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Immunohistochemistry procedure in measurement table

Vocabulary Users
#1

Hi all,

Whilst mapping our data I noticed that Immunohistochemistry procedure is classed as a measurement rather than as a procedure - 4035726. It’s showing as an error on DQD because I have mapped it to procedure but domain_id is incorrect I’m wondering if it is an issue with the vocab or there is a logical reason for it to be located there instead.

Thanks

#2

@tomstone786:

Not sure. Procedures according to the CDM definition are “activities or processes ordered by, or carried out by, a healthcare provider on the patient with a diagnostic or therapeutic purpose”. The key word here is “on the patient”. Immunohistochemistry is done in the path lab, and therefore a measurement. Usually, you would also expect what substance the IHC is testing. The excision or biopsy of a sample is the actual procedure.

The rule of thumb is: It is a procedure when the doc says “this will hurt a little”.

#3

Thanks @Christian_Reich. Is it usual for parent concepts to be a different domain. Without knowing that they are in different domains if one were to search for all Anatomic pathology procedures within procedures then this would be excluded from the results

#4

Ha! You put the finger into the wound, @tomstone786. We are trying to get the correct assignment for each concept, but it doesn’t always work out. Like in this case. There is also a gray zone.

Still: The OMOP model requires that records of concepts that declared procedures (rightly or wrongly) in the Procedure Occurrence table, and measurement table in the Measurement table. Because otherwise it’s not a model supporting remote research.

#5

The logical reason is the data go where the domain_id for the standard concept_id tell them to go. In your case, concept_id = 4035726 has domain_id = Measurement. So, your ETL should put these data in the Measurement table. Check out The Book of OHDSI for further info about how to design your ETL.

Yes, that is why the best practice is to always take your list of concepts and look them up in the Concept table to determine the domain_id for the standard concept before looking for the data in the CDM. The Concept table is the card catalogue of OHDSI. Always look there first because the concepts can be reorganized and move tables and/or fields.

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