pyDOID

Python package with utilities for managing the Human Disease Ontology.

pyDOID was created to provide functionality that is currently unavailable (or difficult to create) in DO.utils the more extensive R package designed with the same purpose.

The functionality provided by pyDOID is encapsulated in three primary classes:

1. The DOrepo class is designed specifically for access and manipulation of the Disease Ontology's git repository and the files within it. DOrepo:
   1. Inherits from the git.repo.Repo class and extends it with methods to check out individual tags, iteratively execute code across a range of tags, and to capture/restore the state of the git repo.
   2. Wraps the pyDOID.owl classes (outlined below) for specific files in the repository (owl.functional: doid-edit.owl; owl.xml: doid.owl and doid-merged.owl).
2. The owl.functional class provides a single method to extract class axioms from OWL files in the functional format.
3. The owl.xml class provides methods to load and execute SPARQL queries against OWL files in the XML format.