medkit.core.text.entity_norm_attribute

Classes:

EntityNormAttribute(kb_name, kb_id[, ...])

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

class EntityNormAttribute(kb_name, kb_id, kb_version=None, term=None, score=None, metadata=None, uid=None)

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

Variables

• uid (str) – Identifier of the attribute

• label (str) – The attribute label, always set to EntityNormAttribute.LABEL

• value (Optional[Any]) – 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_name (Optional[str]) – 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_id (Optional[Any]) – 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_version (Optional[str]) – Optional version of the knowledge base.

• term (Optional[str]) – Optional normalized version of the entity text.

• score (Optional[float]) – Optional score reflecting confidence of this link.

• metadata (Dict[str, Any]) – Metadata of the attribute

Attributes:

LABEL

Label used for all normalization attributes

Methods:

copy()	Create a new attribute that is a copy of the current instance, but with a new identifier
from_dict(data_dict)	Creates an Attribute from a dict
get_subclass_for_data_dict(data_dict)	Return the subclass that corresponds to the class name found in a data dict
to_brat()	Return a value compatible with the brat format
to_spacy()	Return a value compatible with spaCy

LABEL: ClassVar[str] = 'NORMALIZATION'

Label used for all normalization attributes

copy()

Create a new attribute that is a copy of the current instance, but with a new identifier

This is used when we want to duplicate an existing attribute onto a different annotation.

Return type

Attribute

classmethod get_subclass_for_data_dict(data_dict)

Return the subclass that corresponds to the class name found in a data dict

Parameters

data_dict (Dict[str, Any]) – Data dict returned by the to_dict() method of a subclass (or of the base class itself)

Return type

Optional[Type[Self]]

Returns

subclass – Subclass that generated data_dict, or None if data_dict correspond to the base class itself.

to_brat()

Return a value compatible with the brat format

Return type

str

to_spacy()

Return a value compatible with spaCy

Return type

str

classmethod from_dict(data_dict)

Creates an Attribute from a dict

Parameters

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

Return type

Self