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pyDOID is a python package developed with the same intent as DO.utils, to provide methods for updating, maintaining, organizing, and analyzing the Human Disease Ontology. DO.utils, powered by reticulate, wraps pyDOID for functionality that is currently unavailable in R. pyDOID provides two primary classes: the DOrepo class and the owl.xml class. Classes and their methods are accessible via $ notation.

Version

Documentation assumes pyDOID >= v0.1.2

DOrepo class

The DOrepo class inherits the methods & subclasses of the GitPython.repo.Repo class and adds a few additional classes & methods, see DOrepo() for details.

owl.xml class

The owl.xml class thinly wraps a small set of python rdflib methods to enable SPARQL 1.1 queries, see owl_xml() for details.