Detecting Reason of Hospitalisation

In this tutorial we will use the pipe eds.reason to :

Identify spans that corresponds to the reason of hospitalisation
Check if there are named entities overlapping with my span of 'reason of hospitalisation'
Check for all named entities if they are tagged is_reason

import edsnlp, edsnlp.pipes as eds

text = """COMPTE RENDU D'HOSPITALISATION du 11/07/2018 au 12/07/2018
MOTIF D'HOSPITALISATION
Monsieur Dupont Jean Michel, de sexe masculin, âgée de 39 ans, née le 23/11/1978,
a été hospitalisé du 11/08/2019 au 17/08/2019 pour attaque d'asthme.

ANTÉCÉDENTS
Antécédents médicaux :
Premier épisode d'asthme en mai 2018."""

nlp = edsnlp.blank("eds")

# Extraction d'entités nommées
nlp.add_pipe(
    eds.matcher(
        terms=dict(
            respiratoire=[
                "asthmatique",
                "asthme",
                "toux",
            ]
        ),
    ),
)
nlp.add_pipe(eds.normalizer())
nlp.add_pipe(eds.sections())
nlp.add_pipe(eds.reason(use_sections=True))

doc = nlp(text)

The pipe reason will add a key of spans called reasons. We check the first item in this list.

# ↑ Omitted code above ↑

reason = doc.spans["reasons"][0]
reason
# Out: hospitalisé du 11/08/2019 au 17/08/2019 pour attaque d'asthme.

Naturally, all spans included the reasons key have the attribute reason._.is_reason == True.

# ↑ Omitted code above ↑

reason._.is_reason
# Out: True

# ↑ Omitted code above ↑

entities = reason._.ents_reason  # (1)
for e in entities:
    print(
        "Entity:",
        e.text,
        "-- Label:",
        e.label_,
        "-- is_reason:",
        e._.is_reason,
    )
# Out: Entity: asthme -- Label: respiratoire -- is_reason: True

We check if the span include named entities, their labels and the attribute is_reason

We can verify that named entities that do not overlap with the spans of reason, have their attribute reason._.is_reason == False:

for e in doc.ents:
    print(e.start, e, e._.is_reason)
# Out: 42 asthme True
# Out: 54 asthme False