We are ingesting some data from our biobank (FYI, OpenSpecimen) into the specimen table. In source, “paraffin embedded slide” has unit = “count” and value = 1, as there wasn’t a standard vocabulary such as UCUM utilized.
If we are ingesting the fact that we have 1 paraffin embedded slide (specimen_concept_id = 46274042) available for a patient, would the quantity be 1, and unit_concept_id be 0? I cannot find an appropriate concept for such a representation that there is 1 slide specimen available. Measuring the dimensions of the slide is of no scientific interest to our researchers ( ) so I haven’t been able to find a good UCUM approach to this.
Second part of my question:
My assumption is that OMOP would like there to be a row for every individual slide, even if from the same block, as we’re wanting to represent each individual physical specimen on a row. If it’s the case that we ever have “Count” = “3” in OpenSpecimen for a Fixed Tissue Slide sample type, should I explode this specimen out into 3 different rows in the specimen table in OMOP v5.4, each with quantity = 1, and unit_concept_id = 0?
Here’s your original post on specimen table: