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 Command Line)
Examples in Notebooks

Compatibility¶

ontobio requires Python 3.4+.

You can install ontobio with pip:

$ pip install ontobio

Contents:

If you are looking for information on a specific function, class or method, this part of the documentation is for you.