OAK uses a number of different Data Models (See Datamodels) for representing ontologies and ontology-related information.

Command Line Usage

The general pattern is:

$ runoak -i INPUT-SPEC dump -O FORMAT -o OUTPUT-FILE

Converting from Obo Graphs

Currently the only converters implemented are for converting between the OboGraphs data model and other models.

>>> from oaklib.utilities.obograph_utils import load_obograph_document
>>> graph_doc = load_obograph_document("tests/input/go-nucleus.json")