Utilities for managing the Human Disease Ontology.
Project description
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:
- The
DOrepo
class is designed specifically for access and manipulation of the Disease Ontology's git repository and the files within it.DOrepo
:- 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. - 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).
- Inherits from the
- The
owl.functional
class provides a single method to extract class axioms from OWL files in the functional format. - The
owl.xml
class provides methods to load and execute SPARQL queries against OWL files in the XML format.
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