######
Output
######

BioCypher development was initially centred around a Neo4j graph database output
due to the migration of OmniPath to a Neo4j backend. Importantly, we understand
BioCypher as an abstraction of the build process of a biomedical knowledge graph,
and thus are open towards any output format for the knowledge representation. We
are currently working on other output formats, such as RDF, SQL, and ArangoDB,
and will update the documentation accordingly.

The used output format is specified via the ``dbms`` parameter in the
``biocypher_config.yaml`` (see the :ref:`config` for an example).  Currently
supported are ``neo4j``, ``arangodb``, ``rdf``, ``postgres``, and ``sqlite``.

Furthermore, you can specify whether to use the ``offline`` or ``online`` mode.

- For the online mode set ``offline: false``. You need a running database
instance and BioCypher will connect to this instance and directly writes the
output to the database.

- For the offline mode set ``offline: true``. BioCypher will write the knowledge
graph to files in a designated output folder (standard being ``biocypher-out/``
and the current datetime). Furthermore you can generate a bash script to insert
the knowledge graph files into the specified ``dbms`` by running
``bc.write_import_call()``.

.. caution::

   The ``online`` mode is currently only supported for the ``neo4j`` database.

Details about the usage of the ``online`` and ``offline`` mode and the different
supported output formats are described on the following pages:

.. toctree::
    :maxdepth: 2

    neo4j.md
    arangodb.md
    rdf.md
    postgres.md
    sqlite.md