medkit.text.ner.adicap_norm_attribute#

Classes:

ADICAPNormAttribute(code[, sampling_mode, ...])

Attribute describing tissue sample using the ADICAP (Association pour le Développement de l'Informatique en Cytologie et Anatomo-Pathologie) coding.
class ADICAPNormAttribute(code, sampling_mode=None, technic=None, organ=None, pathology=None, pathology_type=None, behaviour_type=None, metadata=None, uid=None)[source]#

Attribute describing tissue sample using the ADICAP (Association pour le Développement de l’Informatique en Cytologie et Anatomo-Pathologie) coding.

Cf https://smt.esante.gouv.fr/wp-json/ans/terminologies/document?terminologyId=terminologie-adicap&fileName=cgts_sem_adicap_fiche-detaillee.pdf for a complete description of the coding.

This class is replicating EDS-NLP’s Adicap class, making it a medkit Attribute.

The code field fully describes the tissue sample. Additional information is derived from code in human readable fields (sampling_code, technic, organ, pathology, pathology_type, behaviour_type)

Variables

  • uid – Identifier of the attribute

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

  • value – ADICAP code prefix with “adicap:” (ex: “adicap:BHGS0040”)

  • code – ADICAP code as a string (ex: “BHGS0040”)

  • kb_id – Same as code

  • sampling_mode (Optional[str]) – Sampling mode (ex: “BIOPSIE CHIRURGICALE”)

  • technic (Optional[str]) – Sampling technic (ex: “HISTOLOGIE ET CYTOLOGIE PAR INCLUSION”)

  • organ (Optional[str]) – Organ and regions (ex: “SEIN (ÉGALEMENT UTILISÉ CHEZ L’HOMME)”)

  • pathology (Optional[str]) – General pathology (ex: “PATHOLOGIE GÉNÉRALE NON TUMORALE”)

  • pathology_type (Optional[str]) – Pathology type (ex: “ETAT SUBNORMAL - LESION MINEURE”)

  • behaviour_type (Optional[str]) – Behaviour type (ex: “CARACTERES GENERAUX”)

  • 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(adicap_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
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(adicap_dict)[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