Hey all,
We are ETL-ing our study on Ventilator-associated Pneumonia to OMOP-CDM.
Under ‘sample type’ in our microbiological identification and antimicrobial susceptibility testing forms, we collect - “Bronchoalveolar Lavage (BAL)” and “Mini-BAL”, as separate options.
Technically, the distinction between “BAL” and “Mini-BAL” is that they are two separate procedures -
- BAL = Bronchoalveolar lavage [37204340] / Bronchoscopic bronchoalveolar lavage [37203792]
- Mini-BAL = Blind bronchoalveolar lavage [37203791]
And, specimen collected through either of these procedures can be categorized as “Bronchoalveolar Lavage Fluid Sample”, which exists in Athena as [4121345] and maps to the SPECIMEN domain in OMOP-CDM.
The challenge we are facing is to distinguish “Bronchoalveolar Lavage Fluid Sample” specimen collected using BAL v/s Mini-BAL.
As we understand, SPECIMEN domain in OMOP-CDM does not allow the use of [value_as_concept_id] or [value_as_string]. Otherwise, we would have tried to map these two data items by using the concept ids for the two procedures in the [value_as_concept_id] field. As, also shown in the screenshot. But, this obviously is not permitted as per the OMOP-CDM SPECIMEN domains rules.
So, I was wondering if any one else has faced this challenge? And, if you could please advise us on how best to tackle this? Perhaps, it makes sense to use the [anatomic_site_concept_id]?
Many thanks in advance for your help.
-Ankur