Anatomic Site Concept ID (Entire vs Structure)

[kyulee-jeon]

In the MI-CDM paper (Fig3), the anatomic_site_concept_id for lung nodule use case was designated as '4118108 (entire thorax)'. If we obtain anatomic site information from DICOM, '4184181 (thoracic cavity structure)' might be more appropriate. p.s. I am seeking input on this matter to avoid confusion for researchers who are following MI-CDM based on our paper.

Rationale:

• (DICOM) DICOM generally uses anatomic concepts with "structure" rather than "entire". For instance, the BodyPartExamined Tag 'CHEST' is defined as SCT '43799004 (thoracic cavity structure)'.
• (OMOP CDM) Both codes are included as Standard Concept IDs in the Specimen Table's Accepted Concepts, but 'Entire' lacks descendants compared to 'Structure'.

Concept Type	OMOP Concept ID	SCT Code	Description
Structure	4184181	43799004	Thoracic cavity structure (body structure)
Entire	4118108	302551006	Entire thorax

References:

• DICOM PS3.16 > Correspondence of Anatomic Region Codes and Body Part Examined Defined Terms
• OMOP CDM v5.4 > Specimen Table > ETL Conventions

[jenpark10]

Agreed. We should follow the DICOM-SNOMED Value Set, which is the Thoracic cavity structure.