from_sssom

from_sssom(path: str | Path, *, mapping_set_id: str | None = None, mapping_set_title: str | None = None, mapping_set_name: str | None = None, mapping_set_confidence: float | None = None, mapping_set_version: str | None = None, license: str | None = None, justification: NormalizedNamableReference | None = None, version: str | None = None, standardize: bool = True, metadata: str | None = None) → list[Mapping][source]

Get mappings from a path to a SSSOM TSV file.

Parameters:

  • path – The local file path or URL to a SSSOM TSV file.

  • mapping_set_title – The title for the SSSOM mapping set, if not given explicitly in each mapping row nor by metadata

  • mapping_set_name – A deprecated alias for mapping_set_title

  • mapping_set_confidence –

    The confidence associated with all mappings in the mapping set. This diverges from the SSSOM data model in that each mapping can specify its own confidence, but there is no global confidence at the set level.

    See also

    https://github.com/mapping-commons/sssom/issues/438

  • mapping_set_version – The title for the SSSOM mapping set, if not given explicitly in each mapping row nor by metadata.

  • license – The license for the SSSOM mapping set, if not given explicitly in each mapping row nor by metadata.

  • justification – The mapping justification for all mappings in the SSSOM mapping set, if not given explicitly in each mapping row nor by metadata. Given as a curies.Reference object using semapv as the prefix.

  • version – Deprecated name for mapping_set_version

  • standardize – Should Bioregistry be applied to standardize all

  • metadata – A URL to a SSSOM metadata file, which can contain an external definition of several of the relevant metadata fields accepted by this function.

Returns:

A list of SeMRA mapping objects

Load a SSSOM file by URL that has external metadata

mappings = from_sssom(
    "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv",
    mapping_set_confidence=0.85,
    metadata="https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.yml",
)