miriam_standardize_identifier

miriam_standardize_identifier(prefix: str, identifier: str) → str | None[source]

Normalize the identifier with the appropriate banana.

Parameters:

prefix – The prefix in the CURIE
identifier – The identifier in the CURIE

Returns:

A normalize identifier, possibly with banana/redundant prefix added. Returns none if the prefix doesn’t map to MIRIAM.

Examples with explicitly annotated bananas:

>>> import bioregistry as br
>>> assert "VariO" == br.get_banana("vario")
>>> miriam_standardize_identifier("vario", "0376")
'VariO:0376'
>>> miriam_standardize_identifier("vario", "VariO:0376")
'VariO:0376'

Examples with bananas from OBO

>>> import bioregistry as br
>>> assert "GO" == br.get_banana("go")
>>> miriam_standardize_identifier("go", "0000001")
'GO:0000001'
>>> miriam_standardize_identifier("go", "GO:0000001")
'GO:0000001'
>>> assert "VariO" == br.get_banana("vario")
>>> miriam_standardize_identifier("vario", "0000001")
'VariO:0000001'
>>> miriam_standardize_identifier("vario", "VariO:0000001")
'VariO:0000001'

Examples from OBO Foundry

>>> miriam_standardize_identifier("chebi", "1234")
'CHEBI:1234'
>>> miriam_standardize_identifier("chebi", "CHEBI:1234")
'CHEBI:1234'

Examples outside of OBO

>>> miriam_standardize_identifier("mgi", "6017782")
'MGI:6017782'
>>> miriam_standardize_identifier("mgi", "MGI:6017782")
'MGI:6017782'

>>> miriam_standardize_identifier("swisslipid", "000000341")
'SLM:000000341'
>>> miriam_standardize_identifier("swisslipid", "SLM:000000341")
'SLM:000000341'

Special cases with underscore-delimited bananas

>>> miriam_standardize_identifier("cellosaurus", "0001")
'CVCL_0001'
>>> miriam_standardize_identifier("cellosaurus", "CVCL_0001")
'CVCL_0001'
>>> miriam_standardize_identifier("ro", "0000001")
'RO_0000001'
>>> miriam_standardize_identifier("ro", "RO_0000001")
'RO_0000001'
>>> miriam_standardize_identifier("geogeo", "000000001")
'GEO_000000001'
>>> miriam_standardize_identifier("geogeo", "GEO_000000001")
'GEO_000000001'
>>> miriam_standardize_identifier("biomodels.kisao", "0000057")
'KISAO_0000057'
>>> miriam_standardize_identifier("biomodels.kisao", "KISAO_0000057")
'KISAO_0000057'

Standard

>>> import bioregistry as br
>>> assert br.get_banana("pdb") is None
>>> assert not br.get_namespace_in_lui("pdb")
>>> miriam_standardize_identifier("pdb", "00000020")
'00000020'