Bioregistry |release| Documentation
===================================

The Bioregistry is an integrative, open, community-driven meta-registry of databases,
ontologies, and other nomenclature resources in the life sciences. It relies on an open
code, open data, and open infrastructure paradigm to support its longevity along with a
sustainable governance model that enables community curation and discussion.

This documentation is specifically for the Python package that can access the
Bioregistry and use it for common tasks like metadata lookup, CURIE expansion, URI
contraction, and more.

.. seealso::

    - `About this project <https://bioregistry.io/summary>`_
    - `Bioregistry Website <https://bioregistry.io>`_
    - `A list of all prefixes <https://bioregistry.io/registry/>`_
    - `Source Code on GitHub <https://github.com/biopragmatics/bioregistry>`_
    - `Data Downloads <https://github.com/biopragmatics/bioregistry/tree/main/exports>`_
    - `Project Governance
      <https://github.com/biopragmatics/bioregistry/blob/main/docs/GOVERNANCE.md>`_
    - `Contribution Guidelines
      <https://github.com/biopragmatics/bioregistry/blob/main/docs/CONTRIBUTING.md>`_
    - `Programming language-agnostic API <https://bioregistry.io/apidocs>`_
    - `Python Package on PyPI <https://pypi.org/project/bioregistry>`_
    - `Docker container on DockerHub
      <https://hub.docker.com/r/biopragmatics/bioregistry>`_

Installation
------------

The most recent release of the Bioregistry Python package can be installed from `PyPI
<https://pypi.org/project/bioregistry>`_ with:

.. code-block:: shell

    $ pip install bioregistry

The most recent code and data can be installed directly from GitHub with:

.. code-block:: shell

    $ pip install git+https://github.com/biopragmatics/bioregistry.git

To install in development mode, use the following:

.. code-block:: shell

    $ git clone git+https://github.com/biopragmatics/bioregistry.git
    $ cd bioregistry
    $ pip install -e .

.. toctree::
    :maxdepth: 2
    :caption: Getting Started
    :name: start

    reference
    alignment
    cli
    pandas
    deployment
    curation
    references
    validation-cli

Indices and Tables
------------------

- :ref:`genindex`
- :ref:`modindex`
- :ref:`search`
