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Question about operator concept in observation domain?


We are trying to ETL data from some pathology reports (breast cancer cases) to the OMOP tables. In one case, we have this in our source data:

Overall grade: at least 2

Following the CAP vocabulary, we have mapped the data to this concept id:

4157601 (“Nottingham combined grade of primary malignant neoplasm of breast”)

which is under the “Observation” domain.

Looking at the Observation table, I imagine we can store “2” in the “value_as_number”. But how about the “at least” portion? Unlike the Measurement table, Observation table does not have “operator_concept_id”. So, I wonder how to specify the “>=” concept to the value? Reading the documentation, the Observation table has the “qualifier_concept_id” field, which is used for “specifying the clinical fact further”. But reading the examples (eg. degrees, severities, drug-drug interaction alerts, etc.), I am not certain if this field is intended to be used for this case. I wonder how other people manage similar situation. I would hope to hear some feedback from the community.

Many thanks!

While others can comment better on what to do with Observations, it seems that in this case you can use a Measurement. There are also options for individual components:


@aostropolets is correct, except for cancers:

All attributes of cancer are Measurements in the Cancer Modifier vocabulary. For the Nottingham grades, you want to pick from these. I would use Nottingham Grade 2 and put into operator the concept_id 4171755 (>=).

Thank you for both of your feedback. This is very helpful! :smile: