Part 4: OboGraphs
=================

So far we have been using the :ref:`basic_ontology_interface` which provides basic lookup operations. All methods in this interface
return 'simple' python objects, such as strings, lists of strings, or dictionaries or :ref:`iterators` composing these elements.

Sometimes more powerful abstractions are required. For example, many bioinformatics applications work with a :term:`Graph` level abstraction
of an ontology which allows for graph-theoretic operations and visualizations. In contrast, many ontology management and QC
applications require an OWL :term:`Axiom` oriented view of an ontology.

OAK does not favor any one view or abstraction or datamodel. The general philosophy is:

- be **pluralistic** - provide different :term:`Interfaces` with different abstractions, and allow the application developer or user to choose
- ensure each interface follows a well-documented :term:`Datamodel`, adhering to standards if they exist

To illustrate this we will first introduce the :ref:`OboGraphInterface` which uses the :ref:`OboGraph` datamodel

OboGraphs
---------

See `OboGraph Datamodel <https://incatools.github.io/ontology-access-kit/datamodels/obograph/index.html>`_

In this datamodel, an ontology is conceived of as a Graph, with a graph consisting of

- :term:`Node` objects
- :term:`Edge` objects

Nodes are typically ontology :term:`Classes<Class>` but are not restricted to this.

Edges are typed relationships between nodes - for example, finger part-of hand.

The OboGraph datamodel is used by the :term:`obographviz` library, which visualizes graphs like this:

.. image:: wing-vein.png

OboGraph Interface
-----------

Like most datamodels in OAK, the OboGraph datamodel follows a Data Access Object (DAO) pattern - the objects are intentionally limited
in their behavior. For example, you cannot ask a node what edges come out or go in; these are stored at the top level graph object.

"Smarter" operations are provided by the interface

Commands
-------

There are a number of commands that work with OBOGraph abstractions:

- :ref:`viz`
- :ref:`tree`
- :ref:`ancestors`
- :ref:`descendants`
- :ref:`similarity`


Code examples
------

TODO: see tests for examples for now