normalize_prefix

normalize_prefix(prefix: str, *, use_preferred: bool = False, strict: Literal[True] = True) → str[source]
normalize_prefix(prefix: str, *, use_preferred: bool = False, strict: Literal[False] = False) → str | None

Get the normalized prefix, or return None if not registered.

Parameters:

  • prefix – The prefix to normalize, which could come from Bioregistry, OBO Foundry, OLS, or any of the curated synonyms in the Bioregistry

  • strict – If true and the prefix could not be looked up, raises an error

  • use_preferred – If set to true, uses the “preferred prefix”, if available, instead of the canonicalized Bioregistry prefix.

Returns:

The canonical Bioregistry prefix, it could be looked up. This will usually take precedence: MIRIAM, OBO Foundry / OLS, Custom except in a few cases, such as NCBITaxon.

This works for synonym prefixes, like:

>>> assert "ncbitaxon" == normalize_prefix("taxonomy")

This works for common mistaken prefixes, like:

>>> assert "pubchem.compound" == normalize_prefix("pubchem")

This works for prefixes that are often written many ways, like:

>>> assert "ec" == normalize_prefix("ec-code")
>>> assert "ec" == normalize_prefix("EC_CODE")

Get a “preferred” prefix:

>>> normalize_prefix("go", use_preferred=True)
'GO'