Welcome to ontobio's documentation! =================================== Library for working with ontologies and ontology associations. Provides: - Transparent access to both local files (`obo-json `__, `GAF `__) and remote services (OntoBee, GO/GOlr, `Monarch `__, Wikidata) - Powerful graph operations for traversing logical structure of ontologies - object model for working with ontology metadata elements (synonyms, etc) - Access to gene product functional annotations in GO - Access to gene/variant/disease/genotype etc info from Monarch - Simple basis for building bioinformatics analyses and applications (e.g. `enrichment `__) - Underpinnings for web service APIs - Rich command line access for non-programmers (see :doc:`commandline`) - Examples in :doc:`notebooks` Compatibility ============= ontobio requires Python 3.4+. Contributing ============ https://github.com/biolink/ontobio Installation ============ You can install ontobio with pip: .. code-block:: console $ pip install ontobio Documentation ============= .. toctree:: :maxdepth: 2 :caption: Contents: installation quickstart commandline notebooks concepts inputs outputs identifiers analyses ontologies_advanced go_rules API Reference ------------- If you are looking for information on a specific function, class or method, this part of the documentation is for you. .. toctree:: :maxdepth: 2 api Additional Notes ---------------- .. toctree:: :maxdepth: 2 contributing changelog Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search`