Proposal for representation of "numeric" concepts

[rimusia]

Numeric concept proposal.docx

[cgreich]

Thanks, @rimusia.

Below is an example of Measurement record representing ‘Tumor size’ (4139794) ‘Described as "less than 2 cm," or "greater than 1 cm," or "between 1 cm and 2 cm"’ (35919956):

And then you list two records in the table.

We need to finalize how to do ranges. Two records is not a good idea, because they are not linked, and a simple query "Give me all tumors larger than 2 cm" will return this record, because nobody checks that at the same day there is not only a record >1, but also not one <2. Forcing people would make querying a lot more complicated and much slower.

I still like the addition of "range_value" or "plusminus", and then have value_as_number=1.5, and plusminus=0.5.

Thoughts?

[vojtechhuser]

just pasting text for others to read quickly from the intro section

Proposal for representing “numeric” concepts

Background
In several vocabularies used in OMOP, there are concepts representing numeric values or numeric ranges. Among them are: LOINC severity scores (“Mild”, LA6752-5, with a corresponding numeric value of 1); SNOMED quantitative concepts (“Between 45-50 degrees C”, 264679004]); SNOMED laboratory or test results (“Bacterial colony size, less than 1 mm. diameter”, 39090004). Often, these concepts contain measurement units. “Numeric” concepts are used to represent laboratory and radiology measurements, adverse event assessments, patient reported outcomes and others.

In OMOP CDM, these concepts are normally used in Measurement and Observation tables to store value_as_concept_id. Analysis of these data is currently possible only if the user knows exactly the concepts used to represent range or value, including their respective units. It is not possible to perform analysis on numeric values of these data, nor is it possible to differentiate numeric values by units. For example, it is not impossible to find tumors which size is less than 2 cm by issuing the following simple query:
SELECT *
FROM measurement
WHERE measurement_concept_id = 4139794 -- Tumor size
AND ( (value_as_number <= 2 and unit_concept_id = 8582) -- Centimeter
OR (value_as_number <= 20 and unit_concept_id = 8588)) --Millimeter
AND COALESCE(operator_concept_id, 4171754) = 4171754 -- Less than or equal

One has to know exactly the concepts that cover this range.

Proposal
We propose the following extension of the OMOP CDM vocabulary to represent concepts containing numeric values or ranges.

[cgreich]

@vojtechhuser:

The question is how to represent the range. This has been discussed several times before.