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`
ontobio requires Python 3.4+.
https://github.com/biolink/ontobio
You can install ontobio with pip:
$ pip install ontobio.. toctree:: :maxdepth: 2 :caption: Contents: installation quickstart commandline notebooks concepts inputs outputs identifiers analyses ontologies_advanced go_rules
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
.. toctree:: :maxdepth: 2 contributing changelog