Purpose: Extract Medical Concepts from Physician Notes

This package simplifies communication with cTAKES NLP servers which produce matches with UMLS Concepts.

• Clinical Text and Knowledge Extraction System (cTAKES)
• Unified Medical Language System (UMLS)

Quickstart

Clinical text fragment or entire physician note.

physician_note = 'Chief Complaint: Patient c/o cough, denies fever, recent COVID test negative. Denies smoking.'
output = await ctakesclient.client.post(physician_note)

Note that ctakesclient uses an async API. If your code is not async, you can simply wrap calls in asyncio.run():

output = asyncio.run(ctakesclient.client.post(physician_note))

Output

This client parses responses into lists of MatchText and UmlsConcept.

CtakesJSON(output)

list_match() -> List[MatchText]

list_concept() -> List[UmlsConcept]

list_sign_symptom() -> List[MatchText]

list_disease_disorder() -> List[MatchText]

list_medication() -> List[MatchText]

list_procedure() -> List[MatchText]

list_anatomical_site() -> List[MatchText]

MatchText: Physician Notes

MatchText(s) are the character positions in the physician note where a UmlsConcept was found.

MatchText: Polarity

UMLS Concept

UMLS Vocabulary

UMLS Semantic Types and Groups

You can browse the list of UMLS Semantic Types at the National Library of Medicine.