medkit.core.text.umls_norm_attribute#

Classes:

UMLSNormAttribute(cui, umls_version[, term, ...])

Normalization attribute linking an entity to a CUI in the UMLS knowledge base

class UMLSNormAttribute(cui, umls_version, term=None, score=None, sem_types=None, metadata=None, uid=None)[source]#

Normalization attribute linking an entity to a CUI in the UMLS knowledge base

Variables

uid – Identifier of the attribute
label – The attribute label, always set to EntityNormAttribute.LABEL
value – CUI prefixed with “umls:” (ex: “umls:C0011849”)
kb_name – Name of the knowledge base. Always “umls”
kb_id – CUI (Concept Unique Identifier) to which the annotation should be linked
cui – Convenience alias of kb_id
kb_version – Version of the UMLS database (ex: “202AB”)
umls_version – Convenience alias of kb_version
term – Optional normalized version of the entity text
score – Optional score reflecting confidence of this link
sem_types (Optional[List[str]]) – Optional IDs of semantic types of the CUI (ex: [“T047”])
metadata – Metadata of the attribute

Methods:

`copy`()	Create a new attribute that is a copy of the current instance, but with a new identifier
`from_dict`(data)	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

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.

classmethod from_dict(data)[source]#

Creates an Attribute from a dict

Parameters: attribute_dict (dict) – A dictionary from a serialized Attribute as generated by to_dict()
Return type: Self

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

to_spacy()#

Return a value compatible with spaCy