Converters

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")

Contents:

• Abstract Class
  • DataModelConverter
    • DataModelConverter.curie_converter
    • DataModelConverter.labeler
    • DataModelConverter.enforce_canonical_ordering
    • DataModelConverter.convert()
    • DataModelConverter.dump()
• OBO Graph to FHIR Converter
  • OboGraphToFHIRConverter
    • OboGraphToFHIRConverter.dump()
    • OboGraphToFHIRConverter.convert()
    • OboGraphToFHIRConverter.code()
• OBO Graph to OBO Format Converter
  • OboGraphToOboFormatConverter
    • OboGraphToOboFormatConverter.dump()
    • OboGraphToOboFormatConverter.dumps()
    • OboGraphToOboFormatConverter.as_bytes_io()
    • OboGraphToOboFormatConverter.convert()
• OBO Graph to OWL Converter