Reference Classes

The curies package provides reusable building blocks for representing pre-parsed compact URIs (CURIEs) in more complex data models with pydantic.

The Bioregistry extends these models using Pydantic’s model validation framework (see pydantic.model_validator()) in order to automatically standardize prefixes and local unique identifiers against the Bioregistry database.

There are two different implementations:

1. Normalized references, which use Bioregistry’s bioregistry.normalize_prefix() to create fully lower-case prefixes

   • bioregistry.NormalizedReference

   • bioregistry.NormalizedNamableReference

   • bioregistry.NormalizedNamedReference

2. Preferred references, which use bioregistry.get_preferred_prefix() to adds case stylization in prefixes that often appears in semantic web applications.

   • bioregistry.StandardReference

   • bioregistry.StandardNamableReference

   • bioregistry.StandardNamedReference

In the following example, the prefix is normalized to lowercase.

>>> from bioregistry import NormalizedReference
>>> NormalizedReference(prefix="oboInOwl", identifier="inSubset")
NormalizedReference(prefix='oboinowl', identifier='inSubset')

In the following example, the prefix is stylized to the preferred prefix.

>>> from bioregistry import StandardReference
>>> StandardReference(prefix="oboInOwl", identifier="inSubset")
StandardReference(prefix='oboInOwl', identifier='inSubset')