the following code in\nyour favorite terminal:\n\n.. code-block:: sh\n\n    $ pip install pybel\n\nor from the latest code on `GitHub <https://github.com/pybel/pybel>`_ with:\n\n.. code-block:: sh\n\n    $ pip install git+https://github.com/pybel/pybel.git\n\nSee the `installation documentation <http://pybel.readthedocs.io/en/latest/installation.html>`_ for more advanced\ninstructions. Also, check the change log at `CHANGELOG.rst <https://github.com/pybel/pybel/blob/develop/CHANGELOG.rst>`_.\n\nContributing\n------------\nContributions, whether filing an issue, making a pull request, or forking, are appreciated. See\n`CONTRIBUTING.rst <https://github.com/pybel/pybel/blob/develop/CONTRIBUTING.rst>`_ for more information on getting\ninvolved. Please add your name to `AUTHORS.rst <https://github.com/pybel/pybel/blob/develop/AUTHORS.rst>`_!\n\nAcknowledgements\n----------------\n- This package was originally developed as part of the master's work of\n  `Charles Tapley Hoyt <https://github.com/cthoyt>`_ at `Fraunhofer SCAI <https://www.scai.fraunhofer.de/>`_.\n- This software is proudly built with Paul McGuire's `PyParsing <http://pyparsing.wikispaces.com/>`_ package.\n- `Scott Colby <https://github.com/scolby33>`_ designed our `logo <https://github.com/pybel/pybel-art>`_ and provided\n  sage advice\n- `Christian Ebeling <https://github.com/cebel>`_ for supervision and consultation\n\nLinks\n-----\n- Specified by `BEL 1.0 <http://openbel.org/language/version_1.0/bel_specification_version_1.0.html>`_ and\n  `BEL 2.0 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html>`_\n- Documented on `Read the Docs <http://pybel.readthedocs.io/>`_\n- Versioned on `GitHub <https://github.com/pybel/pybel>`_\n- Tested on `Travis CI <https://travis-ci.org/pybel/pybel>`_\n- Distributed by `PyPI <https://pypi.python.org/pypi/pybel>`_\n- Chat on `Gitter <https://gitter.im/pybel/Lobby>`_\n\n.. |build| image:: https://travis-ci.org/pybel/pybel.svg?branch=develop\n    :target: https://travis-ci.org/pybel/pybel\n    :alt: Development Build Status\n\n.. |windows_build| image:: https://ci.appveyor.com/api/projects/status/v22l3ymg3bdq525d/branch/develop?svg=true\n    :target: https://ci.appveyor.com/project/cthoyt/pybel\n    :alt: Development Windows Build Status\n\n.. |coverage| image:: https://codecov.io/gh/pybel/pybel/coverage.svg?branch=develop\n    :target: https://codecov.io/gh/pybel/pybel/branch/develop\n    :alt: Development Coverage Status\n\n.. |documentation| image:: https://readthedocs.org/projects/pybel/badge/?version=latest\n    :target: http://pybel.readthedocs.io/en/latest/\n    :alt: Development Documentation Status\n\n.. |climate| image:: https://codeclimate.com/github/pybel/pybel/badges/gpa.svg\n    :target: https://codeclimate.com/github/pybel/pybel\n    :alt: Code Climate\n\n.. |python_versions| image:: https://img.shields.io/pypi/pyversions/PyBEL.svg\n    :target: https://pypi.python.org/pypi/pybel\n    :alt: Stable Supported Python Versions\n\n.. |pypi_version| image:: https://img.shields.io/pypi/v/PyBEL.svg\n    :target: https://pypi.python.org/pypi/pybel\n    :alt: Current version on PyPI\n\n.. |pypi_license| image:: https://img.shields.io/pypi/l/PyBEL.svg\n    :target: https://github.com/pybel/pybel/blob/develop/LICENSE\n    :alt: Apache 2.0 License\n\n.. |zenodo| image:: https://zenodo.org/badge/68376693.svg\n    :target: https://zenodo.org/badge/latestdoi/68376693\n\n\n",
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