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'