CDA Parser
The CdaAnnotator class is responsible for parsing and annotating CDA (Clinical Document Architecture) documents. It extracts information about problems, medications, allergies, and notes from the CDA document into FHIR resources, and allows you to add new information to the CDA document.
The CDA parser is used in the CDA Connector module, but can also be used independently.
Usage
Parsing CDA documents
Parse a CDA document from an XML string:
from healthchain.cda_parser import CdaAnnotator
with open("tests/data/test_cda.xml", "r") as f:
cda_xml_string = f.read()
cda = CdaAnnotator.from_xml(cda_xml_string)
conditions = cda.problem_list
medications = cda.medication_list
allergies = cda.allergy_list
note = cda.note
print([condition.model_dump() for condition in conditions])
print([medication.model_dump() for medication in medications])
print([allergy.model_dump() for allergy in allergies])
print(note)
You can access data parsed from the CDA document in the problem_list, medication_list, allergy_list, and note attributes of the CdaAnnotator instance. They return a list of FHIR Condition, MedicationStatement, and AllergyIntolerance resources.
Adding new information to the CDA document
The methods currently available for adding new information to the CDA document are:
| Method | Description |
|---|---|
.add_to_problem_list() |
Adds a list of FHIR Condition resources |
.add_to_medication_list() |
Adds a list of FHIR MedicationStatement resources |
.add_to_allergy_list() |
Adds a list of FHIR AllergyIntolerance resources |
The overwrite parameter in the add_to_*_list() methods is used to determine whether to overwrite the existing list or append to it. If overwrite is True, the existing list will be replaced with the new list. If overwrite is False, the new list will be appended to the existing list.
Depending on the use case, you don't always need to return the original list of information in the CDA document you receive, although this is mostly useful if you are just developing and don't want the eye-strain of a lengthy CDA document.
Exporting the CDA document
The pretty_print parameter is optional and defaults to True. If pretty_print is True, the XML string will be formatted with newlines and indentation.
Example
from healthchain.cda_parser import CdaAnnotator
from healthchain.fhir import (
create_condition,
create_medication_statement,
create_allergy_intolerance,
)
with open("tests/data/test_cda.xml", "r") as f:
cda_xml_string = f.read()
cda = CdaAnnotator.from_xml(cda_xml_string)
new_problems = [
create_condition(subject="Patient/123", code="123456", display="New Problem")
]
new_medications = [
create_medication_statement(
subject="Patient/123", code="789012", display="New Medication"
)
]
new_allergies = [
create_allergy_intolerance(
patient="Patient/123", code="345678", display="New Allergy"
)
]
# Add new problems, medications, and allergies
cda.add_to_problem_list(new_problems, overwrite=True)
cda.add_to_medication_list(new_medications, overwrite=True)
cda.add_to_allergy_list(new_allergies, overwrite=True)
# Export the modified CDA document
modified_cda_xml = cda.export()
print(modified_cda_xml)
The CDA parser is a work in progress. I'm just gonna be real with you, CDAs are the bane of my existence. If you, for some reason, love working with XML-based documents, please get in touch! We have plans to implement more functionality in the future, including allowing configurable templates, more CDA section methods, and using LLMs as a fallback parsing method.