from_pyobo

from_pyobo(prefix: str, target_prefix: str | None = None, *, standardize: bool = True, version: str | None = None, license: str | None = None, confidence: float | None = None, justification: NormalizedNamableReference | None = None, force_process: bool = False, cache: bool = True) → list[Mapping][source]

Get mappings from a given ontology via pyobo.

Parameters:

  • prefix – The prefix of the ontology to get semantic mappings from

  • target_prefix – The optional prefix for targets for semantic mappings.

  • standardize – Should the local unique identifiers in the first and third columns be standardized using bioregistry.standardize_identifier()? Defaults to true.

  • confidence – The confidence level for the mappings. Defaults to DEFAULT_ONTOLOGY_CONFIDENCE.

  • version – The version of the ontology that’s been loaded (does not proactively load, but you can use bioversions.get_version() to go along with PyOBO).

  • license – The license of the ontology that’s been loaded. If not given, will try and look up with bioregistry.get_license().

  • justification – The justification from the SEMAPV vocabulary (given as a Reference object). If not given, defaults to UNSPECIFIED_MAPPING.

  • force_process – force re-processing of the source data, e.g., the OBO file for external ontologies or the locally cached data for PyOBO custom sources

  • cache – Should the ontology be automatically cached? Turn off to

Returns:

A list of semantic mapping objects