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Storing note data from radiology, coronary angiography, and pathology report

CDM Builders
#1

I converted coronary angiography report into note table of OMOP-CDM ver 5.0.2.
I want to convert all reports from radiology and pathology into CDM, too.

But I’m wonder how I can set relationship between these notes with primary procedure or measurements or specimens.
(How can I know where the coronary angiography report comes from, when the patient has multiple coronary angiography in the same day? Current note table has visit_occurrence_id, so I can tag it. But I don’t find any room for procedure_id or measurement_id)

Is there any established logic for this issue? Or should we extend the note table further?

Oncology radiology imaging integration into CDM
How can i store the discription and report of Head CT scan into CDM?
Relationship options for fact_relationship table
#2

You can use fact_relationship table
https://github.com/OHDSI/CommonDataModel/wiki/FACT_RELATIONSHIP
where
domain_concept_id_1 = ‘Note’
fact_id_1 = Note.visit_occurrence_id
domain_concept_id_2 = ‘Measurement’ (if measurement)
fact_id_2 = Measurement.Measurement_concept_id
relationship_concept_id = ??? “Note of”

We don’t have this relationship currently.
@Christian_Reich, we need to think about new relationships adding process

Representing laterality + general questions about post-coordination
#3

Thank you, @Dymshyts
Your comment really helpful!

But I think we should think about extending note table for these relationships, too!

#4

I agree, @SCYou.

It’s an obvious, when Note describes some other event (Procedure, Measurement, Condition or Drug exposure even),
so analogues of domain_concept_id_2 and fact_id_2 fields should be added

#5

@SCYou, @Dymshyts:

Please submit to the CDM WG as a proposal for changing the NOTE table. It might be relegated to THEMIS as a FACT_RELATIONSHIP convention.

#6

@SCYou @Dymshyts @Christian_Reich

I think we should move to making relationships more explicit. FACT_RELATIONSHIP is opaque. Perhaps follow the lead of how the COST table references other tables with a polymorphic pairing:

cost_event_id
cost_domain_id

note_event_id
note_domain_id

Having the NOTE table be able to to explicitly reference PROCEDURE_OCCURENCE is, I believe, especially important.

#7

We can add reference system just as COST table does now. Thank you for very good comment, @mgurley !

@Christian_Reich Yes, I or we should submit a proposal for changing NOTE table to CDM WG.

#8

Just wondering if any decision was made already or some WG-discussion started?

#9

@Dymshyts, I don’t think so. I’m thinking of making proposal to add reference system just as COST table in Note table.
Do you have any other plan?

#10

I agree! We have EHR data and a LOT of “note” data that is present in most domains (procedures, specimens, measurements, observations, oncology, genomic, etc.). @Christian_Reich’s favorite table, Fact_Relationship, is one way to relate data in the Note table to other OMOP tables, but as @Dymshyts stated, the relationship_concept_ids aren’t representative of the relationships.

#11

Looks like we need to overhaul the NOTE table.

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