Reference

class pyobo.Reference(prefix, identifier, name=None, registry_id=None)

Bases: object

A namespace, identifier, and label.

Attributes Summary

bioregistry_link	Get the bioregistry link.
curie	The CURIE for this reference.
link	Get a link for this term.
name
pair	The pair of namespace/identifier.
registry_id	The namespace's identifier in the registry

Methods Summary

auto(prefix, identifier)	Create a reference and auto-populate its name.
default(identifier[, name])	Return a reference from the PyOBO namespace.
from_curie(curie[, name, strict, auto])	Get a reference from a CURIE.
get_url()	Return a URL for this reference, if possible.
to_dict()	Return the reference as a dictionary.

Attributes Documentation

bioregistry_link

Get the bioregistry link.

curie

The CURIE for this reference.

link

Get a link for this term.

name: Optional[str] = None

pair

The pair of namespace/identifier.

registry_id: Optional[str] = None

The namespace’s identifier in the registry

Methods Documentation

classmethod auto(prefix, identifier)

Create a reference and auto-populate its name.

Return type:

Reference

static default(identifier, name=None)

Return a reference from the PyOBO namespace.

Return type:

Reference

static from_curie(curie, name=None, *, strict=True, auto=False)

Get a reference from a CURIE.

Parameters:

• curie (str) – The compact URI (CURIE) to parse in the form of <prefix>:<identifier>

• name (Optional[str]) – The name associated with the CURIE

• strict (bool) – If true, raises an error if the CURIE can not be parsed.

• auto (bool) – Automatically look up name

Return type:

Optional[Reference]

get_url()

Return a URL for this reference, if possible.

Return type:

Optional[str]

to_dict()

Return the reference as a dictionary.

Return type:

Mapping[str, str]