medkit.core.text.entity_norm_attribute

Classes

EntityNormAttribute

Normalization attribute linking an entity to an ID in a knowledge base.

Module Contents

class medkit.core.text.entity_norm_attribute.EntityNormAttribute(kb_name: str | None, kb_id: Any | None, kb_version: str | None = None, term: str | None = None, score: float | None = None, metadata: dict[str, Any] | None = None, uid: str | None = None)

Bases: medkit.core.attribute.Attribute

Normalization attribute linking an entity to an ID in a knowledge base.

Attributes:

uidstr

Identifier of the attribute

labelstr

The attribute label, always set to EntityNormAttribute.LABEL

valueAny

String representation of the normalization, containing kb_id, along with kb_name if available (ex: “umls:C0011849”). For special cases where only term is available, it is used as value.

kb_namestr, optional

Name of the knowledge base (ex: “icd”). Should always be provided except in special cases when we just want to store a normalized term.

kb_idAny, optional

ID in the knowledge base to which the annotation should be linked. Should always be provided except in special cases when we just want to store a normalized term.

kb_versionstr, optional

Optional version of the knowledge base.

termstr, optional

Optional normalized version of the entity text.

scorefloat, optional

Optional score reflecting confidence of this link.

metadatadict of str to Any

Metadata of the attribute

kb_name: str | None

kb_id: Any | None

kb_version: str | None

term: str | None

score: float | None

LABEL: ClassVar[str] = 'NORMALIZATION'

Label used for all normalization attributes

to_brat() → str

Return a value compatible with the brat format.

to_spacy() → str

Return a value compatible with spaCy.

to_dict() → dict[str, Any]

classmethod from_dict(data_dict: dict[str, Any]) → typing_extensions.Self

Create an Attribute from a dict.

Parameters:

attribute_dict: dict of str to Any

A dictionary from a serialized Attribute as generated by to_dict()