Parse CDA section by code in addition to templateId

[jenniferjiangkells]

Description

CDA (Clinical Document Architecture) is an XML-based standard for encoding clinical documents, designed to facilitate interoperable exchange of medical information between healthcare systems.

Currently, the CDA parser parses problems, medications, and allergies sections, using a dictionary-based internal representation via xmltodict. It finds sections by parsing and checking the templateId field in structuredBody/Component/Section(Reference). However as it is not a required field, sections are sometimes not picked up. To make sure sections are picked up, we should check the code field as well.

Example

This will parse as a medication section because it contains templateId:

HealthChain/resources/uclh_cda.xml

Lines 1506 to 1512 in a4beb13

	<section>
	<templateId root="2.16.840.1.113883.10.20.1.8" />
	<templateId root="2.16.840.1.113883.3.88.11.83.112" />
	<templateId root="1.3.6.1.4.1.19376.1.5.3.1.3.19" />
	<id root="369C0DBE-6FCB-11ED-8917-000C29CBAF7B" />
	<code code="10160-0" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="History of Medication use Narrative" />
	<title>Medication</title>

This will not be parsed as a medication section because it doesn't contain templateId. The identifier is in the code field instead:

HealthChain/resources/epic_cda.xml

Lines 248 to 250 in a4beb13

	<section>
	<code code="10160-0" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="HISTORY OF MEDICATION USE" />
	<title>Current Medications - as of 09/16/2014</title>

Context

CDAs from different regions and providers can be implemented very differently. This is part of a larger effort to make the CDA parser more configurable and adaptable.

Possible Implementation

1. Add a SectionCode enum

class SectionCode(Enum):
    MEDICATION = "10160-0"

2. Add ._find_section_by_code() in CdaAnnotator
3. Update _find_problems_section(), _find_medications_section(), and _find_allergies_section()
4. e.g.

def _find_medications_section(self) -> Optional[Section]:
    return (self._find_section_by_template_id(SectionId.MEDICATION.value) or self._find_section_by_code(SectionId.MEDICATION.value))

Alternative Implementation

We can also make the templateId and code configurable - currently hard-coded.

[Vortex-21]

Hey Can you assign me this issue ? Will start working on it right away!

[jenniferjiangkells]

👋 @Vortex-21 - assigned you the issue, any questions let me know!

[jenniferjiangkells]

@Vortex-21 just checking if you still want to work on this issue! I will unassign you but please still feel free to work on it if you want - we've just decided to to change the issue assignment system.

[Vortex-21]

Yes I would still want to work on this issue !

[Vortex-21]

Here in this component , is the code "51847-2" supposed to be the LOINC code for the NOTE enum ? I could get the exact medication, problem and allergy codes but I am not so sure about the "note" code.

Asking this because the section_id does contain NOTE :

class SectionId(Enum):
    PROBLEM = "2.16.840.1.113883.10.20.1.11"
    MEDICATION = "2.16.840.1.113883.10.20.1.8"
    ALLERGY = "2.16.840.1.113883.10.20.1.2"
    NOTE = "1.2.840.114350.1.72.1.200001"

Apart from this I have made the necessary changes and tested on the uclh_cd.xml document as well as the already existing tests . Everything is working as expected and is ready for a PR .

[jenniferjiangkells]

@Vortex-21 Yes you can assume that's the code for the note section for now!

[Vortex-21]

@Vortex-21 Yes you can assume that's the code for the note section for now!

Yes . Raised the PR using that code only !