7. Ontolopy

This chapter describes Ontolopy: a small Python package that I created for manipulating OBO ontology files. This chapter also includes some uses of ontolopy, for example mapping between samples and phenotypes, and other uses. For example, it is particularly useful for finding inconsistencies/disagreements between data sources, which enabled me to contribute back to improve some of the resources that Ontolopy relies on.

At time of writing, Ontolopy v1.1.1-beta (PyPi, GitHub, Docs) is the current release.

Contributions in this chapter

The contributions in this chapter include:

• Creation of the Ontolopy package and it’s documentation.

• Contributions to improve the FANTOM5 and Uberon ontologies, based on using the package to discover data inconsistencies.