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 andcustom
to refer to the custom prefix map. The default priority list is:1. Custom prefix map (
custom
) 1. First-party IRI (default
) 2. Identifiers.org / MIRIAM (miriam
) 3. Ontology Lookup Service (ols
) 4. OBO PURL (obofoundry
) 5. Name-to-Thing (n2t
) 6. BioPortal (bioportal
)prefix_map – A custom prefix map to go with the
custom
key in the priority listuse_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/displayImage.do?defaultImage=true&imageIndex=0&chebiId=24867’