get_iri

get_iri(prefix: str, identifier: str | None = None, *, priority: Sequence[str] | None = None, prefix_map: Mapping[str, str] | None = None, use_bioregistry_io: bool = True, provider: str | None = None) → str | None[source]

Get the best link for the CURIE, if possible.

Parameters:

  • prefix – The prefix in the CURIE

  • identifier – The identifier in the CURIE. If identifier is given as None, then this function will assume that the first argument (prefix) is actually a full CURIE.

  • priority –

    A user-defined priority list. In addition to the metaprefixes in the Bioregistry corresponding to resources that are resolvers/lookup services, you can also use default to correspond to the first-party IRI and custom to refer to the custom prefix map. The default priority list is:

    1. Custom prefix map (custom)

    2. First-party IRI (default)

    3. Identifiers.org / MIRIAM (miriam)

    4. Ontology Lookup Service (ols)

    5. OBO PURL (obofoundry)

    6. Name-to-Thing (n2t)

    7. BioPortal (bioportal)

  • prefix_map – A custom prefix map to go with the custom key in the priority list

  • use_bioregistry_io – Should the bioregistry resolution IRI be used? Defaults to true.

  • provider – The provider code to use for a custom provider

Returns:

The best possible IRI that can be generated based on the priority list.

A pre-parse CURIE can be given as the first two arguments

>>> get_iri("chebi", "24867")
'http://purl.obolibrary.org/obo/CHEBI_24867'

A CURIE can be given directly as a single argument

>>> get_iri("chebi:24867")
'http://purl.obolibrary.org/obo/CHEBI_24867'

A priority list can be given

>>> priority = ["miriam", "default", "bioregistry"]
>>> get_iri("chebi:24867", priority=priority)
'https://identifiers.org/CHEBI:24867'

A custom prefix map can be supplied

>>> prefix_map = {"chebi": "https://example.org/chebi/"}
>>> get_iri("chebi:24867", prefix_map=prefix_map)
'https://example.org/chebi/24867'

A custom prefix map can be supplied in combination with a priority list

>>> prefix_map = {"lipidmaps": "https://example.org/lipidmaps/"}
>>> priority = ["obofoundry", "custom", "default", "bioregistry"]
>>> get_iri("chebi:24867", prefix_map=prefix_map, priority=priority)
'http://purl.obolibrary.org/obo/CHEBI_24867'
>>> get_iri("lipidmaps:1234", prefix_map=prefix_map, priority=priority)
'https://example.org/lipidmaps/1234'

A custom provider is given, which makes the Bioregistry very extensible

>>> get_iri("chebi:24867", provider="chebi-img")
'https://www.ebi.ac.uk/chebi/backend/api/public/compound/24867/structure/?width=300&height=300'