api.rst

API

.. currentmodule:: ontobio

Ontology Access

Factory

The OntologyFactory class provides a means of creating an ontology object backed by either local files or remote services. See :ref:`inputs` for more details.

.. currentmodule:: ontobio.ontol_factory

.. autoclass:: OntologyFactory
    :members:

Ontology Object Model

.. currentmodule:: ontobio.ontol

.. autoclass:: Ontology
    :members:
    :inherited-members:

.. autoclass:: Synonym
    :members:
    :inherited-members:

.. autoclass:: LogicalDefinition
    :members:
    :inherited-members:

Assocation Access

Factory

.. currentmodule:: ontobio.assoc_factory

.. autoclass:: AssociationSetFactory
    :members:

Assocation Object Model

.. currentmodule:: ontobio.assocmodel

.. autoclass:: AssociationSet
    :members:

TODO - detailed association modeling

Association File Parsers

.. currentmodule:: ontobio.io.gafparser

.. autoclass:: AssocParser
    :members:
    :inherited-members:

.. autoclass:: GafParser
    :members:
    :inherited-members:

.. autoclass:: GpadParser
    :members:
    :inherited-members:

.. autoclass:: HpoaParser
    :members:
    :inherited-members:

.. autoclass:: AssocParserConfig
    :members:

Go Rules

.. automodule:: ontobio.io.qc
    :members:

GoAssociation internal Model

.. automodule:: ontobio.model.association
    :members:

GOlr Queries

.. currentmodule:: ontobio.golr.golr_query

.. autoclass:: GolrAssociationQuery
    :members:

.. autoclass:: GolrSearchQuery
    :members:

Lexmap

.. currentmodule:: ontobio.lexmap

.. autoclass:: LexicalMapEngine
    :members: