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Ophthalmology data extraction into measurement VALUE_AS_NUMBER

CDM Builders
#1

Hi, all. I’m trying to extract Ophthalmology (Kaleidoscope) data into OMOP measurement table using this paper and the mapping below.

https://userweb.epic.com/Thread/128570/Kaleidoscope-to-OMOP-mappings/

However, we have some numeric values with + or - signs. I can put values with - signs like ‘-0.50’ into the value_as_number column but I can’t put ‘+2.50’ into the value_as_number column. Can I just put ‘2.50’ into the value_as_number and ‘+2.50’ into the value_source_value column?

Tagging @MPhilofsky & @karthik

Thanks!

#2

Hi @Jungmi!
In your case you should fill operator_concept_id field (the list of acceptable values is here - Athena). The field value_as_number should be filled according to existing OMOP CDM documentation (OMOP CDM v5.4).
There are nevertheless some exceptions for the negative values of following Measurements (listed as LOINC codes): - 1925-7 Base excess in Arterial blood by calculation - 1927-3 Base excess in Venous blood by calculation - 8632-2 QRS-Axis - 11555-0 Base excess in Blood by calculation - 1926-5 Base excess in Capillary blood by calculation - 28638-5 Base excess in Arterial cord blood by calculation 28639-3 Base excess in Venous cord blood by calculation.

#3

Thanks, @Varvara_Savitskaya for replying!
We do use operator_concept_id field for <, <=, >, >= but there is no specific concepts for + or - from the Meas Value Operator domain.

#4

It isn’t stated in the documentation, but all numbers will be assumed to be positive unless otherwise stated. However, with your use case, I think the ‘+’ sign might be necessary. Is it?

Have you connected with the Eye Care and Vision WG? They are seeking data partners and use cases for their endeavors to transform eye exam data to the OMOP CDM.

EDIT: I forgot to add, you can use the value_source_value to store these data, HOWEVER, this field is not used in standardized analytics; is not available for use in Atlas; and if the data stored in the value_source_value field come from the EHR, many institutions won’t share these data because there are PHI stored in the field. Therefore, it is not recommended to use this field.

#5

Yes.
In fact, if you put 2.50 or 2.5 it will not matter. (per general math)

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