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Question about non-standard CAP code in measurement domain

Implementers
#1

Hello.

The pathology data (CAP) in our source system is stored in question-answer pair. In one case, we have:

Question - Antibody
Answer - 4B5

I can find them in the CAP vocabulary.

The “Antibody” has the concept id “1112134”, which is mapped to another (standard) SNOMED code with concept id “4288455”, under the Measurement domain. So for this record, I thought I would store the concept id “4288455” as the measurement_concept_id; and then, the concept id for “4B5” (concept id: “1112135”) would go to “value_as_concept_id”.

But then, when I look at concept id “1112135” for “4B5”, it is non-standard code, and does not map to any standard code.

Does it mean that the “value_as_concept_id” can have non-standard code? My root question is - how should I store “4B5” in this case?

Thank you!

#2

There is ongoing discussion of survey pairs here: Survey vocabularies in OMOP - #8 by Christian_Reich . This does not provide the answer to your question yet but maybe a good place to pose it. I am curious why we have antibody question with antigen answer - is it a common practice? Both from Observation domain by the way.

#3

Thank you for the reply.

About the question - “is it a common practice?”:

In our hospital, we store pathology report data in one system that uses the CAP coding system (https://cap.org/protocols-and-guidelines/electronic-cancer-protocols).

I am not an expert in the CAP coding system. Reading its documents and the available data, the CAP codes seem to be organized based on the layout of the data collection form, which seems to be in question-answer format all the time. For example, there may be an item on the form called “Specimen Laterality”, with a list of available options, such as “Right”, “Left”, “Not specified”, etc. With this, I can see how our pathology data comes in question-answer format in the database. BTW, the form contains many sections that store different types of information. I used “Antibody” as an example in my previous post, which is just one of the many items on a single form.

To answer your question, I don’t have exposure to other systems for patholgy data. I can’t really tell if it is a common practice. But the CAP code in our system is what our group is working on now.

Also, almost all the data on the data collection form go to either “Observation” and “Measurement” domains, depending on what standard code the “Question” may be mapped to. And I am hoping the “Answer” can be stored in the associated {domain}_value_as_concept_id.

But then, I notice there is a number of non-standard code for the “answer”, which I am not certain how to store in the omop tables. I hope to get some help. Any comment is welcome. Thank you!

#4

Hello. After I re-read the post, I realize you have caught a mistake I made … Your reply has addressed my question. :grin: … I mistakenly thought the code for “Antibody” would go to “Measurement” at the beginning. But you have pointed out it should go to “Observation” instead. Yes, you are right … and in “Observation”, I may store “4B5” in “value_as_string”. This solves the question that I have. Many thanks for helping me solve the problem!! I should be more careful when going through the detail. Thank you!!

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