convert

convert(input_path: str | Path, output_path: str | Path, input_flag: Literal['-i', '-I'] | None = None, *, merge: bool = True, fmt: str | None = None, check: bool = True, reason: bool = False, extra_args: list[str] | None = None, debug: bool = False) → str[source]

Convert an OBO file to an OWL file with ROBOT.

Parameters:

  • input_path – Either a local file path or IRI. If a local file path is used, pass "-i" to flag. If an IRI is used, pass "-I" to flag.

  • output_path – The local file path to save the converted ontology to. Will infer format from the extension, otherwise, use the fmt param.

  • input_flag – The flag to denote if the file is local or remote. Tries to infer from input string if none is given

  • merge – Use ROBOT’s merge command to squash all graphs together

  • fmt – Explicitly set the format

  • check – By default, the OBO writer strictly enforces document structure rules <http://owlcollab.github.io/oboformat/doc/obo-syntax.html#4>. If an ontology violates these, the convert to OBO operation will fail. These checks can be ignored by setting this to false.

  • reason – Turn on ontology reasoning

  • extra_args – Extra positional arguments to pass in the command line

  • debug – Turn on -vvv

Returns:

Output from standard out from running ROBOT