parse_iri

parse_iri(iri, *, prefix_map=None)[source]

Parse a compact identifier from an IRI.

Parameters

iri (str) – A valid IRI
prefix_map (Union[Mapping[str, str], List[Tuple[str, str]], None]) – If None, will use the default prefix map. If a mapping, will convert into a sorted list using ensure_prefix_list(). If you plan to use this function in a loop, pre-compute this and pass it instead. If a list of pairs is passed, will use it directly.

Return type

Union[Tuple[str, str], Tuple[None, None]]

Returns

A pair of prefix/identifier, if can be parsed

IRI from an OBO PURL:

>>> parse_iri("http://purl.obolibrary.org/obo/DRON_00023232")
('dron', '00023232')

IRI from the OLS:

>>> parse_iri("https://www.ebi.ac.uk/ols/ontologies/ecao/terms?iri=http://purl.obolibrary.org/obo/ECAO_0107180")
('ecao', '0107180')

IRI from native provider

>>> parse_iri("https://www.alzforum.org/mutations/1234")
('alzforum.mutation', '1234')

Dog food:

>>> parse_iri("https://bioregistry.io/DRON:00023232")
('dron', '00023232')

IRIs from Identifiers.org (https and http, colon and slash):

>>> parse_iri("https://identifiers.org/aop.relationships:5")
('aop.relationships', '5')
>>> parse_iri("http://identifiers.org/aop.relationships:5")
('aop.relationships', '5')
>>> parse_iri("https://identifiers.org/aop.relationships/5")
('aop.relationships', '5')
>>> parse_iri("http://identifiers.org/aop.relationships/5")
('aop.relationships', '5')

IRI from N2T >>> parse_iri(”https://n2t.net/aop.relationships:5”) (‘aop.relationships’, ‘5’)

Handle either HTTP or HTTPS: >>> parse_iri(”http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=268”) (‘neuronames’, ‘268’) >>> parse_iri(”https://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=268”) (‘neuronames’, ‘268’)

Provide your own prefix map for one-off parsing (i.e., not in bulk): >>> prefix_map = {“chebi”: “https://example.org/chebi:”} >>> parse_iri(”https://example.org/chebi:1234”, prefix_map=prefix_map) (‘chebi’, ‘1234’)

If you provide your own prefix map but want to do parsing in bulk, you should pre-process the prefix map with:

>>> from bioregistry import ensure_prefix_list
>>> prefix_map = {"chebi": "https://example.org/chebi:"}
>>> prefix_list = ensure_prefix_list(prefix_map)
>>> parse_iri("https://example.org/chebi:1234", prefix_map=prefix_list)
('chebi', '1234')

Corner cases:

>>> parse_iri("https://omim.org/MIM:PS214100")
('omim.ps', '214100')