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PyBEL |release| Documentation
=============================
Biological Expression Language (BEL) is a domain-specific language that enables the expression of complex molecular
relationships and their context in a machine-readable form. Its simple grammar and expressive power have led to its
successful use in the to describe complex disease networks with several thousands of relationships.
PyBEL is a pure Python software package that parses BEL documents, validates their semantics, and facilitates data
interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J. Its companion
package, `PyBEL-Tools <http://pybel-tools.readthedocs.io/>`_, contains a library of functions for analysis of
biological networks. For result-oriented guides, see the `PyBEL-Notebooks <https://github.com/pybel/pybel-notebooks>`_
repository.
Installation is as easy as getting the code from `PyPI <https://pypi.python.org/pypi/pybel>`_ with
:code:`python3 -m pip install pybel`. See the :doc:`installation <introduction/installation>` documentation.
For citation information, see the :doc:`references <meta/references>` page.
PyBEL is tested on Python 3.5+ on Mac OS and Linux using
`Travis CI <https://travis-ci.org/pybel/pybel>`_ as well as on Windows using
`AppVeyor <https://ci.appveyor.com/project/cthoyt/pybel>`_.
.. seealso::
- Specified by `BEL 1.0 <https://github.com/OpenBEL/language/raw/master/docs/version_1.0/bel_specification_version_1.0.pdf>`_,
`BEL 2.0 <https://github.com/OpenBEL/language/raw/master/docs/version_2.0/bel_specification_version_2.0.pdf>`_, and
`BEL 2.0+ <https://biological-expression-language.github.io>`_
- Documented on `Read the Docs <http://pybel.readthedocs.io/>`_
- Versioned on `GitHub <https://github.com/pybel/pybel>`_
- Tested on `Travis CI <https://travis-ci.org/pybel/pybel>`_
- Distributed by `PyPI <https://pypi.python.org/pypi/pybel>`_
.. toctree::
:maxdepth: 2
:caption: Getting Started
:name: start
introduction/overview
introduction/installation
.. toctree::
:maxdepth: 2
:caption: Data Structure
:name: data
reference/struct/datamodel
reference/struct/examples
reference/struct/filters
reference/struct/grouping
reference/struct/operators
reference/struct/pipeline
reference/struct/query
reference/struct/summary
.. toctree::
:maxdepth: 2
:caption: Mutations
:name: mutations
reference/mutations/mutations
reference/mutations/collapse
reference/mutations/deletion
reference/mutations/expansion
reference/mutations/induction
reference/mutations/induction_expansion
reference/mutations/inference
reference/mutations/metadata
.. toctree::
:maxdepth: 2
:caption: Conversion
:name: conversion
reference/io
.. toctree::
:caption: Database
:name: database
reference/database/manager
reference/database/models
.. toctree::
:maxdepth: 2
:caption: Topic Guide
:name: topics
topics/cookbook
topics/cli
.. toctree::
:caption: Reference
:name: reference
reference/constants
reference/parser
reference/dsl
reference/logging
.. toctree::
:caption: Project
:name: project
meta/references
meta/postmortem
meta/technology
Indices and Tables
------------------
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
|
