Question about operator concept in observation domain?

[mr.nim.li]

Hello,

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!

[aostropolets (Anna Ostropolets)]

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:

[Christian_Reich]

@mr.nim.li:

@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 (>=).

[mr.nim.li]

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