from_cache_df

from_cache_df(path: str | Path, source_prefix: str, *, prefixes: Collection[str] | None = None, standardize: bool = True, version: str | None = None, license: str | None = None, confidence: float | None = None, justification: NormalizedNamableReference | None = None) → list[Mapping][source]

Get mappings from a pyobo-flavored cache file.

Parameters:

  • path –

    The path to a dataframe containing mappings in the following columns:

    1. Local unique identifiers from the source prefix

    2. Cross-reference prefix

    3. Cross-reference local unique identifier

  • source_prefix – The prefix of the ontology

  • prefixes – A set of prefixes to subset the second column of cross-reference targets

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

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

  • 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.

Returns:

A list of semantic mapping objects