Welcome to ontobio’s documentation!

Library for working with ontologies and ontology associations.


  • 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


ontobio requires Python 3.4+.


You can install ontobio with pip:

$ pip install ontobio

Indices and tables