Family Context

The eds.family component uses a simple rule-based algorithm to detect spans that describe a family member (or family history) of the patient rather than the patient themself.

Examples

The following snippet matches a simple terminology, and checks the family context of the extracted entities. It is complete, and can be run as is.

import edsnlp

nlp = edsnlp.blank("eds")
nlp.add_pipe("eds.sentences")
# Dummy matcher
nlp.add_pipe(
    "eds.matcher",
    config=dict(terms=dict(douleur="douleur", osteoporose="ostéoporose")),
)
nlp.add_pipe("eds.family")

text = (
    "Le patient est admis le 23 août 2021 pour une douleur au bras. "
    "Il a des antécédents familiaux d'ostéoporose"
)

doc = nlp(text)

doc.ents
# Out: (douleur, ostéoporose)

doc.ents[0]._.family
# Out: False

doc.ents[1]._.family
# Out: True

Extensions

The eds.family component declares two extensions, on both Span and Token objects :

The family attribute is a boolean, set to True if the component predicts that the span/token relates to a family member.
The family_ property is a human-readable string, computed from the family attribute. It implements a simple getter function that outputs PATIENT or FAMILY, depending on the value of family.

Parameters

PARAMETER	DESCRIPTION
`nlp`	The pipeline object. TYPE: `PipelineProtocol`
`name`	The component name. TYPE: `Optional[str]`
`attr`	spaCy's attribute to use: a string with the value "TEXT" or "NORM", or a dict with the key 'term_attr' we can also add a key for each regex. TYPE: `str` DEFAULT: `NORM`
`family`	List of terms indicating family reference. TYPE: `Optional[List[str]]` DEFAULT: `None`
`termination`	List of syntagms termination terms. TYPE: `Optional[List[str]]` DEFAULT: `None`
`span_getter`	Which entities should be classified. By default, `doc.ents` TYPE: `SpanGetterArg` DEFAULT: `None`
`on_ents_only`	Deprecated, use `span_getter` instead. Whether to look for matches around detected entities only. Useful for faster inference in downstream tasks. If True, will look in all ents located in `doc.ents` only If an iterable of string is passed, will additionally look in `doc.spans[key]` for each key in the iterable TYPE: `Union[bool, str, List[str], Set[str]]` DEFAULT: `None`
`explain`	Whether to keep track of cues for each entity. TYPE: `bool` DEFAULT: `False`
`use_sections`	Whether to use annotated sections (namely `antécédents familiaux`). TYPE: bool, by default `False` DEFAULT: `True`

Authors and citation

The eds.family component was developed by AP-HP's Data Science team.